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_7650209.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_7650209.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7650209.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: 1.89, per 1000 atoms: 0.56 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: 0.50 Conformation dependent library (CDL) restraints added in 132.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 512 0.91 - 1.16: 1114 1.16 - 1.40: 601 1.40 - 1.65: 859 1.65 - 1.90: 67 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 165 " pdb=" CA ALA A 165 " ideal model delta sigma weight residual 1.459 1.184 0.275 1.19e-02 7.06e+03 5.34e+02 bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.509 -0.188 1.00e-02 1.00e+04 3.52e+02 bond pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 1.332 1.489 -0.157 8.60e-03 1.35e+04 3.33e+02 bond pdb=" CA ARG A 48 " pdb=" C ARG A 48 " ideal model delta sigma weight residual 1.526 1.751 -0.225 1.28e-02 6.10e+03 3.10e+02 bond pdb=" C HIS A 126 " pdb=" O HIS A 126 " ideal model delta sigma weight residual 1.234 1.018 0.216 1.27e-02 6.20e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 2849 4.17 - 8.35: 1898 8.35 - 12.52: 807 12.52 - 16.69: 201 16.69 - 20.86: 22 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 152 " pdb=" C ILE A 152 " pdb=" N ALEU A 153 " ideal model delta sigma weight residual 122.99 137.39 -14.40 1.07e+00 8.73e-01 1.81e+02 angle pdb=" CA BLEU A 153 " pdb=" C BLEU A 153 " pdb=" O BLEU A 153 " ideal model delta sigma weight residual 120.30 134.14 -13.84 1.07e+00 8.73e-01 1.67e+02 angle pdb=" OD1 ASN A 81 " pdb=" CG ASN A 81 " pdb=" ND2 ASN A 81 " ideal model delta sigma weight residual 122.60 110.15 12.45 1.00e+00 1.00e+00 1.55e+02 angle pdb=" C LEU A 77 " pdb=" N GLY A 78 " pdb=" CA GLY A 78 " ideal model delta sigma weight residual 119.94 133.62 -13.68 1.11e+00 8.12e-01 1.52e+02 angle pdb=" O LEU A 7 " pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 123.27 109.53 13.74 1.13e+00 7.83e-01 1.48e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 1278 16.41 - 32.81: 145 32.81 - 49.21: 37 49.21 - 65.62: 16 65.62 - 82.02: 5 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ALA A 2 " pdb=" C ALA A 2 " pdb=" CA ALA A 2 " pdb=" CB ALA A 2 " ideal model delta harmonic sigma weight residual 122.90 140.97 -18.07 0 2.50e+00 1.60e-01 5.22e+01 dihedral pdb=" C BTYR A 67 " pdb=" N BTYR A 67 " pdb=" CA BTYR A 67 " pdb=" CB BTYR A 67 " ideal model delta harmonic sigma weight residual -122.60 -104.87 -17.73 0 2.50e+00 1.60e-01 5.03e+01 dihedral pdb=" C ASP A 68 " pdb=" N ASP A 68 " pdb=" CA ASP A 68 " pdb=" CB ASP A 68 " ideal model delta harmonic sigma weight residual -122.60 -139.97 17.37 0 2.50e+00 1.60e-01 4.83e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.215: 92 0.215 - 0.424: 79 0.424 - 0.634: 44 0.634 - 0.844: 22 0.844 - 1.053: 6 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 -1.54 -1.05 2.00e-01 2.50e+01 2.77e+01 chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.49 -0.98 2.00e-01 2.50e+01 2.38e+01 chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.28e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.110 2.00e-02 2.50e+03 7.83e-02 1.84e+02 pdb=" CG PHE A 119 " -0.167 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.113 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.058 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.043 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.089 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.066 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG TYR A 139 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.092 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.050 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.119 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.053 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.084 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.005 2.00e-02 2.50e+03 5.59e-02 9.38e+01 pdb=" CG PHE A 164 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.080 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.052 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.086 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1035 2.32 - 2.89: 8049 2.89 - 3.46: 10545 3.46 - 4.03: 15207 4.03 - 4.60: 21803 Nonbonded interactions: 56639 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.748 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.846 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.857 2.450 nonbonded pdb=" O LEU A 92 " pdb=" H AGLU A 96 " model vdw 1.866 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.866 2.100 ... (remaining 56634 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_7650209_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= 0.2794 r_free= 0.1811 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.412075 | | target function (ml) not normalized (work): 71665.338555 | | target function (ml) not normalized (free): 3261.716745 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3204 0.2170 7.5908 5.0385| | 2: 3.63 - 2.88 1.00 2711 122 0.2635 0.1697 4.3212 4.3343| | 3: 2.88 - 2.52 1.00 2682 148 0.2583 0.1661 4.1792 4.1806| | 4: 2.52 - 2.29 1.00 2661 139 0.2556 0.1610 3.5005 3.6554| | 5: 2.29 - 2.13 1.00 2678 122 0.2632 0.1541 3.3998 3.4286| | 6: 2.13 - 2.00 1.00 2692 117 0.2773 0.1598 3.315 3.3051| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.58 0.77 0.23 1282.30| | 2: 3.63 - 2.88 2711 122 0.83 23.65 1.31 0.23 1282.30| | 3: 2.88 - 2.52 2682 148 0.73 32.77 1.29 0.23 1282.30| | 4: 2.52 - 2.29 2661 139 0.93 11.49 1.30 0.26 134.75| | 5: 2.29 - 2.13 2678 122 0.92 13.43 1.32 0.26 134.75| | 6: 2.13 - 2.00 2692 117 0.90 16.31 1.34 0.26 134.75| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 134.75 max = 1282.30 mean = 714.92| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.90 mean = 19.21| |phase err.(test): min = 0.00 max = 88.11 mean = 19.16| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.275 1557 Z= 5.637 Angle : 5.171 17.906 2118 Z= 3.655 Chirality : 0.401 1.053 243 Planarity : 0.032 0.108 284 Dihedral : 14.076 82.020 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.08 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % 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: -2.43 (0.46), residues: 224 helix: -2.39 (0.38), residues: 102 sheet: -0.74 (0.75), residues: 38 loop : -0.61 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.016 ARG A 156 TYR 0.061 0.025 TYR A 141 PHE 0.151 0.039 PHE A 119 HIS 0.088 0.044 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= 0.2794 r_free= 0.1811 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.412075 | | target function (ml) not normalized (work): 71665.338555 | | target function (ml) not normalized (free): 3261.716745 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2821 percent. r_work = 0.2922 r_free = 0.1993 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2868 0.2922 0.1993 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2868 0.2922 0.1993 n_refl.: 17050 remove outliers: r(all,work,free)=0.2158 0.2169 0.1993 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2130 0.2141 0.1976 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1616 0.1614 0.1672 n_refl.: 17045 remove outliers: r(all,work,free)=0.1615 0.1613 0.1672 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 0.4025 395.027 364.772 0.651 1.017 0.397 11.894-9.307 99.02 97 4 0.1918 634.030 615.991 0.926 1.018 0.380 9.237-7.194 100.00 213 7 0.2169 518.573 508.338 0.954 1.018 0.381 7.162-5.571 100.00 427 22 0.2311 389.189 376.212 0.923 1.016 0.331 5.546-4.326 100.00 867 58 0.1404 534.295 527.910 0.952 1.013 0.220 4.315-3.360 100.00 1859 96 0.1279 508.119 503.648 1.015 1.008 0.201 3.356-2.611 100.00 3867 181 0.1673 333.806 329.079 1.013 0.999 0.071 2.608-2.000 99.99 8818 434 0.1639 217.584 213.697 1.037 0.982 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4492 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1613 r_free=0.1672 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1613 r_free=0.1672 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.437052 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.835373 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 0.1350 0.1632 0.0282 0.008 1.0 1.0 0.5 0.0 0 11.219 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.32 2.82 3.013 18.453 0.835 0.023 12.77 16.54 3.77 3.591 18.711 0.835 0.020 Individual atomic B min max mean iso aniso Overall: 6.22 113.89 19.97 4.04 1785 0 Protein: 6.22 112.07 17.22 4.04 1519 0 Water: 8.73 113.89 35.98 N/A 258 0 Other: 21.48 37.04 26.25 N/A 8 0 Chain A: 6.22 113.89 19.97 N/A 1785 0 Histogram: Values Number of atoms 6.22 - 16.99 1089 16.99 - 27.75 340 27.75 - 38.52 185 38.52 - 49.29 96 49.29 - 60.06 48 60.06 - 70.82 13 70.82 - 81.59 6 81.59 - 92.36 4 92.36 - 103.13 1 103.13 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1654 r_work=0.1281 r_free=0.1661 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1661 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 = 0.1276 r_free = 0.1657 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.28 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= 0.1276 r_free= 0.1657 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020029 | | target function (ls_wunit_k1) not normalized (work): 325.215333 | | target function (ls_wunit_k1) not normalized (free): 26.841251 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1276 0.1657 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1917 0.1917 0.1985 n_refl.: 17044 remove outliers: r(all,work,free)=0.1917 0.1917 0.1985 n_refl.: 17044 overall B=-0.40 to atoms: r(all,work,free)=0.1888 0.1887 0.1968 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1277 0.1650 n_refl.: 17044 remove outliers: r(all,work,free)=0.1293 0.1275 0.1650 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 0.3518 302.977 279.636 0.629 1.009 0.370 11.894-9.307 99.02 97 4 0.1714 487.291 477.319 0.918 1.010 0.367 9.237-7.194 100.00 213 7 0.1819 398.555 395.491 0.959 1.010 0.351 7.162-5.571 100.00 427 22 0.1816 299.116 294.259 0.932 1.009 0.311 5.546-4.326 100.00 867 58 0.1046 410.638 408.466 0.957 1.008 0.211 4.315-3.360 100.00 1859 96 0.0927 390.521 390.208 1.018 1.005 0.191 3.356-2.611 100.00 3867 181 0.1298 256.550 255.334 1.015 1.000 0.091 2.608-2.000 99.99 8818 434 0.1354 167.227 165.730 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=-1.4100 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1650 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1650 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1650 | n_water=258 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1280 r_free=0.1638 | n_water=254 | time (s): 20.020 (total time: 20.640) Filter (q & B) r_work=0.1281 r_free=0.1638 | n_water=252 | time (s): 1.620 (total time: 22.260) Compute maps r_work=0.1281 r_free=0.1638 | n_water=252 | time (s): 0.600 (total time: 22.860) Filter (map) r_work=0.1316 r_free=0.1629 | n_water=214 | time (s): 1.540 (total time: 24.400) Find peaks r_work=0.1316 r_free=0.1629 | n_water=214 | time (s): 0.430 (total time: 24.830) Add new water r_work=0.1537 r_free=0.1835 | n_water=374 | time (s): 1.440 (total time: 26.270) Refine new water occ: r_work=0.1332 r_free=0.1563 adp: r_work=0.1270 r_free=0.1556 occ: r_work=0.1276 r_free=0.1525 adp: r_work=0.1241 r_free=0.1527 occ: r_work=0.1241 r_free=0.1516 adp: r_work=0.1232 r_free=0.1518 ADP+occupancy (water only), MIN, final r_work=0.1232 r_free=0.1518 r_work=0.1232 r_free=0.1518 | n_water=374 | time (s): 20.690 (total time: 46.960) Filter (q & B) r_work=0.1235 r_free=0.1516 | n_water=363 | time (s): 1.490 (total time: 48.450) Filter (dist only) r_work=0.1235 r_free=0.1516 | n_water=363 | time (s): 27.100 (total time: 75.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.286483 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.981347 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 0.1211 0.1566 0.0354 0.008 0.9 3.2 0.5 0.0 0 12.643 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 15.66 3.54 4.148 21.086 0.981 0.018 11.98 15.83 3.85 4.155 21.339 0.981 0.018 Individual atomic B min max mean iso aniso Overall: 6.59 106.67 21.38 4.21 1890 0 Protein: 6.59 106.67 17.71 4.20 1519 0 Water: 8.77 68.16 36.46 N/A 363 0 Other: 24.97 43.77 33.92 N/A 8 0 Chain A: 6.59 106.67 19.49 N/A 1741 0 Chain S: 18.02 65.65 43.47 N/A 149 0 Histogram: Values Number of atoms 6.59 - 16.60 1008 16.60 - 26.60 392 26.60 - 36.61 225 36.61 - 46.62 150 46.62 - 56.63 76 56.63 - 66.64 27 66.64 - 76.65 5 76.65 - 86.65 3 86.65 - 96.66 2 96.66 - 106.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1583 r_work=0.1199 r_free=0.1585 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1585 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1585 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.28 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= 0.1196 r_free= 0.1585 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016981 | | target function (ls_wunit_k1) not normalized (work): 275.686086 | | target function (ls_wunit_k1) not normalized (free): 23.946251 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1196 0.1585 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1761 0.1757 0.1888 n_refl.: 17042 remove outliers: r(all,work,free)=0.1761 0.1757 0.1888 n_refl.: 17042 overall B=-0.39 to atoms: r(all,work,free)=0.1736 0.1731 0.1870 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1189 0.1575 n_refl.: 17042 remove outliers: r(all,work,free)=0.1207 0.1188 0.1575 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 0.3314 299.820 281.801 0.619 1.002 0.360 11.894-9.307 99.02 97 4 0.1483 487.291 483.378 0.920 1.003 0.355 9.237-7.194 100.00 213 7 0.1638 398.555 398.017 0.978 1.003 0.288 7.162-5.571 100.00 427 22 0.1539 299.116 295.149 0.933 1.003 0.281 5.546-4.326 100.00 867 58 0.0864 410.638 407.268 0.960 1.003 0.216 4.315-3.360 100.00 1859 96 0.0819 390.521 389.392 1.017 1.003 0.211 3.356-2.611 100.00 3867 181 0.1205 256.550 255.916 1.012 1.002 0.111 2.608-2.000 99.99 8818 434 0.1333 167.227 166.637 1.017 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4013 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1575 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=0.1189 r_free=0.1576 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1576 | n_water=363 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.1189 r_free=0.1576 | n_water=363 | time (s): 26.790 (total time: 27.490) Filter (q & B) r_work=0.1189 r_free=0.1576 | n_water=363 | time (s): 0.820 (total time: 28.310) Compute maps r_work=0.1189 r_free=0.1576 | n_water=363 | time (s): 0.630 (total time: 28.940) Filter (map) r_work=0.1257 r_free=0.1613 | n_water=261 | time (s): 1.800 (total time: 30.740) Find peaks r_work=0.1257 r_free=0.1613 | n_water=261 | time (s): 0.660 (total time: 31.400) Add new water r_work=0.1442 r_free=0.1785 | n_water=406 | time (s): 2.080 (total time: 33.480) Refine new water occ: r_work=0.1245 r_free=0.1564 adp: r_work=0.1237 r_free=0.1568 occ: r_work=0.1217 r_free=0.1535 adp: r_work=0.1206 r_free=0.1537 occ: r_work=0.1198 r_free=0.1513 adp: r_work=0.1187 r_free=0.1516 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1516 r_work=0.1187 r_free=0.1516 | n_water=406 | time (s): 39.320 (total time: 72.800) Filter (q & B) r_work=0.1189 r_free=0.1515 | n_water=401 | time (s): 1.880 (total time: 74.680) Filter (dist only) r_work=0.1189 r_free=0.1515 | n_water=401 | time (s): 28.980 (total time: 103.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.047906 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.149827 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 0.1165 0.1517 0.0352 0.010 1.0 3.8 0.5 0.0 0 1.024 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.65 15.17 3.52 4.296 21.491 0.150 4.984 11.45 15.22 3.77 4.832 21.399 0.150 4.961 Individual atomic B min max mean iso aniso Overall: 5.71 104.58 20.85 4.67 1928 0 Protein: 5.71 104.58 16.96 4.66 1519 0 Water: 8.65 63.26 35.31 N/A 401 0 Other: 26.30 44.85 34.07 N/A 8 0 Chain A: 5.71 104.58 18.70 N/A 1736 0 Chain S: 18.58 63.26 40.25 N/A 192 0 Histogram: Values Number of atoms 5.71 - 15.60 1023 15.60 - 25.48 369 25.48 - 35.37 237 35.37 - 45.26 177 45.26 - 55.15 79 55.15 - 65.03 29 65.03 - 74.92 6 74.92 - 84.81 3 84.81 - 94.70 3 94.70 - 104.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1522 r_work=0.1145 r_free=0.1523 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1523 target_work(ml) = 4.961 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1138 r_free = 0.1519 target_work(ml) = 4.956 | | occupancies: max = 1.00 min = 0.19 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= 0.1138 r_free= 0.1519 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.956031 | | target function (ml) not normalized (work): 80456.212666 | | target function (ml) not normalized (free): 4176.578128 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1157 0.1138 0.1519 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1666 0.1659 0.1836 n_refl.: 17041 remove outliers: r(all,work,free)=0.1666 0.1659 0.1836 n_refl.: 17041 overall B=-0.50 to atoms: r(all,work,free)=0.1632 0.1625 0.1821 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1156 0.1138 0.1513 n_refl.: 17041 remove outliers: r(all,work,free)=0.1155 0.1137 0.1513 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 0.3508 296.260 278.578 0.574 1.003 0.340 11.894-9.307 99.02 97 4 0.1711 487.291 482.127 0.920 1.004 0.330 9.237-7.194 100.00 213 7 0.1710 398.555 400.431 0.989 1.004 0.275 7.162-5.571 100.00 427 22 0.1592 299.116 294.515 0.939 1.004 0.251 5.546-4.326 100.00 867 58 0.0940 410.638 406.984 0.965 1.004 0.211 4.315-3.360 100.00 1859 96 0.0882 390.521 388.389 1.012 1.003 0.212 3.356-2.611 100.00 3867 181 0.1266 256.550 254.533 1.010 1.001 0.142 2.608-2.000 99.99 8818 434 0.1092 167.227 165.842 1.007 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1412 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1137 r_free=0.1513 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=0.1137 r_free=0.1511 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1511 | n_water=401 | time (s): 0.910 (total time: 0.910) Filter (dist) r_work=0.1138 r_free=0.1513 | n_water=400 | time (s): 32.490 (total time: 33.400) Filter (q & B) r_work=0.1138 r_free=0.1511 | n_water=399 | time (s): 1.990 (total time: 35.390) Compute maps r_work=0.1138 r_free=0.1511 | n_water=399 | time (s): 0.860 (total time: 36.250) Filter (map) r_work=0.1189 r_free=0.1541 | n_water=314 | time (s): 1.890 (total time: 38.140) Find peaks r_work=0.1189 r_free=0.1541 | n_water=314 | time (s): 0.580 (total time: 38.720) Add new water r_work=0.1333 r_free=0.1687 | n_water=449 | time (s): 2.200 (total time: 40.920) Refine new water occ: r_work=0.1173 r_free=0.1513 adp: r_work=0.1166 r_free=0.1514 occ: r_work=0.1149 r_free=0.1500 adp: r_work=0.1142 r_free=0.1496 occ: r_work=0.1136 r_free=0.1490 adp: r_work=0.1129 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1491 r_work=0.1129 r_free=0.1491 | n_water=449 | time (s): 30.070 (total time: 70.990) Filter (q & B) r_work=0.1133 r_free=0.1493 | n_water=439 | time (s): 1.480 (total time: 72.470) Filter (dist only) r_work=0.1136 r_free=0.1494 | n_water=437 | time (s): 34.260 (total time: 106.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.846696 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.156281 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 0.1129 0.1544 0.0415 0.009 1.0 4.5 0.5 0.0 0 0.923 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.29 15.44 4.15 4.482 20.913 0.156 4.960 11.16 15.44 4.28 4.607 20.909 0.156 4.952 Individual atomic B min max mean iso aniso Overall: 5.60 101.58 20.74 4.74 1964 0 Protein: 5.60 101.58 16.36 4.74 1519 0 Water: 8.34 62.86 35.73 N/A 437 0 Other: 26.13 45.85 34.15 N/A 8 0 Chain A: 5.60 101.58 18.05 N/A 1734 0 Chain S: 16.01 62.86 41.09 N/A 230 0 Histogram: Values Number of atoms 5.60 - 15.20 1030 15.20 - 24.79 375 24.79 - 34.39 209 34.39 - 43.99 194 43.99 - 53.59 111 53.59 - 63.19 30 63.19 - 72.78 5 72.78 - 82.38 5 82.38 - 91.98 2 91.98 - 101.58 3 =========================== Idealize ADP of riding H ========================== r_work=0.1116 r_free=0.1544 r_work=0.1116 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1116 r_free = 0.1544 target_work(ml) = 4.953 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1108 r_free = 0.1554 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.21 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= 0.1108 r_free= 0.1554 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.951384 | | target function (ml) not normalized (work): 80375.809775 | | target function (ml) not normalized (free): 4188.074490 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1108 0.1554 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1587 0.1575 0.1866 n_refl.: 17040 remove outliers: r(all,work,free)=0.1587 0.1575 0.1866 n_refl.: 17040 overall B=-0.26 to atoms: r(all,work,free)=0.1571 0.1558 0.1857 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1127 0.1105 0.1548 n_refl.: 17040 remove outliers: r(all,work,free)=0.1127 0.1105 0.1548 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 0.3683 296.260 275.260 0.546 1.005 0.330 11.894-9.307 99.02 97 4 0.1809 487.291 480.662 0.917 1.005 0.330 9.237-7.194 100.00 213 7 0.1730 398.555 400.938 0.991 1.005 0.235 7.162-5.571 100.00 427 22 0.1525 299.116 293.195 0.937 1.004 0.211 5.546-4.326 100.00 867 58 0.0906 410.638 406.890 0.963 1.004 0.201 4.315-3.360 100.00 1859 96 0.0855 390.521 388.545 1.006 1.003 0.201 3.356-2.611 100.00 3867 181 0.1242 256.550 254.480 1.003 1.001 0.141 2.608-2.000 99.99 8818 434 0.1046 167.227 166.025 0.998 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9160 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1105 r_free=0.1548 After: r_work=0.1107 r_free=0.1547 ================================== NQH flips ================================== r_work=0.1107 r_free=0.1547 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=0.1107 r_free=0.1547 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1107 r_free=0.1547 | n_water=437 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1108 r_free=0.1545 | n_water=435 | time (s): 36.390 (total time: 37.010) Filter (q & B) r_work=0.1108 r_free=0.1545 | n_water=435 | time (s): 0.800 (total time: 37.810) Compute maps r_work=0.1108 r_free=0.1545 | n_water=435 | time (s): 0.750 (total time: 38.560) Filter (map) r_work=0.1175 r_free=0.1553 | n_water=329 | time (s): 1.710 (total time: 40.270) Find peaks r_work=0.1175 r_free=0.1553 | n_water=329 | time (s): 0.530 (total time: 40.800) Add new water r_work=0.1288 r_free=0.1673 | n_water=467 | time (s): 1.520 (total time: 42.320) Refine new water occ: r_work=0.1138 r_free=0.1516 adp: r_work=0.1131 r_free=0.1517 occ: r_work=0.1120 r_free=0.1501 adp: r_work=0.1112 r_free=0.1502 occ: r_work=0.1106 r_free=0.1494 adp: r_work=0.1100 r_free=0.1494 ADP+occupancy (water only), MIN, final r_work=0.1100 r_free=0.1494 r_work=0.1100 r_free=0.1494 | n_water=467 | time (s): 24.570 (total time: 66.890) Filter (q & B) r_work=0.1104 r_free=0.1508 | n_water=456 | time (s): 1.740 (total time: 68.630) Filter (dist only) r_work=0.1104 r_free=0.1509 | n_water=455 | time (s): 34.470 (total time: 103.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.980089 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.148675 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 0.1126 0.1520 0.0394 0.010 1.1 6.1 0.5 0.0 0 0.990 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.20 3.94 4.481 20.664 0.149 4.946 11.16 15.09 3.92 4.617 20.703 0.149 4.940 Individual atomic B min max mean iso aniso Overall: 5.21 100.00 20.74 4.93 1982 0 Protein: 5.21 100.00 16.08 4.92 1519 0 Water: 8.10 65.29 36.04 N/A 455 0 Other: 26.40 45.80 33.42 N/A 8 0 Chain A: 5.21 100.00 17.74 N/A 1734 0 Chain S: 18.60 65.29 41.68 N/A 248 0 Histogram: Values Number of atoms 5.21 - 14.69 1006 14.69 - 24.17 393 24.17 - 33.65 215 33.65 - 43.13 173 43.13 - 52.61 137 52.61 - 62.09 38 62.09 - 71.57 10 71.57 - 81.04 3 81.04 - 90.52 3 90.52 - 100.00 4 =========================== Idealize ADP of riding H ========================== r_work=0.1116 r_free=0.1509 r_work=0.1116 r_free=0.1508 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1116 r_free = 0.1508 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1111 r_free = 0.1506 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1111 r_free= 0.1506 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.934651 | | target function (ml) not normalized (work): 80104.195795 | | target function (ml) not normalized (free): 4166.837952 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1124 0.1404 5.4561 5.6838| | 2: 3.63 - 2.88 1.00 2711 122 0.1097 0.1446 5.2229 5.3247| | 3: 2.88 - 2.52 1.00 2681 148 0.1361 0.1673 5.1282 5.1885| | 4: 2.52 - 2.29 1.00 2661 139 0.0936 0.1491 4.6251 4.9469| | 5: 2.29 - 2.13 1.00 2678 122 0.0962 0.1460 4.576 4.8717| | 6: 2.13 - 2.00 1.00 2692 117 0.1124 0.1807 4.5702 4.8174| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.94 9.15 1.00 0.95 6386.35| | 2: 3.63 - 2.88 2711 122 0.92 12.85 1.01 0.95 6386.35| | 3: 2.88 - 2.52 2681 148 0.87 19.05 0.99 0.95 6386.35| | 4: 2.52 - 2.29 2661 139 0.93 12.12 1.01 0.97 2103.68| | 5: 2.29 - 2.13 2678 122 0.91 14.20 1.00 0.97 2103.68| | 6: 2.13 - 2.00 2692 117 0.89 16.76 0.99 0.97 2103.68| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2103.68 max = 6386.35 mean = 4267.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.87 mean = 13.98| |phase err.(test): min = 0.00 max = 86.26 mean = 13.54| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1111 0.1506 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1570 0.1559 0.1813 n_refl.: 17040 remove outliers: r(all,work,free)=0.1570 0.1559 0.1813 n_refl.: 17040 overall B=-0.21 to atoms: r(all,work,free)=0.1558 0.1547 0.1805 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1130 0.1111 0.1506 n_refl.: 17040 remove outliers: r(all,work,free)=0.1130 0.1111 0.1506 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 0.3622 296.260 276.684 0.546 1.006 0.340 11.894-9.307 99.02 97 4 0.1744 487.291 480.155 0.915 1.006 0.340 9.237-7.194 100.00 213 7 0.1766 398.555 400.929 0.989 1.006 0.240 7.162-5.571 100.00 427 22 0.1587 299.116 294.027 0.933 1.005 0.204 5.546-4.326 100.00 867 58 0.0918 410.638 407.694 0.959 1.004 0.177 4.315-3.360 100.00 1859 96 0.0885 390.521 387.968 1.003 1.003 0.167 3.356-2.611 100.00 3867 181 0.1237 256.550 254.518 1.000 1.000 0.067 2.608-2.000 99.99 8818 434 0.1042 167.227 165.832 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7246 ================= 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 : 0.2794 0.1811 0.084 5.171 8.8 119.3 19.9 258 0.000 1_bss: 0.1613 0.1672 0.084 5.171 8.4 118.9 19.5 258 0.000 1_settarget: 0.1613 0.1672 0.084 5.171 8.4 118.9 19.5 258 0.000 1_nqh: 0.1613 0.1672 0.084 5.171 8.4 118.9 19.5 258 0.000 1_weight: 0.1613 0.1672 0.084 5.171 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1350 0.1632 0.008 0.965 8.4 118.9 19.5 258 0.148 1_adp: 0.1277 0.1654 0.008 0.965 6.2 113.9 20.0 258 0.148 1_regHadp: 0.1281 0.1661 0.008 0.965 6.2 113.9 20.0 258 0.148 1_occ: 0.1276 0.1657 0.008 0.965 6.2 113.9 20.0 258 0.148 2_bss: 0.1275 0.1650 0.008 0.965 5.8 113.5 19.6 258 0.148 2_settarget: 0.1275 0.1650 0.008 0.965 5.8 113.5 19.6 258 0.148 2_updatecdl: 0.1275 0.1650 0.009 0.986 5.8 113.5 19.6 258 0.148 2_nqh: 0.1275 0.1650 0.009 0.986 5.8 113.5 19.6 258 0.148 2_sol: 0.1235 0.1516 0.009 0.986 5.8 111.7 20.9 363 n/a 2_weight: 0.1235 0.1516 0.009 0.986 5.8 111.7 20.9 363 n/a 2_xyzrec: 0.1211 0.1566 0.008 0.947 5.8 111.7 20.9 363 n/a 2_adp: 0.1198 0.1583 0.008 0.947 6.6 106.7 21.4 363 n/a 2_regHadp: 0.1199 0.1585 0.008 0.947 6.6 106.7 21.4 363 n/a 2_occ: 0.1196 0.1585 0.008 0.947 6.6 106.7 21.4 363 n/a 3_bss: 0.1188 0.1575 0.008 0.947 6.2 106.3 21.0 363 n/a 3_settarget: 0.1188 0.1575 0.008 0.947 6.2 106.3 21.0 363 n/a 3_updatecdl: 0.1188 0.1575 0.008 0.943 6.2 106.3 21.0 363 n/a 3_nqh: 0.1189 0.1576 0.008 0.943 6.2 106.3 21.0 363 n/a 3_sol: 0.1189 0.1515 0.008 0.943 6.2 106.3 21.0 401 n/a 3_weight: 0.1189 0.1515 0.008 0.943 6.2 106.3 21.0 401 n/a 3_xyzrec: 0.1165 0.1517 0.010 0.992 6.2 106.3 21.0 401 n/a 3_adp: 0.1145 0.1522 0.010 0.992 5.7 104.6 20.8 401 n/a 3_regHadp: 0.1145 0.1523 0.010 0.992 5.7 104.6 20.8 401 n/a 3_occ: 0.1138 0.1519 0.010 0.992 5.7 104.6 20.8 401 n/a 4_bss: 0.1137 0.1513 0.010 0.992 5.2 104.1 20.3 401 n/a 4_settarget: 0.1137 0.1513 0.010 0.992 5.2 104.1 20.3 401 n/a 4_updatecdl: 0.1137 0.1513 0.010 0.992 5.2 104.1 20.3 401 n/a 4_nqh: 0.1137 0.1511 0.010 0.992 5.2 104.1 20.3 401 n/a 4_sol: 0.1136 0.1494 0.010 0.992 5.2 104.1 20.8 437 n/a 4_weight: 0.1136 0.1494 0.010 0.992 5.2 104.1 20.8 437 n/a 4_xyzrec: 0.1129 0.1544 0.009 0.962 5.2 104.1 20.8 437 n/a 4_adp: 0.1116 0.1544 0.009 0.962 5.6 101.6 20.7 437 n/a 4_regHadp: 0.1116 0.1544 0.009 0.962 5.6 101.6 20.7 437 n/a 4_occ: 0.1108 0.1554 0.009 0.962 5.6 101.6 20.7 437 n/a 5_bss: 0.1105 0.1548 0.009 0.962 5.3 101.3 20.5 437 n/a 5_settarget: 0.1105 0.1548 0.009 0.962 5.3 101.3 20.5 437 n/a 5_updatecdl: 0.1105 0.1548 0.009 0.963 5.3 101.3 20.5 437 n/a 5_setrh: 0.1107 0.1547 0.009 0.963 5.3 101.3 20.5 437 n/a 5_nqh: 0.1107 0.1547 0.009 0.963 5.3 101.3 20.5 437 n/a 5_sol: 0.1104 0.1509 0.009 0.963 5.3 101.3 20.7 455 n/a 5_weight: 0.1104 0.1509 0.009 0.963 5.3 101.3 20.7 455 n/a 5_xyzrec: 0.1126 0.1520 0.010 1.069 5.3 101.3 20.7 455 n/a 5_adp: 0.1116 0.1509 0.010 1.069 5.2 100.0 20.7 455 n/a 5_regHadp: 0.1116 0.1508 0.010 1.069 5.2 100.0 20.7 455 n/a 5_occ: 0.1111 0.1506 0.010 1.069 5.2 100.0 20.7 455 n/a end: 0.1111 0.1506 0.010 1.069 5.0 99.8 20.5 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7650209_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7650209_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2300 Refinement macro-cycles (run) : 923.0800 Write final files (write_after_run_outputs) : 20.7900 Total : 947.1000 Total CPU time: 16.20 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:12 PST -0800 (1735494072.48 s) Start R-work = 0.1613, R-free = 0.1672 Final R-work = 0.1111, R-free = 0.1506 =============================================================================== Job complete usr+sys time: 994.49 seconds wall clock time: 16 minutes 56.86 seconds (1016.86 seconds total)