Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_1u9o.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u9o/1u9o.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_1u9o.prmtop amber.coordinate_file_name=4amber_1u9o.rst7 amber.order_file_name=4amber_1u9o.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_1u9o.rst7 4amber_1u9o.order 4amber_1u9o.prmtop Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "4phenix_1u9o.pdb" } default_model = "4phenix_1u9o.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u9o/1u9o.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u9o/1u9o.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_1u9o.prmtop coordinate_file_name = 4amber_1u9o.rst7 order_file_name = 4amber_1u9o.order } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B GLU 180": "OE1" <-> "OE2" 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: 5976 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain: "B" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Time building chain proxies: 0.79, per 1000 atoms: 0.13 Number of scatterers: 5976 At special positions: 0 Unit cell: (140.5, 140.5, 76.69, 90, 90, 120) Space group: R 3 :H (No. 146) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 586 8.00 N 520 7.00 C 1908 6.00 H 2954 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: 1.09 Conformation dependent library (CDL) restraints added in 183.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 0 sheets defined 71.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 removed outlier: 3.669A pdb=" N LEU A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.704A pdb=" N TYR A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 90 removed outlier: 4.046A pdb=" N LEU A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.952A pdb=" N GLY A 106 " --> pdb=" O MET A 102 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.545A pdb=" N ALA A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.679A pdb=" N LYS A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 187 removed outlier: 3.650A pdb=" N ARG A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'B' and resid 24 through 35 removed outlier: 3.595A pdb=" N ALA B 31 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.658A pdb=" N ALA B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY B 53 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 63 Processing helix chain 'B' and resid 68 through 92 removed outlier: 3.559A pdb=" N THR B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 114 removed outlier: 3.545A pdb=" N TRP B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.719A pdb=" N ALA B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 154 removed outlier: 3.752A pdb=" N PHE B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 187 removed outlier: 3.582A pdb=" N PHE B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.667A pdb=" N ILE B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) 176 hydrogen bonds defined for protein. 501 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: 0.96 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 2954 1.16 - 1.33: 936 1.33 - 1.51: 1031 1.51 - 1.69: 1101 1.69 - 1.86: 16 Bond restraints: 6038 Sorted by residual: bond pdb=" N ALA A 95 " pdb=" H ALA A 95 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH2 ARG B 78 " pdb="HH22 ARG B 78 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLN A 191 " pdb=" H GLN A 191 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLU A 180 " pdb=" H GLU A 180 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ARG B 181 " pdb=" H ARG B 181 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6033 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.85: 324 106.85 - 113.67: 6801 113.67 - 120.49: 2030 120.49 - 127.31: 1705 127.31 - 134.13: 30 Bond angle restraints: 10890 Sorted by residual: angle pdb=" N LEU B 36 " pdb=" CA LEU B 36 " pdb=" C LEU B 36 " ideal model delta sigma weight residual 114.56 103.25 11.31 1.27e+00 6.20e-01 7.92e+01 angle pdb=" N VAL B 109 " pdb=" CA VAL B 109 " pdb=" C VAL B 109 " ideal model delta sigma weight residual 110.30 103.58 6.72 9.70e-01 1.06e+00 4.81e+01 angle pdb=" N ARG B 159 " pdb=" CA ARG B 159 " pdb=" C ARG B 159 " ideal model delta sigma weight residual 112.92 104.87 8.05 1.23e+00 6.61e-01 4.29e+01 angle pdb=" N VAL A 47 " pdb=" CA VAL A 47 " pdb=" C VAL A 47 " ideal model delta sigma weight residual 111.05 103.32 7.73 1.25e+00 6.40e-01 3.83e+01 angle pdb=" N LEU A 90 " pdb=" CA LEU A 90 " pdb=" C LEU A 90 " ideal model delta sigma weight residual 114.39 106.42 7.97 1.45e+00 4.76e-01 3.02e+01 ... (remaining 10885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 2592 18.01 - 36.02: 166 36.02 - 54.02: 61 54.02 - 72.03: 23 72.03 - 90.04: 4 Dihedral angle restraints: 2846 sinusoidal: 1524 harmonic: 1322 Sorted by residual: dihedral pdb=" CB GLU B 180 " pdb=" CG GLU B 180 " pdb=" CD GLU B 180 " pdb=" OE1 GLU B 180 " ideal model delta sinusoidal sigma weight residual 0.00 90.04 -90.04 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU B 26 " pdb=" CG GLU B 26 " pdb=" CD GLU B 26 " pdb=" OE1 GLU B 26 " ideal model delta sinusoidal sigma weight residual 0.00 -88.21 88.21 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" N ASP B 96 " pdb=" CA ASP B 96 " pdb=" CB ASP B 96 " pdb=" CG ASP B 96 " ideal model delta sinusoidal sigma weight residual -180.00 -120.07 -59.93 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 283 0.065 - 0.129: 133 0.129 - 0.194: 50 0.194 - 0.258: 13 0.258 - 0.323: 5 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA VAL B 109 " pdb=" N VAL B 109 " pdb=" C VAL B 109 " pdb=" CB VAL B 109 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA VAL A 47 " pdb=" N VAL A 47 " pdb=" C VAL A 47 " pdb=" CB VAL A 47 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA TYR B 62 " pdb=" N TYR B 62 " pdb=" C TYR B 62 " pdb=" CB TYR B 62 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 481 not shown) Planarity restraints: 922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 148 " 0.157 2.00e-02 2.50e+03 6.20e-02 1.15e+02 pdb=" CG TYR A 148 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 148 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A 148 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR A 148 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 148 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 148 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 148 " 0.109 2.00e-02 2.50e+03 pdb=" HD1 TYR A 148 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 148 " -0.052 2.00e-02 2.50e+03 pdb=" HE1 TYR A 148 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR A 148 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 141 " 0.107 2.00e-02 2.50e+03 3.96e-02 4.70e+01 pdb=" CG PHE A 141 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE A 141 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 141 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 141 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 PHE A 141 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 PHE A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 PHE A 141 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 141 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 141 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 138 " -0.105 2.00e-02 2.50e+03 3.17e-02 4.02e+01 pdb=" CG TRP B 138 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 138 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 138 " 0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP B 138 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 138 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 138 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 138 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 138 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 138 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP B 138 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 TRP B 138 " -0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP B 138 " 0.031 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 138 " -0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 138 " 0.010 2.00e-02 2.50e+03 pdb=" HH2 TRP B 138 " -0.021 2.00e-02 2.50e+03 ... (remaining 919 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.60: 45 1.60 - 2.35: 1578 2.35 - 3.10: 19225 3.10 - 3.85: 25639 3.85 - 4.60: 40401 Warning: very small nonbonded interaction distances. Nonbonded interactions: 86888 Sorted by model distance: nonbonded pdb=" HG SER B 57 " pdb=" HG1 THR B 60 " model vdw 0.851 2.100 nonbonded pdb=" HE1 TRP B 103 " pdb=" HH TYR B 212 " model vdw 0.945 2.100 nonbonded pdb=" HG1 THR A 32 " pdb=" HA ALA A 54 " model vdw 0.956 2.270 nonbonded pdb=" HA2 GLY A 22 " pdb=" HH TYR A 64 " model vdw 1.106 2.270 nonbonded pdb=" HE3 MET B 178 " pdb="HD22 LEU B 203 " model vdw 1.201 2.440 ... (remaining 86883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_1u9o.prmtop atom order : 4amber_1u9o.order coordinates : 4amber_1u9o.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 8 15.96 2 O 586 7.97 1 N 520 6.97 1 C 1908 5.97 2 H 2954 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: 2954 of 5976 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 5976 n_use_u_iso = 5976 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 = 5976 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (5976 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 5976 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 24 through 37 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 42 through 44 helix_type = alpha pi *3_10 unknown } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 47 through 54 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 58 through 64 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 68 through 90 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 101 through 116 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 118 through 127 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 132 through 158 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 168 through 187 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 199 through 211 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'B' and resid 24 through 35 helix_type = alpha pi *3_10 unknown } helix { serial_number = "12" helix_identifier = "12" selection = chain 'B' and resid 47 through 54 } helix { serial_number = "13" helix_identifier = "13" selection = chain 'B' and resid 60 through 63 helix_type = alpha pi *3_10 unknown } helix { serial_number = "14" helix_identifier = "14" selection = chain 'B' and resid 68 through 92 } helix { serial_number = "15" helix_identifier = "15" selection = chain 'B' and resid 99 through 114 } helix { serial_number = "16" helix_identifier = "16" selection = chain 'B' and resid 118 through 130 } helix { serial_number = "17" helix_identifier = "17" selection = chain 'B' and resid 132 through 154 } helix { serial_number = "18" helix_identifier = "18" selection = chain 'B' and resid 168 through 187 } helix { serial_number = "19" helix_identifier = "19" selection = chain 'B' and resid 199 through 212 } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } amber { use_amber = True topology_file_name = "4amber_1u9o.prmtop" coordinate_file_name = "4amber_1u9o.rst7" order_file_name = "4amber_1u9o.order" } } output { prefix = "4phenix_1u9o_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: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.3147 r_free= 0.3646 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ml) (work): 7.003949 | | target function (ml) not normalized (work): 54658.816412 | | target function (ml) not normalized (free): 2915.710281 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.48 - 4.76 0.96 2554 135 0.3297 0.3894 7.6151 7.6432| | 2: 4.76 - 3.79 1.00 2644 139 0.3009 0.3418 7.019 7.1481| | 3: 3.79 - 3.31 0.98 2606 137 0.3026 0.3485 6.3898 6.4985| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.48 - 4.76 2554 135 0.56 48.14 0.92 0.54 844685.67| | 2: 4.76 - 3.79 2644 139 0.62 43.02 1.24 0.73 373540.16| | 3: 3.79 - 3.31 2606 137 0.74 33.71 1.14 0.78 84470.25| |alpha: min = 0.54 max = 0.78 mean = 0.68| |beta: min = 84470.25 max = 844685.67 mean = 431201.55| |figures of merit: min = 0.00 max = 0.99 mean = 0.64| |phase err.(work): min = 6.22 max = 89.67 mean = 41.59| |phase err.(test): min = 8.18 max = 88.24 mean = 39.43| |-----------------------------------------------------------------------------| ----------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 : 0.010 0.071 3084 Z= 0.647 Angle : 1.426 11.305 4206 Z= 0.952 Chirality : 0.088 0.323 484 Planarity : 0.009 0.069 552 Dihedral : 15.917 90.038 1102 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 29.65 Ramachandran Plot: Outliers : 5.73 % Allowed : 20.83 % Favored : 73.44 % Rotamer: Outliers : 7.05 % Allowed : 6.41 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -7.23 (0.24), residues: 384 helix: -4.48 (0.16), residues: 286 sheet: None (None), residues: 0 loop : -4.93 (0.41), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 181 TYR 0.129 0.017 TYR A 148 PHE 0.065 0.014 PHE A 141 TRP 0.072 0.010 TRP B 138 HIS 0.003 0.001 HIS B 169 Individual atomic B min max mean iso aniso Overall: 6.35 60.00 50.91 1.57 3022 0 Protein: 6.35 60.00 50.91 1.57 3022 0 Chain A: 6.35 60.00 49.62 N/A 1511 0 Chain B: 25.19 60.00 52.21 N/A 1511 0 Histogram: Values Number of atoms 6.35 - 11.71 1 11.71 - 17.08 1 17.08 - 22.45 0 22.45 - 27.81 5 27.81 - 33.18 12 33.18 - 38.54 109 38.54 - 43.91 375 43.91 - 49.27 750 49.27 - 54.64 743 54.64 - 60.00 1026 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.3147 r_free= 0.3646 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ml) (work): 7.003949 | | target function (ml) not normalized (work): 54658.816412 | | target function (ml) not normalized (free): 2915.710281 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3174 0.3147 0.3646 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3174 0.3147 0.3646 n_refl.: 8215 remove outliers: r(all,work,free)=0.3174 0.3147 0.3646 n_refl.: 8215 overall B=18.84 to atoms: r(all,work,free)=0.3681 0.3655 0.4131 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2246 0.2220 0.2724 n_refl.: 8215 remove outliers: r(all,work,free)=0.2246 0.2220 0.2724 n_refl.: 8215 ======================== 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 19.484-12.760 91.74 95 5 0.2148 2100.847 1983.633 1.058 1.020 0.362 12.667-10.628 93.40 94 5 0.1453 2797.512 2756.047 1.133 1.017 0.357 10.620-8.919 89.94 153 8 0.1327 2794.097 2744.158 1.124 1.015 0.350 8.899-7.465 94.10 272 15 0.1748 2025.945 1969.239 1.127 1.011 0.341 7.459-6.262 96.09 468 24 0.2324 1345.536 1277.143 1.057 1.006 0.317 6.257-5.249 97.47 805 43 0.2139 1120.207 1078.564 0.925 0.999 0.259 5.246-4.401 98.85 1382 73 0.2031 1249.481 1191.868 0.987 0.989 0.235 4.399-3.690 99.80 2346 123 0.2350 936.742 886.454 1.075 0.974 0.112 3.688-3.311 97.83 2189 115 0.2944 565.762 509.806 1.025 0.959 0.041 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=1.0017 ============================ 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 = 4.412605 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.258442 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 0.2356 0.2761 0.0405 0.014 2.2 0.3 2.1 5.4 0 0.125 0.2262 0.2724 0.0462 0.014 2.1 0.7 2.1 5.8 0 0.250 0.2165 0.2703 0.0538 0.014 2.2 1.3 1.8 5.8 0 0.500 0.2043 0.2685 0.0642 0.015 2.3 2.0 2.6 5.8 0 1.000 0.1926 0.2708 0.0782 0.019 2.8 5.0 2.6 6.4 2 2.000 0.1873 0.2728 0.0855 0.024 3.2 8.7 3.4 7.1 4 3.000 0.1962 0.2751 0.0789 0.027 2.8 11.9 3.4 7.4 0 4.000 0.2048 0.2747 0.0699 0.023 2.1 18.4 4.2 7.7 0 5.000 0.2096 0.2733 0.0638 0.020 1.8 22.6 4.9 7.7 0 6.000 0.2068 0.2738 0.0670 0.023 2.0 22.6 4.9 7.7 0 7.000 0.2078 0.2735 0.0656 0.023 1.9 24.1 5.2 7.7 0 8.000 0.2071 0.2739 0.0668 0.025 1.9 24.3 5.2 7.7 0 9.000 0.2063 0.2739 0.0677 0.026 2.0 24.3 5.2 7.7 0 10.000 0.1987 0.2737 0.0751 0.021 2.7 7.7 2.9 7.7 0 2.206 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2043 0.2685 0.0642 0.015 2.3 2.0 2.6 5.8 0 1.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.43 26.85 6.42 1.120 69.558 0.258 0.045 20.52 26.84 6.32 1.851 69.641 0.008 0.046 20.12 26.79 6.67 1.907 69.737 0.032 0.044 18.88 26.73 7.85 4.468 70.241 0.129 0.039 18.25 26.67 8.42 6.485 70.839 0.258 0.036 17.99 26.72 8.72 7.665 71.206 0.388 0.035 17.84 26.77 8.93 8.493 71.469 0.517 0.035 17.74 26.81 9.07 9.116 71.669 0.646 0.035 17.67 26.84 9.18 9.598 71.824 0.775 0.034 17.61 26.87 9.26 10.029 71.966 0.905 0.034 17.52 26.89 9.37 10.664 72.190 1.034 0.034 17.36 26.86 9.50 11.858 72.660 1.163 0.033 17.29 26.88 9.59 12.522 72.890 1.292 0.033 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.008 Accepted refinement result: 20.52 26.84 6.32 1.851 69.641 0.008 0.046 Individual atomic B min max mean iso aniso Overall: 51.38 80.24 69.92 0.91 3022 0 Protein: 51.38 80.24 69.92 0.91 3022 0 Chain A: 51.38 80.03 68.61 N/A 1511 0 Chain B: 55.44 80.24 71.24 N/A 1511 0 Histogram: Values Number of atoms 51.38 - 54.26 2 54.26 - 57.15 12 57.15 - 60.04 112 60.04 - 62.92 273 62.92 - 65.81 413 65.81 - 68.70 509 68.70 - 71.58 473 71.58 - 74.47 438 74.47 - 77.36 381 77.36 - 80.24 409 =========================== Idealize ADP of riding H ========================== r_work=0.2052 r_free=0.2684 r_work=0.2054 r_free=0.2689 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.2054 r_free= 0.2689 coordinate error (max.-lik. estimate): 0.58 A | | | | normalized target function (ls_wunit_k1) (work): 0.045674 | | target function (ls_wunit_k1) not normalized (work): 356.441616 | | target function (ls_wunit_k1) not normalized (free): 34.935629 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2089 0.2054 0.2689 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3651 0.3623 0.4114 n_refl.: 8215 remove outliers: r(all,work,free)=0.3651 0.3623 0.4114 n_refl.: 8215 overall B=1.28 to atoms: r(all,work,free)=0.3694 0.3666 0.4155 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2068 0.2033 0.2659 n_refl.: 8215 remove outliers: r(all,work,free)=0.2068 0.2033 0.2659 n_refl.: 8215 ======================== 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 19.484-12.760 91.74 95 5 0.1708 1202.334 1167.600 1.156 1.021 0.379 12.667-10.628 93.40 94 5 0.1168 1601.042 1595.933 1.206 1.018 0.379 10.620-8.919 89.94 153 8 0.1017 1599.087 1582.705 1.167 1.016 0.355 8.899-7.465 94.10 272 15 0.1407 1159.467 1144.504 1.175 1.011 0.348 7.459-6.262 96.09 468 24 0.1938 770.062 747.356 1.111 1.006 0.338 6.257-5.249 97.47 805 43 0.2055 641.105 624.333 0.975 0.998 0.277 5.246-4.401 98.85 1382 73 0.1858 715.089 691.455 1.013 0.987 0.246 4.399-3.690 99.80 2346 123 0.2183 536.106 513.823 1.063 0.972 0.118 3.688-3.311 97.83 2189 115 0.2907 323.791 296.049 1.008 0.956 0.019 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.7417 ============================ 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 = 0.978724 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.055473 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 0.2239 0.2614 0.0375 0.013 1.9 0.5 1.6 6.1 0 0.049 0.2079 0.2607 0.0528 0.013 2.1 1.3 2.3 5.4 0 0.147 0.2028 0.2658 0.0630 0.015 2.4 1.8 2.6 5.8 0 0.294 0.2033 0.2659 0.0626 0.015 2.4 2.0 2.6 5.8 0 0.440 0.2033 0.2659 0.0626 0.015 2.4 2.0 2.6 5.8 0 0.587 0.2033 0.2659 0.0626 0.015 2.4 2.0 2.6 5.8 0 0.734 0.2032 0.2660 0.0627 0.015 2.4 2.3 2.6 5.8 0 0.881 0.2030 0.2659 0.0629 0.016 2.4 2.2 2.6 5.8 0 1.028 0.2033 0.2659 0.0626 0.015 2.4 2.0 2.6 5.8 0 0.489 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2239 0.2614 0.0375 0.013 1.9 0.5 1.6 6.1 0 0.049 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.39 26.14 3.75 9.799 77.954 0.055 6.445 22.39 26.13 3.74 9.815 77.942 0.002 6.445 22.39 26.14 3.75 9.799 77.954 0.007 6.445 21.78 25.98 4.20 10.243 77.743 0.028 6.424 20.21 25.45 5.25 11.866 78.650 0.055 6.366 19.97 25.45 5.49 12.546 79.148 0.083 6.360 19.83 25.46 5.63 13.182 79.506 0.111 6.357 19.74 25.47 5.73 13.723 79.775 0.139 6.355 19.68 25.48 5.80 14.188 79.988 0.166 6.353 19.64 25.51 5.87 14.584 80.160 0.194 6.353 19.60 25.52 5.91 14.923 80.303 0.222 6.352 19.58 25.54 5.96 15.214 80.423 0.250 6.352 19.56 25.55 5.99 15.471 80.527 0.277 6.351 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.055 Accepted refinement result: 20.21 25.45 5.25 11.866 78.650 0.055 6.366 Individual atomic B min max mean iso aniso Overall: 47.65 126.20 72.57 7.54 3022 0 Protein: 47.65 126.20 72.57 7.54 3022 0 Chain A: 47.65 123.65 70.52 N/A 1511 0 Chain B: 51.71 126.20 74.63 N/A 1511 0 Histogram: Values Number of atoms 47.65 - 55.51 71 55.51 - 63.36 731 63.36 - 71.22 928 71.22 - 79.07 546 79.07 - 86.93 304 86.93 - 94.78 205 94.78 - 102.64 102 102.64 - 110.49 92 110.49 - 118.35 31 118.35 - 126.20 12 =========================== Idealize ADP of riding H ========================== r_work=0.2021 r_free=0.2545 r_work=0.2012 r_free=0.2536 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.2012 r_free= 0.2536 coordinate error (max.-lik. estimate): 0.50 A | | | | normalized target function (ml) (work): 6.362688 | | target function (ml) not normalized (work): 49654.417621 | | target function (ml) not normalized (free): 2679.184332 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2039 0.2012 0.2536 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3678 0.3657 0.4047 n_refl.: 8215 remove outliers: r(all,work,free)=0.3678 0.3657 0.4047 n_refl.: 8215 overall B=3.46 to atoms: r(all,work,free)=0.3803 0.3782 0.4172 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2030 0.2002 0.2542 n_refl.: 8215 remove outliers: r(all,work,free)=0.2030 0.2002 0.2542 n_refl.: 8215 ======================== 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 19.484-12.760 91.74 95 5 0.1788 1202.334 1160.486 1.130 1.017 0.379 12.667-10.628 93.40 94 5 0.1278 1601.042 1594.620 1.166 1.014 0.378 10.620-8.919 89.94 153 8 0.1091 1599.087 1584.089 1.145 1.013 0.351 8.899-7.465 94.10 272 15 0.1418 1159.467 1137.974 1.169 1.009 0.345 7.459-6.262 96.09 468 24 0.2127 770.062 741.176 1.121 1.005 0.343 6.257-5.249 97.47 805 43 0.2185 641.105 613.868 1.015 0.999 0.292 5.246-4.401 98.85 1382 73 0.1847 715.089 683.606 0.992 0.990 0.231 4.399-3.690 99.80 2346 123 0.2047 536.106 511.440 1.044 0.978 0.114 3.688-3.311 97.83 2189 115 0.2700 323.791 295.989 0.994 0.966 0.028 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.0620 ============================ 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 = 0.978451 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.047862 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 0.1984 0.2476 0.0492 0.013 1.9 0.7 1.6 6.7 0 0.049 0.2002 0.2541 0.0539 0.013 1.9 0.5 1.6 6.1 0 0.147 0.2002 0.2541 0.0539 0.013 1.9 0.5 1.6 6.1 0 0.294 0.2000 0.2540 0.0540 0.013 1.9 0.5 1.6 6.1 0 0.440 0.1998 0.2538 0.0541 0.013 1.9 0.5 1.6 6.1 0 0.587 0.1995 0.2541 0.0546 0.013 1.9 0.5 1.6 6.1 0 0.734 0.1993 0.2538 0.0545 0.013 1.9 0.5 1.6 6.1 0 0.881 0.1979 0.2538 0.0559 0.014 1.9 0.5 1.6 6.1 0 1.027 0.1999 0.2540 0.0540 0.013 1.9 0.5 1.6 6.1 0 0.489 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1998 0.2538 0.0541 0.013 1.9 0.5 1.6 6.1 0 0.587 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.98 25.38 5.41 11.546 82.835 0.048 6.361 22.00 25.84 3.84 7.736 87.681 0.001 6.407 21.25 25.35 4.10 10.832 86.009 0.006 6.391 19.87 25.35 5.48 11.616 82.604 0.024 6.357 19.72 25.38 5.66 11.931 82.561 0.048 6.353 19.17 25.28 6.12 12.653 83.181 0.072 6.339 19.00 25.35 6.35 13.122 83.350 0.096 6.336 18.94 25.39 6.46 13.474 83.458 0.120 6.335 18.89 25.42 6.53 13.763 83.561 0.144 6.335 18.84 25.42 6.58 14.064 83.704 0.168 6.334 18.81 25.46 6.65 14.334 83.828 0.191 6.334 18.78 25.47 6.68 14.567 83.931 0.215 6.334 18.75 25.48 6.73 14.774 84.022 0.239 6.333 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 21.25 25.35 4.10 10.832 86.009 0.006 6.391 Individual atomic B min max mean iso aniso Overall: 53.17 189.63 82.31 4.81 3022 0 Protein: 53.17 189.63 82.31 4.81 3022 0 Chain A: 53.17 180.15 78.13 N/A 1511 0 Chain B: 53.82 189.63 86.50 N/A 1511 0 Histogram: Values Number of atoms 53.17 - 66.82 535 66.82 - 80.47 1075 80.47 - 94.11 720 94.11 - 107.76 487 107.76 - 121.40 123 121.40 - 135.05 54 135.05 - 148.69 23 148.69 - 162.34 0 162.34 - 175.99 3 175.99 - 189.63 2 =========================== Idealize ADP of riding H ========================== r_work=0.2125 r_free=0.2535 r_work=0.2147 r_free=0.2545 ----------X-ray data---------- |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.2147 r_free= 0.2545 coordinate error (max.-lik. estimate): 0.42 A | | | | normalized target function (ml) (work): 6.398327 | | target function (ml) not normalized (work): 49932.541704 | | target function (ml) not normalized (free): 2677.008639 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.48 - 4.76 0.96 2554 135 0.1907 0.2366 6.7035 6.807| | 2: 4.76 - 3.79 1.00 2644 139 0.2125 0.2522 6.4377 6.6207| | 3: 3.79 - 3.31 0.98 2606 137 0.2774 0.3013 6.0593 6.1152| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.48 - 4.76 2554 135 0.84 23.38 0.99 1.02 122878.02| | 2: 4.76 - 3.79 2644 139 0.84 24.42 1.02 1.03 76542.87| | 3: 3.79 - 3.31 2606 137 0.78 30.23 1.01 0.99 37675.75| |alpha: min = 0.99 max = 1.03 mean = 1.01| |beta: min = 37675.75 max = 122878.02 mean = 78727.94| |figures of merit: min = 0.01 max = 1.00 mean = 0.82| |phase err.(work): min = 0.00 max = 89.09 mean = 26.02| |phase err.(test): min = 0.00 max = 85.17 mean = 25.16| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2167 0.2147 0.2545 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3986 0.3969 0.4278 n_refl.: 8215 remove outliers: r(all,work,free)=0.3986 0.3969 0.4278 n_refl.: 8215 overall B=0.00 to atoms: r(all,work,free)=0.3986 0.3969 0.4278 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2158 0.2137 0.2545 n_refl.: 8215 remove outliers: r(all,work,free)=0.2158 0.2137 0.2545 n_refl.: 8215 ======================== 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 19.484-12.760 91.74 95 5 0.1838 1202.334 1158.975 1.027 1.032 0.370 12.667-10.628 93.40 94 5 0.1253 1601.042 1592.814 1.066 1.028 0.360 10.620-8.919 89.94 153 8 0.1096 1599.087 1587.452 1.097 1.025 0.348 8.899-7.465 94.10 272 15 0.1505 1159.467 1137.314 1.117 1.018 0.340 7.459-6.262 96.09 468 24 0.2283 770.062 738.166 1.080 1.009 0.330 6.257-5.249 97.47 805 43 0.2268 641.105 612.426 1.012 0.998 0.290 5.246-4.401 98.85 1382 73 0.2004 715.089 680.536 0.995 0.981 0.220 4.399-3.690 99.80 2346 123 0.2219 536.106 510.144 1.070 0.958 0.120 3.688-3.311 97.83 2189 115 0.2878 323.791 294.243 1.036 0.934 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.7473 ================= 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 : 0.3147 0.3646 0.010 1.426 6.3 60.0 50.9 0 0.000 1_bss: 0.2220 0.2724 0.010 1.426 25.2 78.8 69.8 0 0.000 1_settarget: 0.2220 0.2724 0.010 1.426 25.2 78.8 69.8 0 0.000 1_weight: 0.2220 0.2724 0.010 1.426 25.2 78.8 69.8 0 0.000 1_xyzrec: 0.2043 0.2685 0.015 2.340 25.2 78.8 69.8 0 0.229 1_adp: 0.2052 0.2684 0.015 2.340 51.4 80.2 69.9 0 0.229 1_regHadp: 0.2054 0.2689 0.015 2.340 51.4 80.2 69.9 0 0.229 2_bss: 0.2033 0.2659 0.015 2.340 52.7 81.5 71.2 0 0.229 2_settarget: 0.2033 0.2659 0.015 2.340 52.7 81.5 71.2 0 0.229 2_updatecdl: 0.2033 0.2659 0.015 2.352 52.7 81.5 71.2 0 0.229 2_weight: 0.2033 0.2659 0.015 2.352 52.7 81.5 71.2 0 0.229 2_xyzrec: 0.2239 0.2614 0.013 1.922 52.7 81.5 71.2 0 0.326 2_adp: 0.2021 0.2545 0.013 1.922 47.7 126.2 72.6 0 0.326 2_regHadp: 0.2012 0.2536 0.013 1.922 47.7 126.2 72.6 0 0.326 3_bss: 0.2002 0.2542 0.013 1.922 51.1 129.7 76.0 0 0.326 3_settarget: 0.2002 0.2542 0.013 1.922 51.1 129.7 76.0 0 0.326 3_updatecdl: 0.2002 0.2542 0.013 1.915 51.1 129.7 76.0 0 0.326 3_setrh: 0.2002 0.2542 0.013 1.915 51.1 129.7 76.0 0 0.326 3_weight: 0.2002 0.2542 0.013 1.915 51.1 129.7 76.0 0 0.326 3_xyzrec: 0.1998 0.2538 0.013 1.918 51.1 129.7 76.0 0 0.326 3_adp: 0.2125 0.2535 0.013 1.918 53.2 189.6 82.3 0 0.326 3_regHadp: 0.2147 0.2545 0.013 1.918 53.2 189.6 82.3 0 0.326 end: 0.2137 0.2545 0.013 1.918 53.2 189.6 82.3 0 0.326 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1u9o_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1u9o_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6100 Refinement macro-cycles (run) : 223.1400 Write final files (write_after_run_outputs) : 9.6900 Total : 236.4400 Total CPU time: 4.60 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:38:37 PDT -0700 (1723221517.89 s) Start R-work = 0.2220, R-free = 0.2724 Final R-work = 0.2137, R-free = 0.2545 =============================================================================== Job complete usr+sys time: 284.64 seconds wall clock time: 7 minutes 9.62 seconds (429.62 seconds total)