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_6318584.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_6318584.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6318584.pdb" 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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.24, per 1000 atoms: 0.37 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 114.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 708 0.94 - 1.20: 988 1.20 - 1.47: 751 1.47 - 1.73: 691 1.73 - 1.99: 15 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 1.236 0.983 0.254 1.15e-02 7.56e+03 4.88e+02 bond pdb=" C MET A 134 " pdb=" O MET A 134 " ideal model delta sigma weight residual 1.235 0.961 0.274 1.33e-02 5.65e+03 4.26e+02 bond pdb=" C ILE A 105 " pdb=" O ILE A 105 " ideal model delta sigma weight residual 1.236 1.432 -0.196 1.01e-02 9.80e+03 3.78e+02 bond pdb=" CA TYR A 141 " pdb=" C TYR A 141 " ideal model delta sigma weight residual 1.525 1.273 0.252 1.32e-02 5.74e+03 3.64e+02 bond pdb=" C SER A 161 " pdb=" N PHE A 162 " ideal model delta sigma weight residual 1.334 1.569 -0.234 1.27e-02 6.20e+03 3.40e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.89: 3191 4.89 - 9.78: 1922 9.78 - 14.67: 560 14.67 - 19.56: 96 19.56 - 24.46: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 122.12 138.68 -16.56 1.06e+00 8.90e-01 2.44e+02 angle pdb=" O GLY A 78 " pdb=" C GLY A 78 " pdb=" N ALA A 79 " ideal model delta sigma weight residual 122.18 107.91 14.27 9.60e-01 1.09e+00 2.21e+02 angle pdb=" O BGLN A 80 " pdb=" C BGLN A 80 " pdb=" N ASN A 81 " ideal model delta sigma weight residual 122.12 137.79 -15.67 1.06e+00 8.90e-01 2.18e+02 angle pdb=" O BPRO A 66 " pdb=" C BPRO A 66 " pdb=" N BTYR A 67 " ideal model delta sigma weight residual 121.10 145.56 -24.46 1.90e+00 2.77e-01 1.66e+02 angle pdb=" O ALA A 183 " pdb=" C ALA A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 120.55 108.59 11.96 9.50e-01 1.11e+00 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1317 17.96 - 35.93: 118 35.93 - 53.89: 30 53.89 - 71.85: 14 71.85 - 89.81: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -143.49 20.89 0 2.50e+00 1.60e-01 6.98e+01 dihedral pdb=" C LEU A 77 " pdb=" N LEU A 77 " pdb=" CA LEU A 77 " pdb=" CB LEU A 77 " ideal model delta harmonic sigma weight residual -122.60 -140.98 18.38 0 2.50e+00 1.60e-01 5.41e+01 dihedral pdb=" N ALYS A 99 " pdb=" C ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual 122.80 140.26 -17.46 0 2.50e+00 1.60e-01 4.88e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.213: 86 0.213 - 0.425: 82 0.425 - 0.637: 48 0.637 - 0.849: 21 0.849 - 1.061: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.46 1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CA ALA A 171 " pdb=" N ALA A 171 " pdb=" C ALA A 171 " pdb=" CB ALA A 171 " both_signs ideal model delta sigma weight residual False 2.48 1.49 0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA THR A 19 " pdb=" N THR A 19 " pdb=" C THR A 19 " pdb=" CB THR A 19 " both_signs ideal model delta sigma weight residual False 2.53 3.50 -0.97 2.00e-01 2.50e+01 2.36e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.129 2.00e-02 2.50e+03 6.32e-02 1.20e+02 pdb=" CG TYR A 141 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.089 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.079 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.096 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.046 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.004 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG BTYR A 67 " -0.070 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.110 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.106 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.039 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.052 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.022 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.061 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.017 2.00e-02 2.50e+03 5.97e-02 1.07e+02 pdb=" CG PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.068 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.065 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.080 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 785 2.28 - 2.86: 7830 2.86 - 3.44: 10690 3.44 - 4.02: 15318 4.02 - 4.60: 21984 Nonbonded interactions: 56607 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.699 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.825 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.837 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.850 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H ATHR A 154 " model vdw 1.854 2.450 ... (remaining 56602 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_6318584_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= 0.2781 r_free= 0.1790 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.411486 | | target function (ml) not normalized (work): 71655.766297 | | target function (ml) not normalized (free): 3247.592656 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3185 0.2169 7.6106 5.0346| | 2: 3.63 - 2.88 1.00 2711 122 0.2640 0.1705 4.3209 4.3225| | 3: 2.88 - 2.52 1.00 2682 148 0.2545 0.1661 4.1764 4.1801| | 4: 2.52 - 2.29 1.00 2661 139 0.2571 0.1423 3.494 3.5471| | 5: 2.29 - 2.13 1.00 2678 122 0.2609 0.1436 3.3937 3.4083| | 6: 2.13 - 2.00 1.00 2692 117 0.2751 0.1782 3.3063 3.3525| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.43 0.77 0.23 1288.55| | 2: 3.63 - 2.88 2711 122 0.83 23.64 1.32 0.23 1288.55| | 3: 2.88 - 2.52 2682 148 0.74 32.52 1.29 0.23 1288.55| | 4: 2.52 - 2.29 2661 139 0.94 10.70 1.30 0.26 121.47| | 5: 2.29 - 2.13 2678 122 0.93 12.64 1.31 0.26 121.47| | 6: 2.13 - 2.00 2692 117 0.91 15.42 1.33 0.26 121.47| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 121.47 max = 1288.55 mean = 711.51| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.86 mean = 18.73| |phase err.(test): min = 0.00 max = 88.85 mean = 18.95| |-----------------------------------------------------------------------------| ----------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 0.274 1557 Z= 5.356 Angle : 5.348 24.455 2118 Z= 3.727 Chirality : 0.406 1.061 243 Planarity : 0.030 0.124 284 Dihedral : 14.099 89.814 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 32.43 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.47), residues: 224 helix: -2.38 (0.39), residues: 108 sheet: -0.28 (0.83), residues: 30 loop : -0.84 (0.57), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.099 0.019 ARG A 27 TYR 0.102 0.042 TYR A 141 PHE 0.098 0.032 PHE A 119 HIS 0.041 0.022 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= 0.2781 r_free= 0.1790 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.411486 | | target function (ml) not normalized (work): 71655.766297 | | target function (ml) not normalized (free): 3247.592656 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2588 percent. r_work = 0.2907 r_free = 0.1949 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2853 0.2907 0.1949 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2853 0.2907 0.1949 n_refl.: 17050 remove outliers: r(all,work,free)=0.2140 0.2152 0.1949 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2113 0.2124 0.1932 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1606 0.1605 0.1621 n_refl.: 17045 remove outliers: r(all,work,free)=0.1605 0.1604 0.1621 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 0.4065 394.737 363.140 0.647 1.018 0.393 11.894-9.307 99.02 97 4 0.1899 633.565 610.967 0.921 1.019 0.375 9.237-7.194 100.00 213 7 0.2166 518.193 510.269 0.951 1.018 0.355 7.162-5.571 100.00 427 22 0.2318 388.904 374.562 0.910 1.017 0.288 5.546-4.326 100.00 867 58 0.1399 533.903 527.539 0.956 1.014 0.215 4.315-3.360 100.00 1859 96 0.1292 507.747 503.673 1.014 1.008 0.191 3.356-2.611 100.00 3867 181 0.1649 333.561 329.484 1.014 0.999 0.101 2.608-2.000 99.99 8818 434 0.1626 217.424 213.545 1.035 0.983 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4342 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1604 r_free=0.1621 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 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1604 r_free=0.1621 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.196586 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.897636 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1352 0.1629 0.0276 0.009 1.0 1.6 0.5 0.0 0 11.598 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.29 2.76 3.013 18.457 0.898 0.023 12.79 16.51 3.72 3.588 18.689 0.898 0.021 Individual atomic B min max mean iso aniso Overall: 6.08 113.90 19.92 4.10 1785 0 Protein: 6.08 113.32 17.15 4.10 1519 0 Water: 8.53 113.90 36.09 N/A 258 0 Other: 21.77 36.50 26.09 N/A 8 0 Chain A: 6.08 113.90 19.92 N/A 1785 0 Histogram: Values Number of atoms 6.08 - 16.86 1083 16.86 - 27.64 343 27.64 - 38.42 187 38.42 - 49.21 91 49.21 - 59.99 54 59.99 - 70.77 12 70.77 - 81.55 7 81.55 - 92.33 4 92.33 - 103.12 1 103.12 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1651 r_work=0.1282 r_free=0.1658 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1658 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1277 r_free = 0.1654 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 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= 0.1654 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020089 | | target function (ls_wunit_k1) not normalized (work): 326.179645 | | target function (ls_wunit_k1) not normalized (free): 26.919800 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1295 0.1277 0.1654 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1907 0.1906 0.1984 n_refl.: 17044 remove outliers: r(all,work,free)=0.1907 0.1906 0.1984 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1879 0.1877 0.1968 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1296 0.1279 0.1652 n_refl.: 17044 remove outliers: r(all,work,free)=0.1295 0.1277 0.1652 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 0.3511 303.699 279.178 0.614 1.010 0.360 11.894-9.307 99.02 97 4 0.1686 488.451 478.812 0.917 1.011 0.360 9.237-7.194 100.00 213 7 0.1835 399.504 396.535 0.961 1.010 0.351 7.162-5.571 100.00 427 22 0.1857 299.828 294.950 0.927 1.009 0.301 5.546-4.326 100.00 867 58 0.1044 411.616 409.401 0.958 1.008 0.205 4.315-3.360 100.00 1859 96 0.0932 391.451 391.270 1.018 1.005 0.191 3.356-2.611 100.00 3867 181 0.1299 257.161 255.895 1.016 1.000 0.101 2.608-2.000 99.99 8818 434 0.1352 167.625 166.117 1.023 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.3732 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1652 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1652 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1652 | n_water=258 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1286 r_free=0.1643 | n_water=252 | time (s): 20.250 (total time: 20.920) Filter (q & B) r_work=0.1287 r_free=0.1643 | n_water=249 | time (s): 1.800 (total time: 22.720) Compute maps r_work=0.1287 r_free=0.1643 | n_water=249 | time (s): 0.710 (total time: 23.430) Filter (map) r_work=0.1317 r_free=0.1624 | n_water=213 | time (s): 2.200 (total time: 25.630) Find peaks r_work=0.1317 r_free=0.1624 | n_water=213 | time (s): 0.560 (total time: 26.190) Add new water r_work=0.1517 r_free=0.1852 | n_water=360 | time (s): 1.550 (total time: 27.740) Refine new water occ: r_work=0.1322 r_free=0.1599 adp: r_work=0.1270 r_free=0.1595 occ: r_work=0.1278 r_free=0.1572 adp: r_work=0.1247 r_free=0.1574 occ: r_work=0.1250 r_free=0.1567 adp: r_work=0.1238 r_free=0.1565 ADP+occupancy (water only), MIN, final r_work=0.1238 r_free=0.1565 r_work=0.1238 r_free=0.1565 | n_water=360 | time (s): 12.170 (total time: 39.910) Filter (q & B) r_work=0.1241 r_free=0.1574 | n_water=351 | time (s): 1.440 (total time: 41.350) Filter (dist only) r_work=0.1241 r_free=0.1574 | n_water=351 | time (s): 27.490 (total time: 68.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.381090 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.018501 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 0.1215 0.1613 0.0398 0.008 0.9 1.9 0.5 0.0 0 12.191 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.15 16.13 3.98 4.179 20.908 1.019 0.018 12.00 16.40 4.40 4.268 21.217 1.019 0.018 Individual atomic B min max mean iso aniso Overall: 6.56 107.94 21.21 4.41 1878 0 Protein: 6.56 107.94 17.75 4.39 1519 0 Water: 8.72 65.79 35.86 N/A 351 0 Other: 24.72 47.75 35.07 N/A 8 0 Chain A: 6.56 107.94 19.51 N/A 1740 0 Chain S: 20.66 64.64 42.60 N/A 138 0 Histogram: Values Number of atoms 6.56 - 16.70 1025 16.70 - 26.84 374 26.84 - 36.97 227 36.97 - 47.11 148 47.11 - 57.25 66 57.25 - 67.39 27 67.39 - 77.52 3 77.52 - 87.66 5 87.66 - 97.80 1 97.80 - 107.94 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1640 r_work=0.1201 r_free=0.1643 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1643 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1643 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1197 r_free= 0.1643 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017188 | | target function (ls_wunit_k1) not normalized (work): 279.053817 | | target function (ls_wunit_k1) not normalized (free): 25.201020 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1197 0.1643 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1754 0.1748 0.1907 n_refl.: 17042 remove outliers: r(all,work,free)=0.1754 0.1748 0.1907 n_refl.: 17042 overall B=-0.39 to atoms: r(all,work,free)=0.1729 0.1722 0.1894 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1191 0.1635 n_refl.: 17042 remove outliers: r(all,work,free)=0.1213 0.1191 0.1635 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 0.3378 303.699 281.465 0.603 1.003 0.350 11.894-9.307 99.02 97 4 0.1512 488.451 484.736 0.918 1.003 0.347 9.237-7.194 100.00 213 7 0.1712 399.504 398.207 0.970 1.003 0.331 7.162-5.571 100.00 427 22 0.1559 299.828 295.394 0.934 1.003 0.271 5.546-4.326 100.00 867 58 0.0883 411.616 408.651 0.962 1.003 0.211 4.315-3.360 100.00 1859 96 0.0817 391.451 390.164 1.017 1.002 0.211 3.356-2.611 100.00 3867 181 0.1202 257.161 256.456 1.013 1.001 0.142 2.608-2.000 99.99 8818 434 0.1332 167.625 167.098 1.016 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.4044 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1635 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=0.1193 r_free=0.1638 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1638 | n_water=351 | time (s): 0.760 (total time: 0.760) Filter (dist) r_work=0.1192 r_free=0.1642 | n_water=349 | time (s): 27.460 (total time: 28.220) Filter (q & B) r_work=0.1192 r_free=0.1642 | n_water=349 | time (s): 0.980 (total time: 29.200) Compute maps r_work=0.1192 r_free=0.1642 | n_water=349 | time (s): 0.600 (total time: 29.800) Filter (map) r_work=0.1252 r_free=0.1660 | n_water=267 | time (s): 2.210 (total time: 32.010) Find peaks r_work=0.1252 r_free=0.1660 | n_water=267 | time (s): 0.490 (total time: 32.500) Add new water r_work=0.1438 r_free=0.1836 | n_water=416 | time (s): 1.490 (total time: 33.990) Refine new water occ: r_work=0.1245 r_free=0.1581 adp: r_work=0.1237 r_free=0.1593 occ: r_work=0.1218 r_free=0.1557 adp: r_work=0.1208 r_free=0.1567 occ: r_work=0.1200 r_free=0.1547 adp: r_work=0.1190 r_free=0.1550 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1550 r_work=0.1190 r_free=0.1550 | n_water=416 | time (s): 42.490 (total time: 76.480) Filter (q & B) r_work=0.1194 r_free=0.1552 | n_water=401 | time (s): 1.520 (total time: 78.000) Filter (dist only) r_work=0.1194 r_free=0.1552 | n_water=400 | time (s): 30.880 (total time: 108.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.894911 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.149498 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 0.1171 0.1586 0.0415 0.009 0.9 3.8 0.5 0.0 0 0.947 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.71 15.86 4.15 4.407 21.546 0.149 5.005 11.55 15.89 4.35 4.920 21.434 0.149 4.981 Individual atomic B min max mean iso aniso Overall: 6.29 106.21 20.85 4.66 1927 0 Protein: 6.29 106.21 16.99 4.65 1519 0 Water: 8.98 60.40 35.27 N/A 400 0 Other: 25.83 45.28 33.71 N/A 8 0 Chain A: 6.29 106.21 18.81 N/A 1739 0 Chain S: 16.00 59.97 39.72 N/A 188 0 Histogram: Values Number of atoms 6.29 - 16.29 1070 16.29 - 26.28 345 26.28 - 36.27 225 36.27 - 46.26 173 46.26 - 56.25 76 56.25 - 66.24 26 66.24 - 76.24 4 76.24 - 86.23 3 86.23 - 96.22 3 96.22 - 106.21 2 =========================== Idealize ADP of riding H ========================== r_work=0.1155 r_free=0.1589 r_work=0.1155 r_free=0.1592 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1155 r_free = 0.1592 target_work(ml) = 4.981 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1148 r_free = 0.1598 target_work(ml) = 4.977 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1148 r_free= 0.1598 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.977270 | | target function (ml) not normalized (work): 80805.985164 | | target function (ml) not normalized (free): 4203.441037 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1169 0.1148 0.1598 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1688 0.1680 0.1913 n_refl.: 17042 remove outliers: r(all,work,free)=0.1688 0.1680 0.1913 n_refl.: 17042 overall B=-0.51 to atoms: r(all,work,free)=0.1653 0.1644 0.1897 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1168 0.1146 0.1592 n_refl.: 17042 remove outliers: r(all,work,free)=0.1168 0.1146 0.1592 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 0.3605 303.699 280.762 0.576 1.006 0.340 11.894-9.307 99.02 97 4 0.1729 488.451 483.611 0.912 1.007 0.327 9.237-7.194 100.00 213 7 0.1822 399.504 398.919 0.986 1.007 0.291 7.162-5.571 100.00 427 22 0.1568 299.828 295.107 0.939 1.006 0.239 5.546-4.326 100.00 867 58 0.0935 411.616 408.460 0.964 1.006 0.214 4.315-3.360 100.00 1859 96 0.0891 391.451 388.934 1.011 1.004 0.202 3.356-2.611 100.00 3867 181 0.1292 257.161 254.763 1.010 1.001 0.083 2.608-2.000 99.99 8818 434 0.1085 167.625 166.280 1.012 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1636 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1592 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1146 r_free=0.1592 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1592 | n_water=400 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1146 r_free=0.1596 | n_water=399 | time (s): 34.050 (total time: 34.950) Filter (q & B) r_work=0.1146 r_free=0.1596 | n_water=399 | time (s): 0.920 (total time: 35.870) Compute maps r_work=0.1146 r_free=0.1596 | n_water=399 | time (s): 0.580 (total time: 36.450) Filter (map) r_work=0.1192 r_free=0.1598 | n_water=318 | time (s): 1.680 (total time: 38.130) Find peaks r_work=0.1192 r_free=0.1598 | n_water=318 | time (s): 0.490 (total time: 38.620) Add new water r_work=0.1330 r_free=0.1684 | n_water=458 | time (s): 1.720 (total time: 40.340) Refine new water occ: r_work=0.1165 r_free=0.1535 adp: r_work=0.1158 r_free=0.1535 occ: r_work=0.1147 r_free=0.1531 adp: r_work=0.1138 r_free=0.1527 occ: r_work=0.1133 r_free=0.1527 adp: r_work=0.1126 r_free=0.1526 ADP+occupancy (water only), MIN, final r_work=0.1126 r_free=0.1526 r_work=0.1126 r_free=0.1526 | n_water=458 | time (s): 36.530 (total time: 76.870) Filter (q & B) r_work=0.1127 r_free=0.1533 | n_water=450 | time (s): 1.880 (total time: 78.750) Filter (dist only) r_work=0.1127 r_free=0.1531 | n_water=448 | time (s): 34.900 (total time: 113.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.968184 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.152526 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1119 0.1585 0.0465 0.010 1.0 7.0 0.5 0.0 0 0.984 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.19 15.85 4.65 4.474 20.909 0.153 4.967 11.07 15.74 4.67 4.666 20.920 0.153 4.956 Individual atomic B min max mean iso aniso Overall: 5.81 103.77 20.77 4.79 1975 0 Protein: 5.81 103.77 16.38 4.79 1519 0 Water: 8.38 64.91 35.43 N/A 448 0 Other: 25.39 44.18 32.96 N/A 8 0 Chain A: 5.81 103.77 18.13 N/A 1738 0 Chain S: 14.58 64.91 40.14 N/A 237 0 Histogram: Values Number of atoms 5.81 - 15.61 1063 15.61 - 25.40 354 25.40 - 35.20 223 35.20 - 44.99 199 44.99 - 54.79 97 54.79 - 64.58 24 64.58 - 74.38 7 74.38 - 84.18 3 84.18 - 93.97 3 93.97 - 103.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.1107 r_free=0.1574 r_work=0.1107 r_free=0.1575 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1107 r_free = 0.1575 target_work(ml) = 4.956 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1569 target_work(ml) = 4.953 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1569 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.953398 | | target function (ml) not normalized (work): 80418.412996 | | target function (ml) not normalized (free): 4189.151754 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1102 0.1569 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1583 0.1570 0.1871 n_refl.: 17042 remove outliers: r(all,work,free)=0.1583 0.1570 0.1871 n_refl.: 17042 overall B=-0.26 to atoms: r(all,work,free)=0.1567 0.1554 0.1862 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1100 0.1564 n_refl.: 17042 remove outliers: r(all,work,free)=0.1122 0.1099 0.1564 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 0.3673 300.204 279.541 0.554 1.004 0.340 11.894-9.307 99.02 97 4 0.1764 488.451 482.831 0.909 1.005 0.330 9.237-7.194 100.00 213 7 0.1823 399.504 400.845 0.986 1.005 0.250 7.162-5.571 100.00 427 22 0.1558 299.828 294.060 0.938 1.005 0.215 5.546-4.326 100.00 867 58 0.0918 411.616 408.292 0.965 1.004 0.211 4.315-3.360 100.00 1859 96 0.0854 391.451 388.878 1.005 1.003 0.175 3.356-2.611 100.00 3867 181 0.1232 257.161 254.717 1.003 1.001 0.077 2.608-2.000 99.99 8818 434 0.1027 167.625 166.434 0.997 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.9036 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1099 r_free=0.1564 After: r_work=0.1102 r_free=0.1562 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1562 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1102 r_free=0.1562 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1562 | n_water=448 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1105 r_free=0.1567 | n_water=447 | time (s): 35.710 (total time: 36.340) Filter (q & B) r_work=0.1105 r_free=0.1567 | n_water=447 | time (s): 0.800 (total time: 37.140) Compute maps r_work=0.1105 r_free=0.1567 | n_water=447 | time (s): 0.610 (total time: 37.750) Filter (map) r_work=0.1177 r_free=0.1561 | n_water=342 | time (s): 2.080 (total time: 39.830) Find peaks r_work=0.1177 r_free=0.1561 | n_water=342 | time (s): 0.650 (total time: 40.480) Add new water r_work=0.1288 r_free=0.1687 | n_water=476 | time (s): 2.170 (total time: 42.650) Refine new water occ: r_work=0.1136 r_free=0.1551 adp: r_work=0.1129 r_free=0.1553 occ: r_work=0.1116 r_free=0.1539 adp: r_work=0.1108 r_free=0.1538 occ: r_work=0.1102 r_free=0.1524 adp: r_work=0.1095 r_free=0.1527 ADP+occupancy (water only), MIN, final r_work=0.1095 r_free=0.1527 r_work=0.1095 r_free=0.1527 | n_water=476 | time (s): 34.600 (total time: 77.250) Filter (q & B) r_work=0.1098 r_free=0.1532 | n_water=469 | time (s): 1.930 (total time: 79.180) Filter (dist only) r_work=0.1097 r_free=0.1533 | n_water=468 | time (s): 38.440 (total time: 117.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.925078 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.183641 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 0.1124 0.1553 0.0429 0.010 1.0 6.1 0.5 0.0 0 0.963 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 15.53 4.29 4.496 20.683 0.184 4.952 11.11 15.39 4.28 4.603 20.739 0.184 4.943 Individual atomic B min max mean iso aniso Overall: 5.51 103.00 20.83 5.02 1995 0 Protein: 5.51 103.00 16.09 5.02 1519 0 Water: 8.01 64.69 35.95 N/A 468 0 Other: 26.84 45.67 35.06 N/A 8 0 Chain A: 5.51 103.00 17.84 N/A 1737 0 Chain S: 19.43 64.69 40.94 N/A 258 0 Histogram: Values Number of atoms 5.51 - 15.26 1067 15.26 - 25.00 349 25.00 - 34.75 216 34.75 - 44.50 209 44.50 - 54.25 112 54.25 - 64.00 26 64.00 - 73.75 7 73.75 - 83.50 3 83.50 - 93.25 3 93.25 - 103.00 3 =========================== Idealize ADP of riding H ========================== r_work=0.1111 r_free=0.1539 r_work=0.1111 r_free=0.1540 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1540 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1530 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1103 r_free= 0.1530 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.935863 | | target function (ml) not normalized (work): 80128.796999 | | target function (ml) not normalized (free): 4168.068764 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1111 0.1471 5.4512 5.6849| | 2: 3.63 - 2.88 1.00 2711 122 0.1086 0.1452 5.221 5.3464| | 3: 2.88 - 2.52 1.00 2681 148 0.1366 0.1676 5.1372 5.2034| | 4: 2.52 - 2.29 1.00 2661 139 0.0919 0.1501 4.6246 4.9324| | 5: 2.29 - 2.13 1.00 2678 122 0.0958 0.1533 4.5775 4.9051| | 6: 2.13 - 2.00 1.00 2692 117 0.1125 0.1701 4.5743 4.7674| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2811 159 0.94 9.16 1.00 0.96 6465.51| | 2: 3.63 - 2.88 2711 122 0.92 12.99 1.01 0.96 6465.51| | 3: 2.88 - 2.52 2681 148 0.87 19.10 0.99 0.96 6465.51| | 4: 2.52 - 2.29 2661 139 0.93 12.18 1.01 0.97 2127.12| | 5: 2.29 - 2.13 2678 122 0.91 14.22 1.00 0.97 2127.12| | 6: 2.13 - 2.00 2692 117 0.89 16.83 0.99 0.97 2127.12| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2127.12 max = 6465.51 mean = 4319.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.99 mean = 14.04| |phase err.(test): min = 0.00 max = 85.77 mean = 13.60| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1124 0.1103 0.1530 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1556 0.1547 0.1785 n_refl.: 17041 remove outliers: r(all,work,free)=0.1556 0.1547 0.1785 n_refl.: 17041 overall B=-0.22 to atoms: r(all,work,free)=0.1544 0.1534 0.1779 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1124 0.1104 0.1532 n_refl.: 17041 remove outliers: r(all,work,free)=0.1124 0.1104 0.1532 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 0.3613 300.204 276.644 0.575 1.006 0.340 11.894-9.307 99.02 97 4 0.1710 488.451 483.264 0.955 1.007 0.340 9.237-7.194 100.00 213 7 0.1743 399.504 401.890 1.031 1.007 0.220 7.162-5.571 100.00 427 22 0.1575 299.828 293.888 0.972 1.006 0.210 5.546-4.326 100.00 867 58 0.0930 411.616 408.269 1.000 1.005 0.211 4.315-3.360 100.00 1859 96 0.0858 391.451 388.997 1.038 1.004 0.181 3.356-2.611 100.00 3867 181 0.1240 257.161 254.652 1.035 1.001 0.141 2.608-2.000 99.99 8818 434 0.1033 167.625 166.314 1.025 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9964 b_overall=-0.6438 ================= 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 : 0.2781 0.1790 0.081 5.348 8.8 119.3 19.9 258 0.000 1_bss: 0.1604 0.1621 0.081 5.348 8.4 118.9 19.5 258 0.000 1_settarget: 0.1604 0.1621 0.081 5.348 8.4 118.9 19.5 258 0.000 1_nqh: 0.1604 0.1621 0.081 5.348 8.4 118.9 19.5 258 0.003 1_weight: 0.1604 0.1621 0.081 5.348 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1352 0.1629 0.009 0.977 8.4 118.9 19.5 258 0.143 1_adp: 0.1279 0.1651 0.009 0.977 6.1 113.9 19.9 258 0.143 1_regHadp: 0.1282 0.1658 0.009 0.977 6.1 113.9 19.9 258 0.143 1_occ: 0.1277 0.1654 0.009 0.977 6.1 113.9 19.9 258 0.143 2_bss: 0.1277 0.1652 0.009 0.977 5.7 113.5 19.5 258 0.143 2_settarget: 0.1277 0.1652 0.009 0.977 5.7 113.5 19.5 258 0.143 2_updatecdl: 0.1277 0.1652 0.009 0.990 5.7 113.5 19.5 258 0.143 2_nqh: 0.1277 0.1652 0.009 0.990 5.7 113.5 19.5 258 0.143 2_sol: 0.1241 0.1574 0.009 0.990 5.7 112.9 20.6 351 n/a 2_weight: 0.1241 0.1574 0.009 0.990 5.7 112.9 20.6 351 n/a 2_xyzrec: 0.1215 0.1613 0.008 0.924 5.7 112.9 20.6 351 n/a 2_adp: 0.1200 0.1640 0.008 0.924 6.6 107.9 21.2 351 n/a 2_regHadp: 0.1201 0.1643 0.008 0.924 6.6 107.9 21.2 351 n/a 2_occ: 0.1197 0.1643 0.008 0.924 6.6 107.9 21.2 351 n/a 3_bss: 0.1191 0.1635 0.008 0.924 6.2 107.5 20.8 351 n/a 3_settarget: 0.1191 0.1635 0.008 0.924 6.2 107.5 20.8 351 n/a 3_updatecdl: 0.1191 0.1635 0.008 0.925 6.2 107.5 20.8 351 n/a 3_nqh: 0.1193 0.1638 0.008 0.925 6.2 107.5 20.8 351 n/a 3_sol: 0.1194 0.1552 0.008 0.925 6.2 107.5 21.1 400 n/a 3_weight: 0.1194 0.1552 0.008 0.925 6.2 107.5 21.1 400 n/a 3_xyzrec: 0.1171 0.1586 0.009 0.948 6.2 107.5 21.1 400 n/a 3_adp: 0.1155 0.1589 0.009 0.948 6.3 106.2 20.9 400 n/a 3_regHadp: 0.1155 0.1592 0.009 0.948 6.3 106.2 20.9 400 n/a 3_occ: 0.1148 0.1598 0.009 0.948 6.3 106.2 20.9 400 n/a 4_bss: 0.1146 0.1592 0.009 0.948 5.8 105.7 20.3 400 n/a 4_settarget: 0.1146 0.1592 0.009 0.948 5.8 105.7 20.3 400 n/a 4_updatecdl: 0.1146 0.1592 0.009 0.949 5.8 105.7 20.3 400 n/a 4_nqh: 0.1146 0.1592 0.009 0.949 5.8 105.7 20.3 400 n/a 4_sol: 0.1127 0.1531 0.009 0.949 5.8 105.7 20.7 448 n/a 4_weight: 0.1127 0.1531 0.009 0.949 5.8 105.7 20.7 448 n/a 4_xyzrec: 0.1119 0.1585 0.010 0.985 5.8 105.7 20.7 448 n/a 4_adp: 0.1107 0.1574 0.010 0.985 5.8 103.8 20.8 448 n/a 4_regHadp: 0.1107 0.1575 0.010 0.985 5.8 103.8 20.8 448 n/a 4_occ: 0.1102 0.1569 0.010 0.985 5.8 103.8 20.8 448 n/a 5_bss: 0.1099 0.1564 0.010 0.985 5.5 103.5 20.5 448 n/a 5_settarget: 0.1099 0.1564 0.010 0.985 5.5 103.5 20.5 448 n/a 5_updatecdl: 0.1099 0.1564 0.010 0.987 5.5 103.5 20.5 448 n/a 5_setrh: 0.1102 0.1562 0.010 0.987 5.5 103.5 20.5 448 n/a 5_nqh: 0.1102 0.1562 0.010 0.987 5.5 103.5 20.5 448 n/a 5_sol: 0.1097 0.1533 0.010 0.987 5.5 103.5 20.7 468 n/a 5_weight: 0.1097 0.1533 0.010 0.987 5.5 103.5 20.7 468 n/a 5_xyzrec: 0.1124 0.1553 0.010 1.046 5.5 103.5 20.7 468 n/a 5_adp: 0.1111 0.1539 0.010 1.046 5.5 103.0 20.8 468 n/a 5_regHadp: 0.1111 0.1540 0.010 1.046 5.5 103.0 20.8 468 n/a 5_occ: 0.1103 0.1530 0.010 1.046 5.5 103.0 20.8 468 n/a end: 0.1104 0.1532 0.010 1.046 5.3 102.8 20.6 468 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6318584_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6318584_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7900 Refinement macro-cycles (run) : 933.5000 Write final files (write_after_run_outputs) : 19.9600 Total : 957.2500 Total CPU time: 16.36 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:22 PST -0800 (1735494082.59 s) Start R-work = 0.1604, R-free = 0.1621 Final R-work = 0.1104, R-free = 0.1532 =============================================================================== Job complete usr+sys time: 1001.36 seconds wall clock time: 17 minutes 3.90 seconds (1023.90 seconds total)