Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_1yab.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1yab/1yab.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 amber.topology_file_name=4amber_1yab.prmtop amber.coordinate_file_name=4amber_1yab.rst7 amber.order_file_name=4amber_1yab.order use_amber=True strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Processing files from PHIL: ------------------------------------------------------------------------------- Files not used by program: -------------------------- 4amber_1yab.order 4amber_1yab.prmtop 4amber_1yab.rst7 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "4phenix_1yab.pdb" } default_model = "4phenix_1yab.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1yab/1yab.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1yab/1yab.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 } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } amber { use_amber = True topology_file_name = 4amber_1yab.prmtop coordinate_file_name = 4amber_1yab.rst7 order_file_name = 4amber_1yab.order } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/bootstrap/modules/chem_data/mon_lib" Total number of atoms: 2831 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1401 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "B" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1430 Classifications: {'peptide': 87} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 82} Time building chain proxies: 0.37, per 1000 atoms: 0.13 Number of scatterers: 2831 At special positions: 0 Unit cell: (100.173, 100.173, 87.853, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 257 8.00 N 229 7.00 C 865 6.00 H 1476 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 - 3.50 Amino acid : False - 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: 0.52 Conformation dependent library (CDL) restraints added in 60.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 6 helices and 2 sheets defined 18.6% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 4.330A pdb=" N LEU A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 74' Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'B' and resid 72 through 75 No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 145 through 152 Processing sheet with id= A, first strand: chain 'A' and resid 81 through 84 removed outlier: 6.212A pdb=" N VAL A 118 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU A 127 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE A 139 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL A 129 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL A 137 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE A 131 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 81 through 84 removed outlier: 3.630A pdb=" N ASP B 115 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 118 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU B 127 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE B 139 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 129 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL B 137 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ILE B 131 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) 26 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.43 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 1476 1.15 - 1.32: 248 1.32 - 1.49: 442 1.49 - 1.66: 665 1.66 - 1.83: 8 Bond restraints: 2839 Sorted by residual: bond pdb=" NH1 ARG B 87 " pdb="HH12 ARG B 87 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N VAL A 114 " pdb=" H VAL A 114 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS A 100 " pdb=" H HIS A 100 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N LEU A 75 " pdb=" H LEU A 75 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N ASP A 132 " pdb=" H ASP A 132 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 2834 not shown) Histogram of bond angle deviations from ideal: 97.31 - 104.19: 58 104.19 - 111.06: 3255 111.06 - 117.94: 911 117.94 - 124.81: 927 124.81 - 131.69: 70 Bond angle restraints: 5221 Sorted by residual: angle pdb=" N LYS B 70 " pdb=" CA LYS B 70 " pdb=" C LYS B 70 " ideal model delta sigma weight residual 112.92 102.67 10.25 1.23e+00 6.61e-01 6.95e+01 angle pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N PHE B 135 " ideal model delta sigma weight residual 115.55 123.69 -8.14 1.33e+00 5.65e-01 3.75e+01 angle pdb=" C ASN B 134 " pdb=" N PHE B 135 " pdb=" CA PHE B 135 " ideal model delta sigma weight residual 121.54 131.60 -10.06 1.91e+00 2.74e-01 2.77e+01 angle pdb=" C VAL A 81 " pdb=" CA VAL A 81 " pdb=" CB VAL A 81 " ideal model delta sigma weight residual 110.91 104.61 6.30 1.24e+00 6.50e-01 2.58e+01 angle pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" C ASP B 132 " ideal model delta sigma weight residual 110.80 120.70 -9.90 2.13e+00 2.20e-01 2.16e+01 ... (remaining 5216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.86: 1128 25.86 - 51.72: 115 51.72 - 77.58: 21 77.58 - 103.44: 5 103.44 - 129.30: 1 Dihedral angle restraints: 1270 sinusoidal: 764 harmonic: 506 Sorted by residual: dihedral pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N PHE B 135 " pdb=" CA PHE B 135 " ideal model delta harmonic sigma weight residual 180.00 50.70 129.30 0 5.00e+00 4.00e-02 6.69e+02 dihedral pdb=" C ASP B 132 " pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " ideal model delta harmonic sigma weight residual -122.60 -139.66 17.06 0 2.50e+00 1.60e-01 4.66e+01 dihedral pdb=" N ASP B 132 " pdb=" C ASP B 132 " pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " ideal model delta harmonic sigma weight residual 122.80 139.34 -16.54 0 2.50e+00 1.60e-01 4.38e+01 ... (remaining 1267 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.134: 186 0.134 - 0.267: 45 0.267 - 0.401: 3 0.401 - 0.534: 2 0.534 - 0.667: 2 Chirality restraints: 238 Sorted by residual: chirality pdb=" CA PHE B 135 " pdb=" N PHE B 135 " pdb=" C PHE B 135 " pdb=" CB PHE B 135 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA ASP B 132 " pdb=" N ASP B 132 " pdb=" C ASP B 132 " pdb=" CB ASP B 132 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA ASP A 132 " pdb=" N ASP A 132 " pdb=" C ASP A 132 " pdb=" CB ASP A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 235 not shown) Planarity restraints: 394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 134 " -0.004 2.00e-02 2.50e+03 1.16e-02 2.03e+00 pdb=" CG ASN A 134 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 134 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 134 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 134 " -0.009 2.00e-02 2.50e+03 pdb="HD22 ASN A 134 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 135 " 0.003 2.00e-02 2.50e+03 6.76e-03 1.37e+00 pdb=" CG PHE B 135 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 135 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 135 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 135 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 135 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 135 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE B 135 " -0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE B 135 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 PHE B 135 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE B 135 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE B 135 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 134 " -0.003 2.00e-02 2.50e+03 9.20e-03 1.27e+00 pdb=" CG ASN B 134 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 134 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 134 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 134 " -0.007 2.00e-02 2.50e+03 pdb="HD22 ASN B 134 " 0.012 2.00e-02 2.50e+03 ... (remaining 391 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.84: 90 1.84 - 2.53: 2650 2.53 - 3.22: 8856 3.22 - 3.91: 12174 3.91 - 4.60: 18186 Nonbonded interactions: 41956 Sorted by model distance: nonbonded pdb=" HG3 ARG A 89 " pdb="HH11 ARG A 89 " model vdw 1.154 2.270 nonbonded pdb=" HG1 THR B 88 " pdb=" H ARG B 89 " model vdw 1.172 2.100 nonbonded pdb=" H ILE B 99 " pdb=" HG SER B 102 " model vdw 1.319 2.100 nonbonded pdb=" HA GLU A 147 " pdb=" HB2 GLU A 150 " model vdw 1.324 2.440 nonbonded pdb="HH22 ARG A 94 " pdb="HD12 ILE A 104 " model vdw 1.340 2.270 ... (remaining 41951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_1yab.prmtop atom order : 4amber_1yab.order coordinates : 4amber_1yab.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 4 15.91 1 O 257 7.97 1 N 229 6.97 1 C 865 5.97 1 H 1476 1.00 1 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 ===================== Setting occupancies to: 1.000: selected atoms: 1476 of 2831 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 2831 n_use_u_iso = 2831 n_use_u_aniso = 0 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 = 2831 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (2831 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 2831 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 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 } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 69 through 74 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 92 through 97 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 147 through 151 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'B' and resid 72 through 75 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'B' and resid 94 through 96 helix_type = alpha pi *3_10 unknown } helix { serial_number = "6" helix_identifier = "6" selection = chain 'B' and resid 145 through 152 } sheet { first_strand = chain 'A' and resid 81 through 84 sheet_id = " A" strand { selection = chain 'A' and resid 114 through 118 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 117 and name N bond_start_previous = chain 'A' and resid 82 and name O } strand { selection = chain 'A' and resid 121 through 131 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 126 and name N bond_start_previous = chain 'A' and resid 114 and name O } strand { selection = chain 'A' and resid 134 through 142 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 141 and name N bond_start_previous = chain 'A' and resid 125 and name O } } sheet { first_strand = chain 'B' and resid 81 through 84 sheet_id = " B" strand { selection = chain 'B' and resid 114 through 118 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 117 and name N bond_start_previous = chain 'B' and resid 82 and name O } strand { selection = chain 'B' and resid 121 through 131 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 126 and name N bond_start_previous = chain 'B' and resid 114 and name O } strand { selection = chain 'B' and resid 134 through 142 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 141 and name N bond_start_previous = chain 'B' and resid 125 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } amber { use_amber = True topology_file_name = "4amber_1yab.prmtop" coordinate_file_name = "4amber_1yab.rst7" order_file_name = "4amber_1yab.order" } } output { prefix = "4phenix_1yab_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== WARNING: failed to analyze molecule topology. Atomic model may be wrong. ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.40 - 19.90 A, n_refl.=7246 (all), 4.69 % free)-------------| | | | r_work= 0.4057 r_free= 0.4599 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 5.288894 | | target function (ml) not normalized (work): 36525.100130 | | target function (ml) not normalized (free): 1841.551287 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.90 - 4.27 1.00 3512 170 0.3816 0.4405 5.9301 6.0788| | 2: 4.27 - 3.40 1.00 3394 170 0.4722 0.5142 4.6254 4.7539| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.90 - 4.27 3512 170 0.47 53.91 0.97 0.49 32800.77| | 2: 4.27 - 3.40 3394 170 0.71 34.50 1.68 1.01 2338.72| |alpha: min = 0.49 max = 1.01 mean = 0.75| |beta: min = 2338.72 max = 32800.77 mean = 17829.99| |figures of merit: min = 0.00 max = 1.00 mean = 0.59| |phase err.(work): min = 0.00 max = 90.00 mean = 44.37| |phase err.(test): min = 0.00 max = 89.81 mean = 43.03| |-----------------------------------------------------------------------------| ----------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 : 0.014 0.080 1363 Z= 0.957 Angle : 1.971 12.009 1839 Z= 1.158 Chirality : 0.128 0.667 238 Planarity : 0.005 0.024 230 Dihedral : 23.170 129.301 543 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 8.33 % Allowed : 10.12 % Favored : 81.55 % Rotamer: Outliers : 24.68 % Allowed : 21.52 % Favored : 53.80 % Cbeta Deviations : 2.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.83 % 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: -4.61 (0.52), residues: 168 helix: -4.84 (0.42), residues: 40 sheet: -3.56 (1.49), residues: 10 loop : -2.51 (0.48), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 94 PHE 0.008 0.003 PHE B 135 HIS 0.002 0.001 HIS A 100 Individual atomic B min max mean iso aniso Overall: 93.69 154.06 112.45 1.19 1355 0 Protein: 93.69 154.06 112.45 1.19 1355 0 Chain A: 94.35 154.06 112.30 N/A 669 0 Chain B: 93.69 153.95 112.61 N/A 686 0 Histogram: Values Number of atoms 93.69 - 99.73 219 99.73 - 105.76 346 105.76 - 111.80 259 111.80 - 117.84 158 117.84 - 123.88 111 123.88 - 129.91 104 129.91 - 135.95 47 135.95 - 141.99 29 141.99 - 148.02 23 148.02 - 154.06 59 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7246 (all), 4.69 % free)-------------| | | | r_work= 0.4057 r_free= 0.4599 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 5.288894 | | target function (ml) not normalized (work): 36525.100130 | | target function (ml) not normalized (free): 1841.551287 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4086 0.4057 0.4599 n_refl.: 7246 re-set all scales: r(all,work,free)=0.4086 0.4057 0.4599 n_refl.: 7246 remove outliers: r(all,work,free)=0.4083 0.4054 0.4599 n_refl.: 7245 overall B=-8.11 to atoms: r(all,work,free)=0.3848 0.3818 0.4389 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2254 0.2223 0.2851 n_refl.: 7245 remove outliers: r(all,work,free)=0.2254 0.2223 0.2851 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1924 763.709 732.804 1.331 1.004 0.337 12.965-10.793 93.40 95 4 0.1550 722.010 703.475 1.331 1.002 0.330 10.793-8.919 99.47 176 10 0.1452 676.466 670.332 1.298 1.001 0.327 8.905-7.374 99.69 313 12 0.2058 409.687 396.539 1.159 0.998 0.310 7.364-6.089 99.82 547 20 0.2502 296.177 285.131 1.063 0.994 0.272 6.087-5.031 100.00 938 48 0.2291 234.337 224.148 0.964 0.987 0.214 5.030-4.158 99.88 1640 78 0.1967 247.723 238.431 0.980 0.978 0.144 4.156-3.397 99.85 3105 159 0.2873 111.401 103.468 1.047 0.963 0.058 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.5016 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.841553 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.183874 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.2501 0.2791 0.0290 0.013 2.3 0.7 1.8 19.6 2 0.125 0.2423 0.2793 0.0369 0.013 2.3 0.7 2.4 20.9 4 0.250 0.2318 0.2795 0.0477 0.014 2.3 0.4 2.4 21.5 3 0.500 0.2235 0.2796 0.0561 0.016 2.4 2.5 1.8 18.4 5 1.000 0.2152 0.2759 0.0607 0.021 2.8 4.2 1.8 21.5 4 2.000 0.2091 0.2787 0.0697 0.026 3.4 8.1 5.4 24.1 10 3.000 0.2072 0.2793 0.0722 0.029 3.5 10.6 3.0 27.2 8 4.000 0.2034 0.2740 0.0706 0.033 3.7 12.0 7.1 24.7 10 5.000 0.2020 0.2753 0.0732 0.036 3.7 13.5 6.5 25.3 10 6.000 0.2031 0.2774 0.0744 0.039 4.4 11.3 5.4 31.0 17 7.000 0.2012 0.2769 0.0757 0.041 4.6 12.7 5.4 31.0 19 8.000 0.1993 0.2747 0.0754 0.044 4.2 16.6 6.5 26.6 13 9.000 0.1976 0.2737 0.0761 0.046 4.4 18.1 7.1 26.6 13 10.000 0.2158 0.2762 0.0603 0.020 2.8 4.6 1.8 20.9 4 1.921 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1976 0.2737 0.0761 0.046 4.4 18.1 7.1 26.6 13 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.76 27.37 7.61 0.822 104.100 0.184 0.039 19.97 27.64 7.67 1.995 104.181 0.006 0.039 19.69 27.49 7.79 2.143 104.228 0.023 0.038 19.23 27.07 7.85 2.394 104.236 0.092 0.037 18.89 26.86 7.97 3.425 104.405 0.184 0.035 18.68 26.71 8.03 4.327 104.578 0.276 0.035 18.32 26.57 8.25 6.995 105.181 0.368 0.034 18.25 26.52 8.27 7.485 105.314 0.460 0.033 18.21 26.49 8.29 7.897 105.430 0.552 0.033 18.09 26.40 8.31 8.802 105.730 0.644 0.033 18.07 26.38 8.31 9.116 105.817 0.735 0.033 18.05 26.38 8.33 9.353 105.883 0.827 0.033 18.03 26.36 8.33 9.570 105.946 0.919 0.033 max suggested for this run: 20.82 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 19.97 27.64 7.67 1.995 104.181 0.006 0.039 Individual atomic B min max mean iso aniso Overall: 87.92 145.39 104.51 1.39 1355 0 Protein: 87.92 145.39 104.51 1.39 1355 0 Chain A: 87.94 145.39 104.45 N/A 669 0 Chain B: 87.92 144.93 104.58 N/A 686 0 Histogram: Values Number of atoms 87.92 - 93.67 256 93.67 - 99.42 366 99.42 - 105.16 254 105.16 - 110.91 142 110.91 - 116.65 113 116.65 - 122.40 93 122.40 - 128.15 28 128.15 - 133.89 21 133.89 - 139.64 30 139.64 - 145.39 52 =========================== Idealize ADP of riding H ========================== r_work=0.1997 r_free=0.2764 r_work=0.2013 r_free=0.2780 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.2013 r_free= 0.2780 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ls_wunit_k1) (work): 0.039860 | | target function (ls_wunit_k1) not normalized (work): 275.234453 | | target function (ls_wunit_k1) not normalized (free): 29.848826 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2051 0.2013 0.2780 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3737 0.3708 0.4282 n_refl.: 7245 remove outliers: r(all,work,free)=0.3737 0.3708 0.4282 n_refl.: 7245 overall B=0.00 to atoms: r(all,work,free)=0.3737 0.3708 0.4282 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2024 0.1986 0.2770 n_refl.: 7245 remove outliers: r(all,work,free)=0.2024 0.1986 0.2770 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1776 483.743 465.378 1.479 1.005 0.340 12.965-10.793 95.19 95 4 0.1116 457.331 452.466 1.445 1.003 0.335 10.793-8.919 99.47 176 10 0.1223 428.482 427.301 1.377 1.003 0.331 8.905-7.374 99.69 313 12 0.1576 259.501 255.461 1.190 1.000 0.300 7.364-6.089 99.82 547 20 0.2060 187.603 184.718 1.066 0.997 0.250 6.087-5.031 100.00 938 48 0.2046 148.432 144.388 0.978 0.992 0.200 5.030-4.158 99.88 1640 78 0.1761 156.911 152.628 1.000 0.984 0.130 4.156-3.397 99.85 3105 159 0.2808 70.563 65.876 1.051 0.973 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.8797 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.133335 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.045923 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.2454 0.2741 0.0287 0.013 2.3 1.4 1.8 18.4 3 0.057 0.2261 0.2795 0.0534 0.016 2.5 1.8 1.8 20.3 4 0.170 0.2184 0.2816 0.0632 0.021 3.0 4.6 2.4 25.3 6 0.340 0.2142 0.2803 0.0661 0.026 3.4 7.4 3.0 28.5 10 0.510 0.2098 0.2761 0.0663 0.030 3.8 11.3 7.1 29.7 9 0.680 0.2077 0.2774 0.0696 0.034 4.2 13.8 8.3 29.7 11 0.850 0.2054 0.2794 0.0740 0.038 4.6 14.9 7.7 31.6 16 1.020 0.2031 0.2789 0.0758 0.042 4.8 17.3 6.5 33.5 18 1.190 0.2123 0.2796 0.0673 0.027 3.5 8.1 3.0 29.7 10 0.567 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2454 0.2741 0.0287 0.013 2.3 1.4 1.8 18.4 3 0.057 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.54 27.41 2.87 15.207 115.345 0.046 5.055 25.18 28.74 3.56 13.358 117.246 0.001 5.071 23.51 26.99 3.48 13.806 116.746 0.006 5.016 21.70 25.66 3.96 14.030 118.566 0.023 4.948 21.31 25.87 4.56 15.142 118.717 0.046 4.936 21.07 25.85 4.78 16.308 119.440 0.069 4.926 20.94 25.86 4.92 17.400 119.974 0.092 4.921 21.01 25.60 4.59 16.633 119.275 0.115 4.921 21.08 25.69 4.61 16.415 118.991 0.138 4.924 21.02 25.67 4.65 16.778 119.210 0.161 4.922 20.98 25.67 4.69 17.043 119.345 0.184 4.920 20.93 25.65 4.72 17.468 119.586 0.207 4.918 20.91 25.65 4.73 17.687 119.691 0.230 4.917 max suggested for this run: 23.07 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.115 Accepted refinement result: 21.01 25.60 4.59 16.633 119.275 0.115 4.921 Individual atomic B min max mean iso aniso Overall: 82.92 180.76 112.72 12.89 1355 0 Protein: 82.92 180.76 112.72 12.89 1355 0 Chain A: 82.94 177.96 113.32 N/A 669 0 Chain B: 82.92 180.76 112.14 N/A 686 0 Histogram: Values Number of atoms 82.92 - 92.71 302 92.71 - 102.49 250 102.49 - 112.28 208 112.28 - 122.06 182 122.06 - 131.84 135 131.84 - 141.63 110 141.63 - 151.41 83 151.41 - 161.20 51 161.20 - 170.98 26 170.98 - 180.76 8 =========================== Idealize ADP of riding H ========================== r_work=0.2101 r_free=0.2560 r_work=0.2091 r_free=0.2575 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.2091 r_free= 0.2575 coordinate error (max.-lik. estimate): 0.15 A | | | | normalized target function (ml) (work): 4.918593 | | target function (ml) not normalized (work): 33962.887102 | | target function (ml) not normalized (free): 1732.616899 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2115 0.2091 0.2575 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3909 0.3881 0.4416 n_refl.: 7245 remove outliers: r(all,work,free)=0.3909 0.3881 0.4416 n_refl.: 7245 overall B=-1.50 to atoms: r(all,work,free)=0.3862 0.3834 0.4372 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2094 0.2068 0.2598 n_refl.: 7245 remove outliers: r(all,work,free)=0.2094 0.2068 0.2598 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1703 483.743 483.454 1.537 0.983 0.349 12.965-10.793 95.19 95 4 0.1162 457.331 440.283 1.409 0.983 0.341 10.793-8.919 99.47 176 10 0.1333 428.482 427.336 1.316 0.984 0.311 8.905-7.374 99.69 313 12 0.1933 259.501 248.765 1.132 0.985 0.292 7.364-6.089 99.82 547 20 0.2294 187.603 179.146 1.032 0.986 0.242 6.087-5.031 100.00 938 48 0.2279 148.432 140.904 0.943 0.988 0.182 5.030-4.158 99.88 1640 78 0.1896 156.911 150.491 0.969 0.992 0.112 4.156-3.397 99.85 3105 159 0.2593 70.563 65.961 1.034 0.997 0.041 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=0.8036 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.023177 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.040496 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.2166 0.2586 0.0420 0.013 2.2 1.4 1.8 13.9 3 0.051 0.2053 0.2587 0.0534 0.014 2.3 1.4 1.8 18.4 3 0.153 0.2059 0.2591 0.0532 0.014 2.3 1.4 1.8 18.4 3 0.307 0.2054 0.2587 0.0534 0.014 2.3 1.4 1.8 18.4 3 0.460 0.2033 0.2588 0.0555 0.015 2.3 1.4 1.8 18.4 3 0.614 0.2025 0.2589 0.0564 0.016 2.4 1.4 1.8 18.4 3 0.767 0.2017 0.2591 0.0574 0.017 2.4 1.1 1.8 18.4 3 0.921 0.2009 0.2589 0.0580 0.018 2.4 1.1 1.8 18.4 3 1.074 0.2052 0.2588 0.0536 0.014 2.3 1.4 1.8 18.4 3 0.512 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2166 0.2586 0.0420 0.013 2.2 1.4 1.8 13.9 3 0.051 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.66 25.86 4.20 18.698 122.614 0.040 4.936 26.54 30.45 3.91 13.362 131.340 0.001 5.053 24.77 28.88 4.11 13.034 130.171 0.005 5.015 21.77 25.79 4.03 15.303 125.833 0.020 4.937 20.94 25.26 4.32 16.392 125.187 0.040 4.909 20.61 25.08 4.47 16.875 125.256 0.061 4.894 20.49 25.10 4.61 17.337 125.107 0.081 4.890 20.37 25.07 4.70 17.692 125.407 0.101 4.886 20.28 25.05 4.76 18.090 125.746 0.121 4.882 20.22 25.04 4.82 18.481 126.038 0.142 4.879 20.19 25.04 4.86 18.848 126.287 0.162 4.877 20.16 25.03 4.87 19.189 126.496 0.182 4.875 20.14 25.02 4.88 19.505 126.672 0.202 4.874 max suggested for this run: 24.52 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.202 Accepted refinement result: 20.14 25.02 4.88 19.505 126.672 0.202 4.874 Individual atomic B min max mean iso aniso Overall: 76.42 218.42 119.70 20.84 1355 0 Protein: 76.42 218.42 119.70 20.84 1355 0 Chain A: 77.24 216.33 121.07 N/A 669 0 Chain B: 76.42 218.42 118.37 N/A 686 0 Histogram: Values Number of atoms 76.42 - 90.62 255 90.62 - 104.82 232 104.82 - 119.02 274 119.02 - 133.22 184 133.22 - 147.42 146 147.42 - 161.62 120 161.62 - 175.82 72 175.82 - 190.02 50 190.02 - 204.22 17 204.22 - 218.42 5 =========================== Idealize ADP of riding H ========================== r_work=0.2014 r_free=0.2502 r_work=0.2009 r_free=0.2508 ----------X-ray data---------- |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.2009 r_free= 0.2508 coordinate error (max.-lik. estimate): 0.18 A | | | | normalized target function (ml) (work): 4.871926 | | target function (ml) not normalized (work): 33640.650459 | | target function (ml) not normalized (free): 1714.937209 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.90 - 4.27 0.99 3511 170 0.1903 0.2386 5.3055 5.5078| | 2: 4.27 - 3.40 1.00 3394 170 0.2299 0.2848 4.4234 4.58| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.90 - 4.27 3511 170 0.80 25.87 1.00 0.99 8059.29| | 2: 4.27 - 3.40 3394 170 0.79 27.41 1.03 1.04 1486.07| |alpha: min = 0.99 max = 1.04 mean = 1.02| |beta: min = 1486.07 max = 8059.29 mean = 4828.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.79| |phase err.(work): min = 0.00 max = 89.93 mean = 26.63| |phase err.(test): min = 0.00 max = 89.07 mean = 27.21| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2033 0.2009 0.2508 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3972 0.3945 0.4487 n_refl.: 7245 remove outliers: r(all,work,free)=0.3972 0.3945 0.4487 n_refl.: 7245 overall B=-5.98 to atoms: r(all,work,free)=0.3781 0.3754 0.4306 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2010 0.1989 0.2425 n_refl.: 7245 remove outliers: r(all,work,free)=0.2010 0.1989 0.2425 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1605 483.743 467.386 1.606 1.004 0.362 12.965-10.793 95.19 95 4 0.1138 457.331 453.099 1.416 1.003 0.334 10.793-8.919 99.47 176 10 0.1303 428.482 429.332 1.331 1.003 0.325 8.905-7.374 99.69 313 12 0.1906 259.501 251.732 1.135 1.002 0.276 7.364-6.089 99.82 547 20 0.2253 187.603 182.363 1.049 1.000 0.238 6.087-5.031 100.00 938 48 0.2298 148.432 141.407 0.946 0.997 0.179 5.030-4.158 99.88 1640 78 0.1814 156.911 150.680 0.975 0.993 0.108 4.156-3.397 99.85 3105 159 0.2393 70.563 65.704 1.046 0.987 0.033 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.7031 ================= 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) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.4057 0.4599 0.014 1.971 93.7 154.1 112.5 0 0.000 1_bss: 0.2223 0.2851 0.014 1.971 85.6 146.0 104.3 0 0.000 1_settarget: 0.2223 0.2851 0.014 1.971 85.6 146.0 104.3 0 0.000 1_weight: 0.2223 0.2851 0.014 1.971 85.6 146.0 104.3 0 0.000 1_xyzrec: 0.1976 0.2737 0.046 4.430 85.6 146.0 104.3 0 0.172 1_adp: 0.1997 0.2764 0.046 4.430 87.9 145.4 104.5 0 0.172 1_regHadp: 0.2013 0.2780 0.046 4.430 87.9 145.4 104.5 0 0.172 2_bss: 0.1986 0.2770 0.046 4.430 87.9 145.4 104.5 0 0.172 2_settarget: 0.1986 0.2770 0.046 4.430 87.9 145.4 104.5 0 0.172 2_updatecdl: 0.1986 0.2770 0.046 4.436 87.9 145.4 104.5 0 0.172 2_weight: 0.1986 0.2770 0.046 4.436 87.9 145.4 104.5 0 0.172 2_xyzrec: 0.2454 0.2741 0.013 2.330 87.9 145.4 104.5 0 0.331 2_adp: 0.2101 0.2560 0.013 2.330 82.9 180.8 112.7 0 0.331 2_regHadp: 0.2091 0.2575 0.013 2.330 82.9 180.8 112.7 0 0.331 3_bss: 0.2068 0.2598 0.013 2.330 81.4 179.3 111.2 0 0.331 3_settarget: 0.2068 0.2598 0.013 2.330 81.4 179.3 111.2 0 0.331 3_updatecdl: 0.2068 0.2598 0.013 2.327 81.4 179.3 111.2 0 0.331 3_setrh: 0.2068 0.2598 0.013 2.327 81.4 179.3 111.2 0 0.331 3_weight: 0.2068 0.2598 0.013 2.327 81.4 179.3 111.2 0 0.331 3_xyzrec: 0.2166 0.2586 0.013 2.249 81.4 179.3 111.2 0 0.548 3_adp: 0.2014 0.2502 0.013 2.249 76.4 218.4 119.7 0 0.548 3_regHadp: 0.2009 0.2508 0.013 2.249 76.4 218.4 119.7 0 0.548 end: 0.1989 0.2425 0.013 2.249 70.4 212.4 113.7 0 0.548 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1yab_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1yab_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 1.5700 Refinement macro-cycles (run) : 123.2700 Write final files (write_after_run_outputs) : 7.6400 Total : 132.4800 Total CPU time: 2.52 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:37:02 PDT -0700 (1723221422.88 s) Start R-work = 0.2223, R-free = 0.2851 Final R-work = 0.1989, R-free = 0.2425 =============================================================================== Job complete usr+sys time: 157.93 seconds wall clock time: 5 minutes 32.61 seconds (332.61 seconds total)