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_7427252.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_7427252.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7427252.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 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: 1.19, per 1000 atoms: 0.35 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 194.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 535 0.91 - 1.17: 1114 1.17 - 1.43: 674 1.43 - 1.69: 807 1.69 - 1.95: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 1.236 1.037 0.200 1.15e-02 7.56e+03 3.01e+02 bond pdb=" CA VAL A 146 " pdb=" C VAL A 146 " ideal model delta sigma weight residual 1.522 1.731 -0.209 1.22e-02 6.72e+03 2.95e+02 bond pdb=" CA SER A 83 " pdb=" C SER A 83 " ideal model delta sigma weight residual 1.523 1.742 -0.219 1.35e-02 5.49e+03 2.62e+02 bond pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 1.335 1.531 -0.196 1.23e-02 6.61e+03 2.55e+02 bond pdb=" C SER A 3 " pdb=" N LYS A 4 " ideal model delta sigma weight residual 1.330 1.112 0.218 1.37e-02 5.33e+03 2.52e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 2991 4.35 - 8.71: 1859 8.71 - 13.06: 731 13.06 - 17.42: 168 17.42 - 21.77: 28 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OD1AASN A 97 " pdb=" CG AASN A 97 " pdb=" ND2AASN A 97 " ideal model delta sigma weight residual 122.60 106.78 15.82 1.00e+00 1.00e+00 2.50e+02 angle pdb=" CA MET A 26 " pdb=" C MET A 26 " pdb=" O MET A 26 " ideal model delta sigma weight residual 120.55 105.53 15.02 1.06e+00 8.90e-01 2.01e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.91 109.59 12.32 9.80e-01 1.04e+00 1.58e+02 angle pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 120.53 107.45 13.08 1.07e+00 8.73e-01 1.49e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 129.98 -10.78 9.00e-01 1.23e+00 1.43e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 1303 17.39 - 34.77: 124 34.77 - 52.15: 41 52.15 - 69.54: 10 69.54 - 86.92: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CA THR A 110 " pdb=" CB THR A 110 " ideal model delta harmonic sigma weight residual 123.40 145.69 -22.29 0 2.50e+00 1.60e-01 7.95e+01 dihedral pdb=" N GLU A 143 " pdb=" C GLU A 143 " pdb=" CA GLU A 143 " pdb=" CB GLU A 143 " ideal model delta harmonic sigma weight residual 122.80 143.00 -20.20 0 2.50e+00 1.60e-01 6.53e+01 dihedral pdb=" C THR A 110 " pdb=" N THR A 110 " pdb=" CA THR A 110 " pdb=" CB THR A 110 " ideal model delta harmonic sigma weight residual -122.00 -141.74 19.74 0 2.50e+00 1.60e-01 6.23e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.221: 109 0.221 - 0.441: 73 0.441 - 0.661: 43 0.661 - 0.882: 10 0.882 - 1.102: 8 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 1.42 1.10 2.00e-01 2.50e+01 3.04e+01 chirality pdb=" CA ALA A 79 " pdb=" N ALA A 79 " pdb=" C ALA A 79 " pdb=" CB ALA A 79 " both_signs ideal model delta sigma weight residual False 2.48 1.52 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CA PRO A 184 " pdb=" N PRO A 184 " pdb=" C PRO A 184 " pdb=" CB PRO A 184 " both_signs ideal model delta sigma weight residual False 2.72 1.75 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.065 2.00e-02 2.50e+03 5.92e-02 1.05e+02 pdb=" CG PHE A 162 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.141 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.056 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.070 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.061 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.023 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.005 2.00e-02 2.50e+03 5.88e-02 1.04e+02 pdb=" CG TYR A 139 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.114 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.066 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.043 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.084 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.055 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " -0.001 9.50e-02 1.11e+02 6.73e-02 1.02e+02 pdb=" NE ARG A 28 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " -0.145 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " -0.007 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " 0.129 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.020 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 632 2.25 - 2.84: 7612 2.84 - 3.43: 10742 3.43 - 4.01: 15415 4.01 - 4.60: 22181 Nonbonded interactions: 56582 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.667 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.829 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.837 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.841 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.853 2.450 ... (remaining 56577 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_7427252_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2788 r_free= 0.1846 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.406340 | | target function (ml) not normalized (work): 71572.181319 | | target function (ml) not normalized (free): 3259.888123 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3207 0.2153 7.5866 5.0172| | 2: 3.63 - 2.88 1.00 2711 122 0.2623 0.1760 4.3255 4.3235| | 3: 2.88 - 2.52 1.00 2682 148 0.2565 0.1859 4.1763 4.1926| | 4: 2.52 - 2.29 1.00 2661 139 0.2524 0.1436 3.4908 3.5337| | 5: 2.29 - 2.13 1.00 2678 122 0.2680 0.1529 3.4002 3.4612| | 6: 2.13 - 2.00 1.00 2692 117 0.2741 0.1872 3.2925 3.425| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.51 0.77 0.23 1282.46| | 2: 3.63 - 2.88 2711 122 0.83 23.59 1.31 0.23 1282.46| | 3: 2.88 - 2.52 2682 148 0.73 32.62 1.29 0.23 1282.46| | 4: 2.52 - 2.29 2661 139 0.93 11.18 1.29 0.26 131.58| | 5: 2.29 - 2.13 2678 122 0.92 13.26 1.32 0.26 131.58| | 6: 2.13 - 2.00 2692 117 0.90 15.98 1.33 0.26 131.58| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 131.58 max = 1282.46 mean = 713.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.99 mean = 19.03| |phase err.(test): min = 0.00 max = 89.30 mean = 19.22| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.248 1557 Z= 5.560 Angle : 5.208 15.963 2118 Z= 3.657 Chirality : 0.383 1.102 243 Planarity : 0.030 0.088 284 Dihedral : 13.827 86.922 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.62 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 30.27 % 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: -2.46 (0.44), residues: 224 helix: -2.53 (0.37), residues: 108 sheet: -1.08 (0.81), residues: 28 loop : -0.22 (0.52), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.068 0.024 ARG A 145 TYR 0.084 0.040 TYR A 141 PHE 0.119 0.043 PHE A 162 HIS 0.047 0.024 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2788 r_free= 0.1846 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.406340 | | target function (ml) not normalized (work): 71572.181319 | | target function (ml) not normalized (free): 3259.888123 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2925 percent. r_work = 0.2917 r_free = 0.1996 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2863 0.2917 0.1996 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2863 0.2917 0.1996 n_refl.: 17050 remove outliers: r(all,work,free)=0.2156 0.2167 0.1996 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2127 0.2138 0.1977 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1614 0.1610 0.1688 n_refl.: 17045 remove outliers: r(all,work,free)=0.1612 0.1608 0.1688 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3892 399.244 361.409 0.659 1.010 0.397 11.894-9.307 99.02 97 4 0.1809 634.094 614.665 0.933 1.011 0.380 9.237-7.194 100.00 213 7 0.2159 518.625 510.089 0.962 1.010 0.349 7.162-5.571 100.00 427 22 0.2293 389.229 376.340 0.923 1.009 0.287 5.546-4.326 100.00 867 58 0.1447 534.348 528.730 0.964 1.008 0.215 4.315-3.360 100.00 1859 96 0.1302 508.170 504.032 1.020 1.005 0.191 3.356-2.611 100.00 3867 181 0.1662 333.839 329.110 1.013 1.000 0.039 2.608-2.000 99.99 8818 434 0.1621 217.606 213.790 1.031 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.5004 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1608 r_free=0.1688 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1610 r_free=0.1691 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.964703 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.853795 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1349 0.1631 0.0282 0.009 1.0 1.0 0.5 0.0 0 11.982 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.49 16.31 2.82 3.013 18.438 0.854 0.023 12.79 16.54 3.75 3.626 18.714 0.854 0.020 Individual atomic B min max mean iso aniso Overall: 6.34 113.88 19.99 4.09 1785 0 Protein: 6.34 112.96 17.23 4.09 1519 0 Water: 8.71 113.88 36.03 N/A 258 0 Other: 21.75 36.94 26.32 N/A 8 0 Chain A: 6.34 113.88 19.99 N/A 1785 0 Histogram: Values Number of atoms 6.34 - 17.09 1098 17.09 - 27.85 331 27.85 - 38.60 184 38.60 - 49.36 96 49.36 - 60.11 50 60.11 - 70.86 12 70.86 - 81.62 6 81.62 - 92.37 4 92.37 - 103.12 1 103.12 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1654 r_work=0.1282 r_free=0.1659 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1659 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1276 r_free = 0.1653 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.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1276 r_free= 0.1653 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019968 | | target function (ls_wunit_k1) not normalized (work): 324.204036 | | target function (ls_wunit_k1) not normalized (free): 27.183846 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1276 0.1653 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1903 0.1902 0.1977 n_refl.: 17043 remove outliers: r(all,work,free)=0.1903 0.1902 0.1977 n_refl.: 17043 overall B=-0.39 to atoms: r(all,work,free)=0.1874 0.1873 0.1961 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1294 0.1276 0.1652 n_refl.: 17043 remove outliers: r(all,work,free)=0.1294 0.1276 0.1652 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3533 307.693 287.485 0.656 1.009 0.393 11.894-9.307 99.02 97 4 0.1674 488.690 477.649 0.919 1.010 0.365 9.237-7.194 100.00 213 7 0.1834 399.699 396.996 0.958 1.009 0.351 7.162-5.571 100.00 427 22 0.1873 299.975 294.669 0.930 1.008 0.301 5.546-4.326 100.00 867 58 0.1045 411.817 409.381 0.957 1.007 0.205 4.315-3.360 100.00 1859 96 0.0932 391.642 391.226 1.018 1.004 0.191 3.356-2.611 100.00 3867 181 0.1297 257.286 255.951 1.014 1.000 0.101 2.608-2.000 99.99 8818 434 0.1349 167.707 166.192 1.023 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.4000 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1652 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=0.1651 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1278 r_free=0.1651 | n_water=258 | time (s): 0.740 (total time: 0.740) Filter (dist) r_work=0.1282 r_free=0.1642 | n_water=253 | time (s): 19.430 (total time: 20.170) Filter (q & B) r_work=0.1283 r_free=0.1642 | n_water=251 | time (s): 1.630 (total time: 21.800) Compute maps r_work=0.1283 r_free=0.1642 | n_water=251 | time (s): 0.690 (total time: 22.490) Filter (map) r_work=0.1324 r_free=0.1630 | n_water=207 | time (s): 1.660 (total time: 24.150) Find peaks r_work=0.1324 r_free=0.1630 | n_water=207 | time (s): 0.480 (total time: 24.630) Add new water r_work=0.1546 r_free=0.1866 | n_water=359 | time (s): 1.700 (total time: 26.330) Refine new water occ: r_work=0.1337 r_free=0.1610 adp: r_work=0.1281 r_free=0.1604 occ: r_work=0.1287 r_free=0.1579 adp: r_work=0.1255 r_free=0.1586 occ: r_work=0.1256 r_free=0.1579 adp: r_work=0.1245 r_free=0.1580 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1580 r_work=0.1245 r_free=0.1580 | n_water=359 | time (s): 14.060 (total time: 40.390) Filter (q & B) r_work=0.1247 r_free=0.1584 | n_water=352 | time (s): 1.840 (total time: 42.230) Filter (dist only) r_work=0.1247 r_free=0.1584 | n_water=351 | time (s): 26.280 (total time: 68.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.849560 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.001129 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 0.1219 0.1622 0.0403 0.008 0.9 1.9 0.5 0.0 0 11.925 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.19 16.22 4.03 4.178 21.013 1.001 0.018 12.04 16.36 4.32 4.200 21.186 1.001 0.018 Individual atomic B min max mean iso aniso Overall: 6.70 107.57 21.07 4.21 1878 0 Protein: 6.70 107.57 17.57 4.20 1519 0 Water: 8.27 68.49 35.93 N/A 351 0 Other: 24.64 42.94 33.27 N/A 8 0 Chain A: 6.70 107.57 19.22 N/A 1734 0 Chain S: 18.17 61.41 43.29 N/A 144 0 Histogram: Values Number of atoms 6.70 - 16.79 1046 16.79 - 26.87 355 26.87 - 36.96 228 36.96 - 47.05 144 47.05 - 57.13 75 57.13 - 67.22 19 67.22 - 77.31 4 77.31 - 87.39 5 87.39 - 97.48 0 97.48 - 107.57 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1636 r_work=0.1205 r_free=0.1635 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1635 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1628 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1201 r_free= 0.1628 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017289 | | target function (ls_wunit_k1) not normalized (work): 280.705259 | | target function (ls_wunit_k1) not normalized (free): 25.809625 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1222 0.1201 0.1628 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1806 0.1803 0.1934 n_refl.: 17043 remove outliers: r(all,work,free)=0.1806 0.1803 0.1934 n_refl.: 17043 overall B=-0.50 to atoms: r(all,work,free)=0.1771 0.1768 0.1915 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1197 0.1619 n_refl.: 17043 remove outliers: r(all,work,free)=0.1215 0.1195 0.1619 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 0.3332 307.130 278.402 0.623 1.007 0.370 11.894-9.307 99.02 97 4 0.1493 488.690 484.615 0.919 1.007 0.360 9.237-7.194 100.00 213 7 0.1663 399.699 399.361 0.969 1.006 0.331 7.162-5.571 100.00 427 22 0.1575 299.975 295.391 0.937 1.006 0.245 5.546-4.326 100.00 867 58 0.0894 411.817 409.223 0.960 1.005 0.211 4.315-3.360 100.00 1859 96 0.0833 391.642 391.076 1.014 1.004 0.202 3.356-2.611 100.00 3867 181 0.1208 257.286 256.524 1.008 1.001 0.132 2.608-2.000 99.99 8818 434 0.1330 167.707 166.666 1.010 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1403 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1619 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=0.1196 r_free=0.1623 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1623 | n_water=351 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1196 r_free=0.1624 | n_water=350 | time (s): 29.820 (total time: 30.430) Filter (q & B) r_work=0.1196 r_free=0.1624 | n_water=350 | time (s): 0.810 (total time: 31.240) Compute maps r_work=0.1196 r_free=0.1624 | n_water=350 | time (s): 0.570 (total time: 31.810) Filter (map) r_work=0.1265 r_free=0.1643 | n_water=257 | time (s): 1.550 (total time: 33.360) Find peaks r_work=0.1265 r_free=0.1643 | n_water=257 | time (s): 0.500 (total time: 33.860) Add new water r_work=0.1456 r_free=0.1829 | n_water=403 | time (s): 1.930 (total time: 35.790) Refine new water occ: r_work=0.1258 r_free=0.1567 adp: r_work=0.1253 r_free=0.1575 occ: r_work=0.1229 r_free=0.1539 adp: r_work=0.1221 r_free=0.1544 occ: r_work=0.1208 r_free=0.1528 adp: r_work=0.1201 r_free=0.1533 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1533 r_work=0.1201 r_free=0.1533 | n_water=403 | time (s): 40.360 (total time: 76.150) Filter (q & B) r_work=0.1203 r_free=0.1544 | n_water=395 | time (s): 2.010 (total time: 78.160) Filter (dist only) r_work=0.1203 r_free=0.1543 | n_water=394 | time (s): 31.890 (total time: 110.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.863669 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.166227 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 0.1180 0.1550 0.0370 0.009 1.0 4.2 0.5 0.0 0 0.932 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.80 15.50 3.70 4.295 21.225 0.166 5.002 11.62 15.52 3.91 4.876 21.135 0.166 4.978 Individual atomic B min max mean iso aniso Overall: 5.87 106.06 20.56 4.66 1921 0 Protein: 5.87 106.06 16.73 4.66 1519 0 Water: 8.60 60.26 35.06 N/A 394 0 Other: 26.12 44.57 33.38 N/A 8 0 Chain A: 5.87 106.06 18.43 N/A 1732 0 Chain S: 16.93 60.20 40.02 N/A 189 0 Histogram: Values Number of atoms 5.87 - 15.89 1064 15.89 - 25.91 352 25.91 - 35.93 219 35.93 - 45.95 174 45.95 - 55.97 72 55.97 - 65.98 28 65.98 - 76.00 5 76.00 - 86.02 4 86.02 - 96.04 1 96.04 - 106.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1162 r_free=0.1552 r_work=0.1162 r_free=0.1554 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1162 r_free = 0.1554 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1151 r_free = 0.1556 target_work(ml) = 4.975 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1151 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.974681 | | target function (ml) not normalized (work): 80758.969012 | | target function (ml) not normalized (free): 4196.013189 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1170 0.1151 0.1556 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1655 0.1645 0.1874 n_refl.: 17041 remove outliers: r(all,work,free)=0.1655 0.1645 0.1874 n_refl.: 17041 overall B=-0.34 to atoms: r(all,work,free)=0.1632 0.1623 0.1863 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1168 0.1148 0.1552 n_refl.: 17041 remove outliers: r(all,work,free)=0.1167 0.1147 0.1552 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 0.3383 303.965 282.834 0.590 1.007 0.350 11.894-9.307 99.02 97 4 0.1766 488.690 480.640 0.916 1.008 0.330 9.237-7.194 100.00 213 7 0.1828 399.699 400.739 0.985 1.008 0.280 7.162-5.571 100.00 427 22 0.1682 299.975 293.599 0.937 1.007 0.220 5.546-4.326 100.00 867 58 0.0933 411.817 408.220 0.965 1.006 0.201 4.315-3.360 100.00 1859 96 0.0891 391.642 389.551 1.010 1.004 0.201 3.356-2.611 100.00 3867 181 0.1290 257.286 254.998 1.010 1.000 0.152 2.608-2.000 99.99 8818 434 0.1084 167.707 166.314 1.013 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1652 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1147 r_free=0.1552 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1147 r_free=0.1552 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1147 r_free=0.1552 | n_water=394 | time (s): 0.930 (total time: 0.930) Filter (dist) r_work=0.1147 r_free=0.1552 | n_water=394 | time (s): 28.500 (total time: 29.430) Filter (q & B) r_work=0.1147 r_free=0.1552 | n_water=394 | time (s): 0.810 (total time: 30.240) Compute maps r_work=0.1147 r_free=0.1552 | n_water=394 | time (s): 0.760 (total time: 31.000) Filter (map) r_work=0.1207 r_free=0.1565 | n_water=308 | time (s): 2.090 (total time: 33.090) Find peaks r_work=0.1207 r_free=0.1565 | n_water=308 | time (s): 0.640 (total time: 33.730) Add new water r_work=0.1352 r_free=0.1664 | n_water=453 | time (s): 1.760 (total time: 35.490) Refine new water occ: r_work=0.1182 r_free=0.1499 adp: r_work=0.1175 r_free=0.1501 occ: r_work=0.1157 r_free=0.1473 adp: r_work=0.1149 r_free=0.1471 occ: r_work=0.1140 r_free=0.1457 adp: r_work=0.1134 r_free=0.1455 ADP+occupancy (water only), MIN, final r_work=0.1134 r_free=0.1455 r_work=0.1134 r_free=0.1455 | n_water=453 | time (s): 40.540 (total time: 76.030) Filter (q & B) r_work=0.1138 r_free=0.1473 | n_water=442 | time (s): 1.490 (total time: 77.520) Filter (dist only) r_work=0.1138 r_free=0.1473 | n_water=441 | time (s): 33.280 (total time: 110.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.813349 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.160204 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 0.1523 0.0399 0.009 1.0 3.2 0.5 0.0 0 0.907 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 15.23 3.99 4.460 20.901 0.160 4.959 11.12 15.24 4.12 4.538 20.938 0.160 4.952 Individual atomic B min max mean iso aniso Overall: 5.68 104.31 20.90 4.74 1968 0 Protein: 5.68 104.31 16.40 4.73 1519 0 Water: 8.35 63.76 36.17 N/A 441 0 Other: 25.99 44.20 32.93 N/A 8 0 Chain A: 5.68 104.31 18.05 N/A 1731 0 Chain S: 13.15 63.76 41.68 N/A 237 0 Histogram: Values Number of atoms 5.68 - 15.54 1058 15.54 - 25.40 356 25.40 - 35.27 225 35.27 - 45.13 181 45.13 - 55.00 104 55.00 - 64.86 30 64.86 - 74.72 7 74.72 - 84.59 3 84.59 - 94.45 2 94.45 - 104.31 2 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1524 r_work=0.1112 r_free=0.1526 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1526 target_work(ml) = 4.953 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1104 r_free = 0.1527 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1104 r_free= 0.1527 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.947061 | | target function (ml) not normalized (work): 80305.640448 | | target function (ml) not normalized (free): 4177.532823 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1124 0.1104 0.1527 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1556 0.1543 0.1843 n_refl.: 17040 remove outliers: r(all,work,free)=0.1556 0.1543 0.1843 n_refl.: 17040 overall B=-0.26 to atoms: r(all,work,free)=0.1541 0.1527 0.1835 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1102 0.1524 n_refl.: 17040 remove outliers: r(all,work,free)=0.1121 0.1101 0.1524 n_refl.: 17039 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3543 300.392 279.530 0.559 1.001 0.340 11.894-9.307 99.02 97 4 0.1779 488.690 479.374 0.917 1.002 0.289 9.237-7.194 100.00 213 7 0.1746 399.699 400.733 0.990 1.003 0.250 7.162-5.571 100.00 427 22 0.1554 299.975 293.603 0.941 1.003 0.190 5.546-4.326 100.00 867 58 0.0918 411.817 408.774 0.965 1.003 0.191 4.315-3.360 100.00 1859 96 0.0843 391.642 389.469 1.005 1.002 0.191 3.356-2.611 100.00 3867 181 0.1226 257.286 255.186 1.001 1.001 0.121 2.608-2.000 99.99 8818 434 0.1047 167.707 166.474 0.994 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.8861 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1101 r_free=0.1524 After: r_work=0.1103 r_free=0.1523 ================================== NQH flips ================================== r_work=0.1103 r_free=0.1523 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=0.1104 r_free=0.1518 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1104 r_free=0.1518 | n_water=441 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1104 r_free=0.1517 | n_water=440 | time (s): 37.520 (total time: 38.150) Filter (q & B) r_work=0.1104 r_free=0.1517 | n_water=440 | time (s): 0.940 (total time: 39.090) Compute maps r_work=0.1104 r_free=0.1517 | n_water=440 | time (s): 0.830 (total time: 39.920) Filter (map) r_work=0.1175 r_free=0.1547 | n_water=339 | time (s): 2.350 (total time: 42.270) Find peaks r_work=0.1175 r_free=0.1547 | n_water=339 | time (s): 0.540 (total time: 42.810) Add new water r_work=0.1307 r_free=0.1643 | n_water=490 | time (s): 1.590 (total time: 44.400) Refine new water occ: r_work=0.1146 r_free=0.1471 adp: r_work=0.1138 r_free=0.1473 occ: r_work=0.1122 r_free=0.1457 adp: r_work=0.1112 r_free=0.1455 occ: r_work=0.1106 r_free=0.1447 adp: r_work=0.1098 r_free=0.1444 ADP+occupancy (water only), MIN, final r_work=0.1098 r_free=0.1444 r_work=0.1098 r_free=0.1444 | n_water=490 | time (s): 29.490 (total time: 73.890) Filter (q & B) r_work=0.1101 r_free=0.1454 | n_water=481 | time (s): 1.930 (total time: 75.820) Filter (dist only) r_work=0.1101 r_free=0.1454 | n_water=481 | time (s): 39.700 (total time: 115.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.916234 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.154873 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1123 0.1493 0.0370 0.010 1.0 6.7 0.5 0.0 0 0.958 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.23 14.93 3.70 4.479 20.863 0.155 4.948 11.10 14.81 3.71 4.555 20.940 0.155 4.938 Individual atomic B min max mean iso aniso Overall: 5.21 102.91 21.14 4.88 2008 0 Protein: 5.21 102.91 16.17 4.87 1519 0 Water: 7.98 64.44 36.65 N/A 481 0 Other: 25.61 43.89 32.42 N/A 8 0 Chain A: 5.21 102.91 17.82 N/A 1731 0 Chain S: 14.11 64.44 41.90 N/A 277 0 Histogram: Values Number of atoms 5.21 - 14.98 1035 14.98 - 24.75 370 24.75 - 34.52 218 34.52 - 44.29 209 44.29 - 54.06 118 54.06 - 63.83 38 63.83 - 73.60 11 73.60 - 83.37 4 83.37 - 93.14 3 93.14 - 102.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1110 r_free=0.1481 r_work=0.1110 r_free=0.1482 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1110 r_free = 0.1482 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1483 target_work(ml) = 4.934 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1103 r_free= 0.1483 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.933955 | | target function (ml) not normalized (work): 80087.953613 | | target function (ml) not normalized (free): 4158.756129 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2809 159 0.1097 0.1367 5.4397 5.6286| | 2: 3.63 - 2.88 1.00 2711 122 0.1090 0.1383 5.207 5.325| | 3: 2.88 - 2.52 1.00 2681 148 0.1357 0.1666 5.1178 5.1949| | 4: 2.52 - 2.29 1.00 2661 139 0.0940 0.1525 4.636 4.9701| | 5: 2.29 - 2.13 1.00 2678 122 0.0978 0.1455 4.5932 4.865| | 6: 2.13 - 2.00 1.00 2692 117 0.1124 0.1787 4.5816 4.7944| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2809 159 0.95 8.62 1.00 0.96 6082.76| | 2: 3.63 - 2.88 2711 122 0.93 12.48 1.01 0.96 6082.76| | 3: 2.88 - 2.52 2681 148 0.88 18.48 0.99 0.96 6082.76| | 4: 2.52 - 2.29 2661 139 0.93 12.29 1.01 0.98 2175.40| | 5: 2.29 - 2.13 2678 122 0.91 14.35 1.00 0.98 2175.40| | 6: 2.13 - 2.00 2692 117 0.89 17.09 0.99 0.98 2175.40| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2175.40 max = 6082.76 mean = 4149.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.88 mean = 13.84| |phase err.(test): min = 0.00 max = 88.59 mean = 13.57| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1103 0.1483 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1540 0.1528 0.1792 n_refl.: 17039 remove outliers: r(all,work,free)=0.1540 0.1528 0.1792 n_refl.: 17039 overall B=-0.21 to atoms: r(all,work,free)=0.1529 0.1517 0.1785 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1104 0.1482 n_refl.: 17039 remove outliers: r(all,work,free)=0.1122 0.1104 0.1482 n_refl.: 17039 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3433 300.392 282.103 0.549 1.005 0.328 11.894-9.307 99.02 97 4 0.1691 488.690 482.908 0.916 1.006 0.319 9.237-7.194 100.00 213 7 0.1660 399.699 402.447 0.989 1.006 0.219 7.162-5.571 100.00 427 22 0.1551 299.975 294.589 0.936 1.005 0.190 5.546-4.326 100.00 867 58 0.0930 411.817 408.755 0.964 1.005 0.184 4.315-3.360 100.00 1859 96 0.0859 391.642 389.196 1.000 1.003 0.177 3.356-2.611 100.00 3867 181 0.1240 257.286 255.115 0.998 1.000 0.141 2.608-2.000 99.99 8818 434 0.1044 167.707 166.312 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7251 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2788 0.1846 0.084 5.208 8.8 119.3 19.9 258 0.000 1_bss: 0.1608 0.1688 0.084 5.208 8.4 118.9 19.5 258 0.000 1_settarget: 0.1608 0.1688 0.084 5.208 8.4 118.9 19.5 258 0.000 1_nqh: 0.1610 0.1691 0.084 5.208 8.4 118.9 19.5 258 0.003 1_weight: 0.1610 0.1691 0.084 5.208 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1349 0.1631 0.009 0.991 8.4 118.9 19.5 258 0.140 1_adp: 0.1279 0.1654 0.009 0.991 6.3 113.9 20.0 258 0.140 1_regHadp: 0.1282 0.1659 0.009 0.991 6.3 113.9 20.0 258 0.140 1_occ: 0.1276 0.1653 0.009 0.991 6.3 113.9 20.0 258 0.140 2_bss: 0.1276 0.1652 0.009 0.991 6.0 113.5 19.6 258 0.140 2_settarget: 0.1276 0.1652 0.009 0.991 6.0 113.5 19.6 258 0.140 2_updatecdl: 0.1276 0.1652 0.009 1.012 6.0 113.5 19.6 258 0.140 2_nqh: 0.1278 0.1651 0.009 1.012 6.0 113.5 19.6 258 0.137 2_sol: 0.1247 0.1584 0.009 1.012 6.0 112.6 20.7 351 n/a 2_weight: 0.1247 0.1584 0.009 1.012 6.0 112.6 20.7 351 n/a 2_xyzrec: 0.1219 0.1622 0.008 0.925 6.0 112.6 20.7 351 n/a 2_adp: 0.1204 0.1636 0.008 0.925 6.7 107.6 21.1 351 n/a 2_regHadp: 0.1205 0.1635 0.008 0.925 6.7 107.6 21.1 351 n/a 2_occ: 0.1201 0.1628 0.008 0.925 6.7 107.6 21.1 351 n/a 3_bss: 0.1195 0.1619 0.008 0.925 6.2 107.1 20.6 351 n/a 3_settarget: 0.1195 0.1619 0.008 0.925 6.2 107.1 20.6 351 n/a 3_updatecdl: 0.1195 0.1619 0.008 0.924 6.2 107.1 20.6 351 n/a 3_nqh: 0.1196 0.1623 0.008 0.924 6.2 107.1 20.6 351 n/a 3_sol: 0.1203 0.1543 0.008 0.924 6.2 107.1 20.7 394 n/a 3_weight: 0.1203 0.1543 0.008 0.924 6.2 107.1 20.7 394 n/a 3_xyzrec: 0.1180 0.1550 0.009 0.960 6.2 107.1 20.7 394 n/a 3_adp: 0.1162 0.1552 0.009 0.960 5.9 106.1 20.6 394 n/a 3_regHadp: 0.1162 0.1554 0.009 0.960 5.9 106.1 20.6 394 n/a 3_occ: 0.1151 0.1556 0.009 0.960 5.9 106.1 20.6 394 n/a 4_bss: 0.1147 0.1552 0.009 0.960 5.5 105.7 20.2 394 n/a 4_settarget: 0.1147 0.1552 0.009 0.960 5.5 105.7 20.2 394 n/a 4_updatecdl: 0.1147 0.1552 0.009 0.961 5.5 105.7 20.2 394 n/a 4_nqh: 0.1147 0.1552 0.009 0.961 5.5 105.7 20.2 394 n/a 4_sol: 0.1138 0.1473 0.009 0.961 5.5 105.7 20.8 441 n/a 4_weight: 0.1138 0.1473 0.009 0.961 5.5 105.7 20.8 441 n/a 4_xyzrec: 0.1124 0.1523 0.009 0.963 5.5 105.7 20.8 441 n/a 4_adp: 0.1112 0.1524 0.009 0.963 5.7 104.3 20.9 441 n/a 4_regHadp: 0.1112 0.1526 0.009 0.963 5.7 104.3 20.9 441 n/a 4_occ: 0.1104 0.1527 0.009 0.963 5.7 104.3 20.9 441 n/a 5_bss: 0.1101 0.1524 0.009 0.963 5.4 104.1 20.6 441 n/a 5_settarget: 0.1101 0.1524 0.009 0.963 5.4 104.1 20.6 441 n/a 5_updatecdl: 0.1101 0.1524 0.009 0.963 5.4 104.1 20.6 441 n/a 5_setrh: 0.1103 0.1523 0.009 0.963 5.4 104.1 20.6 441 n/a 5_nqh: 0.1104 0.1518 0.009 0.963 5.4 104.1 20.6 441 n/a 5_sol: 0.1101 0.1454 0.009 0.963 5.4 104.1 21.0 481 n/a 5_weight: 0.1101 0.1454 0.009 0.963 5.4 104.1 21.0 481 n/a 5_xyzrec: 0.1123 0.1493 0.010 1.032 5.4 104.1 21.0 481 n/a 5_adp: 0.1110 0.1481 0.010 1.032 5.2 102.9 21.1 481 n/a 5_regHadp: 0.1110 0.1482 0.010 1.032 5.2 102.9 21.1 481 n/a 5_occ: 0.1103 0.1483 0.010 1.032 5.2 102.9 21.1 481 n/a end: 0.1104 0.1482 0.010 1.032 5.0 102.7 20.9 481 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7427252_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7427252_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.0600 Refinement macro-cycles (run) : 940.8800 Write final files (write_after_run_outputs) : 18.1500 Total : 963.0900 Total CPU time: 16.43 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:27 PST -0800 (1735494087.74 s) Start R-work = 0.1608, R-free = 0.1688 Final R-work = 0.1104, R-free = 0.1482 =============================================================================== Job complete usr+sys time: 1006.67 seconds wall clock time: 17 minutes 9.67 seconds (1029.67 seconds total)