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_8666014.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 { 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" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8666014.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8666014.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 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.03, per 1000 atoms: 0.60 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: 0.44 Conformation dependent library (CDL) restraints added in 187.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.90: 430 0.90 - 1.16: 1197 1.16 - 1.43: 670 1.43 - 1.69: 835 1.69 - 1.96: 21 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.244 1.430 -0.186 1.00e-02 1.00e+04 3.46e+02 bond pdb=" C LEU A 77 " pdb=" N GLY A 78 " ideal model delta sigma weight residual 1.334 1.544 -0.211 1.14e-02 7.69e+03 3.42e+02 bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.447 1.251 0.196 1.08e-02 8.57e+03 3.29e+02 bond pdb=" C ASP A 60 " pdb=" O ASP A 60 " ideal model delta sigma weight residual 1.236 1.451 -0.215 1.19e-02 7.06e+03 3.26e+02 bond pdb=" CD ARG A 145 " pdb=" NE ARG A 145 " ideal model delta sigma weight residual 1.458 1.209 0.249 1.40e-02 5.10e+03 3.15e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 2961 4.39 - 8.79: 1912 8.79 - 13.18: 728 13.18 - 17.57: 152 17.57 - 21.97: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 119.71 106.85 12.86 8.10e-01 1.52e+00 2.52e+02 angle pdb=" CA GLY A 137 " pdb=" C GLY A 137 " pdb=" O GLY A 137 " ideal model delta sigma weight residual 119.82 103.97 15.85 1.14e+00 7.69e-01 1.93e+02 angle pdb=" C LEU A 82 " pdb=" N SER A 83 " pdb=" CA SER A 83 " ideal model delta sigma weight residual 120.28 139.74 -19.46 1.44e+00 4.82e-01 1.83e+02 angle pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 108.40 95.27 13.13 1.00e+00 1.00e+00 1.72e+02 angle pdb=" ND1 HIS A 126 " pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " ideal model delta sigma weight residual 106.10 118.65 -12.55 1.00e+00 1.00e+00 1.57e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 1291 16.76 - 33.53: 135 33.53 - 50.29: 34 50.29 - 67.05: 16 67.05 - 83.81: 5 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C BGLU A 90 " pdb=" N BGLU A 90 " pdb=" CA BGLU A 90 " pdb=" CB BGLU A 90 " ideal model delta harmonic sigma weight residual -122.60 -146.96 24.36 0 2.50e+00 1.60e-01 9.50e+01 dihedral pdb=" C GLU A 116 " pdb=" N GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual -122.60 -142.28 19.68 0 2.50e+00 1.60e-01 6.20e+01 dihedral pdb=" N BGLU A 90 " pdb=" C BGLU A 90 " pdb=" CA BGLU A 90 " pdb=" CB BGLU A 90 " ideal model delta harmonic sigma weight residual 122.80 142.46 -19.66 0 2.50e+00 1.60e-01 6.18e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.240: 108 0.240 - 0.472: 75 0.472 - 0.705: 36 0.705 - 0.937: 19 0.937 - 1.170: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -1.42 -1.17 2.00e-01 2.50e+01 3.42e+01 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 -1.52 -1.07 2.00e-01 2.50e+01 2.88e+01 chirality pdb=" CA BGLU A 90 " pdb=" N BGLU A 90 " pdb=" C BGLU A 90 " pdb=" CB BGLU A 90 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.072 2.00e-02 2.50e+03 6.70e-02 1.35e+02 pdb=" CG TYR A 141 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.110 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.107 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.097 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.011 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.028 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.107 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.058 2.00e-02 2.50e+03 6.22e-02 1.16e+02 pdb=" CG BTYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.128 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.050 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.053 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.074 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.046 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.061 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.041 2.00e-02 2.50e+03 5.42e-02 8.82e+01 pdb=" CG TYR A 139 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.085 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.079 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.087 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.029 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.078 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.052 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1084 2.32 - 2.89: 8132 2.89 - 3.46: 10475 3.46 - 4.03: 15267 4.03 - 4.60: 21704 Nonbonded interactions: 56662 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.755 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.775 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.779 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.814 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.827 2.450 ... (remaining 56657 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_8666014_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= 0.1855 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.393986 | | target function (ml) not normalized (work): 71371.522531 | | target function (ml) not normalized (free): 3262.085856 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3196 0.2241 7.4887 5.0426| | 2: 3.63 - 2.88 1.00 2711 122 0.2628 0.1672 4.3316 4.3374| | 3: 2.88 - 2.52 1.00 2682 148 0.2536 0.1795 4.1883 4.2085| | 4: 2.52 - 2.29 1.00 2661 139 0.2579 0.1587 3.4983 3.597| | 5: 2.29 - 2.13 1.00 2678 122 0.2626 0.1562 3.3879 3.4361| | 6: 2.13 - 2.00 1.00 2692 117 0.2745 0.1659 3.3071 3.3257| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.80 0.77 0.23 1328.73| | 2: 3.63 - 2.88 2711 122 0.82 24.03 1.31 0.23 1328.73| | 3: 2.88 - 2.52 2682 148 0.73 33.18 1.28 0.23 1328.73| | 4: 2.52 - 2.29 2661 139 0.94 11.06 1.30 0.26 128.68| | 5: 2.29 - 2.13 2678 122 0.92 13.16 1.31 0.26 128.68| | 6: 2.13 - 2.00 2692 117 0.90 15.67 1.34 0.26 128.68| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 128.68 max = 1328.73 mean = 735.39| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.94 mean = 19.16| |phase err.(test): min = 0.00 max = 88.85 mean = 19.32| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.249 1557 Z= 5.435 Angle : 5.396 19.459 2118 Z= 3.758 Chirality : 0.408 1.170 243 Planarity : 0.030 0.091 284 Dihedral : 13.832 83.813 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 32.43 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.45), residues: 224 helix: -3.25 (0.33), residues: 105 sheet: -0.98 (0.72), residues: 38 loop : -0.95 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.023 ARG A 98 TYR 0.085 0.037 TYR A 139 PHE 0.090 0.027 PHE A 164 HIS 0.047 0.017 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2783 r_free= 0.1855 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.393986 | | target function (ml) not normalized (work): 71371.522531 | | target function (ml) not normalized (free): 3262.085856 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3285 percent. r_work = 0.2916 r_free = 0.2026 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2862 0.2916 0.2026 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2862 0.2916 0.2026 n_refl.: 17050 remove outliers: r(all,work,free)=0.2155 0.2164 0.2026 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2127 0.2136 0.2008 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1613 0.1608 0.1698 n_refl.: 17045 remove outliers: r(all,work,free)=0.1610 0.1606 0.1698 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 98.94 88 5 0.3898 398.836 359.296 0.641 1.017 0.399 11.894-9.307 99.02 97 4 0.1877 633.446 615.370 0.922 1.018 0.370 9.237-7.194 100.00 213 7 0.2224 518.095 508.996 0.958 1.017 0.350 7.162-5.571 100.00 427 22 0.2241 388.831 377.536 0.917 1.015 0.300 5.546-4.326 100.00 867 58 0.1406 533.802 529.027 0.959 1.013 0.226 4.315-3.360 100.00 1859 96 0.1289 507.651 503.828 1.015 1.008 0.191 3.356-2.611 100.00 3867 181 0.1658 333.498 329.003 1.012 1.000 0.061 2.608-2.000 99.98 8817 434 0.1634 217.327 213.583 1.035 0.985 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4615 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1606 r_free=0.1698 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1609 r_free=0.1704 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.744948 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.888204 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 0.0280 0.009 0.9 1.0 0.5 0.0 0 10.872 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.32 2.80 3.013 18.449 0.888 0.023 12.76 16.51 3.75 3.610 18.702 0.888 0.020 Individual atomic B min max mean iso aniso Overall: 5.93 113.89 19.96 4.11 1785 0 Protein: 5.93 113.16 17.18 4.11 1519 0 Water: 8.93 113.89 36.09 N/A 258 0 Other: 21.48 36.96 26.12 N/A 8 0 Chain A: 5.93 113.89 19.96 N/A 1785 0 Histogram: Values Number of atoms 5.93 - 16.72 1070 16.72 - 27.52 351 27.52 - 38.32 190 38.32 - 49.11 94 49.11 - 59.91 53 59.91 - 70.70 12 70.70 - 81.50 7 81.50 - 92.30 4 92.30 - 103.09 1 103.09 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1651 r_work=0.1279 r_free=0.1659 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1659 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 = 0.1273 r_free = 0.1645 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.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1273 r_free= 0.1645 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019884 | | target function (ls_wunit_k1) not normalized (work): 322.815697 | | target function (ls_wunit_k1) not normalized (free): 26.836879 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1273 0.1645 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1902 0.1901 0.1983 n_refl.: 17042 remove outliers: r(all,work,free)=0.1902 0.1901 0.1983 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1874 0.1872 0.1967 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1292 0.1275 0.1644 n_refl.: 17042 remove outliers: r(all,work,free)=0.1292 0.1275 0.1644 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 96.88 88 5 0.3549 307.532 287.460 0.651 1.010 0.393 11.894-9.307 99.02 97 4 0.1662 488.433 477.764 0.917 1.010 0.380 9.237-7.194 100.00 213 7 0.1804 399.489 397.230 0.960 1.010 0.351 7.162-5.571 100.00 427 22 0.1841 299.817 295.242 0.931 1.009 0.301 5.546-4.326 100.00 867 58 0.1040 411.601 409.340 0.956 1.007 0.205 4.315-3.360 100.00 1859 96 0.0925 391.436 390.963 1.016 1.004 0.191 3.356-2.611 100.00 3867 181 0.1300 257.151 255.835 1.013 1.000 0.091 2.608-2.000 99.98 8817 434 0.1352 167.575 166.010 1.022 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3657 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1644 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1279 r_free=0.1649 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1279 r_free=0.1649 | n_water=258 | time (s): 0.790 (total time: 0.790) Filter (dist) r_work=0.1284 r_free=0.1641 | n_water=253 | time (s): 21.350 (total time: 22.140) Filter (q & B) r_work=0.1285 r_free=0.1640 | n_water=251 | time (s): 1.420 (total time: 23.560) Compute maps r_work=0.1285 r_free=0.1640 | n_water=251 | time (s): 0.610 (total time: 24.170) Filter (map) r_work=0.1320 r_free=0.1631 | n_water=211 | time (s): 1.790 (total time: 25.960) Find peaks r_work=0.1320 r_free=0.1631 | n_water=211 | time (s): 0.650 (total time: 26.610) Add new water r_work=0.1543 r_free=0.1883 | n_water=367 | time (s): 2.100 (total time: 28.710) Refine new water occ: r_work=0.1340 r_free=0.1601 adp: r_work=0.1280 r_free=0.1593 occ: r_work=0.1285 r_free=0.1555 adp: r_work=0.1252 r_free=0.1559 occ: r_work=0.1252 r_free=0.1549 adp: r_work=0.1240 r_free=0.1551 ADP+occupancy (water only), MIN, final r_work=0.1240 r_free=0.1551 r_work=0.1240 r_free=0.1551 | n_water=367 | time (s): 11.600 (total time: 40.310) Filter (q & B) r_work=0.1243 r_free=0.1557 | n_water=360 | time (s): 2.090 (total time: 42.400) Filter (dist only) r_work=0.1244 r_free=0.1559 | n_water=359 | time (s): 30.380 (total time: 72.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.371522 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.998134 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 0.1212 0.1605 0.0392 0.008 0.9 2.2 0.5 0.0 0 12.186 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 16.05 3.92 4.181 21.038 0.998 0.018 11.98 16.26 4.29 4.195 21.282 0.998 0.018 Individual atomic B min max mean iso aniso Overall: 6.68 107.78 21.30 4.26 1886 0 Protein: 6.68 107.78 17.70 4.24 1519 0 Water: 8.20 68.27 36.23 N/A 359 0 Other: 24.33 44.46 34.74 N/A 8 0 Chain A: 6.68 107.78 19.40 N/A 1738 0 Chain S: 18.32 62.39 43.62 N/A 148 0 Histogram: Values Number of atoms 6.68 - 16.79 1032 16.79 - 26.90 368 26.90 - 37.01 221 37.01 - 47.12 160 47.12 - 57.23 68 57.23 - 67.34 26 67.34 - 77.45 4 77.45 - 87.56 4 87.56 - 97.67 1 97.67 - 107.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1626 r_work=0.1199 r_free=0.1627 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1627 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1628 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.26 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= 0.1195 r_free= 0.1628 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017062 | | target function (ls_wunit_k1) not normalized (work): 276.993460 | | target function (ls_wunit_k1) not normalized (free): 25.468122 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1195 0.1628 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1814 0.1811 0.1949 n_refl.: 17042 remove outliers: r(all,work,free)=0.1814 0.1811 0.1949 n_refl.: 17042 overall B=-0.51 to atoms: r(all,work,free)=0.1779 0.1775 0.1925 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1190 0.1621 n_refl.: 17042 remove outliers: r(all,work,free)=0.1210 0.1189 0.1621 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 95.83 87 5 0.3355 309.566 283.435 0.627 1.006 0.374 11.894-9.307 99.02 97 4 0.1532 488.433 484.360 0.915 1.007 0.370 9.237-7.194 100.00 213 7 0.1641 399.489 401.273 0.974 1.006 0.290 7.162-5.571 100.00 427 22 0.1561 299.817 296.681 0.939 1.006 0.271 5.546-4.326 100.00 867 58 0.0885 411.601 409.265 0.958 1.005 0.206 4.315-3.360 100.00 1859 96 0.0815 391.436 390.641 1.014 1.004 0.192 3.356-2.611 100.00 3867 181 0.1200 257.151 256.189 1.007 1.001 0.122 2.608-2.000 99.98 8817 434 0.1330 167.575 166.513 1.010 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1452 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1621 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1621 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1621 | n_water=359 | time (s): 0.790 (total time: 0.790) Filter (dist) r_work=0.1189 r_free=0.1621 | n_water=359 | time (s): 27.660 (total time: 28.450) Filter (q & B) r_work=0.1189 r_free=0.1621 | n_water=359 | time (s): 0.920 (total time: 29.370) Compute maps r_work=0.1189 r_free=0.1621 | n_water=359 | time (s): 0.820 (total time: 30.190) Filter (map) r_work=0.1269 r_free=0.1633 | n_water=255 | time (s): 2.000 (total time: 32.190) Find peaks r_work=0.1269 r_free=0.1633 | n_water=255 | time (s): 0.560 (total time: 32.750) Add new water r_work=0.1459 r_free=0.1849 | n_water=404 | time (s): 1.900 (total time: 34.650) Refine new water occ: r_work=0.1254 r_free=0.1592 adp: r_work=0.1248 r_free=0.1600 occ: r_work=0.1225 r_free=0.1558 adp: r_work=0.1216 r_free=0.1563 occ: r_work=0.1205 r_free=0.1539 adp: r_work=0.1197 r_free=0.1541 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1541 r_work=0.1197 r_free=0.1541 | n_water=404 | time (s): 35.670 (total time: 70.320) Filter (q & B) r_work=0.1199 r_free=0.1547 | n_water=391 | time (s): 1.620 (total time: 71.940) Filter (dist only) r_work=0.1200 r_free=0.1547 | n_water=390 | time (s): 32.510 (total time: 104.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.045178 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.155469 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 0.1547 0.0375 0.009 1.0 3.2 0.5 0.0 0 1.023 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.72 15.47 3.75 4.337 21.338 0.155 4.994 11.53 15.52 3.99 4.880 21.228 0.155 4.972 Individual atomic B min max mean iso aniso Overall: 6.24 104.92 20.59 4.59 1917 0 Protein: 6.24 104.92 16.83 4.58 1519 0 Water: 8.45 63.00 34.94 N/A 390 0 Other: 26.65 44.42 34.63 N/A 8 0 Chain A: 6.24 104.92 18.54 N/A 1734 0 Chain S: 16.68 63.00 40.01 N/A 183 0 Histogram: Values Number of atoms 6.24 - 16.11 1065 16.11 - 25.97 352 25.97 - 35.84 226 35.84 - 45.71 157 45.71 - 55.58 77 55.58 - 65.45 28 65.45 - 75.32 4 75.32 - 85.19 3 85.19 - 95.06 3 95.06 - 104.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1153 r_free=0.1552 r_work=0.1153 r_free=0.1553 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1553 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1142 r_free = 0.1551 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.21 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= 0.1142 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.967040 | | target function (ml) not normalized (work): 80634.922947 | | target function (ml) not normalized (free): 4190.925144 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1142 0.1551 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1671 0.1663 0.1870 n_refl.: 17041 remove outliers: r(all,work,free)=0.1671 0.1663 0.1870 n_refl.: 17041 overall B=-0.34 to atoms: r(all,work,free)=0.1648 0.1639 0.1859 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1158 0.1138 0.1548 n_refl.: 17041 remove outliers: r(all,work,free)=0.1156 0.1136 0.1548 n_refl.: 17038 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3336 300.234 285.818 0.592 1.010 0.350 11.894-9.307 99.02 97 4 0.1731 488.433 480.854 0.909 1.011 0.350 9.237-7.194 100.00 213 7 0.1821 399.489 400.853 0.975 1.010 0.266 7.162-5.571 100.00 427 22 0.1654 299.817 295.326 0.939 1.009 0.263 5.546-4.326 100.00 867 58 0.0937 411.601 407.876 0.961 1.008 0.206 4.315-3.360 100.00 1859 96 0.0872 391.436 389.402 1.011 1.005 0.201 3.356-2.611 100.00 3867 181 0.1269 257.151 255.141 1.010 1.000 0.141 2.608-2.000 99.98 8817 434 0.1082 167.575 166.183 1.017 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9585 b_overall=-1.1780 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1136 r_free=0.1548 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1136 r_free=0.1548 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1136 r_free=0.1548 | n_water=390 | time (s): 0.830 (total time: 0.830) Filter (dist) r_work=0.1136 r_free=0.1548 | n_water=390 | time (s): 28.620 (total time: 29.450) Filter (q & B) r_work=0.1136 r_free=0.1548 | n_water=390 | time (s): 1.190 (total time: 30.640) Compute maps r_work=0.1136 r_free=0.1548 | n_water=390 | time (s): 0.660 (total time: 31.300) Filter (map) r_work=0.1197 r_free=0.1581 | n_water=308 | time (s): 1.590 (total time: 32.890) Find peaks r_work=0.1197 r_free=0.1581 | n_water=308 | time (s): 0.440 (total time: 33.330) Add new water r_work=0.1351 r_free=0.1753 | n_water=456 | time (s): 1.580 (total time: 34.910) Refine new water occ: r_work=0.1174 r_free=0.1508 adp: r_work=0.1167 r_free=0.1519 occ: r_work=0.1146 r_free=0.1476 adp: r_work=0.1137 r_free=0.1485 occ: r_work=0.1128 r_free=0.1466 adp: r_work=0.1120 r_free=0.1472 ADP+occupancy (water only), MIN, final r_work=0.1120 r_free=0.1472 r_work=0.1120 r_free=0.1472 | n_water=456 | time (s): 31.780 (total time: 66.690) Filter (q & B) r_work=0.1123 r_free=0.1481 | n_water=447 | time (s): 1.780 (total time: 68.470) Filter (dist only) r_work=0.1123 r_free=0.1482 | n_water=446 | time (s): 38.310 (total time: 106.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.903324 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.181155 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1118 0.1528 0.0410 0.010 1.0 3.8 0.5 0.0 0 0.952 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.18 15.28 4.10 4.429 20.956 0.181 4.951 11.08 15.16 4.08 4.614 20.984 0.181 4.943 Individual atomic B min max mean iso aniso Overall: 5.73 102.59 20.89 4.88 1973 0 Protein: 5.73 102.59 16.46 4.87 1519 0 Water: 8.36 63.71 35.72 N/A 446 0 Other: 27.27 45.94 35.11 N/A 8 0 Chain A: 5.73 102.59 18.14 N/A 1734 0 Chain S: 17.18 63.71 40.82 N/A 239 0 Histogram: Values Number of atoms 5.73 - 15.41 1047 15.41 - 25.10 360 25.10 - 34.78 226 34.78 - 44.47 190 44.47 - 54.16 99 54.16 - 63.84 36 63.84 - 73.53 7 73.53 - 83.22 2 83.22 - 92.90 4 92.90 - 102.59 2 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1516 r_work=0.1109 r_free=0.1517 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1109 r_free = 0.1517 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1511 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17038 (all), 4.74 % free)------------| | | | r_work= 0.1100 r_free= 0.1511 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.936020 | | target function (ml) not normalized (work): 80116.542824 | | target function (ml) not normalized (free): 4169.865685 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1120 0.1100 0.1511 n_refl.: 17038 re-set all scales: r(all,work,free)=0.1569 0.1559 0.1785 n_refl.: 17038 remove outliers: r(all,work,free)=0.1569 0.1559 0.1785 n_refl.: 17038 overall B=-0.27 to atoms: r(all,work,free)=0.1552 0.1542 0.1774 n_refl.: 17038 bulk-solvent and scaling: r(all,work,free)=0.1118 0.1098 0.1504 n_refl.: 17038 remove outliers: r(all,work,free)=0.1118 0.1098 0.1504 n_refl.: 17038 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3562 300.234 273.058 0.552 1.001 0.330 11.894-9.307 99.02 97 4 0.1699 488.433 485.223 0.923 1.001 0.330 9.237-7.194 100.00 213 7 0.1669 399.489 400.379 0.991 1.002 0.243 7.162-5.571 100.00 427 22 0.1550 299.817 294.376 0.942 1.002 0.220 5.546-4.326 100.00 867 58 0.0911 411.601 407.990 0.965 1.002 0.192 4.315-3.360 100.00 1859 96 0.0842 391.436 389.753 1.008 1.002 0.174 3.356-2.611 100.00 3867 181 0.1229 257.151 254.691 1.002 1.001 0.131 2.608-2.000 99.98 8817 434 0.1047 167.575 166.335 0.997 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9382 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1098 r_free=0.1504 After: r_work=0.1100 r_free=0.1503 ================================== NQH flips ================================== r_work=0.1100 r_free=0.1503 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=0.1100 r_free=0.1503 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1100 r_free=0.1503 | n_water=446 | time (s): 0.930 (total time: 0.930) Filter (dist) r_work=0.1100 r_free=0.1503 | n_water=446 | time (s): 36.510 (total time: 37.440) Filter (q & B) r_work=0.1100 r_free=0.1503 | n_water=446 | time (s): 1.090 (total time: 38.530) Compute maps r_work=0.1100 r_free=0.1503 | n_water=446 | time (s): 0.850 (total time: 39.380) Filter (map) r_work=0.1183 r_free=0.1551 | n_water=332 | time (s): 2.220 (total time: 41.600) Find peaks r_work=0.1183 r_free=0.1551 | n_water=332 | time (s): 0.530 (total time: 42.130) Add new water r_work=0.1306 r_free=0.1626 | n_water=470 | time (s): 2.050 (total time: 44.180) Refine new water occ: r_work=0.1137 r_free=0.1492 adp: r_work=0.1130 r_free=0.1490 occ: r_work=0.1116 r_free=0.1475 adp: r_work=0.1107 r_free=0.1473 occ: r_work=0.1101 r_free=0.1463 adp: r_work=0.1093 r_free=0.1464 ADP+occupancy (water only), MIN, final r_work=0.1093 r_free=0.1464 r_work=0.1093 r_free=0.1464 | n_water=470 | time (s): 31.970 (total time: 76.150) Filter (q & B) r_work=0.1096 r_free=0.1471 | n_water=461 | time (s): 2.120 (total time: 78.270) Filter (dist only) r_work=0.1097 r_free=0.1467 | n_water=459 | time (s): 37.820 (total time: 116.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.854103 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.157953 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1118 0.1486 0.0368 0.010 1.1 5.1 0.5 0.0 0 0.927 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.18 14.86 3.68 4.559 20.728 0.158 4.938 11.06 14.75 3.68 4.649 20.799 0.158 4.930 Individual atomic B min max mean iso aniso Overall: 5.29 101.27 20.83 5.04 1986 0 Protein: 5.29 101.27 16.17 5.03 1519 0 Water: 7.97 66.89 36.00 N/A 459 0 Other: 26.69 45.61 34.67 N/A 8 0 Chain A: 5.29 101.27 17.84 N/A 1734 0 Chain S: 18.21 66.89 41.40 N/A 252 0 Histogram: Values Number of atoms 5.29 - 14.89 1024 14.89 - 24.48 369 24.48 - 34.08 225 34.08 - 43.68 197 43.68 - 53.28 118 53.28 - 62.88 32 62.88 - 72.47 11 72.47 - 82.07 3 82.07 - 91.67 3 91.67 - 101.27 4 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1475 r_work=0.1106 r_free=0.1475 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1475 target_work(ml) = 4.930 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1101 r_free = 0.1477 target_work(ml) = 4.927 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17038 (all), 4.74 % free)------------| | | | r_work= 0.1101 r_free= 0.1477 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.927348 | | target function (ml) not normalized (work): 79975.790381 | | target function (ml) not normalized (free): 4153.128377 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2809 159 0.1115 0.1365 5.4562 5.6318| | 2: 3.63 - 2.88 1.00 2711 122 0.1077 0.1461 5.2054 5.3442| | 3: 2.88 - 2.52 1.00 2681 148 0.1349 0.1541 5.1107 5.1593| | 4: 2.52 - 2.29 1.00 2661 139 0.0937 0.1477 4.6224 4.924| | 5: 2.29 - 2.13 1.00 2678 122 0.0962 0.1531 4.5737 4.9031| | 6: 2.13 - 2.00 1.00 2691 117 0.1112 0.1766 4.566 4.7819| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2809 159 0.95 8.64 1.00 0.96 6035.35| | 2: 3.63 - 2.88 2711 122 0.93 12.40 1.01 0.96 6035.35| | 3: 2.88 - 2.52 2681 148 0.88 18.50 0.99 0.96 6035.35| | 4: 2.52 - 2.29 2661 139 0.93 11.94 1.01 0.97 2082.18| | 5: 2.29 - 2.13 2678 122 0.92 13.95 1.00 0.97 2082.18| | 6: 2.13 - 2.00 2691 117 0.90 16.62 0.99 0.97 2082.18| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2082.18 max = 6035.35 mean = 4079.59| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.64| |phase err.(test): min = 0.00 max = 88.95 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1101 0.1477 n_refl.: 17038 re-set all scales: r(all,work,free)=0.1541 0.1531 0.1754 n_refl.: 17038 remove outliers: r(all,work,free)=0.1541 0.1531 0.1754 n_refl.: 17038 overall B=-0.22 to atoms: r(all,work,free)=0.1529 0.1518 0.1747 n_refl.: 17038 bulk-solvent and scaling: r(all,work,free)=0.1119 0.1101 0.1477 n_refl.: 17038 remove outliers: r(all,work,free)=0.1119 0.1101 0.1477 n_refl.: 17038 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3540 300.234 275.714 0.544 1.005 0.326 11.894-9.307 99.02 97 4 0.1789 488.433 482.724 0.920 1.006 0.323 9.237-7.194 100.00 213 7 0.1736 399.489 401.652 0.986 1.006 0.230 7.162-5.571 100.00 427 22 0.1595 299.817 293.647 0.932 1.005 0.205 5.546-4.326 100.00 867 58 0.0919 411.601 408.245 0.963 1.005 0.195 4.315-3.360 100.00 1859 96 0.0854 391.436 389.212 1.004 1.003 0.191 3.356-2.611 100.00 3867 181 0.1235 257.151 254.788 0.998 1.001 0.111 2.608-2.000 99.98 8817 434 0.1033 167.575 166.313 0.991 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7606 ================= 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 0.1855 0.081 5.396 8.8 119.3 19.9 258 0.000 1_bss: 0.1606 0.1698 0.081 5.396 8.4 118.9 19.5 258 0.000 1_settarget: 0.1606 0.1698 0.081 5.396 8.4 118.9 19.5 258 0.000 1_nqh: 0.1609 0.1704 0.081 5.396 8.4 118.9 19.5 258 0.006 1_weight: 0.1609 0.1704 0.081 5.396 8.4 118.9 19.5 258 0.006 1_xyzrec: 0.1351 0.1632 0.009 0.949 8.4 118.9 19.5 258 0.154 1_adp: 0.1276 0.1651 0.009 0.949 5.9 113.9 20.0 258 0.154 1_regHadp: 0.1279 0.1659 0.009 0.949 5.9 113.9 20.0 258 0.154 1_occ: 0.1273 0.1645 0.009 0.949 5.9 113.9 20.0 258 0.154 2_bss: 0.1275 0.1644 0.009 0.949 5.5 113.5 19.6 258 0.154 2_settarget: 0.1275 0.1644 0.009 0.949 5.5 113.5 19.6 258 0.154 2_updatecdl: 0.1275 0.1644 0.009 0.969 5.5 113.5 19.6 258 0.154 2_nqh: 0.1279 0.1649 0.009 0.969 5.5 113.5 19.6 258 0.148 2_sol: 0.1244 0.1559 0.009 0.969 5.5 112.8 20.9 359 n/a 2_weight: 0.1244 0.1559 0.009 0.969 5.5 112.8 20.9 359 n/a 2_xyzrec: 0.1212 0.1605 0.008 0.924 5.5 112.8 20.9 359 n/a 2_adp: 0.1198 0.1626 0.008 0.924 6.7 107.8 21.3 359 n/a 2_regHadp: 0.1199 0.1627 0.008 0.924 6.7 107.8 21.3 359 n/a 2_occ: 0.1195 0.1628 0.008 0.924 6.7 107.8 21.3 359 n/a 3_bss: 0.1189 0.1621 0.008 0.924 6.2 107.3 20.8 359 n/a 3_settarget: 0.1189 0.1621 0.008 0.924 6.2 107.3 20.8 359 n/a 3_updatecdl: 0.1189 0.1621 0.008 0.924 6.2 107.3 20.8 359 n/a 3_nqh: 0.1189 0.1621 0.008 0.924 6.2 107.3 20.8 359 n/a 3_sol: 0.1200 0.1547 0.008 0.924 6.2 107.3 20.8 390 n/a 3_weight: 0.1200 0.1547 0.008 0.924 6.2 107.3 20.8 390 n/a 3_xyzrec: 0.1172 0.1547 0.009 0.979 6.2 107.3 20.8 390 n/a 3_adp: 0.1153 0.1552 0.009 0.979 6.2 104.9 20.6 390 n/a 3_regHadp: 0.1153 0.1553 0.009 0.979 6.2 104.9 20.6 390 n/a 3_occ: 0.1142 0.1551 0.009 0.979 6.2 104.9 20.6 390 n/a 4_bss: 0.1136 0.1548 0.009 0.979 5.9 104.6 20.2 390 n/a 4_settarget: 0.1136 0.1548 0.009 0.979 5.9 104.6 20.2 390 n/a 4_updatecdl: 0.1136 0.1548 0.009 0.980 5.9 104.6 20.2 390 n/a 4_nqh: 0.1136 0.1548 0.009 0.980 5.9 104.6 20.2 390 n/a 4_sol: 0.1123 0.1482 0.009 0.980 5.9 104.6 20.8 446 n/a 4_weight: 0.1123 0.1482 0.009 0.980 5.9 104.6 20.8 446 n/a 4_xyzrec: 0.1118 0.1528 0.010 0.982 5.9 104.6 20.8 446 n/a 4_adp: 0.1108 0.1516 0.010 0.982 5.7 102.6 20.9 446 n/a 4_regHadp: 0.1109 0.1517 0.010 0.982 5.7 102.6 20.9 446 n/a 4_occ: 0.1100 0.1511 0.010 0.982 5.7 102.6 20.9 446 n/a 5_bss: 0.1098 0.1504 0.010 0.982 5.5 102.3 20.6 446 n/a 5_settarget: 0.1098 0.1504 0.010 0.982 5.5 102.3 20.6 446 n/a 5_updatecdl: 0.1098 0.1504 0.010 0.983 5.5 102.3 20.6 446 n/a 5_setrh: 0.1100 0.1503 0.010 0.983 5.5 102.3 20.6 446 n/a 5_nqh: 0.1100 0.1503 0.010 0.983 5.5 102.3 20.6 446 n/a 5_sol: 0.1097 0.1467 0.010 0.983 5.5 102.3 20.7 459 n/a 5_weight: 0.1097 0.1467 0.010 0.983 5.5 102.3 20.7 459 n/a 5_xyzrec: 0.1118 0.1486 0.010 1.054 5.5 102.3 20.7 459 n/a 5_adp: 0.1106 0.1475 0.010 1.054 5.3 101.3 20.8 459 n/a 5_regHadp: 0.1106 0.1475 0.010 1.054 5.3 101.3 20.8 459 n/a 5_occ: 0.1101 0.1477 0.010 1.054 5.3 101.3 20.8 459 n/a end: 0.1101 0.1477 0.010 1.054 5.1 101.0 20.6 459 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8666014_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8666014_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1700 Refinement macro-cycles (run) : 936.0400 Write final files (write_after_run_outputs) : 20.1100 Total : 959.3200 Total CPU time: 16.39 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:24 PST -0800 (1735494084.94 s) Start R-work = 0.1606, R-free = 0.1698 Final R-work = 0.1101, R-free = 0.1477 =============================================================================== Job complete usr+sys time: 1003.54 seconds wall clock time: 17 minutes 6.67 seconds (1026.67 seconds total)