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_2659048.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_2659048.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2659048.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: 1.28, per 1000 atoms: 0.38 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: 0.41 Conformation dependent library (CDL) restraints added in 180.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 481 0.90 - 1.17: 1162 1.17 - 1.44: 717 1.44 - 1.70: 775 1.70 - 1.97: 18 Bond restraints: 3153 Sorted by residual: bond pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 1.518 1.719 -0.201 1.00e-02 1.00e+04 4.04e+02 bond pdb=" CA LYS A 122 " pdb=" C LYS A 122 " ideal model delta sigma weight residual 1.523 1.755 -0.232 1.30e-02 5.92e+03 3.19e+02 bond pdb=" CA ALA A 178 " pdb=" C ALA A 178 " ideal model delta sigma weight residual 1.523 1.292 0.231 1.30e-02 5.92e+03 3.17e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.187 0.191 1.10e-02 8.26e+03 3.02e+02 bond pdb=" N ACYS A 53 " pdb=" CA ACYS A 53 " ideal model delta sigma weight residual 1.456 1.662 -0.205 1.20e-02 6.94e+03 2.93e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.62: 3624 5.62 - 11.25: 1728 11.25 - 16.87: 393 16.87 - 22.49: 25 22.49 - 28.11: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.91 104.91 17.00 9.80e-01 1.04e+00 3.01e+02 angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH1 ARG A 48 " ideal model delta sigma weight residual 121.50 137.32 -15.82 1.00e+00 1.00e+00 2.50e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 129.38 -10.09 6.50e-01 2.37e+00 2.41e+02 angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 105.33 13.87 9.00e-01 1.23e+00 2.37e+02 angle pdb=" C GLY A 108 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 119.82 105.61 14.21 9.80e-01 1.04e+00 2.10e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.56: 1341 19.56 - 39.13: 97 39.13 - 58.69: 34 58.69 - 78.26: 8 78.26 - 97.82: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -143.24 20.64 0 2.50e+00 1.60e-01 6.82e+01 dihedral pdb=" C ALA A 14 " pdb=" N ALA A 14 " pdb=" CA ALA A 14 " pdb=" CB ALA A 14 " ideal model delta harmonic sigma weight residual -122.60 -102.92 -19.68 0 2.50e+00 1.60e-01 6.20e+01 dihedral pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual 122.80 142.01 -19.21 0 2.50e+00 1.60e-01 5.91e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 104 0.208 - 0.416: 65 0.416 - 0.624: 46 0.624 - 0.832: 21 0.832 - 1.040: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 51 " pdb=" CA VAL A 51 " pdb=" CG1 VAL A 51 " pdb=" CG2 VAL A 51 " both_signs ideal model delta sigma weight residual False -2.63 -1.59 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CA ALA A 14 " pdb=" N ALA A 14 " pdb=" C ALA A 14 " pdb=" CB ALA A 14 " both_signs ideal model delta sigma weight residual False 2.48 3.51 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CB VAL A 33 " pdb=" CA VAL A 33 " pdb=" CG1 VAL A 33 " pdb=" CG2 VAL A 33 " both_signs ideal model delta sigma weight residual False -2.63 -1.66 -0.97 2.00e-01 2.50e+01 2.37e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.044 2.00e-02 2.50e+03 6.38e-02 1.22e+02 pdb=" CG PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.096 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.026 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.137 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.045 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.112 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.005 2.00e-02 2.50e+03 5.42e-02 8.81e+01 pdb=" CG BTYR A 67 " -0.097 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.107 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.039 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.032 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.020 2.00e-02 2.50e+03 4.81e-02 6.95e+01 pdb=" CG PHE A 164 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.090 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.042 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.077 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.062 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 935 2.31 - 2.88: 8022 2.88 - 3.45: 10610 3.45 - 4.03: 15159 4.03 - 4.60: 21975 Nonbonded interactions: 56701 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.733 2.100 nonbonded pdb="HH21 ARG A 145 " pdb=" OE1 GLU A 163 " model vdw 1.834 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.858 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.870 2.450 nonbonded pdb=" H LYS A 12 " pdb=" O HOH A 396 " model vdw 1.888 2.450 ... (remaining 56696 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_2659048_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= 0.2787 r_free= 0.1844 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.408414 | | target function (ml) not normalized (work): 71605.863404 | | target function (ml) not normalized (free): 3278.970992 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3178 0.2187 7.5192 5.0504| | 2: 3.63 - 2.88 1.00 2711 122 0.2654 0.1676 4.3341 4.3027| | 3: 2.88 - 2.52 1.00 2682 148 0.2554 0.1659 4.1795 4.1835| | 4: 2.52 - 2.29 1.00 2661 139 0.2548 0.1597 3.495 3.5961| | 5: 2.29 - 2.13 1.00 2678 122 0.2689 0.1577 3.4265 3.4712| | 6: 2.13 - 2.00 1.00 2692 117 0.2729 0.1959 3.3335 3.4916| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.56 0.77 0.23 1300.50| | 2: 3.63 - 2.88 2711 122 0.83 23.85 1.32 0.23 1300.50| | 3: 2.88 - 2.52 2682 148 0.73 32.94 1.29 0.23 1300.50| | 4: 2.52 - 2.29 2661 139 0.93 11.56 1.30 0.26 143.47| | 5: 2.29 - 2.13 2678 122 0.92 14.00 1.31 0.26 143.47| | 6: 2.13 - 2.00 2692 117 0.90 16.69 1.33 0.26 143.47| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 143.47 max = 1300.50 mean = 728.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.91 mean = 19.44| |phase err.(test): min = 0.00 max = 89.10 mean = 19.62| |-----------------------------------------------------------------------------| ----------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 : 0.085 0.281 1557 Z= 5.601 Angle : 5.394 24.633 2118 Z= 3.839 Chirality : 0.390 1.040 243 Planarity : 0.031 0.098 284 Dihedral : 14.130 97.822 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.11 % Allowed : 3.73 % Favored : 93.17 % Cbeta Deviations : 30.81 % 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: -2.74 (0.46), residues: 224 helix: -2.41 (0.40), residues: 109 sheet: -1.87 (0.85), residues: 28 loop : -0.59 (0.54), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.024 ARG A 27 TYR 0.067 0.027 TYR A 139 PHE 0.111 0.037 PHE A 119 HIS 0.038 0.020 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= 0.2787 r_free= 0.1844 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.408414 | | target function (ml) not normalized (work): 71605.863404 | | target function (ml) not normalized (free): 3278.970992 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2938 percent. r_work = 0.2917 r_free = 0.2012 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2865 0.2917 0.2012 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2865 0.2917 0.2012 n_refl.: 17050 remove outliers: r(all,work,free)=0.2153 0.2162 0.2012 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2126 0.2135 0.1993 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1617 0.1614 0.1674 n_refl.: 17045 remove outliers: r(all,work,free)=0.1616 0.1613 0.1674 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 0.4096 394.811 361.543 0.647 1.012 0.397 11.894-9.307 99.02 97 4 0.1922 633.683 613.034 0.925 1.013 0.380 9.237-7.194 100.00 213 7 0.2228 518.289 508.097 0.960 1.012 0.351 7.162-5.571 100.00 427 22 0.2323 388.976 375.273 0.929 1.011 0.294 5.546-4.326 100.00 867 58 0.1375 534.002 528.687 0.960 1.009 0.230 4.315-3.360 100.00 1859 96 0.1276 507.841 503.877 1.014 1.005 0.201 3.356-2.611 100.00 3867 181 0.1642 333.623 329.408 1.015 1.000 0.034 2.608-2.000 99.99 8818 434 0.1665 217.465 213.306 1.029 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4453 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1613 r_free=0.1674 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1615 r_free=0.1667 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.239551 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.835345 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1351 0.1642 0.0291 0.009 1.0 0.6 0.5 0.0 0 11.620 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.42 2.91 3.013 18.454 0.835 0.023 12.79 16.66 3.87 3.627 18.717 0.835 0.020 Individual atomic B min max mean iso aniso Overall: 6.23 113.89 19.98 4.09 1785 0 Protein: 6.23 112.66 17.22 4.09 1519 0 Water: 9.07 113.89 36.04 N/A 258 0 Other: 21.67 37.77 26.38 N/A 8 0 Chain A: 6.23 113.89 19.98 N/A 1785 0 Histogram: Values Number of atoms 6.23 - 17.00 1088 17.00 - 27.77 342 27.77 - 38.53 181 38.53 - 49.30 100 49.30 - 60.06 48 60.06 - 70.83 12 70.83 - 81.60 6 81.60 - 92.36 4 92.36 - 103.13 1 103.13 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1666 r_work=0.1283 r_free=0.1672 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1283 r_free = 0.1672 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 = 0.1663 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 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= 0.1277 r_free= 0.1663 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020009 | | target function (ls_wunit_k1) not normalized (work): 324.882455 | | target function (ls_wunit_k1) not normalized (free): 27.408756 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1277 0.1663 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1913 0.1911 0.1994 n_refl.: 17044 remove outliers: r(all,work,free)=0.1913 0.1911 0.1994 n_refl.: 17044 overall B=-0.40 to atoms: r(all,work,free)=0.1884 0.1882 0.1978 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1296 0.1278 0.1655 n_refl.: 17044 remove outliers: r(all,work,free)=0.1294 0.1276 0.1655 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 0.3517 303.081 278.709 0.612 1.010 0.360 11.894-9.307 99.02 97 4 0.1725 487.458 476.992 0.914 1.010 0.358 9.237-7.194 100.00 213 7 0.1811 398.691 397.223 0.959 1.010 0.325 7.162-5.571 100.00 427 22 0.1810 299.218 294.618 0.936 1.009 0.301 5.546-4.326 100.00 867 58 0.1044 410.778 408.547 0.958 1.007 0.205 4.315-3.360 100.00 1859 96 0.0925 390.654 390.325 1.017 1.004 0.191 3.356-2.611 100.00 3867 181 0.1302 256.638 255.378 1.017 1.000 0.091 2.608-2.000 99.99 8818 434 0.1356 167.284 165.789 1.024 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.4099 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1655 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1278 r_free=0.1654 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1278 r_free=0.1654 | n_water=258 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1283 r_free=0.1649 | n_water=253 | time (s): 20.710 (total time: 21.480) Filter (q & B) r_work=0.1283 r_free=0.1648 | n_water=251 | time (s): 1.400 (total time: 22.880) Compute maps r_work=0.1283 r_free=0.1648 | n_water=251 | time (s): 0.660 (total time: 23.540) Filter (map) r_work=0.1320 r_free=0.1639 | n_water=212 | time (s): 2.020 (total time: 25.560) Find peaks r_work=0.1320 r_free=0.1639 | n_water=212 | time (s): 0.650 (total time: 26.210) Add new water r_work=0.1526 r_free=0.1853 | n_water=366 | time (s): 1.880 (total time: 28.090) Refine new water occ: r_work=0.1321 r_free=0.1559 adp: r_work=0.1268 r_free=0.1557 occ: r_work=0.1273 r_free=0.1528 adp: r_work=0.1242 r_free=0.1534 occ: r_work=0.1244 r_free=0.1524 adp: r_work=0.1231 r_free=0.1521 ADP+occupancy (water only), MIN, final r_work=0.1231 r_free=0.1521 r_work=0.1231 r_free=0.1521 | n_water=366 | time (s): 14.380 (total time: 42.470) Filter (q & B) r_work=0.1232 r_free=0.1527 | n_water=359 | time (s): 1.660 (total time: 44.130) Filter (dist only) r_work=0.1233 r_free=0.1530 | n_water=358 | time (s): 28.690 (total time: 72.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.766065 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.965200 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 0.1206 0.1567 0.0361 0.008 0.9 2.9 0.5 0.0 0 11.883 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 15.67 3.61 4.175 20.992 0.965 0.018 11.93 15.92 4.00 4.165 21.276 0.965 0.017 Individual atomic B min max mean iso aniso Overall: 6.74 107.27 21.27 4.22 1885 0 Protein: 6.74 107.27 17.75 4.21 1519 0 Water: 8.54 65.78 35.90 N/A 358 0 Other: 25.06 43.99 34.55 N/A 8 0 Chain A: 6.74 107.27 19.48 N/A 1739 0 Chain S: 18.48 65.13 42.56 N/A 146 0 Histogram: Values Number of atoms 6.74 - 16.79 1026 16.79 - 26.85 379 26.85 - 36.90 218 36.90 - 46.95 159 46.95 - 57.00 69 57.00 - 67.06 23 67.06 - 77.11 4 77.11 - 87.16 4 87.16 - 97.22 1 97.22 - 107.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1592 r_work=0.1194 r_free=0.1593 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1593 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1607 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 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= 0.1193 r_free= 0.1607 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016910 | | target function (ls_wunit_k1) not normalized (work): 274.530708 | | target function (ls_wunit_k1) not normalized (free): 23.641334 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1193 0.1607 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1753 0.1743 0.1977 n_refl.: 17042 remove outliers: r(all,work,free)=0.1753 0.1743 0.1977 n_refl.: 17042 overall B=-0.39 to atoms: r(all,work,free)=0.1727 0.1717 0.1960 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1187 0.1600 n_refl.: 17042 remove outliers: r(all,work,free)=0.1206 0.1186 0.1600 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 0.3225 299.922 285.767 0.590 1.004 0.340 11.894-9.307 99.02 97 4 0.1588 487.458 484.126 0.913 1.005 0.340 9.237-7.194 100.00 213 7 0.1664 398.691 399.928 0.971 1.005 0.287 7.162-5.571 100.00 427 22 0.1567 299.218 295.569 0.938 1.005 0.266 5.546-4.326 100.00 867 58 0.0879 410.778 408.341 0.961 1.004 0.215 4.315-3.360 100.00 1859 96 0.0818 390.654 389.664 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1191 256.638 255.839 1.013 1.001 0.058 2.608-2.000 99.99 8818 434 0.1328 167.284 166.307 1.019 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3867 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1600 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1186 r_free=0.1602 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1602 | n_water=358 | time (s): 0.890 (total time: 0.890) Filter (dist) r_work=0.1186 r_free=0.1604 | n_water=357 | time (s): 29.480 (total time: 30.370) Filter (q & B) r_work=0.1186 r_free=0.1604 | n_water=357 | time (s): 0.820 (total time: 31.190) Compute maps r_work=0.1186 r_free=0.1604 | n_water=357 | time (s): 0.720 (total time: 31.910) Filter (map) r_work=0.1255 r_free=0.1643 | n_water=269 | time (s): 2.230 (total time: 34.140) Find peaks r_work=0.1255 r_free=0.1643 | n_water=269 | time (s): 0.650 (total time: 34.790) Add new water r_work=0.1434 r_free=0.1787 | n_water=415 | time (s): 1.640 (total time: 36.430) Refine new water occ: r_work=0.1237 r_free=0.1566 adp: r_work=0.1229 r_free=0.1577 occ: r_work=0.1209 r_free=0.1550 adp: r_work=0.1199 r_free=0.1558 occ: r_work=0.1191 r_free=0.1543 adp: r_work=0.1183 r_free=0.1547 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1547 r_work=0.1183 r_free=0.1547 | n_water=415 | time (s): 27.360 (total time: 63.790) Filter (q & B) r_work=0.1186 r_free=0.1553 | n_water=404 | time (s): 1.670 (total time: 65.460) Filter (dist only) r_work=0.1186 r_free=0.1553 | n_water=404 | time (s): 29.170 (total time: 94.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.941679 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.120035 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 0.1166 0.1550 0.0385 0.009 1.0 3.8 0.5 0.0 0 0.971 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.66 15.50 3.85 4.309 21.552 0.120 4.986 11.45 15.53 4.09 4.802 21.443 0.120 4.961 Individual atomic B min max mean iso aniso Overall: 6.59 104.05 20.88 4.46 1931 0 Protein: 6.59 104.05 17.00 4.46 1519 0 Water: 8.52 62.55 35.20 N/A 404 0 Other: 27.67 44.70 35.09 N/A 8 0 Chain A: 6.59 104.05 18.76 N/A 1737 0 Chain S: 15.00 62.55 39.89 N/A 194 0 Histogram: Values Number of atoms 6.59 - 16.34 1075 16.34 - 26.09 338 26.09 - 35.83 227 35.83 - 45.58 181 45.58 - 55.32 66 55.32 - 65.07 32 65.07 - 74.81 3 74.81 - 84.56 4 84.56 - 94.31 3 94.31 - 104.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1553 r_work=0.1145 r_free=0.1555 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1555 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1138 r_free = 0.1553 target_work(ml) = 4.956 | | 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= 0.1138 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.956201 | | target function (ml) not normalized (work): 80458.961345 | | target function (ml) not normalized (free): 4176.767653 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1158 0.1138 0.1553 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1662 0.1656 0.1822 n_refl.: 17041 remove outliers: r(all,work,free)=0.1662 0.1656 0.1822 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1636 0.1630 0.1809 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1156 0.1136 0.1549 n_refl.: 17041 remove outliers: r(all,work,free)=0.1155 0.1135 0.1549 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 0.3544 296.361 277.882 0.559 1.005 0.334 11.894-9.307 99.02 97 4 0.1669 487.458 481.906 0.913 1.007 0.330 9.237-7.194 100.00 213 7 0.1796 398.691 399.921 0.982 1.007 0.245 7.162-5.571 100.00 427 22 0.1597 299.218 293.836 0.940 1.006 0.225 5.546-4.326 100.00 867 58 0.0945 410.778 407.086 0.965 1.006 0.211 4.315-3.360 100.00 1859 96 0.0882 390.654 388.416 1.011 1.004 0.201 3.356-2.611 100.00 3867 181 0.1269 256.638 254.471 1.012 1.001 0.131 2.608-2.000 99.99 8818 434 0.1078 167.284 165.894 1.019 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3681 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1135 r_free=0.1549 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1137 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1544 | n_water=404 | time (s): 0.910 (total time: 0.910) Filter (dist) r_work=0.1137 r_free=0.1548 | n_water=403 | time (s): 32.650 (total time: 33.560) Filter (q & B) r_work=0.1137 r_free=0.1548 | n_water=403 | time (s): 1.140 (total time: 34.700) Compute maps r_work=0.1137 r_free=0.1548 | n_water=403 | time (s): 0.620 (total time: 35.320) Filter (map) r_work=0.1199 r_free=0.1579 | n_water=312 | time (s): 2.020 (total time: 37.340) Find peaks r_work=0.1199 r_free=0.1579 | n_water=312 | time (s): 0.630 (total time: 37.970) Add new water r_work=0.1340 r_free=0.1695 | n_water=457 | time (s): 1.910 (total time: 39.880) Refine new water occ: r_work=0.1169 r_free=0.1525 adp: r_work=0.1162 r_free=0.1527 occ: r_work=0.1145 r_free=0.1508 adp: r_work=0.1137 r_free=0.1510 occ: r_work=0.1128 r_free=0.1495 adp: r_work=0.1122 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1122 r_free=0.1497 r_work=0.1122 r_free=0.1497 | n_water=457 | time (s): 32.180 (total time: 72.060) Filter (q & B) r_work=0.1127 r_free=0.1502 | n_water=445 | time (s): 1.500 (total time: 73.560) Filter (dist only) r_work=0.1126 r_free=0.1502 | n_water=444 | time (s): 34.900 (total time: 108.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.903010 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.176357 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 0.1114 0.1551 0.0437 0.010 1.0 5.8 0.5 0.0 0 0.952 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.14 15.51 4.37 4.369 21.080 0.176 4.951 11.02 15.46 4.44 4.577 21.118 0.176 4.943 Individual atomic B min max mean iso aniso Overall: 5.90 101.56 21.03 4.84 1971 0 Protein: 5.90 101.56 16.58 4.83 1519 0 Water: 8.44 64.63 36.03 N/A 444 0 Other: 26.96 47.25 35.02 N/A 8 0 Chain A: 5.90 101.56 18.28 N/A 1735 0 Chain S: 18.45 64.63 41.28 N/A 236 0 Histogram: Values Number of atoms 5.90 - 15.46 1030 15.46 - 25.03 376 25.03 - 34.60 212 34.60 - 44.16 201 44.16 - 53.73 94 53.73 - 63.29 41 63.29 - 72.86 7 72.86 - 82.43 5 82.43 - 91.99 3 91.99 - 101.56 2 =========================== Idealize ADP of riding H ========================== r_work=0.1102 r_free=0.1546 r_work=0.1102 r_free=0.1547 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1102 r_free = 0.1547 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1097 r_free = 0.1539 target_work(ml) = 4.938 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1097 r_free= 0.1539 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.937758 | | target function (ml) not normalized (work): 80154.628671 | | target function (ml) not normalized (free): 4178.058055 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1097 0.1539 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1590 0.1578 0.1863 n_refl.: 17040 remove outliers: r(all,work,free)=0.1590 0.1578 0.1863 n_refl.: 17040 overall B=-0.29 to atoms: r(all,work,free)=0.1571 0.1559 0.1853 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1118 0.1096 0.1538 n_refl.: 17040 remove outliers: r(all,work,free)=0.1118 0.1096 0.1538 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 0.3631 296.361 274.326 0.547 1.001 0.330 11.894-9.307 99.02 97 4 0.1694 487.458 482.908 0.925 1.002 0.330 9.237-7.194 100.00 213 7 0.1652 398.691 401.015 0.990 1.002 0.230 7.162-5.571 100.00 427 22 0.1508 299.218 293.755 0.938 1.003 0.210 5.546-4.326 100.00 867 58 0.0918 410.778 408.103 0.967 1.003 0.205 4.315-3.360 100.00 1859 96 0.0859 390.654 388.368 1.008 1.002 0.201 3.356-2.611 100.00 3867 181 0.1232 256.638 254.531 1.004 1.002 0.161 2.608-2.000 99.99 8818 434 0.1034 167.284 166.126 1.000 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0135 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1096 r_free=0.1538 After: r_work=0.1098 r_free=0.1537 ================================== NQH flips ================================== r_work=0.1098 r_free=0.1537 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1098 r_free=0.1537 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1098 r_free=0.1537 | n_water=444 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.1098 r_free=0.1537 | n_water=444 | time (s): 35.060 (total time: 35.650) Filter (q & B) r_work=0.1098 r_free=0.1537 | n_water=443 | time (s): 1.590 (total time: 37.240) Compute maps r_work=0.1098 r_free=0.1537 | n_water=443 | time (s): 0.630 (total time: 37.870) Filter (map) r_work=0.1170 r_free=0.1550 | n_water=334 | time (s): 1.700 (total time: 39.570) Find peaks r_work=0.1170 r_free=0.1550 | n_water=334 | time (s): 0.560 (total time: 40.130) Add new water r_work=0.1287 r_free=0.1652 | n_water=464 | time (s): 2.080 (total time: 42.210) Refine new water occ: r_work=0.1141 r_free=0.1523 adp: r_work=0.1135 r_free=0.1523 occ: r_work=0.1121 r_free=0.1515 adp: r_work=0.1114 r_free=0.1513 occ: r_work=0.1107 r_free=0.1508 adp: r_work=0.1101 r_free=0.1507 ADP+occupancy (water only), MIN, final r_work=0.1101 r_free=0.1507 r_work=0.1101 r_free=0.1507 | n_water=464 | time (s): 45.060 (total time: 87.270) Filter (q & B) r_work=0.1103 r_free=0.1515 | n_water=453 | time (s): 1.930 (total time: 89.200) Filter (dist only) r_work=0.1106 r_free=0.1520 | n_water=452 | time (s): 35.960 (total time: 125.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.943022 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.160564 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 0.1130 0.1550 0.0420 0.010 1.1 4.8 0.5 0.0 0 0.972 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 15.50 4.20 4.545 20.814 0.161 4.956 11.19 15.52 4.33 4.640 20.855 0.161 4.951 Individual atomic B min max mean iso aniso Overall: 5.37 99.93 20.84 4.93 1979 0 Protein: 5.37 99.93 16.23 4.91 1519 0 Water: 8.32 66.73 36.09 N/A 452 0 Other: 26.45 47.13 34.83 N/A 8 0 Chain A: 5.37 99.93 17.89 N/A 1734 0 Chain S: 16.85 66.73 41.72 N/A 245 0 Histogram: Values Number of atoms 5.37 - 14.83 1006 14.83 - 24.28 384 24.28 - 33.74 217 33.74 - 43.20 194 43.20 - 52.65 123 52.65 - 62.11 37 62.11 - 71.56 8 71.56 - 81.02 3 81.02 - 90.47 3 90.47 - 99.93 4 =========================== Idealize ADP of riding H ========================== r_work=0.1119 r_free=0.1552 r_work=0.1119 r_free=0.1552 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1119 r_free = 0.1552 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1113 r_free = 0.1555 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1113 r_free= 0.1555 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.948660 | | target function (ml) not normalized (work): 80331.601277 | | target function (ml) not normalized (free): 4188.205963 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1126 0.1426 5.4675 5.684| | 2: 3.63 - 2.88 1.00 2711 122 0.1106 0.1607 5.2425 5.4112| | 3: 2.88 - 2.52 1.00 2681 148 0.1368 0.1718 5.154 5.2425| | 4: 2.52 - 2.29 1.00 2661 139 0.0935 0.1600 4.6348 4.9991| | 5: 2.29 - 2.13 1.00 2678 122 0.0958 0.1448 4.5856 4.873| | 6: 2.13 - 2.00 1.00 2692 117 0.1117 0.1715 4.5781 4.778| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.94 9.63 1.00 0.95 6909.45| | 2: 3.63 - 2.88 2711 122 0.92 13.50 1.01 0.95 6909.45| | 3: 2.88 - 2.52 2681 148 0.87 19.84 0.99 0.95 6909.45| | 4: 2.52 - 2.29 2661 139 0.93 12.33 1.01 0.97 2177.15| | 5: 2.29 - 2.13 2678 122 0.91 14.38 1.00 0.97 2177.15| | 6: 2.13 - 2.00 2692 117 0.89 17.11 0.99 0.97 2177.15| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2177.15 max = 6909.45 mean = 4568.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.96 mean = 14.43| |phase err.(test): min = 0.00 max = 86.39 mean = 13.86| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1113 0.1555 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1581 0.1571 0.1809 n_refl.: 17040 remove outliers: r(all,work,free)=0.1581 0.1571 0.1809 n_refl.: 17040 overall B=-0.23 to atoms: r(all,work,free)=0.1567 0.1557 0.1801 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1135 0.1114 0.1554 n_refl.: 17040 remove outliers: r(all,work,free)=0.1135 0.1114 0.1554 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 0.3669 296.361 273.171 0.541 1.005 0.327 11.894-9.307 99.02 97 4 0.1711 487.458 481.810 0.917 1.006 0.324 9.237-7.194 100.00 213 7 0.1727 398.691 401.112 0.987 1.006 0.220 7.162-5.571 100.00 427 22 0.1589 299.218 293.805 0.934 1.005 0.211 5.546-4.326 100.00 867 58 0.0932 410.778 407.655 0.964 1.005 0.209 4.315-3.360 100.00 1859 96 0.0895 390.654 388.070 1.004 1.003 0.205 3.356-2.611 100.00 3867 181 0.1241 256.638 254.179 0.999 1.001 0.131 2.608-2.000 99.99 8818 434 0.1039 167.284 165.972 0.994 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8135 ================= 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 : 0.2787 0.1844 0.085 5.394 8.8 119.3 19.9 258 0.000 1_bss: 0.1613 0.1674 0.085 5.394 8.4 118.9 19.5 258 0.000 1_settarget: 0.1613 0.1674 0.085 5.394 8.4 118.9 19.5 258 0.000 1_nqh: 0.1615 0.1667 0.085 5.394 8.4 118.9 19.5 258 0.006 1_weight: 0.1615 0.1667 0.085 5.394 8.4 118.9 19.5 258 0.006 1_xyzrec: 0.1351 0.1642 0.009 0.981 8.4 118.9 19.5 258 0.157 1_adp: 0.1279 0.1666 0.009 0.981 6.2 113.9 20.0 258 0.157 1_regHadp: 0.1283 0.1672 0.009 0.981 6.2 113.9 20.0 258 0.157 1_occ: 0.1277 0.1663 0.009 0.981 6.2 113.9 20.0 258 0.157 2_bss: 0.1276 0.1655 0.009 0.981 5.8 113.5 19.6 258 0.157 2_settarget: 0.1276 0.1655 0.009 0.981 5.8 113.5 19.6 258 0.157 2_updatecdl: 0.1276 0.1655 0.009 1.000 5.8 113.5 19.6 258 0.157 2_nqh: 0.1278 0.1654 0.009 1.000 5.8 113.5 19.6 258 0.154 2_sol: 0.1233 0.1530 0.009 1.000 5.8 112.3 20.7 358 n/a 2_weight: 0.1233 0.1530 0.009 1.000 5.8 112.3 20.7 358 n/a 2_xyzrec: 0.1206 0.1567 0.008 0.926 5.8 112.3 20.7 358 n/a 2_adp: 0.1193 0.1592 0.008 0.926 6.7 107.3 21.3 358 n/a 2_regHadp: 0.1194 0.1593 0.008 0.926 6.7 107.3 21.3 358 n/a 2_occ: 0.1193 0.1607 0.008 0.926 6.7 107.3 21.3 358 n/a 3_bss: 0.1186 0.1600 0.008 0.926 6.4 106.9 20.9 358 n/a 3_settarget: 0.1186 0.1600 0.008 0.926 6.4 106.9 20.9 358 n/a 3_updatecdl: 0.1186 0.1600 0.008 0.930 6.4 106.9 20.9 358 n/a 3_nqh: 0.1186 0.1602 0.008 0.930 6.4 106.9 20.9 358 n/a 3_sol: 0.1186 0.1553 0.008 0.930 6.4 106.9 21.1 404 n/a 3_weight: 0.1186 0.1553 0.008 0.930 6.4 106.9 21.1 404 n/a 3_xyzrec: 0.1166 0.1550 0.009 0.986 6.4 106.9 21.1 404 n/a 3_adp: 0.1145 0.1553 0.009 0.986 6.6 104.1 20.9 404 n/a 3_regHadp: 0.1145 0.1555 0.009 0.986 6.6 104.1 20.9 404 n/a 3_occ: 0.1138 0.1553 0.009 0.986 6.6 104.1 20.9 404 n/a 4_bss: 0.1135 0.1549 0.009 0.986 6.2 103.7 20.5 404 n/a 4_settarget: 0.1135 0.1549 0.009 0.986 6.2 103.7 20.5 404 n/a 4_updatecdl: 0.1135 0.1549 0.009 0.984 6.2 103.7 20.5 404 n/a 4_nqh: 0.1137 0.1544 0.009 0.984 6.2 103.7 20.5 404 n/a 4_sol: 0.1126 0.1502 0.009 0.984 6.2 103.7 21.0 444 n/a 4_weight: 0.1126 0.1502 0.009 0.984 6.2 103.7 21.0 444 n/a 4_xyzrec: 0.1114 0.1551 0.010 0.992 6.2 103.7 21.0 444 n/a 4_adp: 0.1102 0.1546 0.010 0.992 5.9 101.6 21.0 444 n/a 4_regHadp: 0.1102 0.1547 0.010 0.992 5.9 101.6 21.0 444 n/a 4_occ: 0.1097 0.1539 0.010 0.992 5.9 101.6 21.0 444 n/a 5_bss: 0.1096 0.1538 0.010 0.992 5.6 101.3 20.7 444 n/a 5_settarget: 0.1096 0.1538 0.010 0.992 5.6 101.3 20.7 444 n/a 5_updatecdl: 0.1096 0.1538 0.010 0.995 5.6 101.3 20.7 444 n/a 5_setrh: 0.1098 0.1537 0.010 0.995 5.6 101.3 20.7 444 n/a 5_nqh: 0.1098 0.1537 0.010 0.995 5.6 101.3 20.7 444 n/a 5_sol: 0.1106 0.1520 0.010 0.995 5.6 101.3 20.8 452 n/a 5_weight: 0.1106 0.1520 0.010 0.995 5.6 101.3 20.8 452 n/a 5_xyzrec: 0.1130 0.1550 0.010 1.106 5.6 101.3 20.8 452 n/a 5_adp: 0.1119 0.1552 0.010 1.106 5.4 99.9 20.8 452 n/a 5_regHadp: 0.1119 0.1552 0.010 1.106 5.4 99.9 20.8 452 n/a 5_occ: 0.1113 0.1555 0.010 1.106 5.4 99.9 20.8 452 n/a end: 0.1114 0.1554 0.010 1.106 5.1 99.7 20.6 452 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2659048_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2659048_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1800 Refinement macro-cycles (run) : 907.9300 Write final files (write_after_run_outputs) : 20.9600 Total : 932.0700 Total CPU time: 15.94 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:57 PST -0800 (1735494057.56 s) Start R-work = 0.1613, R-free = 0.1674 Final R-work = 0.1114, R-free = 0.1554 =============================================================================== Job complete usr+sys time: 980.72 seconds wall clock time: 16 minutes 43.57 seconds (1003.57 seconds total)