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_8555406.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8555406.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8555406.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" 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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.26, per 1000 atoms: 0.37 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 106.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.90: 449 0.90 - 1.18: 1237 1.18 - 1.47: 788 1.47 - 1.75: 667 1.75 - 2.03: 12 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLY A 136 " pdb=" N GLY A 137 " ideal model delta sigma weight residual 1.329 1.512 -0.183 1.00e-02 1.00e+04 3.34e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.186 0.192 1.10e-02 8.26e+03 3.04e+02 bond pdb=" C LYS A 62 " pdb=" O LYS A 62 " ideal model delta sigma weight residual 1.236 1.458 -0.222 1.29e-02 6.01e+03 2.97e+02 bond pdb=" C GLU A 143 " pdb=" N ASN A 144 " ideal model delta sigma weight residual 1.329 1.562 -0.232 1.36e-02 5.41e+03 2.92e+02 bond pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 1.330 1.551 -0.221 1.30e-02 5.92e+03 2.88e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 3122 4.39 - 8.78: 1743 8.78 - 13.17: 714 13.17 - 17.56: 173 17.56 - 21.95: 25 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 137.65 -14.98 1.09e+00 8.42e-01 1.89e+02 angle pdb=" CA ASN A 144 " pdb=" C ASN A 144 " pdb=" O ASN A 144 " ideal model delta sigma weight residual 121.47 136.75 -15.28 1.15e+00 7.56e-01 1.76e+02 angle pdb=" CA ASP A 42 " pdb=" C ASP A 42 " pdb=" O ASP A 42 " ideal model delta sigma weight residual 120.96 134.69 -13.73 1.09e+00 8.42e-01 1.59e+02 angle pdb=" CA VAL A 44 " pdb=" C VAL A 44 " pdb=" O VAL A 44 " ideal model delta sigma weight residual 120.39 133.57 -13.18 1.05e+00 9.07e-01 1.58e+02 angle pdb=" O ALYS A 132 " pdb=" C ALYS A 132 " pdb=" N MET A 133 " ideal model delta sigma weight residual 122.12 109.26 12.86 1.06e+00 8.90e-01 1.47e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 1273 15.93 - 31.86: 150 31.86 - 47.79: 35 47.79 - 63.71: 20 63.71 - 79.64: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 69 " pdb=" N VAL A 69 " pdb=" CA VAL A 69 " pdb=" CB VAL A 69 " ideal model delta harmonic sigma weight residual -122.00 -140.55 18.55 0 2.50e+00 1.60e-01 5.51e+01 dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -141.15 18.55 0 2.50e+00 1.60e-01 5.51e+01 dihedral pdb=" N ASN A 144 " pdb=" C ASN A 144 " pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " ideal model delta harmonic sigma weight residual 122.80 104.60 18.20 0 2.50e+00 1.60e-01 5.30e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.173: 85 0.173 - 0.345: 59 0.345 - 0.517: 53 0.517 - 0.688: 32 0.688 - 0.860: 14 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BGLN A 80 " pdb=" N BGLN A 80 " pdb=" C BGLN A 80 " pdb=" CB BGLN A 80 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.85e+01 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.79 0.86 2.00e-01 2.50e+01 1.85e+01 chirality pdb=" CA PHE A 164 " pdb=" N PHE A 164 " pdb=" C PHE A 164 " pdb=" CB PHE A 164 " both_signs ideal model delta sigma weight residual False 2.51 3.36 -0.84 2.00e-01 2.50e+01 1.78e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.074 2.00e-02 2.50e+03 7.08e-02 1.50e+02 pdb=" CG PHE A 164 " 0.171 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.090 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.044 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.043 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG BTYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.113 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.024 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.111 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.046 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.043 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.034 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.005 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.051 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.114 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.043 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG TYR A 141 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.083 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.068 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.089 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.067 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.070 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.036 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.065 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 783 2.28 - 2.86: 7873 2.86 - 3.44: 10542 3.44 - 4.02: 15323 4.02 - 4.60: 22055 Nonbonded interactions: 56576 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.698 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.750 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.776 2.100 nonbonded pdb="HH22 ARG A 5 " pdb=" O AGLU A 64 " model vdw 1.794 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.798 2.450 ... (remaining 56571 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_8555406_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= 0.2788 r_free= 0.1899 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.406027 | | target function (ml) not normalized (work): 71567.092488 | | target function (ml) not normalized (free): 3289.964021 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3188 0.2182 7.4908 5.0454| | 2: 3.63 - 2.88 1.00 2711 122 0.2638 0.1840 4.3284 4.3306| | 3: 2.88 - 2.52 1.00 2682 148 0.2569 0.1759 4.1939 4.1954| | 4: 2.52 - 2.29 1.00 2661 139 0.2559 0.1635 3.5148 3.5987| | 5: 2.29 - 2.13 1.00 2678 122 0.2654 0.1582 3.4164 3.5474| | 6: 2.13 - 2.00 1.00 2692 117 0.2746 0.2014 3.3307 3.4658| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.77 0.77 0.23 1330.39| | 2: 3.63 - 2.88 2711 122 0.82 24.05 1.32 0.23 1330.39| | 3: 2.88 - 2.52 2682 148 0.73 33.04 1.28 0.23 1330.39| | 4: 2.52 - 2.29 2661 139 0.93 12.01 1.30 0.26 150.65| | 5: 2.29 - 2.13 2678 122 0.91 14.37 1.32 0.26 150.65| | 6: 2.13 - 2.00 2692 117 0.89 17.30 1.34 0.26 150.65| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 150.65 max = 1330.39 mean = 747.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.97 mean = 19.76| |phase err.(test): min = 0.00 max = 89.91 mean = 20.04| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.232 1557 Z= 5.531 Angle : 5.263 16.495 2118 Z= 3.759 Chirality : 0.374 0.860 243 Planarity : 0.033 0.105 284 Dihedral : 13.785 79.642 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 34.05 % 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: -2.11 (0.48), residues: 224 helix: -2.32 (0.40), residues: 103 sheet: -0.82 (0.75), residues: 28 loop : -0.13 (0.58), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.014 ARG A 48 TYR 0.090 0.055 TYR A 141 PHE 0.147 0.050 PHE A 164 HIS 0.077 0.033 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2788 r_free= 0.1899 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.406027 | | target function (ml) not normalized (work): 71567.092488 | | target function (ml) not normalized (free): 3289.964021 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3334 percent. r_work = 0.2921 r_free = 0.2058 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2870 0.2921 0.2058 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2870 0.2921 0.2058 n_refl.: 17050 remove outliers: r(all,work,free)=0.2162 0.2171 0.2058 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2135 0.2143 0.2041 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1620 0.1615 0.1733 n_refl.: 17045 remove outliers: r(all,work,free)=0.1619 0.1614 0.1733 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 0.4081 394.877 363.383 0.648 1.011 0.397 11.894-9.307 99.02 97 4 0.1863 633.789 614.043 0.932 1.013 0.380 9.237-7.194 100.00 213 7 0.2170 518.375 510.917 0.961 1.013 0.361 7.162-5.571 100.00 427 22 0.2297 389.041 376.545 0.922 1.011 0.294 5.546-4.326 100.00 867 58 0.1400 534.091 528.153 0.958 1.010 0.234 4.315-3.360 100.00 1859 96 0.1270 507.926 504.172 1.019 1.006 0.210 3.356-2.611 100.00 3867 181 0.1655 333.678 329.112 1.013 1.000 0.029 2.608-2.000 99.99 8818 434 0.1662 217.501 213.662 1.031 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4762 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1614 r_free=0.1733 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=0.1614 r_free=0.1733 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.994104 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.880366 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1350 0.1626 0.0276 0.009 1.0 1.3 0.5 0.0 0 11.497 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.26 2.76 3.013 18.445 0.880 0.023 12.78 16.48 3.71 3.623 18.713 0.880 0.020 Individual atomic B min max mean iso aniso Overall: 5.96 113.89 19.98 4.08 1785 0 Protein: 5.96 112.64 17.22 4.09 1519 0 Water: 8.96 113.89 36.04 N/A 258 0 Other: 21.82 36.94 26.30 N/A 8 0 Chain A: 5.96 113.89 19.98 N/A 1785 0 Histogram: Values Number of atoms 5.96 - 16.75 1072 16.75 - 27.54 349 27.54 - 38.33 190 38.33 - 49.13 97 49.13 - 59.92 49 59.92 - 70.71 13 70.71 - 81.51 7 81.51 - 92.30 4 92.30 - 103.09 1 103.09 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1648 r_work=0.1281 r_free=0.1656 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1656 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1276 r_free = 0.1650 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.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1276 r_free= 0.1650 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020043 | | target function (ls_wunit_k1) not normalized (work): 325.445264 | | target function (ls_wunit_k1) not normalized (free): 26.923219 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1276 0.1650 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1916 0.1915 0.1985 n_refl.: 17044 remove outliers: r(all,work,free)=0.1916 0.1915 0.1985 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1887 0.1886 0.1968 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1294 0.1276 0.1645 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1275 0.1645 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 0.3550 303.319 279.596 0.621 1.009 0.368 11.894-9.307 99.02 97 4 0.1698 487.840 477.718 0.915 1.010 0.367 9.237-7.194 100.00 213 7 0.1824 399.004 396.188 0.960 1.010 0.341 7.162-5.571 100.00 427 22 0.1831 299.453 294.730 0.932 1.009 0.301 5.546-4.326 100.00 867 58 0.1039 411.101 408.699 0.956 1.008 0.211 4.315-3.360 100.00 1859 96 0.0926 390.961 390.572 1.019 1.005 0.201 3.356-2.611 100.00 3867 181 0.1296 256.839 255.582 1.015 1.000 0.081 2.608-2.000 99.99 8818 434 0.1354 167.415 165.944 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=-1.4010 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1645 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1645 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1645 | n_water=258 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1279 r_free=0.1634 | n_water=254 | time (s): 23.050 (total time: 23.780) Filter (q & B) r_work=0.1279 r_free=0.1634 | n_water=252 | time (s): 2.080 (total time: 25.860) Compute maps r_work=0.1279 r_free=0.1634 | n_water=252 | time (s): 0.860 (total time: 26.720) Filter (map) r_work=0.1318 r_free=0.1618 | n_water=211 | time (s): 1.990 (total time: 28.710) Find peaks r_work=0.1318 r_free=0.1618 | n_water=211 | time (s): 0.680 (total time: 29.390) Add new water r_work=0.1535 r_free=0.1835 | n_water=367 | time (s): 2.020 (total time: 31.410) Refine new water occ: r_work=0.1333 r_free=0.1559 adp: r_work=0.1273 r_free=0.1548 occ: r_work=0.1280 r_free=0.1521 adp: r_work=0.1246 r_free=0.1527 occ: r_work=0.1248 r_free=0.1517 adp: r_work=0.1237 r_free=0.1517 ADP+occupancy (water only), MIN, final r_work=0.1237 r_free=0.1517 r_work=0.1237 r_free=0.1517 | n_water=367 | time (s): 17.190 (total time: 48.600) Filter (q & B) r_work=0.1239 r_free=0.1530 | n_water=355 | time (s): 2.330 (total time: 50.930) Filter (dist only) r_work=0.1239 r_free=0.1532 | n_water=354 | time (s): 28.090 (total time: 79.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.866382 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.950657 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 0.1218 0.1587 0.0369 0.008 0.9 2.6 0.5 0.0 0 12.433 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.18 15.87 3.69 4.173 21.027 0.951 0.018 12.05 16.11 4.06 4.197 21.313 0.951 0.018 Individual atomic B min max mean iso aniso Overall: 6.98 107.25 21.33 4.25 1881 0 Protein: 6.98 107.25 17.82 4.24 1519 0 Water: 8.58 65.77 36.15 N/A 354 0 Other: 23.45 41.79 32.30 N/A 8 0 Chain A: 6.98 107.25 19.51 N/A 1738 0 Chain S: 18.92 65.46 43.48 N/A 143 0 Histogram: Values Number of atoms 6.98 - 17.00 1040 17.00 - 27.03 373 27.03 - 37.06 213 37.06 - 47.09 151 47.09 - 57.11 67 57.11 - 67.14 27 67.14 - 77.17 3 77.17 - 87.20 3 87.20 - 97.22 2 97.22 - 107.25 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1611 r_work=0.1207 r_free=0.1611 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1611 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1613 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 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= 0.1202 r_free= 0.1613 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017164 | | target function (ls_wunit_k1) not normalized (work): 278.652486 | | target function (ls_wunit_k1) not normalized (free): 24.143691 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1202 0.1613 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1762 0.1755 0.1955 n_refl.: 17042 remove outliers: r(all,work,free)=0.1762 0.1755 0.1955 n_refl.: 17042 overall B=-0.39 to atoms: r(all,work,free)=0.1737 0.1729 0.1938 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1194 0.1605 n_refl.: 17042 remove outliers: r(all,work,free)=0.1212 0.1192 0.1605 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 0.3309 300.157 282.811 0.590 1.005 0.340 11.894-9.307 99.02 97 4 0.1496 487.840 484.731 0.911 1.005 0.337 9.237-7.194 100.00 213 7 0.1681 399.004 398.866 0.970 1.005 0.289 7.162-5.571 100.00 427 22 0.1510 299.453 296.153 0.935 1.005 0.240 5.546-4.326 100.00 867 58 0.0876 411.101 408.655 0.960 1.004 0.216 4.315-3.360 100.00 1859 96 0.0834 390.961 389.968 1.017 1.003 0.211 3.356-2.611 100.00 3867 181 0.1211 256.839 256.127 1.013 1.001 0.111 2.608-2.000 99.99 8818 434 0.1330 167.415 166.426 1.019 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3925 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1605 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=0.1194 r_free=0.1608 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1608 | n_water=354 | time (s): 0.880 (total time: 0.880) Filter (dist) r_work=0.1194 r_free=0.1607 | n_water=352 | time (s): 27.920 (total time: 28.800) Filter (q & B) r_work=0.1194 r_free=0.1607 | n_water=352 | time (s): 0.980 (total time: 29.780) Compute maps r_work=0.1194 r_free=0.1607 | n_water=352 | time (s): 0.770 (total time: 30.550) Filter (map) r_work=0.1255 r_free=0.1628 | n_water=260 | time (s): 2.560 (total time: 33.110) Find peaks r_work=0.1255 r_free=0.1628 | n_water=260 | time (s): 0.480 (total time: 33.590) Add new water r_work=0.1441 r_free=0.1807 | n_water=403 | time (s): 1.580 (total time: 35.170) Refine new water occ: r_work=0.1248 r_free=0.1566 adp: r_work=0.1240 r_free=0.1568 occ: r_work=0.1224 r_free=0.1548 adp: r_work=0.1213 r_free=0.1545 occ: r_work=0.1208 r_free=0.1542 adp: r_work=0.1199 r_free=0.1537 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1537 r_work=0.1199 r_free=0.1537 | n_water=403 | time (s): 37.580 (total time: 72.750) Filter (q & B) r_work=0.1202 r_free=0.1547 | n_water=394 | time (s): 1.620 (total time: 74.370) Filter (dist only) r_work=0.1201 r_free=0.1550 | n_water=393 | time (s): 29.930 (total time: 104.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.911664 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.175150 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 0.1177 0.1533 0.0355 0.009 1.0 3.8 0.5 0.0 0 0.956 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.77 15.33 3.55 4.333 21.469 0.175 4.995 11.55 15.41 3.86 4.848 21.403 0.175 4.971 Individual atomic B min max mean iso aniso Overall: 6.28 104.78 20.76 4.71 1920 0 Protein: 6.28 104.78 17.08 4.70 1519 0 Water: 8.79 60.38 34.71 N/A 393 0 Other: 25.59 44.44 33.44 N/A 8 0 Chain A: 6.28 104.78 18.81 N/A 1736 0 Chain S: 14.05 59.98 39.11 N/A 184 0 Histogram: Values Number of atoms 6.28 - 16.13 1061 16.13 - 25.98 354 25.98 - 35.83 224 35.83 - 45.68 169 45.68 - 55.53 74 55.53 - 65.38 24 65.38 - 75.23 5 75.23 - 85.08 4 85.08 - 94.93 3 94.93 - 104.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.1155 r_free=0.1541 r_work=0.1155 r_free=0.1542 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1155 r_free = 0.1542 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1149 r_free = 0.1532 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.23 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= 0.1149 r_free= 0.1532 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.967154 | | target function (ml) not normalized (work): 80636.782361 | | target function (ml) not normalized (free): 4182.478780 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1167 0.1149 0.1532 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1679 0.1674 0.1826 n_refl.: 17041 remove outliers: r(all,work,free)=0.1679 0.1674 0.1826 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1654 0.1648 0.1814 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1168 0.1149 0.1532 n_refl.: 17041 remove outliers: r(all,work,free)=0.1167 0.1148 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 0.3571 296.594 278.253 0.553 1.006 0.334 11.894-9.307 99.02 97 4 0.1752 487.840 480.895 0.908 1.006 0.330 9.237-7.194 100.00 213 7 0.1834 399.004 399.105 0.981 1.006 0.259 7.162-5.571 100.00 427 22 0.1597 299.453 293.960 0.938 1.006 0.225 5.546-4.326 100.00 867 58 0.0937 411.101 407.684 0.963 1.005 0.207 4.315-3.360 100.00 1859 96 0.0905 390.961 388.763 1.012 1.004 0.195 3.356-2.611 100.00 3867 181 0.1270 256.839 254.739 1.013 1.001 0.152 2.608-2.000 99.99 8818 434 0.1098 167.415 166.013 1.017 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3332 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1148 r_free=0.1532 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1148 r_free=0.1532 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1532 | n_water=393 | time (s): 0.830 (total time: 0.830) Filter (dist) r_work=0.1148 r_free=0.1532 | n_water=393 | time (s): 31.910 (total time: 32.740) Filter (q & B) r_work=0.1148 r_free=0.1532 | n_water=393 | time (s): 1.130 (total time: 33.870) Compute maps r_work=0.1148 r_free=0.1532 | n_water=393 | time (s): 0.840 (total time: 34.710) Filter (map) r_work=0.1200 r_free=0.1546 | n_water=306 | time (s): 2.010 (total time: 36.720) Find peaks r_work=0.1200 r_free=0.1546 | n_water=306 | time (s): 0.540 (total time: 37.260) Add new water r_work=0.1359 r_free=0.1651 | n_water=460 | time (s): 1.450 (total time: 38.710) Refine new water occ: r_work=0.1179 r_free=0.1481 adp: r_work=0.1170 r_free=0.1487 occ: r_work=0.1157 r_free=0.1467 adp: r_work=0.1146 r_free=0.1471 occ: r_work=0.1141 r_free=0.1463 adp: r_work=0.1132 r_free=0.1466 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1466 r_work=0.1132 r_free=0.1466 | n_water=460 | time (s): 36.190 (total time: 74.900) Filter (q & B) r_work=0.1136 r_free=0.1477 | n_water=448 | time (s): 1.990 (total time: 76.890) Filter (dist only) r_work=0.1136 r_free=0.1478 | n_water=447 | time (s): 36.980 (total time: 113.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.940292 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.164661 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 0.1119 0.1549 0.0430 0.010 1.0 4.5 0.5 0.0 0 0.970 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.19 15.49 4.30 4.518 21.207 0.165 4.960 11.08 15.55 4.48 4.707 21.213 0.165 4.954 Individual atomic B min max mean iso aniso Overall: 5.81 103.33 21.08 4.88 1974 0 Protein: 5.81 103.33 16.65 4.88 1519 0 Water: 8.68 63.71 35.95 N/A 447 0 Other: 24.14 42.12 31.33 N/A 8 0 Chain A: 5.81 103.33 18.32 N/A 1735 0 Chain S: 17.90 63.71 41.08 N/A 239 0 Histogram: Values Number of atoms 5.81 - 15.57 1036 15.57 - 25.32 377 25.32 - 35.07 219 35.07 - 44.82 197 44.82 - 54.57 95 54.57 - 64.32 35 64.32 - 74.07 7 74.07 - 83.83 3 83.83 - 93.58 2 93.58 - 103.33 3 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1555 r_work=0.1108 r_free=0.1557 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1557 target_work(ml) = 4.955 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1573 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1573 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.953606 | | target function (ml) not normalized (work): 80411.885315 | | target function (ml) not normalized (free): 4193.222585 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1102 0.1573 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1586 0.1573 0.1858 n_refl.: 17040 remove outliers: r(all,work,free)=0.1586 0.1573 0.1858 n_refl.: 17040 overall B=-0.31 to atoms: r(all,work,free)=0.1566 0.1553 0.1846 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1100 0.1570 n_refl.: 17040 remove outliers: r(all,work,free)=0.1122 0.1100 0.1570 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 0.3770 296.594 273.393 0.527 1.003 0.318 11.894-9.307 99.02 97 4 0.1793 487.840 479.268 0.909 1.004 0.310 9.237-7.194 100.00 213 7 0.1736 399.004 401.197 0.988 1.004 0.240 7.162-5.571 100.00 427 22 0.1547 299.453 294.024 0.941 1.004 0.210 5.546-4.326 100.00 867 58 0.0916 411.101 407.239 0.967 1.004 0.204 4.315-3.360 100.00 1859 96 0.0858 390.961 388.703 1.009 1.003 0.201 3.356-2.611 100.00 3867 181 0.1221 256.839 254.569 1.007 1.001 0.161 2.608-2.000 99.99 8818 434 0.1037 167.415 166.259 1.006 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0764 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1100 r_free=0.1570 After: r_work=0.1102 r_free=0.1570 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1570 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1102 r_free=0.1570 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1570 | n_water=447 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1108 r_free=0.1571 | n_water=443 | time (s): 37.390 (total time: 38.120) Filter (q & B) r_work=0.1108 r_free=0.1571 | n_water=442 | time (s): 2.350 (total time: 40.470) Compute maps r_work=0.1108 r_free=0.1571 | n_water=442 | time (s): 0.690 (total time: 41.160) Filter (map) r_work=0.1178 r_free=0.1558 | n_water=335 | time (s): 2.380 (total time: 43.540) Find peaks r_work=0.1178 r_free=0.1558 | n_water=335 | time (s): 0.610 (total time: 44.150) Add new water r_work=0.1305 r_free=0.1671 | n_water=473 | time (s): 1.860 (total time: 46.010) Refine new water occ: r_work=0.1147 r_free=0.1528 adp: r_work=0.1140 r_free=0.1528 occ: r_work=0.1128 r_free=0.1507 adp: r_work=0.1119 r_free=0.1509 occ: r_work=0.1113 r_free=0.1490 adp: r_work=0.1107 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1107 r_free=0.1491 r_work=0.1107 r_free=0.1491 | n_water=473 | time (s): 28.350 (total time: 74.360) Filter (q & B) r_work=0.1110 r_free=0.1502 | n_water=461 | time (s): 1.720 (total time: 76.080) Filter (dist only) r_work=0.1110 r_free=0.1503 | n_water=460 | time (s): 39.660 (total time: 115.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.887150 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.154732 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 0.1133 0.1530 0.0396 0.009 1.0 5.1 0.5 0.0 0 0.944 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 15.30 3.96 4.577 20.878 0.155 4.957 11.20 15.16 3.96 4.647 20.928 0.155 4.946 Individual atomic B min max mean iso aniso Overall: 5.55 102.28 20.93 4.96 1987 0 Protein: 5.55 102.28 16.28 4.96 1519 0 Water: 8.15 66.08 36.14 N/A 460 0 Other: 22.46 40.16 29.93 N/A 8 0 Chain A: 5.55 102.28 17.92 N/A 1734 0 Chain S: 18.59 66.08 41.60 N/A 253 0 Histogram: Values Number of atoms 5.55 - 15.22 1040 15.22 - 24.89 370 24.89 - 34.57 226 34.57 - 44.24 187 44.24 - 53.91 109 53.91 - 63.58 36 63.58 - 73.26 10 73.26 - 82.93 2 82.93 - 92.60 3 92.60 - 102.28 4 =========================== Idealize ADP of riding H ========================== r_work=0.1120 r_free=0.1516 r_work=0.1120 r_free=0.1516 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1120 r_free = 0.1516 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1114 r_free = 0.1522 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1114 r_free= 0.1522 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.943410 | | target function (ml) not normalized (work): 80246.381322 | | target function (ml) not normalized (free): 4165.249294 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1129 0.1350 5.4651 5.628| | 2: 3.63 - 2.88 1.00 2711 122 0.1091 0.1505 5.2218 5.355| | 3: 2.88 - 2.52 1.00 2681 148 0.1361 0.1758 5.1305 5.2046| | 4: 2.52 - 2.29 1.00 2661 139 0.0942 0.1598 4.6369 4.9805| | 5: 2.29 - 2.13 1.00 2678 122 0.0981 0.1456 4.5957 4.8727| | 6: 2.13 - 2.00 1.00 2692 117 0.1127 0.1759 4.5811 4.7866| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.95 8.95 1.00 0.95 6295.20| | 2: 3.63 - 2.88 2711 122 0.92 12.78 1.01 0.95 6295.20| | 3: 2.88 - 2.52 2681 148 0.88 18.75 0.99 0.95 6295.20| | 4: 2.52 - 2.29 2661 139 0.93 12.33 1.00 0.97 2175.90| | 5: 2.29 - 2.13 2678 122 0.91 14.29 1.00 0.97 2175.90| | 6: 2.13 - 2.00 2692 117 0.89 17.11 0.99 0.97 2175.90| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2175.90 max = 6295.20 mean = 4257.25| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.80 mean = 14.00| |phase err.(test): min = 0.00 max = 87.65 mean = 13.68| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1134 0.1114 0.1522 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1583 0.1571 0.1837 n_refl.: 17040 remove outliers: r(all,work,free)=0.1583 0.1571 0.1837 n_refl.: 17040 overall B=-0.23 to atoms: r(all,work,free)=0.1570 0.1558 0.1829 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1135 0.1116 0.1521 n_refl.: 17040 remove outliers: r(all,work,free)=0.1134 0.1114 0.1521 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 0.3533 298.760 273.672 0.532 1.004 0.323 11.894-9.307 99.02 97 4 0.1788 487.840 482.900 0.915 1.005 0.318 9.237-7.194 100.00 213 7 0.1728 399.004 400.729 0.988 1.005 0.227 7.162-5.571 100.00 427 22 0.1559 299.453 294.415 0.936 1.004 0.204 5.546-4.326 100.00 867 58 0.0936 411.101 408.170 0.963 1.004 0.195 4.315-3.360 100.00 1859 96 0.0881 390.961 388.643 1.004 1.002 0.181 3.356-2.611 100.00 3867 181 0.1246 256.839 254.387 1.003 1.000 0.063 2.608-2.000 99.99 8818 434 0.1046 167.415 166.121 0.993 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-0.7923 ================= 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 : 0.2788 0.1899 0.082 5.263 8.8 119.3 19.9 258 0.000 1_bss: 0.1614 0.1733 0.082 5.263 8.4 118.9 19.5 258 0.000 1_settarget: 0.1614 0.1733 0.082 5.263 8.4 118.9 19.5 258 0.000 1_nqh: 0.1614 0.1733 0.082 5.263 8.4 118.9 19.5 258 0.000 1_weight: 0.1614 0.1733 0.082 5.263 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1350 0.1626 0.009 0.973 8.4 118.9 19.5 258 0.149 1_adp: 0.1278 0.1648 0.009 0.973 6.0 113.9 20.0 258 0.149 1_regHadp: 0.1281 0.1656 0.009 0.973 6.0 113.9 20.0 258 0.149 1_occ: 0.1276 0.1650 0.009 0.973 6.0 113.9 20.0 258 0.149 2_bss: 0.1275 0.1645 0.009 0.973 5.6 113.5 19.6 258 0.149 2_settarget: 0.1275 0.1645 0.009 0.973 5.6 113.5 19.6 258 0.149 2_updatecdl: 0.1275 0.1645 0.009 0.993 5.6 113.5 19.6 258 0.149 2_nqh: 0.1275 0.1645 0.009 0.993 5.6 113.5 19.6 258 0.149 2_sol: 0.1239 0.1532 0.009 0.993 5.6 112.3 20.8 354 n/a 2_weight: 0.1239 0.1532 0.009 0.993 5.6 112.3 20.8 354 n/a 2_xyzrec: 0.1218 0.1587 0.008 0.938 5.6 112.3 20.8 354 n/a 2_adp: 0.1205 0.1611 0.008 0.938 7.0 107.3 21.3 354 n/a 2_regHadp: 0.1207 0.1611 0.008 0.938 7.0 107.3 21.3 354 n/a 2_occ: 0.1202 0.1613 0.008 0.938 7.0 107.3 21.3 354 n/a 3_bss: 0.1192 0.1605 0.008 0.938 6.6 106.9 20.9 354 n/a 3_settarget: 0.1192 0.1605 0.008 0.938 6.6 106.9 20.9 354 n/a 3_updatecdl: 0.1192 0.1605 0.008 0.937 6.6 106.9 20.9 354 n/a 3_nqh: 0.1194 0.1608 0.008 0.937 6.6 106.9 20.9 354 n/a 3_sol: 0.1201 0.1550 0.008 0.937 6.6 106.9 20.9 393 n/a 3_weight: 0.1201 0.1550 0.008 0.937 6.6 106.9 20.9 393 n/a 3_xyzrec: 0.1177 0.1533 0.009 0.964 6.6 106.9 20.9 393 n/a 3_adp: 0.1155 0.1541 0.009 0.964 6.3 104.8 20.8 393 n/a 3_regHadp: 0.1155 0.1542 0.009 0.964 6.3 104.8 20.8 393 n/a 3_occ: 0.1149 0.1532 0.009 0.964 6.3 104.8 20.8 393 n/a 4_bss: 0.1148 0.1532 0.009 0.964 5.9 104.4 20.4 393 n/a 4_settarget: 0.1148 0.1532 0.009 0.964 5.9 104.4 20.4 393 n/a 4_updatecdl: 0.1148 0.1532 0.009 0.964 5.9 104.4 20.4 393 n/a 4_nqh: 0.1148 0.1532 0.009 0.964 5.9 104.4 20.4 393 n/a 4_sol: 0.1136 0.1478 0.009 0.964 5.9 104.4 21.1 447 n/a 4_weight: 0.1136 0.1478 0.009 0.964 5.9 104.4 21.1 447 n/a 4_xyzrec: 0.1119 0.1549 0.010 0.977 5.9 104.4 21.1 447 n/a 4_adp: 0.1108 0.1555 0.010 0.977 5.8 103.3 21.1 447 n/a 4_regHadp: 0.1108 0.1557 0.010 0.977 5.8 103.3 21.1 447 n/a 4_occ: 0.1102 0.1573 0.010 0.977 5.8 103.3 21.1 447 n/a 5_bss: 0.1100 0.1570 0.010 0.977 5.5 103.0 20.8 447 n/a 5_settarget: 0.1100 0.1570 0.010 0.977 5.5 103.0 20.8 447 n/a 5_updatecdl: 0.1100 0.1570 0.010 0.978 5.5 103.0 20.8 447 n/a 5_setrh: 0.1102 0.1570 0.010 0.978 5.5 103.0 20.8 447 n/a 5_nqh: 0.1102 0.1570 0.010 0.978 5.5 103.0 20.8 447 n/a 5_sol: 0.1110 0.1503 0.010 0.978 5.5 103.0 20.8 460 n/a 5_weight: 0.1110 0.1503 0.010 0.978 5.5 103.0 20.8 460 n/a 5_xyzrec: 0.1133 0.1530 0.009 1.021 5.5 103.0 20.8 460 n/a 5_adp: 0.1120 0.1516 0.009 1.021 5.5 102.3 20.9 460 n/a 5_regHadp: 0.1120 0.1516 0.009 1.021 5.5 102.3 20.9 460 n/a 5_occ: 0.1114 0.1522 0.009 1.021 5.5 102.3 20.9 460 n/a end: 0.1114 0.1521 0.009 1.021 5.3 102.0 20.7 460 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8555406_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8555406_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.0600 Refinement macro-cycles (run) : 949.7100 Write final files (write_after_run_outputs) : 19.4300 Total : 973.2000 Total CPU time: 16.58 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:35 PST -0800 (1735494095.06 s) Start R-work = 0.1614, R-free = 0.1733 Final R-work = 0.1114, R-free = 0.1521 =============================================================================== Job complete usr+sys time: 1014.28 seconds wall clock time: 17 minutes 16.59 seconds (1036.59 seconds total)