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_3941866.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_3941866.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3941866.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.99, per 1000 atoms: 0.59 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: 0.35 Conformation dependent library (CDL) restraints added in 107.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 577 0.92 - 1.18: 1076 1.18 - 1.43: 652 1.43 - 1.68: 822 1.68 - 1.94: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.462 1.282 0.180 9.50e-03 1.11e+04 3.59e+02 bond pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.336 1.561 -0.225 1.25e-02 6.40e+03 3.25e+02 bond pdb=" CA ILE A 91 " pdb=" CB ILE A 91 " ideal model delta sigma weight residual 1.538 1.353 0.185 1.06e-02 8.90e+03 3.05e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.496 -0.175 1.00e-02 1.00e+04 3.05e+02 bond pdb=" C THR A 110 " pdb=" N ALA A 111 " ideal model delta sigma weight residual 1.335 1.560 -0.225 1.31e-02 5.83e+03 2.94e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 3369 5.06 - 10.13: 1881 10.13 - 15.19: 452 15.19 - 20.26: 64 20.26 - 25.32: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " ideal model delta sigma weight residual 123.46 109.43 14.03 9.90e-01 1.02e+00 2.01e+02 angle pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 121.10 136.58 -15.48 1.10e+00 8.26e-01 1.98e+02 angle pdb=" O GLU A 84 " pdb=" C GLU A 84 " pdb=" N SER A 85 " ideal model delta sigma weight residual 122.34 137.76 -15.42 1.25e+00 6.40e-01 1.52e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.82 108.08 12.74 1.05e+00 9.07e-01 1.47e+02 angle pdb=" O BASN A 76 " pdb=" C BASN A 76 " pdb=" N LEU A 77 " ideal model delta sigma weight residual 122.07 134.36 -12.29 1.03e+00 9.43e-01 1.42e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 15.87: 1273 15.87 - 31.71: 141 31.71 - 47.55: 42 47.55 - 63.39: 22 63.39 - 79.23: 3 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 -145.59 22.99 0 2.50e+00 1.60e-01 8.46e+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 122.80 143.05 -20.25 0 2.50e+00 1.60e-01 6.56e+01 dihedral pdb=" N PRO A 158 " pdb=" C PRO A 158 " pdb=" CA PRO A 158 " pdb=" CB PRO A 158 " ideal model delta harmonic sigma weight residual 115.10 134.01 -18.91 0 2.50e+00 1.60e-01 5.72e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.254: 108 0.254 - 0.503: 80 0.503 - 0.753: 42 0.753 - 1.002: 10 1.002 - 1.251: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -3.88 1.25 2.00e-01 2.50e+01 3.91e+01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.62 -1.18 2.00e-01 2.50e+01 3.49e+01 chirality pdb=" CA MET A 133 " pdb=" N MET A 133 " pdb=" C MET A 133 " pdb=" CB MET A 133 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.71e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.039 2.00e-02 2.50e+03 5.81e-02 1.01e+02 pdb=" CG ATYR A 67 " 0.127 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.009 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.043 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.008 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.020 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.066 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.089 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.058 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.068 2.00e-02 2.50e+03 5.36e-02 8.62e+01 pdb=" CG BTYR A 67 " 0.042 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.052 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.041 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.115 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.036 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.029 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.013 2.00e-02 2.50e+03 5.28e-02 8.37e+01 pdb=" CG TYR A 139 " -0.097 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.086 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.058 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.053 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 598 2.24 - 2.83: 7500 2.83 - 3.42: 10849 3.42 - 4.01: 15322 4.01 - 4.60: 22313 Nonbonded interactions: 56582 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.652 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.749 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.794 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.811 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.827 2.100 ... (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_3941866_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= 0.1791 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.420450 | | target function (ml) not normalized (work): 71801.372415 | | target function (ml) not normalized (free): 3262.701843 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3202 0.2079 7.6263 5.0395| | 2: 3.63 - 2.88 1.00 2711 122 0.2644 0.1726 4.3209 4.3226| | 3: 2.88 - 2.52 1.00 2682 148 0.2552 0.1591 4.1776 4.1716| | 4: 2.52 - 2.29 1.00 2661 139 0.2541 0.1546 3.5212 3.5805| | 5: 2.29 - 2.13 1.00 2678 122 0.2657 0.1574 3.403 3.4814| | 6: 2.13 - 2.00 1.00 2692 117 0.2732 0.1860 3.3065 3.3695| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.40 0.77 0.23 1288.12| | 2: 3.63 - 2.88 2711 122 0.83 23.57 1.32 0.23 1288.12| | 3: 2.88 - 2.52 2682 148 0.73 32.60 1.28 0.23 1288.12| | 4: 2.52 - 2.29 2661 139 0.93 11.12 1.29 0.26 131.53| | 5: 2.29 - 2.13 2678 122 0.92 13.21 1.32 0.26 131.53| | 6: 2.13 - 2.00 2692 117 0.90 16.03 1.33 0.26 131.53| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 131.53 max = 1288.12 mean = 716.27| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.97 mean = 18.99| |phase err.(test): min = 0.00 max = 89.35 mean = 19.15| |-----------------------------------------------------------------------------| ----------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 : 0.079 0.225 1557 Z= 5.386 Angle : 5.321 17.827 2118 Z= 3.702 Chirality : 0.409 1.251 243 Planarity : 0.032 0.116 284 Dihedral : 13.882 79.230 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 1.08 % Allowed : 5.41 % Favored : 93.51 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 35.68 % 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: -2.87 (0.49), residues: 224 helix: -3.19 (0.32), residues: 103 sheet: -1.11 (0.77), residues: 38 loop : -0.05 (0.68), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.092 0.028 ARG A 5 TYR 0.072 0.032 TYR A 141 PHE 0.058 0.025 PHE A 164 HIS 0.050 0.017 HIS A 115 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= 0.1791 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.420450 | | target function (ml) not normalized (work): 71801.372415 | | target function (ml) not normalized (free): 3262.701843 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3224 percent. r_work = 0.2920 r_free = 0.1981 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2920 0.1981 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2920 0.1981 n_refl.: 17050 remove outliers: r(all,work,free)=0.2155 0.2167 0.1981 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2129 0.2141 0.1965 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1622 0.1619 0.1684 n_refl.: 17045 remove outliers: r(all,work,free)=0.1621 0.1618 0.1684 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 0.4066 394.767 364.767 0.659 1.012 0.403 11.894-9.307 99.02 97 4 0.1869 633.612 617.299 0.930 1.014 0.390 9.237-7.194 100.00 213 7 0.2165 518.231 508.480 0.963 1.013 0.351 7.162-5.571 100.00 427 22 0.2358 388.933 375.979 0.920 1.012 0.341 5.546-4.326 100.00 867 58 0.1403 533.943 528.003 0.961 1.010 0.221 4.315-3.360 100.00 1859 96 0.1292 507.785 503.358 1.016 1.006 0.211 3.356-2.611 100.00 3867 181 0.1670 333.586 329.009 1.008 1.000 0.048 2.608-2.000 99.99 8818 434 0.1647 217.441 213.584 1.028 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3936 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1618 r_free=0.1684 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1618 r_free=0.1684 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.151733 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.909431 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 0.1353 0.1643 0.0291 0.008 1.0 1.6 0.5 0.0 0 11.076 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.53 16.43 2.91 3.013 18.469 0.909 0.023 12.80 16.67 3.87 3.530 18.642 0.909 0.021 Individual atomic B min max mean iso aniso Overall: 6.06 113.91 19.82 4.06 1785 0 Protein: 6.06 113.27 17.04 4.06 1519 0 Water: 8.60 113.91 36.02 N/A 258 0 Other: 21.23 37.57 25.94 N/A 8 0 Chain A: 6.06 113.91 19.82 N/A 1785 0 Histogram: Values Number of atoms 6.06 - 16.84 1094 16.84 - 27.63 338 27.63 - 38.41 178 38.41 - 49.20 98 49.20 - 59.98 50 59.98 - 70.77 12 70.77 - 81.55 7 81.55 - 92.34 4 92.34 - 103.12 1 103.12 - 113.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1280 r_free=0.1667 r_work=0.1283 r_free=0.1672 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1283 r_free = 0.1672 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1278 r_free = 0.1665 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1278 r_free= 0.1665 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020122 | | target function (ls_wunit_k1) not normalized (work): 326.717018 | | target function (ls_wunit_k1) not normalized (free): 27.265708 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1278 0.1665 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1903 0.1903 0.1971 n_refl.: 17044 remove outliers: r(all,work,free)=0.1903 0.1903 0.1971 n_refl.: 17044 overall B=-0.46 to atoms: r(all,work,free)=0.1871 0.1869 0.1953 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1654 n_refl.: 17044 remove outliers: r(all,work,free)=0.1291 0.1273 0.1654 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 0.3484 304.016 278.778 0.615 1.006 0.360 11.894-9.307 99.02 97 4 0.1728 488.962 477.320 0.919 1.007 0.358 9.237-7.194 100.00 213 7 0.1820 399.921 396.814 0.962 1.007 0.351 7.162-5.571 100.00 427 22 0.1844 300.141 294.657 0.933 1.006 0.311 5.546-4.326 100.00 867 58 0.1044 412.046 409.653 0.960 1.006 0.211 4.315-3.360 100.00 1859 96 0.0926 391.860 391.346 1.016 1.004 0.202 3.356-2.611 100.00 3867 181 0.1298 257.430 256.073 1.009 1.001 0.101 2.608-2.000 99.99 8818 434 0.1347 167.800 166.501 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9584 b_overall=-1.1473 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1654 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1654 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1654 | n_water=258 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1281 r_free=0.1643 | n_water=252 | time (s): 19.790 (total time: 20.420) Filter (q & B) r_work=0.1281 r_free=0.1642 | n_water=249 | time (s): 1.780 (total time: 22.200) Compute maps r_work=0.1281 r_free=0.1642 | n_water=249 | time (s): 0.570 (total time: 22.770) Filter (map) r_work=0.1320 r_free=0.1625 | n_water=211 | time (s): 1.440 (total time: 24.210) Find peaks r_work=0.1320 r_free=0.1625 | n_water=211 | time (s): 0.550 (total time: 24.760) Add new water r_work=0.1538 r_free=0.1862 | n_water=373 | time (s): 1.700 (total time: 26.460) Refine new water occ: r_work=0.1325 r_free=0.1571 adp: r_work=0.1267 r_free=0.1563 occ: r_work=0.1272 r_free=0.1533 adp: r_work=0.1240 r_free=0.1538 occ: r_work=0.1240 r_free=0.1524 adp: r_work=0.1228 r_free=0.1527 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1527 r_work=0.1228 r_free=0.1527 | n_water=373 | time (s): 22.080 (total time: 48.540) Filter (q & B) r_work=0.1232 r_free=0.1538 | n_water=360 | time (s): 1.980 (total time: 50.520) Filter (dist only) r_work=0.1233 r_free=0.1541 | n_water=359 | time (s): 28.960 (total time: 79.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.346851 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.986444 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 0.1208 0.1586 0.0378 0.008 0.9 1.9 0.5 0.0 0 12.173 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 15.86 3.78 4.148 20.821 0.986 0.018 11.93 16.07 4.14 4.218 21.143 0.986 0.017 Individual atomic B min max mean iso aniso Overall: 6.57 107.81 21.23 4.27 1886 0 Protein: 6.57 107.81 17.62 4.26 1519 0 Water: 8.24 65.73 36.20 N/A 359 0 Other: 25.70 45.79 35.69 N/A 8 0 Chain A: 6.57 107.81 19.35 N/A 1738 0 Chain S: 16.87 65.17 43.38 N/A 148 0 Histogram: Values Number of atoms 6.57 - 16.69 1026 16.69 - 26.82 376 26.82 - 36.94 225 36.94 - 47.06 156 47.06 - 57.19 63 57.19 - 67.31 30 67.31 - 77.44 3 77.44 - 87.56 5 87.56 - 97.68 0 97.68 - 107.81 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1607 r_work=0.1195 r_free=0.1608 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1608 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1604 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1188 r_free= 0.1604 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.016819 | | target function (ls_wunit_k1) not normalized (work): 273.063227 | | target function (ls_wunit_k1) not normalized (free): 24.362034 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1188 0.1604 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1760 0.1752 0.1956 n_refl.: 17042 remove outliers: r(all,work,free)=0.1760 0.1752 0.1956 n_refl.: 17042 overall B=-0.41 to atoms: r(all,work,free)=0.1734 0.1725 0.1940 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1184 0.1601 n_refl.: 17042 remove outliers: r(all,work,free)=0.1204 0.1184 0.1601 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 0.3356 304.016 285.027 0.603 1.006 0.350 11.894-9.307 99.02 97 4 0.1456 488.962 487.889 0.918 1.007 0.339 9.237-7.194 100.00 213 7 0.1625 399.921 401.841 0.973 1.007 0.295 7.162-5.571 100.00 427 22 0.1514 300.141 297.309 0.936 1.006 0.281 5.546-4.326 100.00 867 58 0.0873 412.046 409.669 0.960 1.005 0.216 4.315-3.360 100.00 1859 96 0.0820 391.860 391.127 1.016 1.004 0.212 3.356-2.611 100.00 3867 181 0.1196 257.430 256.515 1.009 1.000 0.132 2.608-2.000 99.99 8818 434 0.1329 167.800 166.678 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1475 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1184 r_free=0.1601 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.1185 r_free=0.1602 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1602 | n_water=359 | time (s): 0.830 (total time: 0.830) Filter (dist) r_work=0.1186 r_free=0.1601 | n_water=358 | time (s): 29.850 (total time: 30.680) Filter (q & B) r_work=0.1186 r_free=0.1601 | n_water=358 | time (s): 1.250 (total time: 31.930) Compute maps r_work=0.1186 r_free=0.1601 | n_water=358 | time (s): 0.760 (total time: 32.690) Filter (map) r_work=0.1254 r_free=0.1615 | n_water=262 | time (s): 2.080 (total time: 34.770) Find peaks r_work=0.1254 r_free=0.1615 | n_water=262 | time (s): 0.680 (total time: 35.450) Add new water r_work=0.1458 r_free=0.1777 | n_water=412 | time (s): 2.020 (total time: 37.470) Refine new water occ: r_work=0.1253 r_free=0.1571 adp: r_work=0.1242 r_free=0.1567 occ: r_work=0.1225 r_free=0.1549 adp: r_work=0.1212 r_free=0.1542 occ: r_work=0.1204 r_free=0.1541 adp: r_work=0.1192 r_free=0.1535 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1535 r_work=0.1192 r_free=0.1535 | n_water=412 | time (s): 38.580 (total time: 76.050) Filter (q & B) r_work=0.1195 r_free=0.1545 | n_water=401 | time (s): 1.820 (total time: 77.870) Filter (dist only) r_work=0.1195 r_free=0.1545 | n_water=401 | time (s): 31.550 (total time: 109.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.917335 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.153654 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 0.1543 0.0372 0.009 1.0 6.1 0.5 0.0 0 0.959 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.71 15.43 3.72 4.327 21.372 0.154 4.994 11.52 15.62 4.10 4.886 21.235 0.154 4.972 Individual atomic B min max mean iso aniso Overall: 6.21 105.45 20.68 4.63 1928 0 Protein: 6.21 105.45 16.79 4.61 1519 0 Water: 8.42 61.04 35.19 N/A 401 0 Other: 23.89 43.36 31.91 N/A 8 0 Chain A: 6.21 105.45 18.51 N/A 1734 0 Chain S: 15.88 61.04 40.04 N/A 194 0 Histogram: Values Number of atoms 6.21 - 16.14 1074 16.14 - 26.06 339 26.06 - 35.99 236 35.99 - 45.91 161 45.91 - 55.83 79 55.83 - 65.76 27 65.76 - 75.68 5 75.68 - 85.61 3 85.61 - 95.53 2 95.53 - 105.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1152 r_free=0.1562 r_work=0.1153 r_free=0.1564 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1564 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1148 r_free = 0.1564 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.15 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= 0.1564 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.967519 | | target function (ml) not normalized (work): 80647.671164 | | target function (ml) not normalized (free): 4186.240279 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1168 0.1148 0.1564 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1671 0.1663 0.1886 n_refl.: 17042 remove outliers: r(all,work,free)=0.1671 0.1663 0.1886 n_refl.: 17042 overall B=-0.33 to atoms: r(all,work,free)=0.1649 0.1640 0.1874 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1167 0.1147 0.1563 n_refl.: 17042 remove outliers: r(all,work,free)=0.1166 0.1146 0.1563 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 0.3614 300.518 280.234 0.570 1.006 0.340 11.894-9.307 99.02 97 4 0.1777 488.962 482.952 0.915 1.007 0.325 9.237-7.194 100.00 213 7 0.1727 399.921 400.900 0.991 1.007 0.280 7.162-5.571 100.00 427 22 0.1592 300.141 294.574 0.939 1.007 0.251 5.546-4.326 100.00 867 58 0.0952 412.046 409.177 0.964 1.006 0.206 4.315-3.360 100.00 1859 96 0.0884 391.860 389.264 1.012 1.004 0.201 3.356-2.611 100.00 3867 181 0.1283 257.430 255.175 1.009 1.001 0.162 2.608-2.000 99.99 8818 434 0.1095 167.800 166.325 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1511 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1563 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1146 r_free=0.1563 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1563 | n_water=401 | time (s): 0.740 (total time: 0.740) Filter (dist) r_work=0.1149 r_free=0.1563 | n_water=398 | time (s): 30.830 (total time: 31.570) Filter (q & B) r_work=0.1150 r_free=0.1561 | n_water=396 | time (s): 1.800 (total time: 33.370) Compute maps r_work=0.1150 r_free=0.1561 | n_water=396 | time (s): 0.740 (total time: 34.110) Filter (map) r_work=0.1198 r_free=0.1549 | n_water=315 | time (s): 2.270 (total time: 36.380) Find peaks r_work=0.1198 r_free=0.1549 | n_water=315 | time (s): 0.460 (total time: 36.840) Add new water r_work=0.1343 r_free=0.1661 | n_water=447 | time (s): 1.630 (total time: 38.470) Refine new water occ: r_work=0.1184 r_free=0.1533 adp: r_work=0.1176 r_free=0.1532 occ: r_work=0.1163 r_free=0.1516 adp: r_work=0.1153 r_free=0.1516 occ: r_work=0.1147 r_free=0.1505 adp: r_work=0.1139 r_free=0.1506 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1506 r_work=0.1139 r_free=0.1506 | n_water=447 | time (s): 27.940 (total time: 66.410) Filter (q & B) r_work=0.1142 r_free=0.1513 | n_water=440 | time (s): 1.500 (total time: 67.910) Filter (dist only) r_work=0.1145 r_free=0.1513 | n_water=438 | time (s): 35.100 (total time: 103.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.874517 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.151296 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 0.1131 0.1554 0.0423 0.009 1.0 4.2 0.5 0.0 0 0.937 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 15.54 4.23 4.443 20.894 0.151 4.960 11.19 15.52 4.33 4.608 20.892 0.151 4.951 Individual atomic B min max mean iso aniso Overall: 5.65 102.10 20.78 4.74 1965 0 Protein: 5.65 102.10 16.35 4.73 1519 0 Water: 8.37 63.96 35.94 N/A 438 0 Other: 23.40 42.62 31.13 N/A 8 0 Chain A: 5.65 102.10 17.99 N/A 1731 0 Chain S: 15.85 63.96 41.42 N/A 234 0 Histogram: Values Number of atoms 5.65 - 15.29 1028 15.29 - 24.94 380 24.94 - 34.58 213 34.58 - 44.23 185 44.23 - 53.88 103 53.88 - 63.52 42 63.52 - 73.17 6 73.17 - 82.81 3 82.81 - 92.46 3 92.46 - 102.10 2 =========================== Idealize ADP of riding H ========================== r_work=0.1119 r_free=0.1552 r_work=0.1119 r_free=0.1551 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1119 r_free = 0.1551 target_work(ml) = 4.950 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1112 r_free = 0.1558 target_work(ml) = 4.948 | | 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.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1112 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.948236 | | target function (ml) not normalized (work): 80329.664963 | | target function (ml) not normalized (free): 4179.576587 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1112 0.1558 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1583 0.1570 0.1872 n_refl.: 17041 remove outliers: r(all,work,free)=0.1583 0.1570 0.1872 n_refl.: 17041 overall B=-0.27 to atoms: r(all,work,free)=0.1567 0.1553 0.1864 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1130 0.1108 0.1559 n_refl.: 17041 remove outliers: r(all,work,free)=0.1130 0.1108 0.1559 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 0.3763 300.518 276.563 0.544 1.003 0.318 11.894-9.307 99.02 97 4 0.1904 488.962 478.875 0.910 1.004 0.310 9.237-7.194 100.00 213 7 0.1788 399.921 399.921 0.988 1.005 0.229 7.162-5.571 100.00 427 22 0.1561 300.141 294.840 0.940 1.004 0.209 5.546-4.326 100.00 867 58 0.0912 412.046 408.360 0.962 1.004 0.181 4.315-3.360 100.00 1859 96 0.0858 391.860 389.275 1.006 1.003 0.181 3.356-2.611 100.00 3867 181 0.1237 257.430 255.293 1.003 1.001 0.151 2.608-2.000 99.99 8818 434 0.1040 167.800 166.564 0.998 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9244 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1108 r_free=0.1559 After: r_work=0.1110 r_free=0.1558 ================================== NQH flips ================================== r_work=0.1110 r_free=0.1558 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1110 r_free=0.1558 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1110 r_free=0.1558 | n_water=438 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1110 r_free=0.1555 | n_water=436 | time (s): 35.200 (total time: 35.820) Filter (q & B) r_work=0.1110 r_free=0.1555 | n_water=436 | time (s): 0.960 (total time: 36.780) Compute maps r_work=0.1110 r_free=0.1555 | n_water=436 | time (s): 0.780 (total time: 37.560) Filter (map) r_work=0.1190 r_free=0.1558 | n_water=333 | time (s): 1.770 (total time: 39.330) Find peaks r_work=0.1190 r_free=0.1558 | n_water=333 | time (s): 0.440 (total time: 39.770) Add new water r_work=0.1308 r_free=0.1674 | n_water=474 | time (s): 1.700 (total time: 41.470) Refine new water occ: r_work=0.1145 r_free=0.1534 adp: r_work=0.1138 r_free=0.1538 occ: r_work=0.1125 r_free=0.1518 adp: r_work=0.1117 r_free=0.1523 occ: r_work=0.1111 r_free=0.1507 adp: r_work=0.1105 r_free=0.1510 ADP+occupancy (water only), MIN, final r_work=0.1105 r_free=0.1510 r_work=0.1105 r_free=0.1510 | n_water=474 | time (s): 45.040 (total time: 86.510) Filter (q & B) r_work=0.1109 r_free=0.1520 | n_water=463 | time (s): 2.290 (total time: 88.800) Filter (dist only) r_work=0.1109 r_free=0.1520 | n_water=463 | time (s): 36.860 (total time: 125.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.898778 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.170934 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 0.1129 0.1542 0.0413 0.010 1.1 6.4 0.5 0.0 0 0.949 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.29 15.42 4.13 4.468 20.666 0.171 4.954 11.19 15.37 4.19 4.610 20.726 0.171 4.947 Individual atomic B min max mean iso aniso Overall: 5.53 99.54 20.83 5.02 1990 0 Protein: 5.53 99.54 16.08 5.02 1519 0 Water: 8.02 65.69 36.28 N/A 463 0 Other: 22.74 38.93 29.53 N/A 8 0 Chain A: 5.53 99.54 17.72 N/A 1731 0 Chain S: 14.70 65.69 41.67 N/A 259 0 Histogram: Values Number of atoms 5.53 - 14.93 1030 14.93 - 24.33 380 24.33 - 33.73 196 33.73 - 43.13 198 43.13 - 52.54 123 52.54 - 61.94 43 61.94 - 71.34 10 71.34 - 80.74 3 80.74 - 90.14 3 90.14 - 99.54 4 =========================== Idealize ADP of riding H ========================== r_work=0.1119 r_free=0.1537 r_work=0.1119 r_free=0.1538 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1119 r_free = 0.1538 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1112 r_free = 0.1543 target_work(ml) = 4.945 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1112 r_free= 0.1543 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.944866 | | target function (ml) not normalized (work): 80274.952642 | | target function (ml) not normalized (free): 4173.444098 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1127 0.1383 5.4706 5.6379| | 2: 3.63 - 2.88 1.00 2711 122 0.1108 0.1654 5.241 5.4229| | 3: 2.88 - 2.52 1.00 2681 148 0.1362 0.1728 5.1509 5.2319| | 4: 2.52 - 2.29 1.00 2661 139 0.0928 0.1469 4.6283 4.9217| | 5: 2.29 - 2.13 1.00 2678 122 0.0954 0.1473 4.5767 4.8837| | 6: 2.13 - 2.00 1.00 2692 117 0.1119 0.1798 4.5716 4.7963| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.43 1.00 0.96 6767.30| | 2: 3.63 - 2.88 2711 122 0.92 13.29 1.01 0.96 6767.30| | 3: 2.88 - 2.52 2681 148 0.87 19.53 0.99 0.96 6767.30| | 4: 2.52 - 2.29 2661 139 0.93 11.97 1.01 0.97 2116.93| | 5: 2.29 - 2.13 2678 122 0.91 14.12 1.00 0.97 2116.93| | 6: 2.13 - 2.00 2692 117 0.89 16.78 0.99 0.97 2116.93| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2116.93 max = 6767.30 mean = 4466.75| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.90 mean = 14.15| |phase err.(test): min = 0.00 max = 87.92 mean = 13.94| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1112 0.1543 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1566 0.1553 0.1843 n_refl.: 17041 remove outliers: r(all,work,free)=0.1566 0.1553 0.1843 n_refl.: 17041 overall B=-0.21 to atoms: r(all,work,free)=0.1554 0.1541 0.1837 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1112 0.1542 n_refl.: 17041 remove outliers: r(all,work,free)=0.1133 0.1112 0.1542 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 0.3749 300.518 275.829 0.543 1.005 0.324 11.894-9.307 99.02 97 4 0.1784 488.962 480.069 0.913 1.006 0.320 9.237-7.194 100.00 213 7 0.1768 399.921 400.918 0.986 1.006 0.220 7.162-5.571 100.00 427 22 0.1560 300.141 295.394 0.934 1.005 0.202 5.546-4.326 100.00 867 58 0.0942 412.046 408.317 0.961 1.004 0.180 4.315-3.360 100.00 1859 96 0.0869 391.860 389.395 1.003 1.003 0.167 3.356-2.611 100.00 3867 181 0.1251 257.430 255.081 0.999 1.000 0.131 2.608-2.000 99.99 8818 434 0.1035 167.800 166.460 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7103 ================= 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 0.1791 0.079 5.321 8.8 119.3 19.9 258 0.000 1_bss: 0.1618 0.1684 0.079 5.321 8.5 118.9 19.5 258 0.000 1_settarget: 0.1618 0.1684 0.079 5.321 8.5 118.9 19.5 258 0.000 1_nqh: 0.1618 0.1684 0.079 5.321 8.5 118.9 19.5 258 0.000 1_weight: 0.1618 0.1684 0.079 5.321 8.5 118.9 19.5 258 0.000 1_xyzrec: 0.1353 0.1643 0.008 0.960 8.5 118.9 19.5 258 0.154 1_adp: 0.1280 0.1667 0.008 0.960 6.1 113.9 19.8 258 0.154 1_regHadp: 0.1283 0.1672 0.008 0.960 6.1 113.9 19.8 258 0.154 1_occ: 0.1278 0.1665 0.008 0.960 6.1 113.9 19.8 258 0.154 2_bss: 0.1273 0.1654 0.008 0.960 5.6 113.4 19.4 258 0.154 2_settarget: 0.1273 0.1654 0.008 0.960 5.6 113.4 19.4 258 0.154 2_updatecdl: 0.1273 0.1654 0.009 0.983 5.6 113.4 19.4 258 0.154 2_nqh: 0.1273 0.1654 0.009 0.983 5.6 113.4 19.4 258 0.154 2_sol: 0.1233 0.1541 0.009 0.983 5.6 112.8 20.6 359 n/a 2_weight: 0.1233 0.1541 0.009 0.983 5.6 112.8 20.6 359 n/a 2_xyzrec: 0.1208 0.1586 0.008 0.931 5.6 112.8 20.6 359 n/a 2_adp: 0.1193 0.1607 0.008 0.931 6.6 107.8 21.2 359 n/a 2_regHadp: 0.1195 0.1608 0.008 0.931 6.6 107.8 21.2 359 n/a 2_occ: 0.1188 0.1604 0.008 0.931 6.6 107.8 21.2 359 n/a 3_bss: 0.1184 0.1601 0.008 0.931 6.2 107.4 20.8 359 n/a 3_settarget: 0.1184 0.1601 0.008 0.931 6.2 107.4 20.8 359 n/a 3_updatecdl: 0.1184 0.1601 0.008 0.932 6.2 107.4 20.8 359 n/a 3_nqh: 0.1185 0.1602 0.008 0.932 6.2 107.4 20.8 359 n/a 3_sol: 0.1195 0.1545 0.008 0.932 6.2 107.4 20.9 401 n/a 3_weight: 0.1195 0.1545 0.008 0.932 6.2 107.4 20.9 401 n/a 3_xyzrec: 0.1171 0.1543 0.009 0.963 6.2 107.4 20.9 401 n/a 3_adp: 0.1152 0.1562 0.009 0.963 6.2 105.5 20.7 401 n/a 3_regHadp: 0.1153 0.1564 0.009 0.963 6.2 105.5 20.7 401 n/a 3_occ: 0.1148 0.1564 0.009 0.963 6.2 105.5 20.7 401 n/a 4_bss: 0.1146 0.1563 0.009 0.963 5.9 105.1 20.3 401 n/a 4_settarget: 0.1146 0.1563 0.009 0.963 5.9 105.1 20.3 401 n/a 4_updatecdl: 0.1146 0.1563 0.009 0.964 5.9 105.1 20.3 401 n/a 4_nqh: 0.1146 0.1563 0.009 0.964 5.9 105.1 20.3 401 n/a 4_sol: 0.1145 0.1513 0.009 0.964 5.9 105.1 20.8 438 n/a 4_weight: 0.1145 0.1513 0.009 0.964 5.9 105.1 20.8 438 n/a 4_xyzrec: 0.1131 0.1554 0.009 0.965 5.9 105.1 20.8 438 n/a 4_adp: 0.1119 0.1552 0.009 0.965 5.6 102.1 20.8 438 n/a 4_regHadp: 0.1119 0.1551 0.009 0.965 5.6 102.1 20.8 438 n/a 4_occ: 0.1112 0.1558 0.009 0.965 5.6 102.1 20.8 438 n/a 5_bss: 0.1108 0.1559 0.009 0.965 5.4 101.8 20.5 438 n/a 5_settarget: 0.1108 0.1559 0.009 0.965 5.4 101.8 20.5 438 n/a 5_updatecdl: 0.1108 0.1559 0.009 0.965 5.4 101.8 20.5 438 n/a 5_setrh: 0.1110 0.1558 0.009 0.965 5.4 101.8 20.5 438 n/a 5_nqh: 0.1110 0.1558 0.009 0.965 5.4 101.8 20.5 438 n/a 5_sol: 0.1109 0.1520 0.009 0.965 5.4 101.8 20.7 463 n/a 5_weight: 0.1109 0.1520 0.009 0.965 5.4 101.8 20.7 463 n/a 5_xyzrec: 0.1129 0.1542 0.010 1.058 5.4 101.8 20.7 463 n/a 5_adp: 0.1119 0.1537 0.010 1.058 5.5 99.5 20.8 463 n/a 5_regHadp: 0.1119 0.1538 0.010 1.058 5.5 99.5 20.8 463 n/a 5_occ: 0.1112 0.1543 0.010 1.058 5.5 99.5 20.8 463 n/a end: 0.1112 0.1542 0.010 1.058 5.3 99.3 20.6 463 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3941866_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3941866_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9400 Refinement macro-cycles (run) : 955.2000 Write final files (write_after_run_outputs) : 16.2500 Total : 974.3900 Total CPU time: 16.62 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:38 PST -0800 (1735494098.77 s) Start R-work = 0.1618, R-free = 0.1684 Final R-work = 0.1112, R-free = 0.1542 =============================================================================== Job complete usr+sys time: 1015.76 seconds wall clock time: 17 minutes 18.67 seconds (1038.67 seconds total)