Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3025539.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_3025539.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3025539.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 3 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: 1.87, 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: 0.53 Conformation dependent library (CDL) restraints added in 156.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 578 0.92 - 1.18: 1086 1.18 - 1.43: 640 1.43 - 1.68: 822 1.68 - 1.94: 27 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " ideal model delta sigma weight residual 1.522 1.733 -0.211 1.14e-02 7.69e+03 3.42e+02 bond pdb=" N GLY A 40 " pdb=" CA GLY A 40 " ideal model delta sigma weight residual 1.447 1.643 -0.197 1.12e-02 7.97e+03 3.09e+02 bond pdb=" CA ALYS A 175 " pdb=" C ALYS A 175 " ideal model delta sigma weight residual 1.524 1.744 -0.221 1.27e-02 6.20e+03 3.02e+02 bond pdb=" N GLU A 84 " pdb=" CA GLU A 84 " ideal model delta sigma weight residual 1.456 1.685 -0.229 1.33e-02 5.65e+03 2.96e+02 bond pdb=" CA ILE A 21 " pdb=" C ILE A 21 " ideal model delta sigma weight residual 1.524 1.698 -0.173 1.05e-02 9.07e+03 2.72e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 3192 4.70 - 9.40: 1847 9.40 - 14.09: 621 14.09 - 18.79: 104 18.79 - 23.48: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 139.29 -16.69 1.00e+00 1.00e+00 2.79e+02 angle pdb=" O PHE A 162 " pdb=" C PHE A 162 " pdb=" N GLU A 163 " ideal model delta sigma weight residual 122.07 136.88 -14.81 1.03e+00 9.43e-01 2.07e+02 angle pdb=" O ALA A 179 " pdb=" C ALA A 179 " pdb=" N GLN A 180 " ideal model delta sigma weight residual 122.07 136.31 -14.24 1.03e+00 9.43e-01 1.91e+02 angle pdb=" O AGLU A 96 " pdb=" C AGLU A 96 " pdb=" N AASN A 97 " ideal model delta sigma weight residual 122.07 108.59 13.48 1.03e+00 9.43e-01 1.71e+02 angle pdb=" CD1 TYR A 141 " pdb=" CG TYR A 141 " pdb=" CD2 TYR A 141 " ideal model delta sigma weight residual 118.10 99.46 18.64 1.50e+00 4.44e-01 1.54e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.84: 1315 17.84 - 35.67: 118 35.67 - 53.50: 36 53.50 - 71.33: 11 71.33 - 89.16: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ASP A 60 " pdb=" N ASP A 60 " pdb=" CA ASP A 60 " pdb=" CB ASP A 60 " ideal model delta harmonic sigma weight residual -122.60 -142.88 20.28 0 2.50e+00 1.60e-01 6.58e+01 dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -142.58 19.98 0 2.50e+00 1.60e-01 6.39e+01 dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 140.72 -17.92 0 2.50e+00 1.60e-01 5.14e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.201: 107 0.201 - 0.401: 66 0.401 - 0.601: 44 0.601 - 0.800: 20 0.800 - 1.000: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 3.44 -1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CA ASP A 60 " pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CB ASP A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CB VAL A 186 " pdb=" CA VAL A 186 " pdb=" CG1 VAL A 186 " pdb=" CG2 VAL A 186 " both_signs ideal model delta sigma weight residual False -2.63 -3.59 0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.042 2.00e-02 2.50e+03 7.73e-02 1.79e+02 pdb=" CG PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.142 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.111 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.153 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.053 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.083 2.00e-02 2.50e+03 5.37e-02 8.66e+01 pdb=" CG BTYR A 67 " -0.084 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.062 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.085 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.032 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.025 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.052 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.044 2.00e-02 2.50e+03 5.27e-02 8.34e+01 pdb=" CG TYR A 141 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.114 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.055 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.066 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.009 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1099 2.33 - 2.90: 8192 2.90 - 3.47: 10526 3.47 - 4.03: 15223 4.03 - 4.60: 21520 Nonbonded interactions: 56560 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.764 2.100 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.767 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.818 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.824 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.831 2.450 ... (remaining 56555 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_3025539_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= 0.2777 r_free= 0.1837 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.408977 | | target function (ml) not normalized (work): 71615.014773 | | target function (ml) not normalized (free): 3272.668132 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3176 0.2174 7.5734 5.0351| | 2: 3.63 - 2.88 1.00 2711 122 0.2632 0.1759 4.3224 4.3233| | 3: 2.88 - 2.52 1.00 2682 148 0.2536 0.1655 4.1749 4.1797| | 4: 2.52 - 2.29 1.00 2661 139 0.2538 0.1496 3.4966 3.5615| | 5: 2.29 - 2.13 1.00 2678 122 0.2653 0.1516 3.3898 3.4884| | 6: 2.13 - 2.00 1.00 2692 117 0.2760 0.1986 3.3314 3.465| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.47 0.77 0.23 1290.62| | 2: 3.63 - 2.88 2711 122 0.83 23.69 1.31 0.23 1290.62| | 3: 2.88 - 2.52 2682 148 0.73 32.62 1.29 0.23 1290.62| | 4: 2.52 - 2.29 2661 139 0.93 11.59 1.30 0.26 139.78| | 5: 2.29 - 2.13 2678 122 0.92 13.93 1.32 0.26 139.78| | 6: 2.13 - 2.00 2692 117 0.89 16.79 1.33 0.26 139.78| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 139.78 max = 1290.62 mean = 721.61| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 19.35| |phase err.(test): min = 0.00 max = 89.20 mean = 19.59| |-----------------------------------------------------------------------------| ----------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 0.229 1557 Z= 5.385 Angle : 5.286 18.642 2118 Z= 3.693 Chirality : 0.363 1.000 243 Planarity : 0.034 0.118 284 Dihedral : 13.779 89.165 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 28.65 % 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: -2.56 (0.47), residues: 224 helix: -2.53 (0.38), residues: 109 sheet: -1.12 (0.81), residues: 28 loop : -0.37 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.069 0.015 ARG A 28 TYR 0.101 0.033 TYR A 141 PHE 0.107 0.047 PHE A 164 HIS 0.062 0.021 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= 0.2777 r_free= 0.1837 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.408977 | | target function (ml) not normalized (work): 71615.014773 | | target function (ml) not normalized (free): 3272.668132 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3075 percent. r_work = 0.2907 r_free = 0.1991 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2854 0.2907 0.1991 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2854 0.2907 0.1991 n_refl.: 17050 remove outliers: r(all,work,free)=0.2147 0.2158 0.1991 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2119 0.2129 0.1973 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1606 0.1602 0.1676 n_refl.: 17045 remove outliers: r(all,work,free)=0.1604 0.1600 0.1676 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3848 399.105 361.903 0.653 1.012 0.399 11.894-9.307 99.02 97 4 0.1858 633.873 615.678 0.937 1.013 0.375 9.237-7.194 100.00 213 7 0.2209 518.444 509.588 0.963 1.012 0.360 7.162-5.571 100.00 427 22 0.2283 389.093 376.779 0.923 1.011 0.304 5.546-4.326 100.00 867 58 0.1379 534.162 528.934 0.959 1.009 0.225 4.315-3.360 100.00 1859 96 0.1308 507.993 503.590 1.017 1.006 0.191 3.356-2.611 100.00 3867 181 0.1626 333.723 329.577 1.015 1.000 0.091 2.608-2.000 99.99 8818 434 0.1637 217.530 213.528 1.032 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4949 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1600 r_free=0.1676 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN Total number of N/Q/H flips: 1 r_work=0.1601 r_free=0.1675 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.062192 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.765282 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 0.1349 0.1637 0.0288 0.009 1.0 1.0 0.5 0.0 0 12.031 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.49 16.37 2.88 3.013 18.439 0.765 0.023 12.78 16.56 3.78 3.563 18.729 0.765 0.020 Individual atomic B min max mean iso aniso Overall: 6.52 113.88 20.01 4.00 1785 0 Protein: 6.52 112.60 17.28 4.00 1519 0 Water: 8.74 113.88 35.93 N/A 258 0 Other: 21.99 36.24 26.18 N/A 8 0 Chain A: 6.52 113.88 20.01 N/A 1785 0 Histogram: Values Number of atoms 6.52 - 17.26 1102 17.26 - 27.99 331 27.99 - 38.73 180 38.73 - 49.46 98 49.46 - 60.20 47 60.20 - 70.94 14 70.94 - 81.67 5 81.67 - 92.41 5 92.41 - 103.14 0 103.14 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1656 r_work=0.1281 r_free=0.1664 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1664 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 = 0.1277 r_free = 0.1657 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1277 r_free= 0.1657 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020050 | | target function (ls_wunit_k1) not normalized (work): 325.528162 | | target function (ls_wunit_k1) not normalized (free): 27.241475 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1295 0.1277 0.1657 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1909 0.1908 0.1985 n_refl.: 17043 remove outliers: r(all,work,free)=0.1909 0.1908 0.1985 n_refl.: 17043 overall B=-0.40 to atoms: r(all,work,free)=0.1880 0.1879 0.1969 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1296 0.1278 0.1655 n_refl.: 17043 remove outliers: r(all,work,free)=0.1296 0.1278 0.1655 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3590 307.176 283.666 0.649 1.009 0.387 11.894-9.307 99.02 97 4 0.1684 487.869 477.085 0.919 1.010 0.364 9.237-7.194 100.00 213 7 0.1846 399.027 395.756 0.960 1.009 0.351 7.162-5.571 100.00 427 22 0.1877 299.470 294.127 0.930 1.008 0.301 5.546-4.326 100.00 867 58 0.1055 411.125 408.473 0.957 1.007 0.205 4.315-3.360 100.00 1859 96 0.0928 390.984 390.500 1.018 1.004 0.191 3.356-2.611 100.00 3867 181 0.1300 256.854 255.613 1.015 1.000 0.101 2.608-2.000 99.99 8818 434 0.1348 167.425 165.951 1.025 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.4309 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1278 r_free=0.1655 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN Total number of N/Q/H flips: 1 r_work=0.1279 r_free=0.1657 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1279 r_free=0.1657 | n_water=258 | time (s): 0.780 (total time: 0.780) Filter (dist) r_work=0.1287 r_free=0.1646 | n_water=252 | time (s): 19.150 (total time: 19.930) Filter (q & B) r_work=0.1288 r_free=0.1646 | n_water=250 | time (s): 1.580 (total time: 21.510) Compute maps r_work=0.1288 r_free=0.1646 | n_water=250 | time (s): 0.520 (total time: 22.030) Filter (map) r_work=0.1329 r_free=0.1639 | n_water=209 | time (s): 1.430 (total time: 23.460) Find peaks r_work=0.1329 r_free=0.1639 | n_water=209 | time (s): 0.550 (total time: 24.010) Add new water r_work=0.1548 r_free=0.1872 | n_water=360 | time (s): 1.420 (total time: 25.430) Refine new water occ: r_work=0.1343 r_free=0.1585 adp: r_work=0.1285 r_free=0.1585 occ: r_work=0.1292 r_free=0.1557 adp: r_work=0.1260 r_free=0.1564 occ: r_work=0.1261 r_free=0.1557 adp: r_work=0.1251 r_free=0.1559 ADP+occupancy (water only), MIN, final r_work=0.1251 r_free=0.1559 r_work=0.1251 r_free=0.1559 | n_water=360 | time (s): 10.770 (total time: 36.200) Filter (q & B) r_work=0.1254 r_free=0.1562 | n_water=350 | time (s): 1.600 (total time: 37.800) Filter (dist only) r_work=0.1254 r_free=0.1563 | n_water=349 | time (s): 28.470 (total time: 66.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.625114 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.052894 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 0.1225 0.1607 0.0383 0.008 0.9 1.9 0.5 0.0 0 12.313 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 16.07 3.83 4.135 21.010 1.053 0.019 12.05 16.30 4.25 4.271 21.241 1.053 0.018 Individual atomic B min max mean iso aniso Overall: 6.91 107.20 21.15 4.29 1876 0 Protein: 6.91 107.20 17.67 4.27 1519 0 Water: 8.48 68.14 35.99 N/A 349 0 Other: 24.67 45.96 34.82 N/A 8 0 Chain A: 6.91 107.20 19.39 N/A 1736 0 Chain S: 17.95 61.98 42.97 N/A 140 0 Histogram: Values Number of atoms 6.91 - 16.94 1042 16.94 - 26.97 358 26.97 - 36.99 217 36.99 - 47.02 155 47.02 - 57.05 74 57.05 - 67.08 19 67.08 - 77.11 4 77.11 - 87.14 5 87.14 - 97.17 0 97.17 - 107.20 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1630 r_work=0.1207 r_free=0.1632 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1632 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 = 0.1203 r_free = 0.1629 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1203 r_free= 0.1629 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017342 | | target function (ls_wunit_k1) not normalized (work): 281.566443 | | target function (ls_wunit_k1) not normalized (free): 25.366181 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1223 0.1203 0.1629 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1811 0.1807 0.1962 n_refl.: 17043 remove outliers: r(all,work,free)=0.1811 0.1807 0.1962 n_refl.: 17043 overall B=-0.40 to atoms: r(all,work,free)=0.1782 0.1778 0.1944 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1198 0.1617 n_refl.: 17043 remove outliers: r(all,work,free)=0.1217 0.1196 0.1617 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 0.3294 306.614 279.927 0.616 1.003 0.360 11.894-9.307 99.02 97 4 0.1610 487.869 484.327 0.915 1.003 0.347 9.237-7.194 100.00 213 7 0.1742 399.027 396.430 0.972 1.003 0.321 7.162-5.571 100.00 427 22 0.1595 299.470 294.723 0.935 1.003 0.251 5.546-4.326 100.00 867 58 0.0905 411.125 407.446 0.960 1.003 0.211 4.315-3.360 100.00 1859 96 0.0823 390.984 389.741 1.019 1.003 0.201 3.356-2.611 100.00 3867 181 0.1202 256.854 255.964 1.013 1.002 0.048 2.608-2.000 99.99 8818 434 0.1330 167.425 166.839 1.018 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.4409 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1617 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1617 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1617 | n_water=349 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1196 r_free=0.1617 | n_water=349 | time (s): 27.660 (total time: 28.270) Filter (q & B) r_work=0.1196 r_free=0.1617 | n_water=349 | time (s): 0.860 (total time: 29.130) Compute maps r_work=0.1196 r_free=0.1617 | n_water=349 | time (s): 0.550 (total time: 29.680) Filter (map) r_work=0.1262 r_free=0.1625 | n_water=262 | time (s): 1.680 (total time: 31.360) Find peaks r_work=0.1262 r_free=0.1625 | n_water=262 | time (s): 0.460 (total time: 31.820) Add new water r_work=0.1438 r_free=0.1812 | n_water=409 | time (s): 1.350 (total time: 33.170) Refine new water occ: r_work=0.1249 r_free=0.1570 adp: r_work=0.1240 r_free=0.1582 occ: r_work=0.1225 r_free=0.1547 adp: r_work=0.1213 r_free=0.1556 occ: r_work=0.1207 r_free=0.1534 adp: r_work=0.1197 r_free=0.1537 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1537 r_work=0.1197 r_free=0.1537 | n_water=409 | time (s): 38.190 (total time: 71.360) Filter (q & B) r_work=0.1201 r_free=0.1538 | n_water=399 | time (s): 1.530 (total time: 72.890) Filter (dist only) r_work=0.1201 r_free=0.1540 | n_water=398 | time (s): 31.120 (total time: 104.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.904935 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.161600 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 0.1179 0.1544 0.0365 0.009 1.0 3.2 0.5 0.0 0 0.952 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.79 15.44 3.65 4.338 21.412 0.162 4.997 11.61 15.55 3.94 4.820 21.326 0.162 4.976 Individual atomic B min max mean iso aniso Overall: 6.10 105.53 20.74 4.60 1925 0 Protein: 6.10 105.53 16.93 4.59 1519 0 Water: 8.82 63.08 35.01 N/A 398 0 Other: 27.09 45.81 34.37 N/A 8 0 Chain A: 6.10 105.53 18.58 N/A 1730 0 Chain S: 17.37 63.08 39.93 N/A 195 0 Histogram: Values Number of atoms 6.10 - 16.04 1066 16.04 - 25.99 350 25.99 - 35.93 225 35.93 - 45.87 168 45.87 - 55.82 79 55.82 - 65.76 25 65.76 - 75.70 4 75.70 - 85.64 4 85.64 - 95.59 2 95.59 - 105.53 2 =========================== Idealize ADP of riding H ========================== r_work=0.1161 r_free=0.1555 r_work=0.1161 r_free=0.1556 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1161 r_free = 0.1556 target_work(ml) = 4.976 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1151 r_free = 0.1551 target_work(ml) = 4.969 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1151 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.969118 | | target function (ml) not normalized (work): 80668.661871 | | target function (ml) not normalized (free): 4191.877686 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1170 0.1151 0.1551 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1656 0.1647 0.1870 n_refl.: 17041 remove outliers: r(all,work,free)=0.1656 0.1647 0.1870 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1631 0.1622 0.1856 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1168 0.1149 0.1545 n_refl.: 17041 remove outliers: r(all,work,free)=0.1167 0.1148 0.1545 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 0.3398 303.454 280.776 0.574 1.006 0.340 11.894-9.307 99.02 97 4 0.1730 487.869 482.288 0.908 1.006 0.340 9.237-7.194 100.00 213 7 0.1833 399.027 399.524 0.980 1.006 0.254 7.162-5.571 100.00 427 22 0.1638 299.470 293.141 0.939 1.006 0.221 5.546-4.326 100.00 867 58 0.0967 411.125 407.359 0.962 1.005 0.195 4.315-3.360 100.00 1859 96 0.0903 390.984 388.468 1.012 1.003 0.181 3.356-2.611 100.00 3867 181 0.1287 256.854 254.530 1.013 1.000 0.131 2.608-2.000 99.99 8818 434 0.1079 167.425 166.099 1.018 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3318 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1148 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1148 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1545 | n_water=398 | time (s): 0.910 (total time: 0.910) Filter (dist) r_work=0.1148 r_free=0.1545 | n_water=398 | time (s): 31.180 (total time: 32.090) Filter (q & B) r_work=0.1148 r_free=0.1545 | n_water=398 | time (s): 1.240 (total time: 33.330) Compute maps r_work=0.1148 r_free=0.1545 | n_water=398 | time (s): 0.650 (total time: 33.980) Filter (map) r_work=0.1196 r_free=0.1570 | n_water=309 | time (s): 1.780 (total time: 35.760) Find peaks r_work=0.1196 r_free=0.1570 | n_water=309 | time (s): 0.600 (total time: 36.360) Add new water r_work=0.1338 r_free=0.1705 | n_water=452 | time (s): 2.100 (total time: 38.460) Refine new water occ: r_work=0.1175 r_free=0.1521 adp: r_work=0.1168 r_free=0.1526 occ: r_work=0.1152 r_free=0.1503 adp: r_work=0.1143 r_free=0.1505 occ: r_work=0.1135 r_free=0.1492 adp: r_work=0.1127 r_free=0.1492 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1492 r_work=0.1127 r_free=0.1492 | n_water=452 | time (s): 33.170 (total time: 71.630) Filter (q & B) r_work=0.1131 r_free=0.1506 | n_water=442 | time (s): 1.530 (total time: 73.160) Filter (dist only) r_work=0.1131 r_free=0.1506 | n_water=442 | time (s): 33.320 (total time: 106.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.006614 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.157202 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 0.1116 0.1566 0.0450 0.010 1.0 3.5 0.5 0.0 0 1.003 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.66 4.50 4.434 20.982 0.157 4.959 11.04 15.63 4.58 4.604 21.020 0.157 4.955 Individual atomic B min max mean iso aniso Overall: 5.82 103.70 20.90 4.76 1969 0 Protein: 5.82 103.70 16.53 4.75 1519 0 Water: 8.48 65.78 35.71 N/A 442 0 Other: 25.36 43.69 33.00 N/A 8 0 Chain A: 5.82 103.70 18.12 N/A 1729 0 Chain S: 20.10 65.78 40.98 N/A 240 0 Histogram: Values Number of atoms 5.82 - 15.60 1052 15.60 - 25.39 361 25.39 - 35.18 231 35.18 - 44.97 183 44.97 - 54.76 96 54.76 - 64.55 31 64.55 - 74.34 8 74.34 - 84.12 2 84.12 - 93.91 3 93.91 - 103.70 2 =========================== Idealize ADP of riding H ========================== r_work=0.1104 r_free=0.1563 r_work=0.1104 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1104 r_free = 0.1563 target_work(ml) = 4.955 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1099 r_free = 0.1563 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.15 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= 0.1099 r_free= 0.1563 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.951165 | | target function (ml) not normalized (work): 80372.268321 | | target function (ml) not normalized (free): 4192.789239 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1121 0.1099 0.1563 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1574 0.1559 0.1882 n_refl.: 17040 remove outliers: r(all,work,free)=0.1574 0.1559 0.1882 n_refl.: 17040 overall B=-0.30 to atoms: r(all,work,free)=0.1556 0.1540 0.1871 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1119 0.1097 0.1557 n_refl.: 17040 remove outliers: r(all,work,free)=0.1118 0.1096 0.1557 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 0.3576 299.887 280.718 0.561 1.004 0.340 11.894-9.307 99.02 97 4 0.1695 487.869 481.467 0.916 1.004 0.340 9.237-7.194 100.00 213 7 0.1774 399.027 399.136 0.981 1.004 0.233 7.162-5.571 100.00 427 22 0.1524 299.470 293.878 0.940 1.004 0.192 5.546-4.326 100.00 867 58 0.0930 411.125 407.654 0.964 1.003 0.184 4.315-3.360 100.00 1859 96 0.0844 390.984 388.827 1.007 1.003 0.181 3.356-2.611 100.00 3867 181 0.1224 256.854 254.623 1.006 1.001 0.141 2.608-2.000 99.99 8818 434 0.1035 167.425 166.257 1.003 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.0182 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1096 r_free=0.1557 After: r_work=0.1098 r_free=0.1556 ================================== NQH flips ================================== r_work=0.1098 r_free=0.1556 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=0.1100 r_free=0.1559 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1100 r_free=0.1559 | n_water=442 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1101 r_free=0.1556 | n_water=441 | time (s): 35.010 (total time: 35.650) Filter (q & B) r_work=0.1101 r_free=0.1556 | n_water=441 | time (s): 1.060 (total time: 36.710) Compute maps r_work=0.1101 r_free=0.1556 | n_water=441 | time (s): 0.810 (total time: 37.520) Filter (map) r_work=0.1166 r_free=0.1549 | n_water=347 | time (s): 2.200 (total time: 39.720) Find peaks r_work=0.1166 r_free=0.1549 | n_water=347 | time (s): 0.590 (total time: 40.310) Add new water r_work=0.1278 r_free=0.1614 | n_water=487 | time (s): 2.090 (total time: 42.400) Refine new water occ: r_work=0.1132 r_free=0.1485 adp: r_work=0.1125 r_free=0.1488 occ: r_work=0.1112 r_free=0.1474 adp: r_work=0.1104 r_free=0.1476 occ: r_work=0.1098 r_free=0.1472 adp: r_work=0.1092 r_free=0.1471 ADP+occupancy (water only), MIN, final r_work=0.1092 r_free=0.1471 r_work=0.1092 r_free=0.1471 | n_water=487 | time (s): 40.340 (total time: 82.740) Filter (q & B) r_work=0.1099 r_free=0.1480 | n_water=471 | time (s): 1.960 (total time: 84.700) Filter (dist only) r_work=0.1099 r_free=0.1481 | n_water=469 | time (s): 40.330 (total time: 125.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.905559 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.151241 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 0.1121 0.1498 0.0377 0.010 1.0 5.4 0.5 0.0 0 0.953 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.21 14.98 3.77 4.488 20.850 0.151 4.942 11.10 14.85 3.75 4.577 20.939 0.151 4.932 Individual atomic B min max mean iso aniso Overall: 5.37 101.81 21.09 4.94 1996 0 Protein: 5.37 101.81 16.30 4.93 1519 0 Water: 8.07 63.96 36.40 N/A 469 0 Other: 26.14 43.80 33.30 N/A 8 0 Chain A: 5.37 101.81 17.86 N/A 1729 0 Chain S: 16.55 63.96 42.00 N/A 267 0 Histogram: Values Number of atoms 5.37 - 15.01 1015 15.01 - 24.66 397 24.66 - 34.30 211 34.30 - 43.95 195 43.95 - 53.59 123 53.59 - 63.24 37 63.24 - 72.88 9 72.88 - 82.52 3 82.52 - 92.17 2 92.17 - 101.81 4 =========================== Idealize ADP of riding H ========================== r_work=0.1110 r_free=0.1485 r_work=0.1110 r_free=0.1484 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1110 r_free = 0.1484 target_work(ml) = 4.931 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1497 target_work(ml) = 4.927 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1497 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.927246 | | target function (ml) not normalized (work): 79979.053859 | | target function (ml) not normalized (free): 4154.675222 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2809 159 0.1108 0.1378 5.45 5.6459| | 2: 3.63 - 2.88 1.00 2711 122 0.1084 0.1513 5.2152 5.3625| | 3: 2.88 - 2.52 1.00 2681 148 0.1348 0.1596 5.122 5.1746| | 4: 2.52 - 2.29 1.00 2661 139 0.0939 0.1575 4.615 4.9662| | 5: 2.29 - 2.13 1.00 2678 122 0.0966 0.1401 4.5698 4.8266| | 6: 2.13 - 2.00 1.00 2692 117 0.1123 0.1746 4.562 4.7672| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2809 159 0.95 8.91 1.00 0.96 6277.13| | 2: 3.63 - 2.88 2711 122 0.92 12.72 1.01 0.96 6277.13| | 3: 2.88 - 2.52 2681 148 0.88 18.89 0.99 0.96 6277.13| | 4: 2.52 - 2.29 2661 139 0.93 11.78 1.01 0.98 2035.77| | 5: 2.29 - 2.13 2678 122 0.92 13.75 1.00 0.98 2035.77| | 6: 2.13 - 2.00 2692 117 0.90 16.50 0.99 0.98 2035.77| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2035.77 max = 6277.13 mean = 4178.66| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 13.72| |phase err.(test): min = 0.00 max = 89.51 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1121 0.1102 0.1497 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1565 0.1554 0.1801 n_refl.: 17039 remove outliers: r(all,work,free)=0.1565 0.1554 0.1801 n_refl.: 17039 overall B=-0.25 to atoms: r(all,work,free)=0.1550 0.1539 0.1791 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1103 0.1498 n_refl.: 17039 remove outliers: r(all,work,free)=0.1122 0.1103 0.1498 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 0.3385 299.887 280.485 0.558 1.005 0.340 11.894-9.307 99.02 97 4 0.1713 487.869 482.036 0.906 1.006 0.340 9.237-7.194 100.00 213 7 0.1745 399.027 399.196 0.981 1.006 0.230 7.162-5.571 100.00 427 22 0.1548 299.470 293.734 0.936 1.005 0.200 5.546-4.326 100.00 867 58 0.0925 411.125 407.725 0.963 1.005 0.180 4.315-3.360 100.00 1859 96 0.0870 390.984 389.096 1.004 1.003 0.181 3.356-2.611 100.00 3867 181 0.1230 256.854 254.442 1.002 1.001 0.141 2.608-2.000 99.99 8818 434 0.1041 167.425 166.078 0.998 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8806 ================= 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 : 0.2777 0.1837 0.081 5.286 8.8 119.3 19.9 258 0.000 1_bss: 0.1600 0.1676 0.081 5.286 8.4 118.9 19.5 258 0.000 1_settarget: 0.1600 0.1676 0.081 5.286 8.4 118.9 19.5 258 0.000 1_nqh: 0.1601 0.1675 0.081 5.286 8.4 118.9 19.5 258 0.003 1_weight: 0.1601 0.1675 0.081 5.286 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1349 0.1637 0.009 0.998 8.4 118.9 19.5 258 0.141 1_adp: 0.1278 0.1656 0.009 0.998 6.5 113.9 20.0 258 0.141 1_regHadp: 0.1281 0.1664 0.009 0.998 6.5 113.9 20.0 258 0.141 1_occ: 0.1277 0.1657 0.009 0.998 6.5 113.9 20.0 258 0.141 2_bss: 0.1278 0.1655 0.009 0.998 6.1 113.5 19.6 258 0.141 2_settarget: 0.1278 0.1655 0.009 0.998 6.1 113.5 19.6 258 0.141 2_updatecdl: 0.1278 0.1655 0.009 1.008 6.1 113.5 19.6 258 0.141 2_nqh: 0.1279 0.1657 0.009 1.008 6.1 113.5 19.6 258 0.138 2_sol: 0.1254 0.1563 0.009 1.008 6.1 112.2 20.7 349 n/a 2_weight: 0.1254 0.1563 0.009 1.008 6.1 112.2 20.7 349 n/a 2_xyzrec: 0.1225 0.1607 0.008 0.926 6.1 112.2 20.7 349 n/a 2_adp: 0.1205 0.1630 0.008 0.926 6.9 107.2 21.1 349 n/a 2_regHadp: 0.1207 0.1632 0.008 0.926 6.9 107.2 21.1 349 n/a 2_occ: 0.1203 0.1629 0.008 0.926 6.9 107.2 21.1 349 n/a 3_bss: 0.1196 0.1617 0.008 0.926 6.5 106.8 20.7 349 n/a 3_settarget: 0.1196 0.1617 0.008 0.926 6.5 106.8 20.7 349 n/a 3_updatecdl: 0.1196 0.1617 0.008 0.927 6.5 106.8 20.7 349 n/a 3_nqh: 0.1196 0.1617 0.008 0.927 6.5 106.8 20.7 349 n/a 3_sol: 0.1201 0.1540 0.008 0.927 6.5 106.8 20.9 398 n/a 3_weight: 0.1201 0.1540 0.008 0.927 6.5 106.8 20.9 398 n/a 3_xyzrec: 0.1179 0.1544 0.009 0.950 6.5 106.8 20.9 398 n/a 3_adp: 0.1161 0.1555 0.009 0.950 6.1 105.5 20.7 398 n/a 3_regHadp: 0.1161 0.1556 0.009 0.950 6.1 105.5 20.7 398 n/a 3_occ: 0.1151 0.1551 0.009 0.950 6.1 105.5 20.7 398 n/a 4_bss: 0.1148 0.1545 0.009 0.950 5.7 105.2 20.4 398 n/a 4_settarget: 0.1148 0.1545 0.009 0.950 5.7 105.2 20.4 398 n/a 4_updatecdl: 0.1148 0.1545 0.009 0.951 5.7 105.2 20.4 398 n/a 4_nqh: 0.1148 0.1545 0.009 0.951 5.7 105.2 20.4 398 n/a 4_sol: 0.1131 0.1506 0.009 0.951 5.7 105.2 20.8 442 n/a 4_weight: 0.1131 0.1506 0.009 0.951 5.7 105.2 20.8 442 n/a 4_xyzrec: 0.1116 0.1566 0.010 0.983 5.7 105.2 20.8 442 n/a 4_adp: 0.1104 0.1563 0.010 0.983 5.8 103.7 20.9 442 n/a 4_regHadp: 0.1104 0.1563 0.010 0.983 5.8 103.7 20.9 442 n/a 4_occ: 0.1099 0.1563 0.010 0.983 5.8 103.7 20.9 442 n/a 5_bss: 0.1096 0.1557 0.010 0.983 5.5 103.4 20.6 442 n/a 5_settarget: 0.1096 0.1557 0.010 0.983 5.5 103.4 20.6 442 n/a 5_updatecdl: 0.1096 0.1557 0.010 0.985 5.5 103.4 20.6 442 n/a 5_setrh: 0.1098 0.1556 0.010 0.985 5.5 103.4 20.6 442 n/a 5_nqh: 0.1100 0.1559 0.010 0.985 5.5 103.4 20.6 442 n/a 5_sol: 0.1099 0.1481 0.010 0.985 5.5 103.4 20.9 469 n/a 5_weight: 0.1099 0.1481 0.010 0.985 5.5 103.4 20.9 469 n/a 5_xyzrec: 0.1121 0.1498 0.010 1.036 5.5 103.4 20.9 469 n/a 5_adp: 0.1110 0.1485 0.010 1.036 5.4 101.8 21.1 469 n/a 5_regHadp: 0.1110 0.1484 0.010 1.036 5.4 101.8 21.1 469 n/a 5_occ: 0.1102 0.1497 0.010 1.036 5.4 101.8 21.1 469 n/a end: 0.1103 0.1498 0.010 1.036 5.1 101.6 20.8 469 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3025539_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3025539_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6000 Refinement macro-cycles (run) : 916.8700 Write final files (write_after_run_outputs) : 22.4200 Total : 942.8900 Total CPU time: 16.11 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:07 PST -0800 (1735494067.54 s) Start R-work = 0.1600, R-free = 0.1676 Final R-work = 0.1103, R-free = 0.1498 =============================================================================== Job complete usr+sys time: 989.55 seconds wall clock time: 16 minutes 52.53 seconds (1012.53 seconds total)