Starting phenix.refine on Sat Dec 28 21:06:31 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9255201.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 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9255201.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9255201.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.12, per 1000 atoms: 0.63 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: 0.56 Conformation dependent library (CDL) restraints added in 216.6 milliseconds Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.93: 647 0.93 - 1.19: 1037 1.19 - 1.46: 743 1.46 - 1.72: 709 1.72 - 1.98: 17 Bond restraints: 3153 Sorted by residual: bond pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 1.520 1.342 0.178 7.00e-03 2.04e+04 6.43e+02 bond pdb=" N BLEU A 153 " pdb=" CA BLEU A 153 " ideal model delta sigma weight residual 1.456 1.687 -0.230 1.21e-02 6.83e+03 3.62e+02 bond pdb=" C LEU A 7 " pdb=" O LEU A 7 " ideal model delta sigma weight residual 1.236 1.025 0.211 1.14e-02 7.69e+03 3.41e+02 bond pdb=" N VAL A 25 " pdb=" CA VAL A 25 " ideal model delta sigma weight residual 1.461 1.666 -0.206 1.19e-02 7.06e+03 2.99e+02 bond pdb=" N ARG A 28 " pdb=" CA ARG A 28 " ideal model delta sigma weight residual 1.459 1.676 -0.218 1.28e-02 6.10e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.16: 3405 5.16 - 10.31: 1802 10.31 - 15.47: 494 15.47 - 20.62: 69 20.62 - 25.78: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 121.38 105.91 15.47 8.20e-01 1.49e+00 3.56e+02 angle pdb=" CA HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 118.83 131.47 -12.64 8.70e-01 1.32e+00 2.11e+02 angle pdb=" O VAL A 23 " pdb=" C VAL A 23 " pdb=" N ASP A 24 " ideal model delta sigma weight residual 121.94 136.77 -14.83 1.03e+00 9.43e-01 2.07e+02 angle pdb=" OE1 GLN A 95 " pdb=" CD GLN A 95 " pdb=" NE2 GLN A 95 " ideal model delta sigma weight residual 122.60 136.83 -14.23 1.00e+00 1.00e+00 2.03e+02 angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 131.68 -12.48 9.00e-01 1.23e+00 1.92e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 928 16.03 - 32.06: 116 32.06 - 48.09: 47 48.09 - 64.12: 17 64.12 - 80.15: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 152.30 27.70 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 106 0.219 - 0.438: 72 0.438 - 0.657: 38 0.657 - 0.876: 19 0.876 - 1.095: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -3.72 1.09 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA ALA A 14 " pdb=" N ALA A 14 " pdb=" C ALA A 14 " pdb=" CB ALA A 14 " both_signs ideal model delta sigma weight residual False 2.48 3.53 -1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" CA BGLU A 64 " pdb=" N BGLU A 64 " pdb=" C BGLU A 64 " pdb=" CB BGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.072 2.00e-02 2.50e+03 7.07e-02 1.13e+02 pdb=" CG HIS A 115 " 0.112 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.096 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.098 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " -0.034 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.005 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG BTYR A 67 " -0.013 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.100 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.040 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.109 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.048 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.060 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " 0.201 9.50e-02 1.11e+02 8.74e-02 7.56e+01 pdb=" NE ARG A 145 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.082 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " -0.091 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " 0.016 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " 0.081 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.065 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " 0.018 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 760 2.28 - 2.86: 7840 2.86 - 3.44: 10641 3.44 - 4.02: 15227 4.02 - 4.60: 22108 Nonbonded interactions: 56576 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.696 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.736 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.763 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.837 2.100 nonbonded pdb=" H GLU A 147 " pdb=" O THR A 154 " model vdw 1.837 2.450 ... (remaining 56571 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 3 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 } pdb_interpretation { c_beta_restraints = False } ordered_solvent { 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_9255201_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: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2604 r_free= 0.1939 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.796906 | | target function (ml) not normalized (work): 232999.079967 | | target function (ml) not normalized (free): 11894.983064 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3031 0.2098 7.0895 4.9493| | 2: 3.57 - 2.84 1.00 2876 122 0.2433 0.1669 4.3463 4.3172| | 3: 2.84 - 2.48 1.00 2833 165 0.2358 0.1658 4.1287 4.1574| | 4: 2.47 - 2.25 1.00 2825 136 0.2343 0.1311 3.8281 3.8186| | 5: 2.25 - 2.09 1.00 2756 127 0.2443 0.1560 3.7921 3.8244| | 6: 2.09 - 1.97 1.00 2846 113 0.2508 0.1830 3.46 3.5537| | 7: 1.97 - 1.87 1.00 2787 165 0.2559 0.1976 3.1485 3.2617| | 8: 1.87 - 1.79 1.00 2789 144 0.2473 0.1927 3.078 3.1626| | 9: 1.79 - 1.72 1.00 2745 138 0.2455 0.1996 2.9136 2.9368| | 10: 1.72 - 1.66 1.00 2789 158 0.2414 0.2057 2.8172 2.9154| | 11: 1.66 - 1.61 1.00 2740 147 0.2497 0.1879 2.7709 2.8155| | 12: 1.61 - 1.56 1.00 2787 146 0.2528 0.1994 2.6396 2.6892| | 13: 1.56 - 1.52 1.00 2745 130 0.2560 0.2065 2.5814 2.6611| | 14: 1.52 - 1.48 1.00 2803 134 0.2542 0.1937 2.51 2.5505| | 15: 1.48 - 1.45 1.00 2738 128 0.2550 0.2168 2.4071 2.5712| | 16: 1.45 - 1.42 1.00 2756 161 0.2660 0.1944 2.4033 2.4236| | 17: 1.42 - 1.39 1.00 2785 139 0.2696 0.2056 2.3417 2.3455| | 18: 1.39 - 1.36 1.00 2741 179 0.2673 0.2347 2.2809 2.4595| | 19: 1.36 - 1.34 1.00 2807 134 0.2673 0.2277 2.2683 2.3361| | 20: 1.34 - 1.32 1.00 2696 147 0.2693 0.2030 2.1936 2.1413| | 21: 1.32 - 1.30 1.00 2785 112 0.2665 0.2074 2.1641 2.1347| | 22: 1.29 - 1.27 1.00 2704 152 0.2747 0.2590 2.1471 2.2057| | 23: 1.27 - 1.26 1.00 2802 156 0.2728 0.2172 2.0995 2.08| | 24: 1.26 - 1.24 1.00 2744 132 0.2758 0.2710 2.0751 2.219| | 25: 1.24 - 1.22 1.00 2734 148 0.2845 0.2748 2.047 2.1948| | 26: 1.22 - 1.21 1.00 2727 135 0.2864 0.2405 2.0258 2.087| | 27: 1.21 - 1.19 1.00 2814 148 0.2993 0.2598 2.0205 2.035| | 28: 1.19 - 1.18 1.00 2671 147 0.2987 0.2941 1.9825 2.0471| | 29: 1.18 - 1.16 1.00 2800 134 0.2932 0.2649 1.9567 2.0217| | 30: 1.16 - 1.15 1.00 2740 148 0.3089 0.2968 1.933 1.9661| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.58 2941 171 0.87 18.66 0.76 0.23 1459.12| | 2: 3.57 - 2.84 2876 122 0.81 25.96 1.27 0.23 1459.12| | 3: 2.84 - 2.48 2833 165 0.74 31.79 1.24 0.23 1211.50| | 4: 2.47 - 2.25 2825 136 0.81 25.60 1.26 0.25 568.85| | 5: 2.25 - 2.09 2756 127 0.77 29.41 1.28 0.25 568.85| | 6: 2.09 - 1.97 2846 113 0.83 23.01 1.29 0.25 314.74| | 7: 1.97 - 1.87 2787 165 0.89 17.40 1.28 0.26 98.01| | 8: 1.87 - 1.79 2789 144 0.85 21.89 1.25 0.26 98.01| | 9: 1.79 - 1.72 2745 138 0.87 19.46 1.24 0.26 59.96| | 10: 1.72 - 1.66 2789 158 0.86 21.07 1.23 0.26 52.34| | 11: 1.66 - 1.61 2740 147 0.85 22.09 1.24 0.25 50.55| | 12: 1.61 - 1.56 2787 146 0.87 19.51 1.24 0.25 32.38| | 13: 1.56 - 1.52 2745 130 0.86 21.44 1.25 0.25 32.38| | 14: 1.52 - 1.48 2803 134 0.86 21.56 1.23 0.25 28.68| | 15: 1.48 - 1.45 2738 128 0.86 21.03 1.23 0.25 21.89| | 16: 1.45 - 1.42 2756 161 0.85 22.43 1.24 0.25 21.89| | 17: 1.42 - 1.39 2785 139 0.86 21.57 1.23 0.24 18.35| | 18: 1.39 - 1.36 2741 179 0.86 21.62 1.22 0.24 16.30| | 19: 1.36 - 1.34 2807 134 0.85 22.33 1.21 0.24 16.30| | 20: 1.34 - 1.32 2696 147 0.86 21.20 1.21 0.24 13.05| | 21: 1.32 - 1.30 2785 112 0.86 21.72 1.20 0.24 12.82| | 22: 1.29 - 1.27 2704 152 0.85 22.38 1.21 0.24 12.56| | 23: 1.27 - 1.26 2802 156 0.86 22.13 1.21 0.24 11.20| | 24: 1.26 - 1.24 2744 132 0.85 22.93 1.19 0.24 11.20| | 25: 1.24 - 1.22 2734 148 0.84 24.08 1.20 0.24 10.79| | 26: 1.22 - 1.21 2727 135 0.84 24.48 1.19 0.23 10.33| | 27: 1.21 - 1.19 2814 148 0.83 25.25 1.20 0.23 10.33| | 28: 1.19 - 1.18 2671 147 0.82 26.36 1.19 0.23 9.91| | 29: 1.18 - 1.16 2800 134 0.81 26.78 1.16 0.22 9.75| | 30: 1.16 - 1.15 2740 148 0.79 28.55 1.15 0.22 9.75| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.75 max = 1459.12 mean = 214.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 23.12| |phase err.(test): min = 0.00 max = 89.64 mean = 22.86| |-----------------------------------------------------------------------------| ----------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 0.303 1557 Z= 5.547 Angle : 5.376 15.872 2118 Z= 3.761 Chirality : 0.394 1.095 243 Planarity : 0.029 0.122 284 Dihedral : 13.828 80.154 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 31.35 % 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: -2.41 (0.48), residues: 224 helix: -2.71 (0.35), residues: 109 sheet: 0.13 (1.00), residues: 28 loop : -0.30 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.094 0.020 ARG A 27 TYR 0.049 0.023 TYR A 139 PHE 0.103 0.039 PHE A 119 HIS 0.056 0.029 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 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: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2604 r_free= 0.1939 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.796906 | | target function (ml) not normalized (work): 232999.079967 | | target function (ml) not normalized (free): 11894.983064 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2562 0.2604 0.1940 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2562 0.2604 0.1940 n_refl.: 87602 remove outliers: r(all,work,free)=0.1977 0.1981 0.1940 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2003 0.2008 0.1955 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1650 0.1644 0.1762 n_refl.: 87594 remove outliers: r(all,work,free)=0.1650 0.1644 0.1762 n_refl.: 87593 ======================== 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 0.3963 386.280 358.245 0.684 1.001 0.410 11.894-9.307 99.02 97 4 0.1771 613.587 593.639 0.929 1.001 0.390 9.237-7.194 100.00 213 7 0.2157 501.839 488.918 0.950 1.002 0.357 7.162-5.571 100.00 427 22 0.2230 376.602 364.205 0.931 1.002 0.292 5.546-4.326 100.00 867 58 0.1291 516.982 510.203 0.964 1.002 0.224 4.315-3.360 100.00 1859 96 0.1146 491.653 488.652 1.004 1.002 0.147 3.356-2.611 100.00 3867 181 0.1444 322.991 319.530 0.999 1.001 0.048 2.608-2.026 99.99 8198 413 0.1363 214.113 211.650 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1654 104.562 103.780 1.011 1.001 0.000 1.573-1.221 100.00 36679 1900 0.2068 46.367 45.095 1.000 1.001 0.000 1.221-1.150 99.97 13689 708 0.2593 29.214 26.807 0.965 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0500 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1644 r_free=0.1762 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=0.1647 r_free=0.1764 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.872533 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2020.153657 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1210 0.1465 0.0255 0.007 0.9 1.0 0.5 0.0 0 12.436 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 14.65 2.55 3.012 19.077 2020.154 0.017 12.46 15.50 3.04 3.309 19.632 2020.154 0.016 Individual atomic B min max mean iso aniso Overall: 8.57 119.07 21.16 2.87 0 1785 Protein: 8.57 119.07 17.99 2.86 0 1519 Water: 11.07 114.52 39.54 N/A 0 258 Other: 23.39 37.42 29.86 N/A 0 8 Chain A: 8.57 119.07 21.16 N/A 0 1785 Histogram: Values Number of atoms 8.57 - 19.62 1207 19.62 - 30.67 228 30.67 - 41.72 164 41.72 - 52.77 102 52.77 - 63.82 53 63.82 - 74.87 16 74.87 - 85.92 8 85.92 - 96.97 3 96.97 - 108.02 1 108.02 - 119.07 3 =========================== Idealize ADP of riding H ========================== r_work=0.1247 r_free=0.1550 r_work=0.1251 r_free=0.1555 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1251 r_free = 0.1555 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1249 r_free = 0.1555 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1249 r_free= 0.1555 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015411 | | target function (ls_wunit_k1) not normalized (work): 1283.704353 | | target function (ls_wunit_k1) not normalized (free): 115.637377 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1264 0.1249 0.1555 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1705 0.1704 0.1777 n_refl.: 87593 remove outliers: r(all,work,free)=0.1705 0.1704 0.1777 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1726 0.1725 0.1792 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1262 0.1247 0.1547 n_refl.: 87593 remove outliers: r(all,work,free)=0.1261 0.1247 0.1547 n_refl.: 87592 ======================== 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 0.3582 298.183 277.899 0.630 1.001 0.374 11.894-9.307 99.02 97 4 0.1608 477.673 466.720 0.907 1.002 0.369 9.237-7.194 100.00 213 7 0.1817 390.677 385.167 0.946 1.002 0.340 7.162-5.571 100.00 427 22 0.1724 293.182 287.916 0.925 1.002 0.254 5.546-4.326 100.00 867 58 0.0908 402.466 400.131 0.950 1.002 0.204 4.315-3.360 100.00 1859 96 0.0766 382.748 381.795 0.994 1.002 0.143 3.356-2.611 100.00 3867 181 0.1016 251.446 250.734 1.000 1.001 0.052 2.608-2.026 99.99 8198 413 0.0978 166.685 166.073 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1220 81.401 81.579 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1666 36.096 35.557 1.005 0.999 0.000 1.221-1.150 99.97 13689 708 0.2369 22.743 21.262 0.969 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0489 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1247 r_free=0.1547 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=0.1248 r_free=0.1548 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1248 r_free=0.1548 | n_water=258 | time (s): 2.570 (total time: 2.570) Filter (dist) r_work=0.1258 r_free=0.1545 | n_water=252 | time (s): 26.280 (total time: 28.850) Filter (q & B) r_work=0.1261 r_free=0.1545 | n_water=249 | time (s): 3.710 (total time: 32.560) Compute maps r_work=0.1261 r_free=0.1545 | n_water=249 | time (s): 1.810 (total time: 34.370) Filter (map) r_work=0.1277 r_free=0.1553 | n_water=237 | time (s): 3.880 (total time: 38.250) Find peaks r_work=0.1277 r_free=0.1553 | n_water=237 | time (s): 0.730 (total time: 38.980) Add new water r_work=0.1421 r_free=0.1700 | n_water=454 | time (s): 3.790 (total time: 42.770) Refine new water occ: r_work=0.1335 r_free=0.1582 adp: r_work=0.1257 r_free=0.1526 occ: r_work=0.1270 r_free=0.1520 adp: r_work=0.1237 r_free=0.1504 occ: r_work=0.1241 r_free=0.1496 adp: r_work=0.1233 r_free=0.1496 ADP+occupancy (water only), MIN, final r_work=0.1233 r_free=0.1496 r_work=0.1233 r_free=0.1496 | n_water=454 | time (s): 80.290 (total time: 123.060) Filter (q & B) r_work=0.1237 r_free=0.1495 | n_water=431 | time (s): 3.900 (total time: 126.960) Filter (dist only) r_work=0.1237 r_free=0.1494 | n_water=430 | time (s): 43.470 (total time: 170.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.998235 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1498.844007 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1233 0.1513 0.0280 0.007 0.9 2.6 0.5 0.0 0 12.499 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.33 15.13 2.80 3.809 23.301 1498.844 0.015 12.03 14.78 2.74 4.160 23.139 1498.844 0.015 Individual atomic B min max mean iso aniso Overall: 9.02 115.89 23.31 2.60 193 1764 Protein: 9.02 115.89 17.81 2.61 0 1519 Water: 10.95 72.88 42.63 N/A 193 237 Other: 25.45 36.97 30.18 N/A 0 8 Chain A: 9.02 115.89 20.55 N/A 0 1764 Chain S: 17.75 68.10 48.58 N/A 193 0 Histogram: Values Number of atoms 9.02 - 19.71 1218 19.71 - 30.39 245 30.39 - 41.08 193 41.08 - 51.77 131 51.77 - 62.45 112 62.45 - 73.14 46 73.14 - 83.83 6 83.83 - 94.51 3 94.51 - 105.20 1 105.20 - 115.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1478 r_work=0.1203 r_free=0.1477 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1477 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1473 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1203 r_free= 0.1473 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013894 | | target function (ls_wunit_k1) not normalized (work): 1157.339577 | | target function (ls_wunit_k1) not normalized (free): 102.963866 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1203 0.1473 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1603 0.1599 0.1722 n_refl.: 87592 remove outliers: r(all,work,free)=0.1603 0.1599 0.1722 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1609 0.1605 0.1726 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1200 0.1471 n_refl.: 87592 remove outliers: r(all,work,free)=0.1212 0.1199 0.1471 n_refl.: 87589 ======================== 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 0.3445 294.131 272.168 0.594 1.002 0.370 11.894-9.307 99.02 97 4 0.1524 477.673 474.690 0.910 1.003 0.360 9.237-7.194 100.00 213 7 0.1717 390.677 390.053 0.975 1.003 0.290 7.162-5.571 100.00 427 22 0.1453 293.182 290.425 0.944 1.003 0.224 5.546-4.326 100.00 867 58 0.0829 402.466 400.281 0.954 1.002 0.189 4.315-3.360 100.00 1859 96 0.0713 382.748 381.627 1.000 1.002 0.170 3.356-2.611 100.00 3867 181 0.0956 251.446 250.802 1.009 1.002 0.130 2.608-2.026 99.99 8198 413 0.0954 166.685 166.290 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1184 81.401 81.589 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1624 36.096 35.593 1.017 0.998 0.000 1.221-1.150 99.97 13689 708 0.2348 22.743 21.273 0.977 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0595 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1471 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1471 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1471 | n_water=430 | time (s): 1.600 (total time: 1.600) Filter (dist) r_work=0.1200 r_free=0.1470 | n_water=428 | time (s): 36.660 (total time: 38.260) Filter (q & B) r_work=0.1200 r_free=0.1470 | n_water=428 | time (s): 1.110 (total time: 39.370) Compute maps r_work=0.1200 r_free=0.1470 | n_water=428 | time (s): 1.180 (total time: 40.550) Filter (map) r_work=0.1235 r_free=0.1463 | n_water=297 | time (s): 2.790 (total time: 43.340) Find peaks r_work=0.1235 r_free=0.1463 | n_water=297 | time (s): 0.660 (total time: 44.000) Add new water r_work=0.1359 r_free=0.1589 | n_water=493 | time (s): 3.350 (total time: 47.350) Refine new water occ: r_work=0.1260 r_free=0.1517 adp: r_work=0.1261 r_free=0.1516 occ: r_work=0.1239 r_free=0.1499 adp: r_work=0.1237 r_free=0.1495 occ: r_work=0.1226 r_free=0.1490 adp: r_work=0.1218 r_free=0.1483 ADP+occupancy (water only), MIN, final r_work=0.1218 r_free=0.1483 r_work=0.1218 r_free=0.1483 | n_water=493 | time (s): 202.020 (total time: 249.370) Filter (q & B) r_work=0.1221 r_free=0.1481 | n_water=454 | time (s): 2.950 (total time: 252.320) Filter (dist only) r_work=0.1221 r_free=0.1479 | n_water=453 | time (s): 38.560 (total time: 290.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.003713 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.704733 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1230 0.1442 0.0212 0.006 0.9 2.2 0.5 0.0 0 1.002 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 14.42 2.12 3.651 22.354 48.705 3.727 12.14 14.05 1.91 4.244 22.123 48.705 3.654 Individual atomic B min max mean iso aniso Overall: 9.30 110.93 21.86 2.36 217 1763 Protein: 9.30 110.93 17.29 2.36 0 1519 Water: 11.54 71.83 37.07 N/A 217 236 Other: 21.17 32.81 26.97 N/A 0 8 Chain A: 9.30 110.93 20.03 N/A 0 1763 Chain S: 16.07 64.08 36.73 N/A 217 0 Histogram: Values Number of atoms 9.30 - 19.47 1237 19.47 - 29.63 277 29.63 - 39.79 219 39.79 - 49.95 132 49.95 - 60.12 80 60.12 - 70.28 22 70.28 - 80.44 8 80.44 - 90.60 2 90.60 - 100.76 1 100.76 - 110.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1214 r_free=0.1406 r_work=0.1215 r_free=0.1407 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1215 r_free = 0.1407 target_work(ml) = 3.654 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1406 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1210 r_free= 0.1406 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.651749 | | target function (ml) not normalized (work): 304165.140363 | | target function (ml) not normalized (free): 16069.531332 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1210 0.1406 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1540 0.1538 0.1599 n_refl.: 87589 remove outliers: r(all,work,free)=0.1540 0.1538 0.1599 n_refl.: 87589 overall B=-0.02 to atoms: r(all,work,free)=0.1537 0.1535 0.1597 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1200 0.1377 n_refl.: 87589 remove outliers: r(all,work,free)=0.1207 0.1199 0.1377 n_refl.: 87585 ======================== 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 91.67 83 5 0.3983 296.318 261.234 0.471 1.001 0.304 11.894-9.307 98.04 96 4 0.2453 477.796 461.262 0.850 1.001 0.287 9.237-7.194 99.09 211 7 0.2333 385.233 386.038 0.952 1.002 0.180 7.162-5.571 100.00 427 22 0.1985 293.182 284.290 0.916 1.002 0.162 5.546-4.326 100.00 867 58 0.1086 402.466 398.609 0.952 1.002 0.157 4.315-3.360 100.00 1859 96 0.0921 382.748 380.197 0.995 1.002 0.153 3.356-2.611 100.00 3867 181 0.1161 251.446 249.452 0.999 1.002 0.062 2.608-2.026 99.99 8198 413 0.1052 166.685 165.784 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1014 81.401 81.560 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1293 36.096 35.682 1.022 0.999 0.000 1.221-1.150 99.97 13689 708 0.2133 22.743 21.374 0.981 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0475 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1377 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1377 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1377 | n_water=453 | time (s): 2.090 (total time: 2.090) Filter (dist) r_work=0.1198 r_free=0.1377 | n_water=452 | time (s): 37.700 (total time: 39.790) Filter (q & B) r_work=0.1198 r_free=0.1377 | n_water=452 | time (s): 1.070 (total time: 40.860) Compute maps r_work=0.1198 r_free=0.1377 | n_water=452 | time (s): 1.490 (total time: 42.350) Filter (map) r_work=0.1226 r_free=0.1387 | n_water=315 | time (s): 2.650 (total time: 45.000) Find peaks r_work=0.1226 r_free=0.1387 | n_water=315 | time (s): 0.540 (total time: 45.540) Add new water r_work=0.1293 r_free=0.1452 | n_water=480 | time (s): 2.610 (total time: 48.150) Refine new water occ: r_work=0.1220 r_free=0.1367 adp: r_work=0.1220 r_free=0.1370 occ: r_work=0.1205 r_free=0.1357 adp: r_work=0.1203 r_free=0.1357 occ: r_work=0.1194 r_free=0.1358 adp: r_work=0.1190 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1354 r_work=0.1190 r_free=0.1354 | n_water=480 | time (s): 202.580 (total time: 250.730) Filter (q & B) r_work=0.1195 r_free=0.1354 | n_water=450 | time (s): 3.520 (total time: 254.250) Filter (dist only) r_work=0.1195 r_free=0.1353 | n_water=449 | time (s): 35.950 (total time: 290.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.008722 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.379678 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1361 0.0163 0.006 1.0 2.6 0.5 0.0 0 1.004 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.61 1.63 3.454 21.606 43.380 3.636 11.86 13.52 1.66 3.699 21.529 43.380 3.624 Individual atomic B min max mean iso aniso Overall: 9.23 106.26 21.43 2.19 215 1761 Protein: 9.23 106.26 17.11 2.19 0 1519 Water: 11.54 71.13 35.96 N/A 215 234 Other: 20.65 30.34 25.84 N/A 0 8 Chain A: 9.23 106.26 19.77 N/A 0 1761 Chain S: 15.56 59.43 34.99 N/A 215 0 Histogram: Values Number of atoms 9.23 - 18.93 1226 18.93 - 28.64 284 28.64 - 38.34 220 38.34 - 48.04 127 48.04 - 57.74 81 57.74 - 67.45 24 67.45 - 77.15 9 77.15 - 86.85 2 86.85 - 96.55 1 96.55 - 106.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.1186 r_free=0.1352 r_work=0.1186 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1186 r_free = 0.1352 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1183 r_free = 0.1352 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1183 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.622806 | | target function (ml) not normalized (work): 301739.923650 | | target function (ml) not normalized (free): 15937.411024 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1183 0.1352 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1501 0.1501 0.1543 n_refl.: 87585 remove outliers: r(all,work,free)=0.1501 0.1501 0.1543 n_refl.: 87585 overall B=-0.02 to atoms: r(all,work,free)=0.1498 0.1498 0.1541 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1182 0.1352 n_refl.: 87585 remove outliers: r(all,work,free)=0.1188 0.1180 0.1352 n_refl.: 87578 ======================== 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 88.54 80 5 0.4056 288.873 258.168 0.456 1.000 0.299 11.894-9.307 97.06 95 4 0.2338 481.653 465.400 0.843 1.002 0.277 9.237-7.194 97.73 208 7 0.2445 383.315 378.255 0.919 1.002 0.150 7.162-5.571 100.00 427 22 0.2142 293.182 283.429 0.905 1.002 0.133 5.546-4.326 100.00 867 58 0.1122 402.466 398.314 0.951 1.002 0.130 4.315-3.360 100.00 1859 96 0.0942 382.748 380.187 0.994 1.002 0.130 3.356-2.611 100.00 3867 181 0.1156 251.446 249.564 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1020 166.685 165.799 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0971 81.401 81.657 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.096 35.715 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2124 22.743 21.372 0.982 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0458 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1180 r_free=0.1352 After: r_work=0.1180 r_free=0.1352 ================================== NQH flips ================================== r_work=0.1180 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1180 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1180 r_free=0.1352 | n_water=449 | time (s): 1.760 (total time: 1.760) Filter (dist) r_work=0.1180 r_free=0.1352 | n_water=449 | time (s): 33.620 (total time: 35.380) Filter (q & B) r_work=0.1181 r_free=0.1353 | n_water=445 | time (s): 2.610 (total time: 37.990) Compute maps r_work=0.1181 r_free=0.1353 | n_water=445 | time (s): 1.570 (total time: 39.560) Filter (map) r_work=0.1208 r_free=0.1373 | n_water=327 | time (s): 3.370 (total time: 42.930) Find peaks r_work=0.1208 r_free=0.1373 | n_water=327 | time (s): 0.670 (total time: 43.600) Add new water r_work=0.1264 r_free=0.1423 | n_water=498 | time (s): 2.840 (total time: 46.440) Refine new water occ: r_work=0.1193 r_free=0.1351 adp: r_work=0.1194 r_free=0.1353 occ: r_work=0.1181 r_free=0.1343 adp: r_work=0.1179 r_free=0.1344 occ: r_work=0.1171 r_free=0.1341 adp: r_work=0.1168 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1168 r_free=0.1339 r_work=0.1168 r_free=0.1339 | n_water=498 | time (s): 148.010 (total time: 194.450) Filter (q & B) r_work=0.1176 r_free=0.1347 | n_water=459 | time (s): 2.600 (total time: 197.050) Filter (dist only) r_work=0.1176 r_free=0.1346 | n_water=458 | time (s): 37.370 (total time: 234.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.946363 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.422177 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1211 0.1378 0.0167 0.007 1.1 2.6 0.5 0.0 0 0.973 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 13.78 1.67 3.344 21.386 48.422 3.636 12.12 13.81 1.69 3.752 21.266 48.422 3.627 Individual atomic B min max mean iso aniso Overall: 9.23 101.24 21.17 2.06 226 1759 Protein: 9.23 101.24 16.79 2.06 0 1519 Water: 11.50 69.89 35.64 N/A 226 232 Other: 20.41 28.46 24.78 N/A 0 8 Chain A: 9.23 101.24 19.41 N/A 0 1759 Chain S: 14.36 59.15 34.89 N/A 226 0 Histogram: Values Number of atoms 9.23 - 18.43 1213 18.43 - 27.64 292 27.64 - 36.84 215 36.84 - 46.04 141 46.04 - 55.24 78 55.24 - 64.44 29 64.44 - 73.64 12 73.64 - 82.84 2 82.84 - 92.04 1 92.04 - 101.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.1212 r_free=0.1381 r_work=0.1212 r_free=0.1381 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1212 r_free = 0.1381 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1376 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1208 r_free= 0.1376 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.625088 | | target function (ml) not normalized (work): 301904.551296 | | target function (ml) not normalized (free): 15964.830098 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1454 0.1441 5.7174 5.6735| | 2: 3.57 - 2.84 1.00 2888 124 0.1134 0.1428 5.2145 5.2658| | 3: 2.83 - 2.48 1.00 2820 163 0.1243 0.1243 5.0216 5.0192| | 4: 2.47 - 2.25 1.00 2825 136 0.1033 0.1183 4.7216 4.7776| | 5: 2.25 - 2.09 1.00 2756 127 0.0998 0.1168 4.6612 4.7358| | 6: 2.09 - 1.97 1.00 2846 113 0.0985 0.1155 4.366 4.487| | 7: 1.97 - 1.87 1.00 2787 165 0.0989 0.1264 4.0792 4.2215| | 8: 1.87 - 1.79 1.00 2789 144 0.1027 0.1235 4.0008 4.0776| | 9: 1.79 - 1.72 1.00 2745 138 0.0946 0.1337 3.7192 3.9276| | 10: 1.72 - 1.66 1.00 2831 160 0.1008 0.1310 3.6425 3.8046| | 11: 1.66 - 1.61 1.00 2712 147 0.0963 0.1064 3.5738 3.6036| | 12: 1.61 - 1.56 1.00 2773 144 0.0915 0.1149 3.3452 3.4775| | 13: 1.56 - 1.52 1.00 2745 130 0.0978 0.1070 3.3359 3.4317| | 14: 1.52 - 1.48 1.00 2803 134 0.0988 0.1144 3.2584 3.3536| | 15: 1.48 - 1.45 1.00 2738 128 0.1016 0.1291 3.1659 3.3089| | 16: 1.45 - 1.42 1.00 2756 161 0.1067 0.1226 3.1468 3.2344| | 17: 1.42 - 1.39 1.00 2785 139 0.1120 0.1315 3.1143 3.2365| | 18: 1.39 - 1.36 1.00 2741 179 0.1147 0.1398 3.0831 3.2736| | 19: 1.36 - 1.34 1.00 2807 134 0.1219 0.1643 3.0942 3.2766| | 20: 1.34 - 1.32 1.00 2696 147 0.1325 0.1485 3.0884 3.1433| | 21: 1.32 - 1.30 1.00 2785 112 0.1414 0.1586 3.0862 3.1458| | 22: 1.29 - 1.27 1.00 2704 152 0.1482 0.1914 3.0842 3.2818| | 23: 1.27 - 1.26 1.00 2802 156 0.1571 0.1869 3.1012 3.2067| | 24: 1.26 - 1.24 1.00 2744 132 0.1626 0.1762 3.0926 3.1876| | 25: 1.24 - 1.22 1.00 2733 148 0.1793 0.2312 3.1068 3.2912| | 26: 1.22 - 1.21 1.00 2727 135 0.1859 0.1801 3.1191 3.2075| | 27: 1.21 - 1.19 1.00 2814 148 0.2013 0.2111 3.1382 3.1559| | 28: 1.19 - 1.18 1.00 2671 147 0.2147 0.2321 3.138 3.1682| | 29: 1.18 - 1.16 1.00 2800 134 0.2219 0.2356 3.1247 3.2145| | 30: 1.16 - 1.15 1.00 2739 148 0.2380 0.2460 3.113 3.1611| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.58 2920 171 0.94 9.35 1.00 0.97 6525.08| | 2: 3.57 - 2.84 2888 124 0.92 13.68 1.01 0.97 6525.08| | 3: 2.83 - 2.48 2820 163 0.88 17.84 0.99 0.97 5468.93| | 4: 2.47 - 2.25 2825 136 0.91 14.96 1.00 0.98 2745.46| | 5: 2.25 - 2.09 2756 127 0.89 17.23 1.01 0.98 2745.46| | 6: 2.09 - 1.97 2846 113 0.91 13.91 1.02 0.97 1610.73| | 7: 1.97 - 1.87 2787 165 0.94 11.06 1.02 0.97 642.97| | 8: 1.87 - 1.79 2789 144 0.91 14.67 1.00 0.97 642.97| | 9: 1.79 - 1.72 2745 138 0.93 11.64 0.98 0.97 347.69| | 10: 1.72 - 1.66 2831 160 0.93 12.49 0.98 0.97 288.56| | 11: 1.66 - 1.61 2712 147 0.92 13.15 0.98 0.97 275.04| | 12: 1.61 - 1.56 2773 144 0.95 9.56 0.99 0.97 147.60| | 13: 1.56 - 1.52 2745 130 0.94 11.16 1.02 0.97 147.60| | 14: 1.52 - 1.48 2803 134 0.94 11.31 1.02 0.97 131.87| | 15: 1.48 - 1.45 2738 128 0.95 10.44 1.01 0.98 103.07| | 16: 1.45 - 1.42 2756 161 0.94 11.62 1.02 0.98 103.07| | 17: 1.42 - 1.39 2785 139 0.94 11.49 1.01 0.98 93.22| | 18: 1.39 - 1.36 2741 179 0.94 11.79 1.01 0.98 87.51| | 19: 1.36 - 1.34 2807 134 0.94 12.32 1.00 0.98 87.51| | 20: 1.34 - 1.32 2696 147 0.94 12.52 0.99 0.96 82.59| | 21: 1.32 - 1.30 2785 112 0.93 13.43 0.99 0.96 82.25| | 22: 1.29 - 1.27 2704 152 0.93 13.99 0.98 0.96 82.37| | 23: 1.27 - 1.26 2802 156 0.92 14.89 0.98 0.95 83.00| | 24: 1.26 - 1.24 2744 132 0.92 15.04 0.97 0.95 83.00| | 25: 1.24 - 1.22 2733 148 0.91 16.38 0.96 0.94 84.42| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.02 0.93 86.00| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.00| | 28: 1.19 - 1.18 2671 147 0.88 20.23 1.01 0.93 89.04| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.99 0.92 90.19| | 30: 1.16 - 1.15 2739 148 0.86 21.93 0.98 0.92 90.19| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.25 max = 6525.08 mean = 1013.47| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.17| |phase err.(test): min = 0.00 max = 89.15 mean = 14.27| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1208 0.1376 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1519 0.1518 0.1565 n_refl.: 87578 remove outliers: r(all,work,free)=0.1519 0.1518 0.1565 n_refl.: 87578 overall B=-0.01 to atoms: r(all,work,free)=0.1516 0.1515 0.1563 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1208 0.1377 n_refl.: 87578 remove outliers: r(all,work,free)=0.1214 0.1206 0.1377 n_refl.: 87574 ======================== 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 87.50 79 5 0.4016 285.424 252.149 0.430 1.000 0.294 11.894-9.307 95.10 93 4 0.2532 474.975 455.479 0.840 1.002 0.231 9.237-7.194 97.27 207 7 0.2605 382.843 375.596 0.903 1.002 0.155 7.162-5.571 100.00 427 22 0.2285 293.182 282.010 0.899 1.002 0.136 5.546-4.326 100.00 867 58 0.1212 402.466 397.911 0.951 1.002 0.111 4.315-3.360 100.00 1859 96 0.1003 382.748 379.931 0.994 1.002 0.108 3.356-2.611 100.00 3867 181 0.1208 251.446 249.452 1.000 1.002 0.048 2.608-2.026 99.99 8198 413 0.1048 166.685 165.747 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0978 81.401 81.643 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1227 36.096 35.724 1.024 0.996 0.000 1.221-1.150 99.97 13689 708 0.2117 22.743 21.376 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0393 ================= 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 : 0.2604 0.1939 0.084 5.376 8.8 119.3 19.9 258 0.000 1_bss: 0.1644 0.1762 0.084 5.376 9.1 119.5 20.1 258 0.000 1_settarget: 0.1644 0.1762 0.084 5.376 9.1 119.5 20.1 258 0.000 1_nqh: 0.1647 0.1764 0.084 5.376 9.1 119.5 20.1 258 0.003 1_weight: 0.1647 0.1764 0.084 5.376 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1210 0.1465 0.007 0.934 9.1 119.5 20.1 258 0.128 1_adp: 0.1247 0.1550 0.007 0.934 8.6 119.1 21.2 258 0.128 1_regHadp: 0.1251 0.1555 0.007 0.934 8.6 119.1 21.2 258 0.128 1_occ: 0.1249 0.1555 0.007 0.934 8.6 119.1 21.2 258 0.128 2_bss: 0.1247 0.1547 0.007 0.934 8.7 119.2 21.3 258 0.128 2_settarget: 0.1247 0.1547 0.007 0.934 8.7 119.2 21.3 258 0.128 2_updatecdl: 0.1247 0.1547 0.007 0.946 8.7 119.2 21.3 258 0.128 2_nqh: 0.1248 0.1548 0.007 0.946 8.7 119.2 21.3 258 0.131 2_sol: 0.1237 0.1494 0.007 0.946 8.7 119.2 23.6 430 n/a 2_weight: 0.1237 0.1494 0.007 0.946 8.7 119.2 23.6 430 n/a 2_xyzrec: 0.1233 0.1513 0.007 0.866 8.7 119.2 23.6 430 n/a 2_adp: 0.1203 0.1478 0.007 0.866 9.0 115.9 23.3 430 n/a 2_regHadp: 0.1203 0.1477 0.007 0.866 9.0 115.9 23.3 430 n/a 2_occ: 0.1203 0.1473 0.007 0.866 9.0 115.9 23.3 430 n/a 3_bss: 0.1199 0.1471 0.007 0.866 9.1 115.9 23.3 430 n/a 3_settarget: 0.1199 0.1471 0.007 0.866 9.1 115.9 23.3 430 n/a 3_updatecdl: 0.1199 0.1471 0.007 0.866 9.1 115.9 23.3 430 n/a 3_nqh: 0.1199 0.1471 0.007 0.866 9.1 115.9 23.3 430 n/a 3_sol: 0.1221 0.1479 0.007 0.866 9.1 115.9 22.3 453 n/a 3_weight: 0.1221 0.1479 0.007 0.866 9.1 115.9 22.3 453 n/a 3_xyzrec: 0.1230 0.1442 0.006 0.912 9.1 115.9 22.3 453 n/a 3_adp: 0.1214 0.1406 0.006 0.912 9.3 110.9 21.9 453 n/a 3_regHadp: 0.1215 0.1407 0.006 0.912 9.3 110.9 21.9 453 n/a 3_occ: 0.1210 0.1406 0.006 0.912 9.3 110.9 21.9 453 n/a 4_bss: 0.1199 0.1377 0.006 0.912 9.3 110.9 21.8 453 n/a 4_settarget: 0.1199 0.1377 0.006 0.912 9.3 110.9 21.8 453 n/a 4_updatecdl: 0.1199 0.1377 0.006 0.911 9.3 110.9 21.8 453 n/a 4_nqh: 0.1199 0.1377 0.006 0.911 9.3 110.9 21.8 453 n/a 4_sol: 0.1195 0.1353 0.006 0.911 9.3 110.9 21.6 449 n/a 4_weight: 0.1195 0.1353 0.006 0.911 9.3 110.9 21.6 449 n/a 4_xyzrec: 0.1198 0.1361 0.006 0.950 9.3 110.9 21.6 449 n/a 4_adp: 0.1186 0.1352 0.006 0.950 9.2 106.3 21.4 449 n/a 4_regHadp: 0.1186 0.1352 0.006 0.950 9.2 106.3 21.4 449 n/a 4_occ: 0.1183 0.1352 0.006 0.950 9.2 106.3 21.4 449 n/a 5_bss: 0.1180 0.1352 0.006 0.950 9.2 106.2 21.4 449 n/a 5_settarget: 0.1180 0.1352 0.006 0.950 9.2 106.2 21.4 449 n/a 5_updatecdl: 0.1180 0.1352 0.006 0.952 9.2 106.2 21.4 449 n/a 5_setrh: 0.1180 0.1352 0.006 0.952 9.2 106.2 21.4 449 n/a 5_nqh: 0.1180 0.1352 0.006 0.952 9.2 106.2 21.4 449 n/a 5_sol: 0.1176 0.1346 0.006 0.952 9.2 106.2 21.4 458 n/a 5_weight: 0.1176 0.1346 0.006 0.952 9.2 106.2 21.4 458 n/a 5_xyzrec: 0.1211 0.1378 0.007 1.074 9.2 106.2 21.4 458 n/a 5_adp: 0.1212 0.1381 0.007 1.074 9.2 101.2 21.2 458 n/a 5_regHadp: 0.1212 0.1381 0.007 1.074 9.2 101.2 21.2 458 n/a 5_occ: 0.1208 0.1376 0.007 1.074 9.2 101.2 21.2 458 n/a end: 0.1206 0.1377 0.007 1.074 9.2 101.2 21.2 458 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_9255201_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_9255201_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8700 Refinement macro-cycles (run) : 3414.8200 Write final files (write_after_run_outputs) : 73.7600 Total : 3493.4500 Total CPU time: 58.82 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:47 PST -0800 (1735452587.32 s) Start R-work = 0.1644, R-free = 0.1762 Final R-work = 0.1206, R-free = 0.1377 =============================================================================== Job complete usr+sys time: 3648.27 seconds wall clock time: 65 minutes 19.82 seconds (3919.82 seconds total)