Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530786.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 { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530786.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530786.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { 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: 1.33, per 1000 atoms: 0.39 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: 0.31 Conformation dependent library (CDL) restraints added in 103.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 390 0.89 - 1.14: 1213 1.14 - 1.39: 566 1.39 - 1.64: 903 1.64 - 1.89: 81 Bond restraints: 3153 Sorted by residual: bond pdb=" C SER A 3 " pdb=" O SER A 3 " ideal model delta sigma weight residual 1.234 0.998 0.235 1.17e-02 7.31e+03 4.05e+02 bond pdb=" ND1 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 1.321 1.522 -0.201 1.00e-02 1.00e+04 4.04e+02 bond pdb=" C BGLU A 96 " pdb=" O BGLU A 96 " ideal model delta sigma weight residual 1.237 1.455 -0.218 1.17e-02 7.31e+03 3.49e+02 bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.144 0.182 1.10e-02 8.26e+03 2.75e+02 bond pdb=" N SER A 3 " pdb=" CA SER A 3 " ideal model delta sigma weight residual 1.454 1.261 0.194 1.17e-02 7.31e+03 2.74e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 3259 4.94 - 9.87: 1874 9.87 - 14.81: 580 14.81 - 19.74: 60 19.74 - 24.67: 4 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 109.00 124.34 -15.34 1.00e+00 1.00e+00 2.35e+02 angle pdb=" O ALEU A 153 " pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 123.27 139.65 -16.38 1.16e+00 7.43e-01 1.99e+02 angle pdb=" CA ALEU A 153 " pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 116.39 102.10 14.29 1.17e+00 7.31e-01 1.49e+02 angle pdb=" O ASN A 81 " pdb=" C ASN A 81 " pdb=" N LEU A 82 " ideal model delta sigma weight residual 122.12 109.28 12.84 1.06e+00 8.90e-01 1.47e+02 angle pdb=" CA ASP A 60 " pdb=" C ASP A 60 " pdb=" O ASP A 60 " ideal model delta sigma weight residual 120.70 132.95 -12.25 1.03e+00 9.43e-01 1.41e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.23: 1317 17.23 - 34.46: 108 34.46 - 51.68: 33 51.68 - 68.91: 20 68.91 - 86.13: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 172 " pdb=" N LEU A 172 " pdb=" CA LEU A 172 " pdb=" CB LEU A 172 " ideal model delta harmonic sigma weight residual -122.60 -105.65 -16.95 0 2.50e+00 1.60e-01 4.60e+01 dihedral pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CA ASP A 60 " pdb=" CB ASP A 60 " ideal model delta harmonic sigma weight residual 122.80 139.21 -16.41 0 2.50e+00 1.60e-01 4.31e+01 dihedral pdb=" C THR A 125 " pdb=" N THR A 125 " pdb=" CA THR A 125 " pdb=" CB THR A 125 " ideal model delta harmonic sigma weight residual -122.00 -106.82 -15.18 0 2.50e+00 1.60e-01 3.69e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.214: 105 0.214 - 0.426: 61 0.426 - 0.638: 49 0.638 - 0.850: 21 0.850 - 1.062: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.53 -1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.67 0.98 2.00e-01 2.50e+01 2.38e+01 chirality pdb=" CA AGLN A 80 " pdb=" N AGLN A 80 " pdb=" C AGLN A 80 " pdb=" CB AGLN A 80 " both_signs ideal model delta sigma weight residual False 2.51 3.47 -0.96 2.00e-01 2.50e+01 2.31e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.028 2.00e-02 2.50e+03 5.93e-02 1.05e+02 pdb=" CG PHE A 162 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.111 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.047 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.082 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.095 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.052 2.00e-02 2.50e+03 5.35e-02 8.59e+01 pdb=" CG BTYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.051 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.027 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.042 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.106 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.020 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.017 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.030 2.00e-02 2.50e+03 5.32e-02 8.50e+01 pdb=" CG PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.100 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.035 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.035 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.074 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 1575 2.39 - 2.94: 8485 2.94 - 3.50: 10405 3.50 - 4.05: 15006 4.05 - 4.60: 21120 Nonbonded interactions: 56591 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.839 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.851 2.100 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.865 2.270 nonbonded pdb=" H BTYR A 67 " pdb=" O HOH A 324 " model vdw 1.870 2.450 nonbonded pdb=" HB3 SER A 142 " pdb=" HG SER A 142 " model vdw 1.874 1.816 ... (remaining 56586 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_8530786_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= 0.2783 r_free= 0.1850 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.393728 | | target function (ml) not normalized (work): 71367.320097 | | target function (ml) not normalized (free): 3268.167985 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3194 0.2154 7.4698 5.0354| | 2: 3.63 - 2.88 1.00 2711 122 0.2636 0.1815 4.3359 4.3322| | 3: 2.88 - 2.52 1.00 2682 148 0.2579 0.1717 4.19 4.1924| | 4: 2.52 - 2.29 1.00 2661 139 0.2528 0.1611 3.5019 3.6125| | 5: 2.29 - 2.13 1.00 2678 122 0.2638 0.1531 3.3959 3.4525| | 6: 2.13 - 2.00 1.00 2692 117 0.2719 0.1776 3.3078 3.3778| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.72 0.77 0.23 1320.98| | 2: 3.63 - 2.88 2711 122 0.82 24.02 1.31 0.23 1320.98| | 3: 2.88 - 2.52 2682 148 0.73 33.23 1.29 0.23 1320.98| | 4: 2.52 - 2.29 2661 139 0.93 11.24 1.30 0.26 133.54| | 5: 2.29 - 2.13 2678 122 0.92 13.41 1.31 0.26 133.54| | 6: 2.13 - 2.00 2692 117 0.90 16.07 1.33 0.26 133.54| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 133.54 max = 1320.98 mean = 733.87| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.96 mean = 19.28| |phase err.(test): min = 0.00 max = 89.01 mean = 19.60| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.254 1557 Z= 5.582 Angle : 5.191 16.376 2118 Z= 3.628 Chirality : 0.397 1.062 243 Planarity : 0.029 0.101 284 Dihedral : 13.965 86.132 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 27.03 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.48), residues: 224 helix: -2.12 (0.37), residues: 109 sheet: -0.42 (0.91), residues: 28 loop : -0.32 (0.63), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.014 ARG A 5 TYR 0.083 0.032 TYR A 139 PHE 0.088 0.041 PHE A 162 HIS 0.033 0.013 HIS A 126 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= 0.2783 r_free= 0.1850 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.393728 | | target function (ml) not normalized (work): 71367.320097 | | target function (ml) not normalized (free): 3268.167985 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3286 percent. r_work = 0.2915 r_free = 0.2011 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2863 0.2915 0.2011 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2863 0.2915 0.2011 n_refl.: 17050 remove outliers: r(all,work,free)=0.2153 0.2162 0.2011 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2127 0.2136 0.1993 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1619 0.1615 0.1694 n_refl.: 17045 remove outliers: r(all,work,free)=0.1617 0.1613 0.1694 n_refl.: 17043 ======================== 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 0.3837 399.179 362.676 0.651 1.011 0.397 11.894-9.307 99.02 97 4 0.1838 633.991 616.679 0.932 1.011 0.370 9.237-7.194 100.00 213 7 0.2151 518.541 510.605 0.960 1.011 0.361 7.162-5.571 100.00 427 22 0.2332 389.166 375.853 0.917 1.010 0.288 5.546-4.326 100.00 867 58 0.1388 534.262 529.392 0.963 1.008 0.210 4.315-3.360 100.00 1859 96 0.1268 508.088 504.304 1.019 1.005 0.181 3.356-2.611 100.00 3867 181 0.1667 333.785 329.124 1.014 0.999 0.048 2.608-2.000 99.99 8818 434 0.1660 217.571 213.614 1.028 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4305 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1613 r_free=0.1694 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1615 r_free=0.1694 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.079901 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.847754 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 0.1351 0.1632 0.0282 0.008 1.0 0.6 0.5 0.0 0 11.040 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.32 2.82 3.012 18.457 0.848 0.023 12.78 16.56 3.79 3.640 18.705 0.848 0.020 Individual atomic B min max mean iso aniso Overall: 6.07 113.90 19.95 4.10 1785 0 Protein: 6.07 112.83 17.19 4.11 1519 0 Water: 8.75 113.90 36.04 N/A 258 0 Other: 22.03 37.97 26.52 N/A 8 0 Chain A: 6.07 113.90 19.95 N/A 1785 0 Histogram: Values Number of atoms 6.07 - 16.85 1072 16.85 - 27.63 352 27.63 - 38.42 187 38.42 - 49.20 99 49.20 - 59.98 48 59.98 - 70.77 12 70.77 - 81.55 7 81.55 - 92.33 4 92.33 - 103.11 1 103.11 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1656 r_work=0.1281 r_free=0.1662 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1662 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 = 0.1275 r_free = 0.1655 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1275 r_free= 0.1655 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019932 | | target function (ls_wunit_k1) not normalized (work): 323.612955 | | target function (ls_wunit_k1) not normalized (free): 27.238699 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1655 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1896 0.1895 0.1981 n_refl.: 17043 remove outliers: r(all,work,free)=0.1896 0.1895 0.1981 n_refl.: 17043 overall B=-0.51 to atoms: r(all,work,free)=0.1860 0.1858 0.1960 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1291 0.1273 0.1650 n_refl.: 17043 remove outliers: r(all,work,free)=0.1289 0.1271 0.1650 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 0.3456 307.041 280.749 0.623 1.006 0.366 11.894-9.307 99.02 97 4 0.1700 488.548 477.190 0.918 1.007 0.364 9.237-7.194 100.00 213 7 0.1835 399.583 395.759 0.959 1.007 0.341 7.162-5.571 100.00 427 22 0.1834 299.888 294.533 0.932 1.006 0.303 5.546-4.326 100.00 867 58 0.1040 411.697 409.132 0.958 1.005 0.201 4.315-3.360 100.00 1859 96 0.0921 391.528 391.012 1.016 1.004 0.192 3.356-2.611 100.00 3867 181 0.1297 257.212 255.925 1.010 1.001 0.091 2.608-2.000 99.99 8818 434 0.1348 167.658 166.340 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1577 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1271 r_free=0.1650 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1271 r_free=0.1650 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1271 r_free=0.1650 | n_water=258 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1280 r_free=0.1639 | n_water=252 | time (s): 19.510 (total time: 20.190) Filter (q & B) r_work=0.1280 r_free=0.1639 | n_water=250 | time (s): 2.200 (total time: 22.390) Compute maps r_work=0.1280 r_free=0.1639 | n_water=250 | time (s): 0.690 (total time: 23.080) Filter (map) r_work=0.1312 r_free=0.1628 | n_water=212 | time (s): 1.970 (total time: 25.050) Find peaks r_work=0.1312 r_free=0.1628 | n_water=212 | time (s): 0.680 (total time: 25.730) Add new water r_work=0.1531 r_free=0.1841 | n_water=370 | time (s): 1.670 (total time: 27.400) Refine new water occ: r_work=0.1324 r_free=0.1577 adp: r_work=0.1268 r_free=0.1566 occ: r_work=0.1274 r_free=0.1544 adp: r_work=0.1242 r_free=0.1546 occ: r_work=0.1243 r_free=0.1535 adp: r_work=0.1231 r_free=0.1535 ADP+occupancy (water only), MIN, final r_work=0.1231 r_free=0.1535 r_work=0.1231 r_free=0.1535 | n_water=370 | time (s): 17.590 (total time: 44.990) Filter (q & B) r_work=0.1233 r_free=0.1536 | n_water=363 | time (s): 1.650 (total time: 46.640) Filter (dist only) r_work=0.1233 r_free=0.1540 | n_water=362 | time (s): 30.030 (total time: 76.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.291894 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.972776 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 0.1204 0.1566 0.0362 0.008 0.9 2.6 0.5 0.0 0 12.146 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 15.66 3.62 4.183 20.901 0.973 0.018 11.91 15.96 4.05 4.182 21.166 0.973 0.017 Individual atomic B min max mean iso aniso Overall: 6.52 107.32 21.17 4.23 1889 0 Protein: 6.52 107.32 17.59 4.22 1519 0 Water: 8.67 65.67 35.93 N/A 362 0 Other: 23.90 45.31 34.08 N/A 8 0 Chain A: 6.52 107.32 19.32 N/A 1739 0 Chain S: 17.23 61.56 42.69 N/A 150 0 Histogram: Values Number of atoms 6.52 - 16.60 1024 16.60 - 26.68 377 26.68 - 36.76 231 36.76 - 46.84 149 46.84 - 56.92 70 56.92 - 67.00 28 67.00 - 77.08 2 77.08 - 87.16 5 87.16 - 97.24 1 97.24 - 107.32 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1596 r_work=0.1192 r_free=0.1597 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1597 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1585 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1188 r_free= 0.1585 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016773 | | target function (ls_wunit_k1) not normalized (work): 272.285788 | | target function (ls_wunit_k1) not normalized (free): 23.640367 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1188 0.1585 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1739 0.1729 0.1946 n_refl.: 17041 remove outliers: r(all,work,free)=0.1739 0.1729 0.1946 n_refl.: 17041 overall B=-0.41 to atoms: r(all,work,free)=0.1713 0.1704 0.1928 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1184 0.1584 n_refl.: 17041 remove outliers: r(all,work,free)=0.1204 0.1184 0.1584 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 0.3367 307.041 286.211 0.595 1.005 0.350 11.894-9.307 99.02 97 4 0.1507 488.548 486.608 0.911 1.006 0.337 9.237-7.194 100.00 213 7 0.1638 399.583 402.487 0.976 1.006 0.285 7.162-5.571 100.00 427 22 0.1532 299.888 297.128 0.938 1.006 0.272 5.546-4.326 100.00 867 58 0.0867 411.697 408.947 0.960 1.005 0.221 4.315-3.360 100.00 1859 96 0.0821 391.528 390.921 1.015 1.003 0.212 3.356-2.611 100.00 3867 181 0.1193 257.212 256.368 1.010 1.000 0.058 2.608-2.000 99.99 8818 434 0.1328 167.658 166.587 1.011 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1457 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1184 r_free=0.1584 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1184 r_free=0.1585 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1585 | n_water=362 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1186 r_free=0.1579 | n_water=361 | time (s): 30.270 (total time: 30.920) Filter (q & B) r_work=0.1186 r_free=0.1579 | n_water=361 | time (s): 1.240 (total time: 32.160) Compute maps r_work=0.1186 r_free=0.1579 | n_water=361 | time (s): 0.790 (total time: 32.950) Filter (map) r_work=0.1250 r_free=0.1609 | n_water=264 | time (s): 1.840 (total time: 34.790) Find peaks r_work=0.1250 r_free=0.1609 | n_water=264 | time (s): 0.670 (total time: 35.460) Add new water r_work=0.1435 r_free=0.1789 | n_water=405 | time (s): 1.890 (total time: 37.350) Refine new water occ: r_work=0.1242 r_free=0.1567 adp: r_work=0.1235 r_free=0.1579 occ: r_work=0.1217 r_free=0.1533 adp: r_work=0.1207 r_free=0.1543 occ: r_work=0.1200 r_free=0.1512 adp: r_work=0.1190 r_free=0.1520 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1520 r_work=0.1190 r_free=0.1520 | n_water=405 | time (s): 37.480 (total time: 74.830) Filter (q & B) r_work=0.1193 r_free=0.1522 | n_water=396 | time (s): 2.460 (total time: 77.290) Filter (dist only) r_work=0.1193 r_free=0.1522 | n_water=396 | time (s): 30.870 (total time: 108.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.849385 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.138418 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 0.1172 0.1554 0.0382 0.009 1.0 3.5 0.5 0.0 0 0.925 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.72 15.54 3.82 4.303 21.307 0.138 4.992 11.52 15.68 4.15 4.828 21.215 0.138 4.972 Individual atomic B min max mean iso aniso Overall: 6.49 104.75 20.65 4.56 1923 0 Protein: 6.49 104.75 16.82 4.55 1519 0 Water: 8.80 63.00 35.14 N/A 396 0 Other: 22.83 42.69 31.00 N/A 8 0 Chain A: 6.49 104.75 18.54 N/A 1735 0 Chain S: 17.95 63.00 40.18 N/A 188 0 Histogram: Values Number of atoms 6.49 - 16.32 1079 16.32 - 26.14 340 26.14 - 35.97 222 35.97 - 45.80 169 45.80 - 55.62 70 55.62 - 65.45 30 65.45 - 75.27 4 75.27 - 85.10 4 85.10 - 94.93 3 94.93 - 104.75 2 =========================== Idealize ADP of riding H ========================== r_work=0.1152 r_free=0.1568 r_work=0.1152 r_free=0.1569 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1152 r_free = 0.1569 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1147 r_free = 0.1558 target_work(ml) = 4.967 | | 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= 0.1147 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.966596 | | target function (ml) not normalized (work): 80627.712020 | | target function (ml) not normalized (free): 4187.794249 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1167 0.1147 0.1558 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1661 0.1654 0.1850 n_refl.: 17041 remove outliers: r(all,work,free)=0.1661 0.1654 0.1850 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1636 0.1628 0.1838 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1165 0.1145 0.1556 n_refl.: 17041 remove outliers: r(all,work,free)=0.1165 0.1145 0.1556 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 0.3574 307.041 283.304 0.571 1.006 0.340 11.894-9.307 99.02 97 4 0.1773 488.548 482.027 0.910 1.007 0.315 9.237-7.194 100.00 213 7 0.1760 399.583 401.291 0.986 1.007 0.255 7.162-5.571 100.00 427 22 0.1638 299.888 294.546 0.941 1.006 0.251 5.546-4.326 100.00 867 58 0.0971 411.697 407.550 0.964 1.006 0.216 4.315-3.360 100.00 1859 96 0.0892 391.528 389.345 1.012 1.004 0.211 3.356-2.611 100.00 3867 181 0.1268 257.212 254.969 1.011 1.001 0.152 2.608-2.000 99.99 8818 434 0.1087 167.658 166.291 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1785 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1556 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1145 r_free=0.1556 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1556 | n_water=396 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1145 r_free=0.1556 | n_water=396 | time (s): 32.280 (total time: 33.000) Filter (q & B) r_work=0.1145 r_free=0.1556 | n_water=396 | time (s): 0.890 (total time: 33.890) Compute maps r_work=0.1145 r_free=0.1556 | n_water=396 | time (s): 0.850 (total time: 34.740) Filter (map) r_work=0.1197 r_free=0.1584 | n_water=312 | time (s): 2.310 (total time: 37.050) Find peaks r_work=0.1197 r_free=0.1584 | n_water=312 | time (s): 0.570 (total time: 37.620) Add new water r_work=0.1342 r_free=0.1728 | n_water=445 | time (s): 2.090 (total time: 39.710) Refine new water occ: r_work=0.1181 r_free=0.1539 adp: r_work=0.1174 r_free=0.1541 occ: r_work=0.1158 r_free=0.1509 adp: r_work=0.1149 r_free=0.1510 occ: r_work=0.1140 r_free=0.1494 adp: r_work=0.1133 r_free=0.1493 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1493 r_work=0.1133 r_free=0.1493 | n_water=445 | time (s): 22.050 (total time: 61.760) Filter (q & B) r_work=0.1136 r_free=0.1499 | n_water=435 | time (s): 2.220 (total time: 63.980) Filter (dist only) r_work=0.1136 r_free=0.1499 | n_water=435 | time (s): 34.660 (total time: 98.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.006046 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.162329 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 0.1125 0.1554 0.0429 0.010 1.0 7.4 0.5 0.0 0 1.003 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.25 15.54 4.29 4.406 20.856 0.162 4.961 11.14 15.47 4.34 4.594 20.870 0.162 4.951 Individual atomic B min max mean iso aniso Overall: 5.92 103.03 20.75 4.80 1962 0 Protein: 5.92 103.03 16.38 4.79 1519 0 Water: 8.48 67.14 35.85 N/A 435 0 Other: 22.73 42.04 30.08 N/A 8 0 Chain A: 5.92 103.03 18.04 N/A 1734 0 Chain S: 16.14 67.14 41.43 N/A 228 0 Histogram: Values Number of atoms 5.92 - 15.63 1054 15.63 - 25.34 367 25.34 - 35.05 215 35.05 - 44.76 180 44.76 - 54.48 97 54.48 - 64.19 35 64.19 - 73.90 7 73.90 - 83.61 2 83.61 - 93.32 3 93.32 - 103.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1114 r_free=0.1547 r_work=0.1114 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1114 r_free = 0.1548 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1555 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1103 r_free= 0.1555 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.946364 | | target function (ml) not normalized (work): 80299.280232 | | target function (ml) not normalized (free): 4182.911647 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1103 0.1555 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1584 0.1570 0.1892 n_refl.: 17041 remove outliers: r(all,work,free)=0.1584 0.1570 0.1892 n_refl.: 17041 overall B=-0.26 to atoms: r(all,work,free)=0.1569 0.1553 0.1883 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1101 0.1554 n_refl.: 17041 remove outliers: r(all,work,free)=0.1123 0.1101 0.1554 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 0.3689 307.041 280.594 0.566 1.003 0.340 11.894-9.307 99.02 97 4 0.1749 488.548 482.227 0.912 1.004 0.338 9.237-7.194 100.00 213 7 0.1678 399.583 401.526 0.987 1.004 0.230 7.162-5.571 100.00 427 22 0.1522 299.888 294.780 0.941 1.004 0.220 5.546-4.326 100.00 867 58 0.0925 411.697 408.378 0.962 1.003 0.205 4.315-3.360 100.00 1859 96 0.0841 391.528 389.307 1.006 1.002 0.201 3.356-2.611 100.00 3867 181 0.1237 257.212 255.176 1.002 1.001 0.141 2.608-2.000 99.99 8818 434 0.1042 167.658 166.479 0.997 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9020 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1101 r_free=0.1554 After: r_work=0.1103 r_free=0.1553 ================================== NQH flips ================================== r_work=0.1103 r_free=0.1553 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=0.1105 r_free=0.1555 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1105 r_free=0.1555 | n_water=435 | time (s): 0.930 (total time: 0.930) Filter (dist) r_work=0.1105 r_free=0.1555 | n_water=435 | time (s): 35.030 (total time: 35.960) Filter (q & B) r_work=0.1106 r_free=0.1555 | n_water=432 | time (s): 2.380 (total time: 38.340) Compute maps r_work=0.1106 r_free=0.1555 | n_water=432 | time (s): 0.690 (total time: 39.030) Filter (map) r_work=0.1180 r_free=0.1547 | n_water=328 | time (s): 1.570 (total time: 40.600) Find peaks r_work=0.1180 r_free=0.1547 | n_water=328 | time (s): 0.470 (total time: 41.070) Add new water r_work=0.1307 r_free=0.1650 | n_water=452 | time (s): 1.810 (total time: 42.880) Refine new water occ: r_work=0.1152 r_free=0.1509 adp: r_work=0.1146 r_free=0.1512 occ: r_work=0.1130 r_free=0.1490 adp: r_work=0.1122 r_free=0.1494 occ: r_work=0.1115 r_free=0.1480 adp: r_work=0.1109 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1109 r_free=0.1482 r_work=0.1109 r_free=0.1482 | n_water=452 | time (s): 42.330 (total time: 85.210) Filter (q & B) r_work=0.1111 r_free=0.1490 | n_water=444 | time (s): 2.080 (total time: 87.290) Filter (dist only) r_work=0.1111 r_free=0.1490 | n_water=444 | time (s): 34.540 (total time: 121.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.902687 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.142691 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 0.1138 0.1507 0.0369 0.009 1.0 7.7 0.5 0.0 0 0.951 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.38 15.07 3.69 4.503 20.630 0.143 4.957 11.27 15.05 3.78 4.597 20.682 0.143 4.948 Individual atomic B min max mean iso aniso Overall: 5.74 101.24 20.72 4.89 1971 0 Protein: 5.74 101.24 16.14 4.88 1519 0 Water: 8.02 62.85 36.24 N/A 444 0 Other: 20.22 39.54 28.48 N/A 8 0 Chain A: 5.74 101.24 17.74 N/A 1733 0 Chain S: 18.82 62.85 42.40 N/A 238 0 Histogram: Values Number of atoms 5.74 - 15.29 1055 15.29 - 24.84 365 24.84 - 34.39 188 34.39 - 43.94 190 43.94 - 53.49 122 53.49 - 63.04 33 63.04 - 72.59 8 72.59 - 82.14 4 82.14 - 91.69 2 91.69 - 101.24 4 =========================== Idealize ADP of riding H ========================== r_work=0.1127 r_free=0.1505 r_work=0.1127 r_free=0.1505 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1127 r_free = 0.1505 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1119 r_free = 0.1498 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1119 r_free= 0.1498 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.943160 | | target function (ml) not normalized (work): 80247.260449 | | target function (ml) not normalized (free): 4165.095394 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1134 0.1354 5.4834 5.641| | 2: 3.63 - 2.88 1.00 2711 122 0.1099 0.1547 5.2238 5.3888| | 3: 2.88 - 2.52 1.00 2681 148 0.1363 0.1647 5.1284 5.189| | 4: 2.52 - 2.29 1.00 2661 139 0.0954 0.1465 4.634 4.9408| | 5: 2.29 - 2.13 1.00 2678 122 0.0975 0.1452 4.5811 4.8655| | 6: 2.13 - 2.00 1.00 2692 117 0.1135 0.1792 4.5777 4.8069| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2811 159 0.95 8.77 1.00 0.96 6306.86| | 2: 3.63 - 2.88 2711 122 0.92 12.73 1.01 0.96 6306.86| | 3: 2.88 - 2.52 2681 148 0.88 18.85 0.99 0.96 6306.86| | 4: 2.52 - 2.29 2661 139 0.93 11.90 1.01 0.98 2095.66| | 5: 2.29 - 2.13 2678 122 0.92 14.00 1.00 0.98 2095.66| | 6: 2.13 - 2.00 2692 117 0.90 16.69 0.99 0.98 2095.66| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2095.66 max = 6306.86 mean = 4223.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.92 mean = 13.78| |phase err.(test): min = 0.00 max = 88.43 mean = 13.20| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1138 0.1119 0.1498 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1574 0.1561 0.1827 n_refl.: 17041 remove outliers: r(all,work,free)=0.1574 0.1561 0.1827 n_refl.: 17041 overall B=-0.22 to atoms: r(all,work,free)=0.1561 0.1549 0.1819 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1120 0.1500 n_refl.: 17041 remove outliers: r(all,work,free)=0.1137 0.1119 0.1500 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 0.3630 303.544 281.364 0.554 1.006 0.338 11.894-9.307 99.02 97 4 0.1817 488.548 479.083 0.909 1.007 0.299 9.237-7.194 100.00 213 7 0.1744 399.583 399.989 0.980 1.007 0.239 7.162-5.571 100.00 427 22 0.1582 299.888 294.596 0.936 1.007 0.217 5.546-4.326 100.00 867 58 0.0950 411.697 408.652 0.959 1.006 0.200 4.315-3.360 100.00 1859 96 0.0873 391.528 389.584 1.003 1.003 0.201 3.356-2.611 100.00 3867 181 0.1248 257.212 254.975 1.000 1.000 0.121 2.608-2.000 99.99 8818 434 0.1051 167.658 166.360 0.994 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.7523 ================= 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 : 0.2783 0.1850 0.083 5.191 8.8 119.3 19.9 258 0.000 1_bss: 0.1613 0.1694 0.083 5.191 8.4 118.9 19.5 258 0.000 1_settarget: 0.1613 0.1694 0.083 5.191 8.4 118.9 19.5 258 0.000 1_nqh: 0.1615 0.1694 0.083 5.191 8.4 118.9 19.5 258 0.003 1_weight: 0.1615 0.1694 0.083 5.191 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1351 0.1632 0.008 0.965 8.4 118.9 19.5 258 0.155 1_adp: 0.1278 0.1656 0.008 0.965 6.1 113.9 20.0 258 0.155 1_regHadp: 0.1281 0.1662 0.008 0.965 6.1 113.9 20.0 258 0.155 1_occ: 0.1275 0.1655 0.008 0.965 6.1 113.9 20.0 258 0.155 2_bss: 0.1271 0.1650 0.008 0.965 5.6 113.4 19.4 258 0.155 2_settarget: 0.1271 0.1650 0.008 0.965 5.6 113.4 19.4 258 0.155 2_updatecdl: 0.1271 0.1650 0.009 0.977 5.6 113.4 19.4 258 0.155 2_nqh: 0.1271 0.1650 0.009 0.977 5.6 113.4 19.4 258 0.155 2_sol: 0.1233 0.1540 0.009 0.977 5.6 112.3 20.7 362 n/a 2_weight: 0.1233 0.1540 0.009 0.977 5.6 112.3 20.7 362 n/a 2_xyzrec: 0.1204 0.1566 0.008 0.929 5.6 112.3 20.7 362 n/a 2_adp: 0.1191 0.1596 0.008 0.929 6.5 107.3 21.2 362 n/a 2_regHadp: 0.1192 0.1597 0.008 0.929 6.5 107.3 21.2 362 n/a 2_occ: 0.1188 0.1585 0.008 0.929 6.5 107.3 21.2 362 n/a 3_bss: 0.1184 0.1584 0.008 0.929 6.1 106.9 20.8 362 n/a 3_settarget: 0.1184 0.1584 0.008 0.929 6.1 106.9 20.8 362 n/a 3_updatecdl: 0.1184 0.1584 0.008 0.928 6.1 106.9 20.8 362 n/a 3_nqh: 0.1184 0.1585 0.008 0.928 6.1 106.9 20.8 362 n/a 3_sol: 0.1193 0.1522 0.008 0.928 6.1 106.9 20.8 396 n/a 3_weight: 0.1193 0.1522 0.008 0.928 6.1 106.9 20.8 396 n/a 3_xyzrec: 0.1172 0.1554 0.009 0.961 6.1 106.9 20.8 396 n/a 3_adp: 0.1152 0.1568 0.009 0.961 6.5 104.8 20.7 396 n/a 3_regHadp: 0.1152 0.1569 0.009 0.961 6.5 104.8 20.7 396 n/a 3_occ: 0.1147 0.1558 0.009 0.961 6.5 104.8 20.7 396 n/a 4_bss: 0.1145 0.1556 0.009 0.961 6.1 104.4 20.3 396 n/a 4_settarget: 0.1145 0.1556 0.009 0.961 6.1 104.4 20.3 396 n/a 4_updatecdl: 0.1145 0.1556 0.009 0.961 6.1 104.4 20.3 396 n/a 4_nqh: 0.1145 0.1556 0.009 0.961 6.1 104.4 20.3 396 n/a 4_sol: 0.1136 0.1499 0.009 0.961 6.1 104.4 20.7 435 n/a 4_weight: 0.1136 0.1499 0.009 0.961 6.1 104.4 20.7 435 n/a 4_xyzrec: 0.1125 0.1554 0.010 1.002 6.1 104.4 20.7 435 n/a 4_adp: 0.1114 0.1547 0.010 1.002 5.9 103.0 20.8 435 n/a 4_regHadp: 0.1114 0.1548 0.010 1.002 5.9 103.0 20.8 435 n/a 4_occ: 0.1103 0.1555 0.010 1.002 5.9 103.0 20.8 435 n/a 5_bss: 0.1101 0.1554 0.010 1.002 5.7 102.8 20.5 435 n/a 5_settarget: 0.1101 0.1554 0.010 1.002 5.7 102.8 20.5 435 n/a 5_updatecdl: 0.1101 0.1554 0.010 1.003 5.7 102.8 20.5 435 n/a 5_setrh: 0.1103 0.1553 0.010 1.003 5.7 102.8 20.5 435 n/a 5_nqh: 0.1105 0.1555 0.010 1.003 5.7 102.8 20.5 435 n/a 5_sol: 0.1111 0.1490 0.010 1.003 5.7 102.8 20.6 444 n/a 5_weight: 0.1111 0.1490 0.010 1.003 5.7 102.8 20.6 444 n/a 5_xyzrec: 0.1138 0.1507 0.009 1.017 5.7 102.8 20.6 444 n/a 5_adp: 0.1127 0.1505 0.009 1.017 5.7 101.2 20.7 444 n/a 5_regHadp: 0.1127 0.1505 0.009 1.017 5.7 101.2 20.7 444 n/a 5_occ: 0.1119 0.1498 0.009 1.017 5.7 101.2 20.7 444 n/a end: 0.1119 0.1500 0.009 1.017 5.5 101.0 20.5 444 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8530786_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8530786_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2400 Refinement macro-cycles (run) : 951.4800 Write final files (write_after_run_outputs) : 17.9300 Total : 972.6500 Total CPU time: 16.58 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:36 PST -0800 (1735494096.50 s) Start R-work = 0.1613, R-free = 0.1694 Final R-work = 0.1119, R-free = 0.1500 =============================================================================== Job complete usr+sys time: 1014.05 seconds wall clock time: 17 minutes 17.53 seconds (1037.53 seconds total)