Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2226169.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2226169.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2226169.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 1.87, per 1000 atoms: 0.55 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 208.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.94: 722 0.94 - 1.20: 976 1.20 - 1.46: 712 1.46 - 1.71: 720 1.71 - 1.97: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.515 -0.194 1.00e-02 1.00e+04 3.77e+02 bond pdb=" CA VAL A 181 " pdb=" CB VAL A 181 " ideal model delta sigma weight residual 1.540 1.775 -0.235 1.29e-02 6.01e+03 3.33e+02 bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.237 1.424 -0.187 1.13e-02 7.83e+03 2.74e+02 bond pdb=" C LYS A 32 " pdb=" O LYS A 32 " ideal model delta sigma weight residual 1.235 1.430 -0.194 1.19e-02 7.06e+03 2.67e+02 bond pdb=" N HIS A 115 " pdb=" CA HIS A 115 " ideal model delta sigma weight residual 1.456 1.250 0.205 1.26e-02 6.30e+03 2.65e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 3198 4.76 - 9.52: 1843 9.52 - 14.28: 618 14.28 - 19.03: 108 19.03 - 23.79: 10 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH2 ARG A 98 " ideal model delta sigma weight residual 119.20 104.39 14.81 9.00e-01 1.23e+00 2.71e+02 angle pdb=" OE1BGLN A 80 " pdb=" CD BGLN A 80 " pdb=" NE2BGLN A 80 " ideal model delta sigma weight residual 122.60 137.81 -15.21 1.00e+00 1.00e+00 2.31e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH2 ARG A 28 " ideal model delta sigma weight residual 119.20 132.19 -12.99 9.00e-01 1.23e+00 2.08e+02 angle pdb=" CA ALA A 103 " pdb=" C ALA A 103 " pdb=" N ALA A 104 " ideal model delta sigma weight residual 116.37 132.58 -16.21 1.19e+00 7.06e-01 1.85e+02 angle pdb=" CA LEU A 38 " pdb=" C LEU A 38 " pdb=" O LEU A 38 " ideal model delta sigma weight residual 120.63 106.13 14.50 1.08e+00 8.57e-01 1.80e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 1284 16.26 - 32.51: 136 32.51 - 48.77: 36 48.77 - 65.03: 21 65.03 - 81.28: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CA LYS A 32 " pdb=" CB LYS A 32 " ideal model delta harmonic sigma weight residual 122.80 102.76 20.04 0 2.50e+00 1.60e-01 6.42e+01 dihedral pdb=" C ALA A 103 " pdb=" N ALA A 103 " pdb=" CA ALA A 103 " pdb=" CB ALA A 103 " ideal model delta harmonic sigma weight residual -122.60 -142.30 19.70 0 2.50e+00 1.60e-01 6.21e+01 dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -142.23 19.63 0 2.50e+00 1.60e-01 6.17e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.185: 66 0.185 - 0.368: 79 0.368 - 0.551: 54 0.551 - 0.734: 30 0.734 - 0.917: 14 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 103 " pdb=" N ALA A 103 " pdb=" C ALA A 103 " pdb=" CB ALA A 103 " both_signs ideal model delta sigma weight residual False 2.48 1.57 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA LEU A 77 " pdb=" N LEU A 77 " pdb=" C LEU A 77 " pdb=" CB LEU A 77 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb=" CA VAL A 169 " pdb=" N VAL A 169 " pdb=" C VAL A 169 " pdb=" CB VAL A 169 " both_signs ideal model delta sigma weight residual False 2.44 3.35 -0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.062 2.00e-02 2.50e+03 6.70e-02 1.35e+02 pdb=" CG TYR A 139 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.072 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.017 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.114 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.133 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.029 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.040 2.00e-02 2.50e+03 5.91e-02 1.05e+02 pdb=" CG ATYR A 67 " 0.094 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.023 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.082 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.017 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.023 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.087 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.009 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.087 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.060 2.00e-02 2.50e+03 5.74e-02 9.89e+01 pdb=" CG PHE A 162 " 0.113 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.070 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.060 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.050 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.053 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.039 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.063 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 1001 2.31 - 2.88: 8055 2.88 - 3.46: 10524 3.46 - 4.03: 15242 4.03 - 4.60: 21875 Nonbonded interactions: 56697 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.739 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.768 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.792 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.812 2.450 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.821 2.270 ... (remaining 56692 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_2226169_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= 0.1829 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.405088 | | target function (ml) not normalized (work): 71551.847159 | | target function (ml) not normalized (free): 3258.323497 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3197 0.2146 7.5965 5.0461| | 2: 3.63 - 2.88 1.00 2711 122 0.2640 0.1709 4.319 4.32| | 3: 2.88 - 2.52 1.00 2682 148 0.2573 0.1710 4.1815 4.1783| | 4: 2.52 - 2.29 1.00 2661 139 0.2529 0.1570 3.4906 3.5557| | 5: 2.29 - 2.13 1.00 2678 122 0.2631 0.1606 3.3836 3.4737| | 6: 2.13 - 2.00 1.00 2692 117 0.2719 0.1776 3.2926 3.3551| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.46 0.77 0.23 1301.03| | 2: 3.63 - 2.88 2711 122 0.83 23.76 1.31 0.23 1301.03| | 3: 2.88 - 2.52 2682 148 0.73 32.74 1.29 0.23 1301.03| | 4: 2.52 - 2.29 2661 139 0.94 11.02 1.29 0.26 130.09| | 5: 2.29 - 2.13 2678 122 0.92 13.11 1.32 0.26 130.09| | 6: 2.13 - 2.00 2692 117 0.90 15.87 1.33 0.26 130.09| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 130.09 max = 1301.03 mean = 722.09| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 90.00 mean = 19.00| |phase err.(test): min = 0.00 max = 89.46 mean = 19.37| |-----------------------------------------------------------------------------| ----------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 0.235 1557 Z= 5.403 Angle : 5.373 18.971 2118 Z= 3.821 Chirality : 0.404 0.917 243 Planarity : 0.031 0.107 284 Dihedral : 13.852 81.283 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 36.22 % 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 (0.48), residues: 224 helix: -2.67 (0.36), residues: 108 sheet: 0.02 (0.93), residues: 28 loop : -0.40 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.019 ARG A 48 TYR 0.080 0.032 TYR A 141 PHE 0.117 0.042 PHE A 162 HIS 0.086 0.038 HIS A 138 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= 0.1829 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.405088 | | target function (ml) not normalized (work): 71551.847159 | | target function (ml) not normalized (free): 3258.323497 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3293 percent. r_work = 0.2916 r_free = 0.1989 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2864 0.2916 0.1989 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2864 0.2916 0.1989 n_refl.: 17050 remove outliers: r(all,work,free)=0.2151 0.2162 0.1989 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2125 0.2136 0.1972 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1612 0.1610 0.1668 n_refl.: 17045 remove outliers: r(all,work,free)=0.1611 0.1609 0.1668 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 0.4093 394.585 361.459 0.651 1.019 0.404 11.894-9.307 99.02 97 4 0.1881 633.321 617.303 0.918 1.019 0.400 9.237-7.194 100.00 213 7 0.2107 517.993 509.276 0.952 1.019 0.371 7.162-5.571 100.00 427 22 0.2310 388.754 375.517 0.913 1.017 0.321 5.546-4.326 100.00 867 58 0.1398 533.697 527.387 0.956 1.014 0.210 4.315-3.360 100.00 1859 96 0.1293 507.551 503.389 1.011 1.008 0.191 3.356-2.611 100.00 3867 181 0.1669 333.432 328.711 1.012 0.999 0.071 2.608-2.000 99.99 8818 434 0.1629 217.341 213.493 1.033 0.983 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3789 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1609 r_free=0.1668 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1609 r_free=0.1673 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.327552 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.823554 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1352 0.1640 0.0288 0.008 1.0 1.3 0.5 0.0 0 11.164 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.40 2.88 3.013 18.473 0.824 0.023 12.79 16.66 3.87 3.577 18.722 0.824 0.021 Individual atomic B min max mean iso aniso Overall: 6.10 113.91 19.97 4.03 1785 0 Protein: 6.10 112.45 17.21 4.03 1519 0 Water: 8.57 113.91 36.01 N/A 258 0 Other: 21.55 37.05 26.27 N/A 8 0 Chain A: 6.10 113.91 19.97 N/A 1785 0 Histogram: Values Number of atoms 6.10 - 16.88 1081 16.88 - 27.66 346 27.66 - 38.45 180 38.45 - 49.23 103 49.23 - 60.01 48 60.01 - 70.79 12 70.79 - 81.57 7 81.57 - 92.35 5 92.35 - 103.13 0 103.13 - 113.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1666 r_work=0.1283 r_free=0.1671 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1283 r_free = 0.1671 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 = 0.1281 r_free = 0.1673 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.13 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= 0.1281 r_free= 0.1673 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020217 | | target function (ls_wunit_k1) not normalized (work): 328.271538 | | target function (ls_wunit_k1) not normalized (free): 27.760401 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1300 0.1281 0.1673 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1917 0.1917 0.1990 n_refl.: 17044 remove outliers: r(all,work,free)=0.1917 0.1917 0.1990 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1888 0.1887 0.1974 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1298 0.1280 0.1662 n_refl.: 17044 remove outliers: r(all,work,free)=0.1297 0.1278 0.1662 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 0.3552 302.585 279.087 0.626 1.009 0.370 11.894-9.307 99.02 97 4 0.1698 486.660 475.304 0.914 1.010 0.370 9.237-7.194 100.00 213 7 0.1833 398.039 394.274 0.959 1.010 0.351 7.162-5.571 100.00 427 22 0.1879 298.729 293.580 0.930 1.009 0.311 5.546-4.326 100.00 867 58 0.1050 410.106 407.570 0.959 1.008 0.211 4.315-3.360 100.00 1859 96 0.0926 390.015 389.665 1.017 1.005 0.181 3.356-2.611 100.00 3867 181 0.1300 256.218 255.042 1.016 1.000 0.101 2.608-2.000 99.99 8818 434 0.1354 167.010 165.530 1.024 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4022 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1278 r_free=0.1662 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1280 r_free=0.1662 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1280 r_free=0.1662 | n_water=258 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1288 r_free=0.1649 | n_water=253 | time (s): 21.230 (total time: 21.840) Filter (q & B) r_work=0.1288 r_free=0.1648 | n_water=251 | time (s): 1.870 (total time: 23.710) Compute maps r_work=0.1288 r_free=0.1648 | n_water=251 | time (s): 0.600 (total time: 24.310) Filter (map) r_work=0.1324 r_free=0.1649 | n_water=213 | time (s): 1.480 (total time: 25.790) Find peaks r_work=0.1324 r_free=0.1649 | n_water=213 | time (s): 0.430 (total time: 26.220) Add new water r_work=0.1540 r_free=0.1870 | n_water=372 | time (s): 1.730 (total time: 27.950) Refine new water occ: r_work=0.1341 r_free=0.1553 adp: r_work=0.1282 r_free=0.1554 occ: r_work=0.1285 r_free=0.1532 adp: r_work=0.1254 r_free=0.1538 occ: r_work=0.1253 r_free=0.1526 adp: r_work=0.1244 r_free=0.1527 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1527 r_work=0.1244 r_free=0.1527 | n_water=372 | time (s): 18.450 (total time: 46.400) Filter (q & B) r_work=0.1246 r_free=0.1539 | n_water=363 | time (s): 1.990 (total time: 48.390) Filter (dist only) r_work=0.1246 r_free=0.1542 | n_water=362 | time (s): 28.640 (total time: 77.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.901430 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.962980 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 0.1217 0.1584 0.0367 0.008 0.9 1.9 0.5 0.0 0 12.451 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.17 15.84 3.67 4.143 21.088 0.963 0.018 12.02 16.09 4.06 4.285 21.356 0.963 0.018 Individual atomic B min max mean iso aniso Overall: 6.52 107.06 21.40 4.32 1889 0 Protein: 6.52 107.06 17.79 4.31 1519 0 Water: 8.04 65.80 36.29 N/A 362 0 Other: 24.76 43.43 33.86 N/A 8 0 Chain A: 6.52 107.06 19.49 N/A 1740 0 Chain S: 16.87 63.39 43.66 N/A 149 0 Histogram: Values Number of atoms 6.52 - 16.57 1012 16.57 - 26.63 387 26.63 - 36.68 211 36.68 - 46.73 165 46.73 - 56.79 76 56.79 - 66.84 27 66.84 - 76.90 3 76.90 - 86.95 6 86.95 - 97.00 0 97.00 - 107.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1609 r_work=0.1204 r_free=0.1612 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1612 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1615 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 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= 0.1615 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017225 | | target function (ls_wunit_k1) not normalized (work): 279.640524 | | target function (ls_wunit_k1) not normalized (free): 24.861003 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1196 0.1615 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1750 0.1739 0.2003 n_refl.: 17042 remove outliers: r(all,work,free)=0.1750 0.1739 0.2003 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1725 0.1713 0.1987 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1190 0.1607 n_refl.: 17042 remove outliers: r(all,work,free)=0.1209 0.1189 0.1607 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 0.3263 299.431 283.640 0.584 1.004 0.340 11.894-9.307 99.02 97 4 0.1618 486.660 483.030 0.907 1.005 0.335 9.237-7.194 100.00 213 7 0.1735 398.039 396.871 0.969 1.005 0.320 7.162-5.571 100.00 427 22 0.1611 298.729 294.316 0.936 1.005 0.271 5.546-4.326 100.00 867 58 0.0873 410.106 407.284 0.962 1.004 0.221 4.315-3.360 100.00 1859 96 0.0811 390.015 389.328 1.015 1.003 0.181 3.356-2.611 100.00 3867 181 0.1198 256.218 255.512 1.014 1.001 0.121 2.608-2.000 99.99 8818 434 0.1326 167.010 165.957 1.018 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3702 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1607 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=0.1191 r_free=0.1606 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1606 | n_water=362 | time (s): 0.910 (total time: 0.910) Filter (dist) r_work=0.1191 r_free=0.1605 | n_water=361 | time (s): 28.660 (total time: 29.570) Filter (q & B) r_work=0.1191 r_free=0.1605 | n_water=361 | time (s): 0.800 (total time: 30.370) Compute maps r_work=0.1191 r_free=0.1605 | n_water=361 | time (s): 0.650 (total time: 31.020) Filter (map) r_work=0.1261 r_free=0.1623 | n_water=265 | time (s): 1.620 (total time: 32.640) Find peaks r_work=0.1261 r_free=0.1623 | n_water=265 | time (s): 0.550 (total time: 33.190) Add new water r_work=0.1455 r_free=0.1825 | n_water=422 | time (s): 1.620 (total time: 34.810) Refine new water occ: r_work=0.1253 r_free=0.1576 adp: r_work=0.1245 r_free=0.1583 occ: r_work=0.1226 r_free=0.1543 adp: r_work=0.1215 r_free=0.1553 occ: r_work=0.1208 r_free=0.1521 adp: r_work=0.1196 r_free=0.1527 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1527 r_work=0.1196 r_free=0.1527 | n_water=422 | time (s): 40.270 (total time: 75.080) Filter (q & B) r_work=0.1199 r_free=0.1538 | n_water=412 | time (s): 1.520 (total time: 76.600) Filter (dist only) r_work=0.1199 r_free=0.1538 | n_water=412 | time (s): 33.750 (total time: 110.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.903550 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.144174 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 0.1175 0.1557 0.0383 0.009 1.0 3.5 0.5 0.0 0 0.952 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.75 15.57 3.83 4.371 21.627 0.144 4.995 11.57 15.76 4.20 4.933 21.513 0.144 4.977 Individual atomic B min max mean iso aniso Overall: 5.80 104.92 20.96 4.61 1939 0 Protein: 5.80 104.92 17.00 4.60 1519 0 Water: 9.00 63.23 35.37 N/A 412 0 Other: 24.75 43.13 32.49 N/A 8 0 Chain A: 5.80 104.92 18.70 N/A 1734 0 Chain S: 17.94 63.23 40.07 N/A 205 0 Histogram: Values Number of atoms 5.80 - 15.71 1023 15.71 - 25.63 384 25.63 - 35.54 222 35.54 - 45.45 186 45.45 - 55.36 79 55.36 - 65.27 31 65.27 - 75.19 6 75.19 - 85.10 4 85.10 - 95.01 2 95.01 - 104.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1157 r_free=0.1576 r_work=0.1157 r_free=0.1579 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1157 r_free = 0.1579 target_work(ml) = 4.977 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1156 r_free = 0.1579 target_work(ml) = 4.976 | | occupancies: max = 1.00 min = 0.25 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= 0.1156 r_free= 0.1579 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.975895 | | target function (ml) not normalized (work): 80778.684582 | | target function (ml) not normalized (free): 4198.874257 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1176 0.1156 0.1579 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1682 0.1672 0.1929 n_refl.: 17041 remove outliers: r(all,work,free)=0.1682 0.1672 0.1929 n_refl.: 17041 overall B=-0.39 to atoms: r(all,work,free)=0.1655 0.1644 0.1916 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1172 0.1152 0.1578 n_refl.: 17041 remove outliers: r(all,work,free)=0.1172 0.1152 0.1578 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 0.3660 299.431 276.769 0.559 1.007 0.340 11.894-9.307 99.02 97 4 0.1752 486.660 480.189 0.909 1.007 0.340 9.237-7.194 100.00 213 7 0.1785 398.039 398.255 0.981 1.007 0.261 7.162-5.571 100.00 427 22 0.1643 298.729 293.360 0.938 1.006 0.243 5.546-4.326 100.00 867 58 0.0973 410.106 405.776 0.965 1.005 0.211 4.315-3.360 100.00 1859 96 0.0909 390.015 387.974 1.013 1.004 0.201 3.356-2.611 100.00 3867 181 0.1298 256.218 253.660 1.013 1.001 0.132 2.608-2.000 99.99 8818 434 0.1073 167.010 165.571 1.021 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3934 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1152 r_free=0.1578 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=0.1152 r_free=0.1577 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1152 r_free=0.1577 | n_water=412 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1152 r_free=0.1577 | n_water=412 | time (s): 32.760 (total time: 33.490) Filter (q & B) r_work=0.1152 r_free=0.1577 | n_water=412 | time (s): 1.310 (total time: 34.800) Compute maps r_work=0.1152 r_free=0.1577 | n_water=412 | time (s): 0.750 (total time: 35.550) Filter (map) r_work=0.1199 r_free=0.1554 | n_water=314 | time (s): 1.970 (total time: 37.520) Find peaks r_work=0.1199 r_free=0.1554 | n_water=314 | time (s): 0.650 (total time: 38.170) Add new water r_work=0.1350 r_free=0.1681 | n_water=459 | time (s): 2.060 (total time: 40.230) Refine new water occ: r_work=0.1180 r_free=0.1519 adp: r_work=0.1171 r_free=0.1524 occ: r_work=0.1156 r_free=0.1503 adp: r_work=0.1147 r_free=0.1507 occ: r_work=0.1141 r_free=0.1495 adp: r_work=0.1133 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1497 r_work=0.1133 r_free=0.1497 | n_water=459 | time (s): 25.740 (total time: 65.970) Filter (q & B) r_work=0.1135 r_free=0.1500 | n_water=450 | time (s): 2.220 (total time: 68.190) Filter (dist only) r_work=0.1139 r_free=0.1501 | n_water=449 | time (s): 35.790 (total time: 103.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.041643 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.162701 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1125 0.1541 0.0416 0.010 1.0 3.8 0.5 0.0 0 1.021 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.25 15.41 4.16 4.449 21.081 0.163 4.957 11.11 15.39 4.28 4.622 21.140 0.163 4.947 Individual atomic B min max mean iso aniso Overall: 5.31 102.30 21.07 4.81 1976 0 Protein: 5.31 102.30 16.66 4.80 1519 0 Water: 8.01 60.33 35.87 N/A 449 0 Other: 19.36 37.91 27.12 N/A 8 0 Chain A: 5.31 102.30 18.27 N/A 1732 0 Chain S: 16.74 60.33 40.93 N/A 244 0 Histogram: Values Number of atoms 5.31 - 15.01 979 15.01 - 24.71 420 24.71 - 34.41 212 34.41 - 44.11 208 44.11 - 53.81 105 53.81 - 63.51 37 63.51 - 73.20 7 73.20 - 82.90 3 82.90 - 92.60 3 92.60 - 102.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.1111 r_free=0.1539 r_work=0.1111 r_free=0.1538 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1538 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1539 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1539 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.942352 | | target function (ml) not normalized (work): 80234.148966 | | target function (ml) not normalized (free): 4178.855095 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1102 0.1539 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1599 0.1585 0.1896 n_refl.: 17041 remove outliers: r(all,work,free)=0.1599 0.1585 0.1896 n_refl.: 17041 overall B=-0.32 to atoms: r(all,work,free)=0.1578 0.1564 0.1884 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1101 0.1532 n_refl.: 17041 remove outliers: r(all,work,free)=0.1121 0.1100 0.1532 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 0.3679 295.876 283.014 0.543 0.999 0.315 11.894-9.307 99.02 97 4 0.1866 486.660 479.426 0.916 1.001 0.304 9.237-7.194 100.00 213 7 0.1772 398.039 397.473 0.986 1.001 0.230 7.162-5.571 100.00 427 22 0.1519 298.729 292.245 0.944 1.001 0.220 5.546-4.326 100.00 867 58 0.0928 410.106 406.262 0.969 1.002 0.200 4.315-3.360 100.00 1859 96 0.0863 390.015 387.673 1.011 1.001 0.191 3.356-2.611 100.00 3867 181 0.1223 256.218 254.091 1.008 1.001 0.131 2.608-2.000 99.99 8818 434 0.1032 167.010 165.825 1.005 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1147 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1100 r_free=0.1532 After: r_work=0.1102 r_free=0.1531 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1531 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1102 r_free=0.1531 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1531 | n_water=449 | time (s): 0.930 (total time: 0.930) Filter (dist) r_work=0.1102 r_free=0.1531 | n_water=449 | time (s): 38.570 (total time: 39.500) Filter (q & B) r_work=0.1102 r_free=0.1531 | n_water=449 | time (s): 1.020 (total time: 40.520) Compute maps r_work=0.1102 r_free=0.1531 | n_water=449 | time (s): 0.620 (total time: 41.140) Filter (map) r_work=0.1174 r_free=0.1541 | n_water=339 | time (s): 1.950 (total time: 43.090) Find peaks r_work=0.1174 r_free=0.1541 | n_water=339 | time (s): 0.590 (total time: 43.680) Add new water r_work=0.1304 r_free=0.1625 | n_water=487 | time (s): 2.220 (total time: 45.900) Refine new water occ: r_work=0.1139 r_free=0.1492 adp: r_work=0.1131 r_free=0.1491 occ: r_work=0.1119 r_free=0.1480 adp: r_work=0.1110 r_free=0.1478 occ: r_work=0.1104 r_free=0.1476 adp: r_work=0.1098 r_free=0.1475 ADP+occupancy (water only), MIN, final r_work=0.1098 r_free=0.1475 r_work=0.1098 r_free=0.1475 | n_water=487 | time (s): 41.580 (total time: 87.480) Filter (q & B) r_work=0.1104 r_free=0.1498 | n_water=471 | time (s): 2.140 (total time: 89.620) Filter (dist only) r_work=0.1104 r_free=0.1498 | n_water=471 | time (s): 36.620 (total time: 126.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.942585 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.178947 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 0.1123 0.1516 0.0393 0.010 1.1 6.7 0.5 0.0 0 0.971 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.23 15.16 3.93 4.529 20.868 0.179 4.948 11.12 15.06 3.95 4.617 20.976 0.179 4.939 Individual atomic B min max mean iso aniso Overall: 5.07 100.32 21.07 5.06 1998 0 Protein: 5.07 100.32 16.39 5.06 1519 0 Water: 7.94 64.89 36.06 N/A 471 0 Other: 19.49 35.18 26.10 N/A 8 0 Chain A: 5.07 100.32 17.96 N/A 1730 0 Chain S: 17.21 64.89 41.15 N/A 268 0 Histogram: Values Number of atoms 5.07 - 14.59 981 14.59 - 24.12 407 24.12 - 33.65 229 33.65 - 43.17 201 43.17 - 52.70 118 52.70 - 62.22 37 62.22 - 71.75 15 71.75 - 81.27 4 81.27 - 90.80 1 90.80 - 100.32 5 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1506 r_work=0.1112 r_free=0.1507 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1507 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1508 target_work(ml) = 4.936 | | 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= 0.1103 r_free= 0.1508 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.935561 | | target function (ml) not normalized (work): 80118.964847 | | target function (ml) not normalized (free): 4172.035808 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1113 0.1369 5.4408 5.6502| | 2: 3.63 - 2.88 1.00 2711 122 0.1096 0.1543 5.2183 5.382| | 3: 2.88 - 2.52 1.00 2681 148 0.1345 0.1657 5.1268 5.19| | 4: 2.52 - 2.29 1.00 2661 139 0.0926 0.1517 4.6295 4.9827| | 5: 2.29 - 2.13 1.00 2678 122 0.0954 0.1465 4.5869 4.8766| | 6: 2.13 - 2.00 1.00 2692 117 0.1127 0.1745 4.5823 4.7983| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.25 1.00 0.96 6426.39| | 2: 3.63 - 2.88 2711 122 0.92 12.91 1.01 0.96 6426.39| | 3: 2.88 - 2.52 2681 148 0.87 19.08 0.99 0.96 6426.39| | 4: 2.52 - 2.29 2661 139 0.93 12.41 1.01 0.97 2191.34| | 5: 2.29 - 2.13 2678 122 0.91 14.40 1.00 0.97 2191.34| | 6: 2.13 - 2.00 2692 117 0.89 17.27 0.99 0.97 2191.34| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2191.34 max = 6426.39 mean = 4331.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.92 mean = 14.18| |phase err.(test): min = 0.00 max = 89.82 mean = 13.80| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1123 0.1103 0.1508 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1576 0.1561 0.1883 n_refl.: 17040 remove outliers: r(all,work,free)=0.1576 0.1561 0.1883 n_refl.: 17040 overall B=-0.26 to atoms: r(all,work,free)=0.1561 0.1545 0.1872 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1104 0.1508 n_refl.: 17040 remove outliers: r(all,work,free)=0.1122 0.1103 0.1508 n_refl.: 17039 ======================== 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 0.3457 298.037 275.626 0.528 1.003 0.310 11.894-9.307 99.02 97 4 0.1846 486.660 478.209 0.914 1.004 0.297 9.237-7.194 100.00 213 7 0.1739 398.039 398.377 0.982 1.004 0.220 7.162-5.571 100.00 427 22 0.1548 298.729 291.987 0.937 1.004 0.210 5.546-4.326 100.00 867 58 0.0910 410.106 406.461 0.966 1.003 0.181 4.315-3.360 100.00 1859 96 0.0878 390.015 387.778 1.007 1.002 0.171 3.356-2.611 100.00 3867 181 0.1234 256.218 254.103 1.005 1.000 0.151 2.608-2.000 99.99 8818 434 0.1031 167.010 165.738 0.998 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-0.8920 ================= 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 0.1829 0.081 5.373 8.8 119.3 19.9 258 0.000 1_bss: 0.1609 0.1668 0.081 5.373 8.5 118.9 19.5 258 0.000 1_settarget: 0.1609 0.1668 0.081 5.373 8.5 118.9 19.5 258 0.000 1_nqh: 0.1609 0.1673 0.081 5.373 8.5 118.9 19.5 258 0.003 1_weight: 0.1609 0.1673 0.081 5.373 8.5 118.9 19.5 258 0.003 1_xyzrec: 0.1352 0.1640 0.008 0.966 8.5 118.9 19.5 258 0.156 1_adp: 0.1279 0.1666 0.008 0.966 6.1 113.9 20.0 258 0.156 1_regHadp: 0.1283 0.1671 0.008 0.966 6.1 113.9 20.0 258 0.156 1_occ: 0.1281 0.1673 0.008 0.966 6.1 113.9 20.0 258 0.156 2_bss: 0.1278 0.1662 0.008 0.966 5.7 113.5 19.6 258 0.156 2_settarget: 0.1278 0.1662 0.008 0.966 5.7 113.5 19.6 258 0.156 2_updatecdl: 0.1278 0.1662 0.008 0.978 5.7 113.5 19.6 258 0.156 2_nqh: 0.1280 0.1662 0.008 0.978 5.7 113.5 19.6 258 0.153 2_sol: 0.1246 0.1542 0.008 0.978 5.7 112.1 20.9 362 n/a 2_weight: 0.1246 0.1542 0.008 0.978 5.7 112.1 20.9 362 n/a 2_xyzrec: 0.1217 0.1584 0.008 0.939 5.7 112.1 20.9 362 n/a 2_adp: 0.1202 0.1609 0.008 0.939 6.5 107.1 21.4 362 n/a 2_regHadp: 0.1204 0.1612 0.008 0.939 6.5 107.1 21.4 362 n/a 2_occ: 0.1196 0.1615 0.008 0.939 6.5 107.1 21.4 362 n/a 3_bss: 0.1189 0.1607 0.008 0.939 6.1 106.7 21.0 362 n/a 3_settarget: 0.1189 0.1607 0.008 0.939 6.1 106.7 21.0 362 n/a 3_updatecdl: 0.1189 0.1607 0.008 0.939 6.1 106.7 21.0 362 n/a 3_nqh: 0.1191 0.1606 0.008 0.939 6.1 106.7 21.0 362 n/a 3_sol: 0.1199 0.1538 0.008 0.939 6.1 106.7 21.2 412 n/a 3_weight: 0.1199 0.1538 0.008 0.939 6.1 106.7 21.2 412 n/a 3_xyzrec: 0.1175 0.1557 0.009 0.956 6.1 106.7 21.2 412 n/a 3_adp: 0.1157 0.1576 0.009 0.956 5.8 104.9 21.0 412 n/a 3_regHadp: 0.1157 0.1579 0.009 0.956 5.8 104.9 21.0 412 n/a 3_occ: 0.1156 0.1579 0.009 0.956 5.8 104.9 21.0 412 n/a 4_bss: 0.1152 0.1578 0.009 0.956 5.4 104.5 20.6 412 n/a 4_settarget: 0.1152 0.1578 0.009 0.956 5.4 104.5 20.6 412 n/a 4_updatecdl: 0.1152 0.1578 0.009 0.956 5.4 104.5 20.6 412 n/a 4_nqh: 0.1152 0.1577 0.009 0.956 5.4 104.5 20.6 412 n/a 4_sol: 0.1139 0.1501 0.009 0.956 5.4 104.5 21.0 449 n/a 4_weight: 0.1139 0.1501 0.009 0.956 5.4 104.5 21.0 449 n/a 4_xyzrec: 0.1125 0.1541 0.010 0.995 5.4 104.5 21.0 449 n/a 4_adp: 0.1111 0.1539 0.010 0.995 5.3 102.3 21.1 449 n/a 4_regHadp: 0.1111 0.1538 0.010 0.995 5.3 102.3 21.1 449 n/a 4_occ: 0.1102 0.1539 0.010 0.995 5.3 102.3 21.1 449 n/a 5_bss: 0.1100 0.1532 0.010 0.995 5.0 102.0 20.7 449 n/a 5_settarget: 0.1100 0.1532 0.010 0.995 5.0 102.0 20.7 449 n/a 5_updatecdl: 0.1100 0.1532 0.010 0.997 5.0 102.0 20.7 449 n/a 5_setrh: 0.1102 0.1531 0.010 0.997 5.0 102.0 20.7 449 n/a 5_nqh: 0.1102 0.1531 0.010 0.997 5.0 102.0 20.7 449 n/a 5_sol: 0.1104 0.1498 0.010 0.997 5.0 102.0 20.9 471 n/a 5_weight: 0.1104 0.1498 0.010 0.997 5.0 102.0 20.9 471 n/a 5_xyzrec: 0.1123 0.1516 0.010 1.089 5.0 102.0 20.9 471 n/a 5_adp: 0.1112 0.1506 0.010 1.089 5.1 100.3 21.1 471 n/a 5_regHadp: 0.1112 0.1507 0.010 1.089 5.1 100.3 21.1 471 n/a 5_occ: 0.1103 0.1508 0.010 1.089 5.1 100.3 21.1 471 n/a end: 0.1103 0.1508 0.010 1.089 4.8 100.1 20.8 471 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2226169_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2226169_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.0800 Refinement macro-cycles (run) : 953.9600 Write final files (write_after_run_outputs) : 16.6100 Total : 974.6500 Total CPU time: 16.63 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:38 PST -0800 (1735494098.91 s) Start R-work = 0.1609, R-free = 0.1668 Final R-work = 0.1103, R-free = 0.1508 =============================================================================== Job complete usr+sys time: 1016.77 seconds wall clock time: 17 minutes 19.57 seconds (1039.57 seconds total)