Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_2h1g.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2h1g/2h1g.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_2h1g.prmtop amber.coordinate_file_name=4amber_2h1g.rst7 amber.order_file_name=4amber_2h1g.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_2h1g.order 4amber_2h1g.prmtop 4amber_2h1g.rst7 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2h1g/2h1g.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2h1g/2h1g.mtz" model { file = "4phenix_2h1g.pdb" } default_model = "4phenix_2h1g.pdb" } 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_2h1g.prmtop coordinate_file_name = 4amber_2h1g.rst7 order_file_name = 4amber_2h1g.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: 4293 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2139 Classifications: {'peptide': 136} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 127} Chain: "B" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2154 Classifications: {'peptide': 137} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Time building chain proxies: 0.52, per 1000 atoms: 0.12 Number of scatterers: 4293 At special positions: 0 Unit cell: (47.031, 59.522, 109.562, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 405 8.00 N 349 7.00 C 1391 6.00 H 2138 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: 0.79 Conformation dependent library (CDL) restraints added in 90.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 506 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 4 sheets defined 37.0% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 57 through 60 Processing helix chain 'A' and resid 75 through 94 removed outlier: 3.530A pdb=" N LYS A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.782A pdb=" N HIS A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N SER A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN A 94 " --> pdb=" O HIS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'B' and resid 57 through 60 Processing helix chain 'B' and resid 75 through 94 removed outlier: 3.792A pdb=" N GLU B 80 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE B 81 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Proline residue: B 82 - end of helix removed outlier: 3.504A pdb=" N ALA B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 88 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 91 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS B 92 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 93 " --> pdb=" O HIS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 162 through 172 Processing sheet with id= A, first strand: chain 'A' and resid 46 through 48 Processing sheet with id= B, first strand: chain 'A' and resid 152 through 157 removed outlier: 6.765A pdb=" N LEU A 145 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL A 155 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR A 143 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 46 through 48 Processing sheet with id= D, first strand: chain 'B' and resid 152 through 157 removed outlier: 6.774A pdb=" N LEU B 145 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL B 155 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 143 " --> pdb=" O VAL B 155 " (cutoff:3.500A) 81 hydrogen bonds defined for protein. 210 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: 0.77 Time building geometry restraints manager: 0.91 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: 2140 1.16 - 1.33: 536 1.33 - 1.51: 996 1.51 - 1.68: 655 1.68 - 1.86: 20 Bond restraints: 4347 Sorted by residual: bond pdb=" NE2 HIS B 166 " pdb=" HE2 HIS B 166 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N LYS B 89 " pdb=" H LYS B 89 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ASP A 41 " pdb=" H ASP A 41 " 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 B 166 " pdb=" H HIS B 166 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LYS B 115 " pdb=" H LYS B 115 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 4342 not shown) Histogram of bond angle deviations from ideal: 98.40 - 106.27: 294 106.27 - 114.14: 5068 114.14 - 122.01: 1765 122.01 - 129.88: 740 129.88 - 137.75: 22 Bond angle restraints: 7889 Sorted by residual: angle pdb=" N TRP B 73 " pdb=" CA TRP B 73 " pdb=" C TRP B 73 " ideal model delta sigma weight residual 111.82 119.27 -7.45 1.16e+00 7.43e-01 4.13e+01 angle pdb=" N ASP A 41 " pdb=" CA ASP A 41 " pdb=" C ASP A 41 " ideal model delta sigma weight residual 110.23 118.37 -8.14 1.45e+00 4.76e-01 3.15e+01 angle pdb=" N ASP B 41 " pdb=" CA ASP B 41 " pdb=" C ASP B 41 " ideal model delta sigma weight residual 110.24 118.13 -7.89 1.41e+00 5.03e-01 3.13e+01 angle pdb=" O VAL A 137 " pdb=" C VAL A 137 " pdb=" N SER A 138 " ideal model delta sigma weight residual 122.72 129.05 -6.33 1.18e+00 7.18e-01 2.88e+01 angle pdb=" C LYS B 173 " pdb=" N PRO B 174 " pdb=" CA PRO B 174 " ideal model delta sigma weight residual 119.84 126.44 -6.60 1.25e+00 6.40e-01 2.79e+01 ... (remaining 7884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 1808 17.76 - 35.52: 157 35.52 - 53.28: 72 53.28 - 71.04: 13 71.04 - 88.80: 5 Dihedral angle restraints: 2055 sinusoidal: 1106 harmonic: 949 Sorted by residual: dihedral pdb=" C SER B 138 " pdb=" N SER B 138 " pdb=" CA SER B 138 " pdb=" CB SER B 138 " ideal model delta harmonic sigma weight residual -122.60 -144.10 21.50 0 2.50e+00 1.60e-01 7.39e+01 dihedral pdb=" N SER B 138 " pdb=" C SER B 138 " pdb=" CA SER B 138 " pdb=" CB SER B 138 " ideal model delta harmonic sigma weight residual 122.80 143.41 -20.61 0 2.50e+00 1.60e-01 6.80e+01 dihedral pdb=" CA PRO B 139 " pdb=" C PRO B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual -180.00 -150.85 -29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 2052 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.153: 264 0.153 - 0.305: 60 0.305 - 0.456: 4 0.456 - 0.607: 2 0.607 - 0.759: 1 Chirality restraints: 331 Sorted by residual: chirality pdb=" CA SER B 138 " pdb=" N SER B 138 " pdb=" C SER B 138 " pdb=" CB SER B 138 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA VAL B 137 " pdb=" N VAL B 137 " pdb=" C VAL B 137 " pdb=" CB VAL B 137 " both_signs ideal model delta sigma weight residual False 2.44 2.91 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA MET A 169 " pdb=" N MET A 169 " pdb=" C MET A 169 " pdb=" CB MET A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 328 not shown) Planarity restraints: 641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 73 " 0.047 2.00e-02 2.50e+03 1.93e-02 1.48e+01 pdb=" CG TRP B 73 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP B 73 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 73 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 73 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 73 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 73 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 73 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 73 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 73 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP B 73 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP B 73 " -0.025 2.00e-02 2.50e+03 pdb=" HE3 TRP B 73 " -0.040 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 73 " 0.005 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 73 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP B 73 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 135 " -0.025 2.00e-02 2.50e+03 2.02e-02 1.23e+01 pdb=" CG TYR A 135 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 135 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 135 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 135 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 135 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 135 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 135 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TYR A 135 " -0.030 2.00e-02 2.50e+03 pdb=" HD2 TYR A 135 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 135 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 TYR A 135 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 135 " 0.039 2.00e-02 2.50e+03 1.86e-02 1.03e+01 pdb=" CG TYR B 135 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 135 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 135 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 135 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 135 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 135 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 135 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 TYR B 135 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR B 135 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR B 135 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 TYR B 135 " -0.000 2.00e-02 2.50e+03 ... (remaining 638 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.03: 163 2.03 - 2.67: 5876 2.67 - 3.31: 13164 3.31 - 3.96: 18010 3.96 - 4.60: 26899 Nonbonded interactions: 64112 Sorted by model distance: nonbonded pdb=" HH TYR A 88 " pdb=" OE1 GLU A 97 " model vdw 1.383 2.450 nonbonded pdb="HD12 LEU B 145 " pdb=" HB3 LYS B 154 " model vdw 1.385 2.440 nonbonded pdb="HD21 ASN B 44 " pdb=" HB3 SER B 58 " model vdw 1.410 2.270 nonbonded pdb=" OD1 ASP A 49 " pdb=" H ASN A 51 " model vdw 1.472 2.450 nonbonded pdb=" HH TYR B 88 " pdb=" OE1 GLU B 97 " model vdw 1.474 2.450 ... (remaining 64107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_2h1g.prmtop atom order : 4amber_2h1g.order coordinates : 4amber_2h1g.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 10 15.96 2 O 405 7.97 1 N 349 6.97 1 C 1391 5.97 2 H 2138 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: 2138 of 4293 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4293 n_use_u_iso = 4293 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 = 4293 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4293 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4293 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 57 through 60 helix_type = alpha pi *3_10 unknown } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 75 through 94 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 107 through 116 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 130 through 135 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 162 through 172 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'B' and resid 57 through 60 helix_type = alpha pi *3_10 unknown } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 75 through 94 helix_type = alpha pi *3_10 unknown } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 107 through 116 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'B' and resid 130 through 134 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'B' and resid 162 through 172 } sheet { first_strand = chain 'A' and resid 46 through 48 sheet_id = " A" strand { selection = chain 'A' and resid 54 through 56 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 55 and name N bond_start_previous = chain 'A' and resid 47 and name O } } sheet { first_strand = chain 'A' and resid 152 through 157 sheet_id = " B" strand { selection = chain 'A' and resid 142 through 146 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 145 and name N bond_start_previous = chain 'A' and resid 153 and name O } strand { selection = chain 'A' and resid 64 through 70 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 69 and name N bond_start_previous = chain 'A' and resid 142 and name O } strand { selection = chain 'A' and resid 96 through 102 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 97 and name N bond_start_previous = chain 'A' and resid 64 and name O } strand { selection = chain 'A' and resid 123 through 125 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 124 and name N bond_start_previous = chain 'A' and resid 100 and name O } } sheet { first_strand = chain 'B' and resid 46 through 48 sheet_id = " C" strand { selection = chain 'B' and resid 54 through 56 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 55 and name N bond_start_previous = chain 'B' and resid 47 and name O } } sheet { first_strand = chain 'B' and resid 152 through 157 sheet_id = " D" strand { selection = chain 'B' and resid 142 through 146 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 145 and name N bond_start_previous = chain 'B' and resid 153 and name O } strand { selection = chain 'B' and resid 64 through 70 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 69 and name N bond_start_previous = chain 'B' and resid 142 and name O } strand { selection = chain 'B' and resid 96 through 102 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 97 and name N bond_start_previous = chain 'B' and resid 64 and name O } strand { selection = chain 'B' and resid 123 through 125 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 124 and name N bond_start_previous = chain 'B' and resid 100 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_2h1g.prmtop" coordinate_file_name = "4amber_2h1g.rst7" order_file_name = "4amber_2h1g.order" } } output { prefix = "4phenix_2h1g_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: 3.10 - 36.90 A, n_refl.=5695 (all), 5.23 % free)-------------| | | | r_work= 0.3522 r_free= 0.3459 coordinate error (max.-lik. estimate): 0.23 A | | | | normalized target function (ml) (work): 6.130617 | | target function (ml) not normalized (work): 33086.941057 | | target function (ml) not normalized (free): 1924.260534 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 36.90 - 3.91 0.97 2809 138 0.3664 0.3361 6.3583 6.4625| | 2: 3.91 - 3.10 0.94 2588 160 0.3327 0.3584 5.8835 6.4527| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 36.90 - 3.91 2809 138 0.76 28.36 0.89 0.78 61384.45| | 2: 3.91 - 3.10 2588 160 0.88 18.57 1.37 1.02 18157.98| |alpha: min = 0.10 max = 1.08 mean = 0.90| |beta: min = 12743.78 max = 259705.32 mean = 40656.25| |figures of merit: min = 0.00 max = 1.00 mean = 0.82| |phase err.(work): min = 0.00 max = 89.98 mean = 23.66| |phase err.(test): min = 0.00 max = 89.21 mean = 22.22| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.153 2209 Z= 1.602 Angle : 2.035 10.752 2998 Z= 1.276 Chirality : 0.130 0.759 331 Planarity : 0.006 0.021 386 Dihedral : 17.709 88.802 808 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 1.49 % Allowed : 4.83 % Favored : 93.68 % Rotamer: Outliers : 6.69 % Allowed : 12.55 % Favored : 80.75 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 18.75 % 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: -2.93 (0.45), residues: 269 helix: -2.28 (0.39), residues: 93 sheet: -1.31 (0.58), residues: 77 loop : -1.82 (0.56), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 129 TYR 0.040 0.010 TYR B 135 PHE 0.021 0.006 PHE A 91 TRP 0.027 0.008 TRP B 73 HIS 0.010 0.006 HIS A 90 Individual atomic B min max mean iso aniso Overall: 2.00 37.24 13.06 1.53 2155 0 Protein: 2.00 37.24 13.06 1.53 2155 0 Chain A: 2.00 33.66 13.04 N/A 1073 0 Chain B: 2.00 37.24 13.09 N/A 1082 0 Histogram: Values Number of atoms 2.00 - 5.52 154 5.52 - 9.05 509 9.05 - 12.57 430 12.57 - 16.10 443 16.10 - 19.62 315 19.62 - 23.14 170 23.14 - 26.67 71 26.67 - 30.19 32 30.19 - 33.72 26 33.72 - 37.24 5 |-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: 3.10 - 36.90 A, n_refl.=5695 (all), 5.23 % free)-------------| | | | r_work= 0.3522 r_free= 0.3459 coordinate error (max.-lik. estimate): 0.23 A | | | | normalized target function (ml) (work): 6.130617 | | target function (ml) not normalized (work): 33086.941057 | | target function (ml) not normalized (free): 1924.260534 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3516 0.3522 0.3459 n_refl.: 5695 re-set all scales: r(all,work,free)=0.3516 0.3522 0.3459 n_refl.: 5695 remove outliers: r(all,work,free)=0.3515 0.3521 0.3459 n_refl.: 5694 overall B=1.11 to atoms: r(all,work,free)=0.3563 0.3571 0.3480 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1929 0.1898 0.2497 n_refl.: 5694 remove outliers: r(all,work,free)=0.1929 0.1898 0.2497 n_refl.: 5694 ======================== 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 36.902-12.728 94.29 95 4 0.2926 541.923 491.493 0.930 1.188 0.390 12.598-9.947 96.15 96 4 0.1351 773.518 776.541 1.022 1.165 0.399 9.931-7.830 97.01 189 6 0.1615 683.542 672.307 1.067 1.151 0.408 7.826-6.174 96.81 381 14 0.2173 462.079 447.028 0.987 1.121 0.462 6.172-4.868 97.27 748 36 0.1783 518.993 507.798 0.949 1.072 0.471 4.862-3.836 96.79 1456 84 0.1628 627.979 611.267 1.025 0.995 0.471 3.836-3.102 94.30 2431 150 0.2131 446.529 420.897 1.120 0.882 0.205 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.0151 ============================ 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 = 3.936114 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.984279 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 0.2038 0.2373 0.0336 0.014 1.9 0.2 0.4 1.7 1 0.125 0.1905 0.2357 0.0452 0.013 1.9 0.0 0.4 2.5 1 0.250 0.1812 0.2400 0.0588 0.014 2.0 0.2 0.7 4.6 1 0.500 0.1697 0.2404 0.0707 0.015 2.2 0.5 0.7 4.6 1 1.000 0.1576 0.2378 0.0802 0.019 2.7 1.9 0.7 7.5 2 2.000 0.1487 0.2386 0.0898 0.022 3.0 3.7 1.1 6.7 4 3.000 0.1472 0.2430 0.0958 0.026 3.4 3.7 1.1 8.8 9 4.000 0.1441 0.2432 0.0991 0.029 3.7 4.7 1.1 8.8 10 5.000 0.1391 0.2421 0.1030 0.032 4.1 6.8 2.2 10.5 14 6.000 0.1383 0.2426 0.1043 0.035 4.2 7.2 2.2 11.3 18 7.000 0.1357 0.2433 0.1076 0.038 4.5 8.4 2.2 11.3 19 8.000 0.1333 0.2472 0.1139 0.040 4.7 9.3 2.6 10.9 20 9.000 0.1324 0.2489 0.1165 0.043 4.9 9.3 3.0 11.3 26 10.000 0.1579 0.2371 0.0792 0.018 2.7 1.9 0.7 7.1 2 1.968 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2038 0.2373 0.0336 0.014 1.9 0.2 0.4 1.7 1 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.38 23.73 3.36 1.092 14.031 0.984 0.050 20.50 23.87 3.37 1.845 14.264 0.030 0.051 19.69 23.70 4.01 2.065 14.286 0.123 0.047 18.15 23.62 5.47 4.674 14.771 0.492 0.040 17.36 23.52 6.17 7.003 15.434 0.984 0.037 17.00 23.58 6.58 8.413 15.828 1.476 0.035 16.41 23.93 7.52 12.514 17.329 1.969 0.033 16.30 24.07 7.77 13.618 17.622 2.461 0.032 16.25 24.24 8.00 14.552 17.871 2.953 0.032 16.07 24.45 8.37 16.661 18.604 3.445 0.031 16.02 24.58 8.55 17.645 18.881 3.937 0.031 16.05 24.62 8.57 17.730 18.836 4.429 0.031 16.03 24.71 8.68 18.331 18.999 4.921 0.031 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.492 Accepted refinement result: 18.15 23.62 5.47 4.674 14.771 0.492 0.040 Individual atomic B min max mean iso aniso Overall: 2.68 46.72 15.65 4.90 2155 0 Protein: 2.68 46.72 15.65 4.90 2155 0 Chain A: 3.08 43.27 15.93 N/A 1073 0 Chain B: 2.68 46.72 15.38 N/A 1082 0 Histogram: Values Number of atoms 2.68 - 7.08 200 7.08 - 11.49 573 11.49 - 15.89 497 15.89 - 20.29 377 20.29 - 24.70 233 24.70 - 29.10 126 29.10 - 33.51 74 33.51 - 37.91 48 37.91 - 42.31 20 42.31 - 46.72 7 =========================== Idealize ADP of riding H ========================== r_work=0.1815 r_free=0.2362 r_work=0.1800 r_free=0.2353 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1800 r_free= 0.2353 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.039283 | | target function (ls_wunit_k1) not normalized (work): 211.973011 | | target function (ls_wunit_k1) not normalized (free): 19.088406 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1828 0.1800 0.2353 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3572 0.3582 0.3447 n_refl.: 5694 remove outliers: r(all,work,free)=0.3572 0.3582 0.3447 n_refl.: 5694 overall B=1.08 to atoms: r(all,work,free)=0.3619 0.3629 0.3470 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1823 0.1793 0.2358 n_refl.: 5694 remove outliers: r(all,work,free)=0.1823 0.1793 0.2358 n_refl.: 5694 ======================== 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 36.902-12.728 94.29 95 4 0.2783 377.089 341.790 0.958 1.261 0.400 12.598-9.947 96.15 96 4 0.1278 538.242 531.364 0.983 1.232 0.399 9.931-7.830 97.01 189 6 0.1458 475.633 462.070 1.047 1.210 0.437 7.826-6.174 96.81 381 14 0.2093 321.531 308.931 0.923 1.169 0.442 6.172-4.868 97.27 748 36 0.1790 361.134 351.536 0.900 1.101 0.436 4.862-3.836 96.79 1456 84 0.1544 436.971 428.342 1.028 0.993 0.404 3.836-3.102 94.30 2431 150 0.1985 310.711 303.420 1.200 0.835 0.216 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.8557 ============================ 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 = 0.600818 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.111675 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 0.1684 0.2296 0.0612 0.013 1.9 0.0 0.7 2.1 0 0.030 0.1762 0.2354 0.0592 0.014 1.9 0.2 0.4 1.7 1 0.090 0.1675 0.2325 0.0649 0.016 2.0 0.0 0.4 1.7 0 0.180 0.1631 0.2308 0.0677 0.018 2.1 0.0 0.4 2.1 0 0.270 0.1595 0.2300 0.0705 0.020 2.3 0.5 0.7 2.5 0 0.360 0.1498 0.2283 0.0785 0.026 2.7 0.5 0.7 3.3 1 0.451 0.1481 0.2290 0.0809 0.028 2.8 0.5 0.7 3.3 1 0.541 0.1459 0.2289 0.0830 0.031 3.0 0.5 0.7 3.3 2 0.631 0.1620 0.2305 0.0685 0.019 2.2 0.0 0.7 2.1 0 0.300 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1762 0.2354 0.0592 0.014 1.9 0.2 0.4 1.7 1 0.090 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.62 23.54 5.92 4.239 18.128 0.112 5.754 19.37 23.26 3.89 3.829 18.667 0.003 5.829 18.40 23.09 4.68 3.475 18.682 0.014 5.779 16.93 22.91 5.98 5.566 18.784 0.056 5.695 16.38 23.16 6.78 7.690 19.004 0.112 5.657 16.16 23.38 7.22 8.977 19.205 0.168 5.642 16.04 23.59 7.55 10.761 19.666 0.223 5.632 15.98 23.70 7.72 11.593 19.854 0.279 5.628 15.96 23.84 7.88 12.302 20.024 0.335 5.625 15.94 23.93 7.99 12.870 20.165 0.391 5.624 15.93 24.00 8.07 13.360 20.290 0.447 5.623 15.94 24.07 8.13 13.772 20.398 0.503 5.623 15.94 24.12 8.19 14.112 20.489 0.558 5.622 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.056 Accepted refinement result: 16.93 22.91 5.98 5.566 18.784 0.056 5.695 Individual atomic B min max mean iso aniso Overall: 2.30 61.40 18.04 6.99 2155 0 Protein: 2.30 61.40 18.04 6.99 2155 0 Chain A: 3.12 60.34 18.53 N/A 1073 0 Chain B: 2.30 61.40 17.55 N/A 1082 0 Histogram: Values Number of atoms 2.30 - 8.21 270 8.21 - 14.12 663 14.12 - 20.03 519 20.03 - 25.94 296 25.94 - 31.85 182 31.85 - 37.76 92 37.76 - 43.67 71 43.67 - 49.58 33 49.58 - 55.49 20 55.49 - 61.40 9 =========================== Idealize ADP of riding H ========================== r_work=0.1693 r_free=0.2291 r_work=0.1690 r_free=0.2296 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1690 r_free= 0.2296 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 5.690541 | | target function (ml) not normalized (work): 30706.158835 | | target function (ml) not normalized (free): 1846.677198 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1721 0.1690 0.2296 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3588 0.3598 0.3450 n_refl.: 5694 remove outliers: r(all,work,free)=0.3588 0.3598 0.3450 n_refl.: 5694 overall B=0.00 to atoms: r(all,work,free)=0.3588 0.3598 0.3450 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1774 0.1745 0.2306 n_refl.: 5694 remove outliers: r(all,work,free)=0.1774 0.1745 0.2306 n_refl.: 5694 ======================== 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 36.902-12.728 94.29 95 4 0.2802 377.089 352.688 1.128 1.080 0.400 12.598-9.947 96.15 96 4 0.1300 538.242 549.243 1.145 1.068 0.400 9.931-7.830 97.01 189 6 0.1457 475.633 477.044 1.202 1.063 0.433 7.826-6.174 96.81 381 14 0.1966 321.531 316.755 1.049 1.051 0.460 6.172-4.868 97.27 748 36 0.1696 361.134 355.017 0.971 1.030 0.460 4.862-3.836 96.79 1456 84 0.1458 436.971 427.912 1.017 0.996 0.460 3.836-3.102 94.30 2431 150 0.1972 310.711 297.524 1.036 0.944 0.190 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.3818 ============================ 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 = 0.566528 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.093940 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 0.1648 0.2238 0.0591 0.014 1.9 0.0 0.4 2.1 0 0.028 0.1741 0.2307 0.0566 0.014 1.9 0.2 0.4 1.7 1 0.085 0.1653 0.2276 0.0623 0.016 2.0 0.0 0.4 2.5 0 0.170 0.1600 0.2270 0.0670 0.019 2.2 0.2 0.4 2.5 1 0.255 0.1569 0.2274 0.0704 0.021 2.3 0.5 0.7 2.9 1 0.340 0.1544 0.2266 0.0722 0.023 2.5 0.5 0.7 2.9 1 0.425 0.1472 0.2257 0.0784 0.028 2.9 0.5 0.7 3.8 2 0.510 0.1459 0.2261 0.0802 0.031 3.0 0.5 0.7 4.2 2 0.595 0.1588 0.2273 0.0685 0.019 2.2 0.5 0.7 2.5 1 0.283 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1648 0.2238 0.0591 0.014 1.9 0.0 0.4 2.1 0 0.028 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 16.48 22.38 5.91 5.757 19.744 0.094 5.623 18.15 21.82 3.68 5.094 20.504 0.003 5.736 17.42 21.94 4.52 4.810 20.269 0.012 5.686 16.20 22.18 5.98 6.044 20.134 0.047 5.595 15.81 22.62 6.81 7.386 20.175 0.094 5.559 15.56 22.98 7.41 8.911 20.449 0.141 5.533 15.51 23.19 7.68 9.645 20.575 0.188 5.525 15.47 23.35 7.88 10.355 20.732 0.235 5.520 15.50 23.40 7.90 10.336 20.715 0.282 5.522 15.52 23.48 7.96 10.392 20.725 0.329 5.524 15.54 23.52 7.98 10.384 20.714 0.376 5.526 15.54 23.56 8.02 10.550 20.755 0.423 5.526 15.55 23.61 8.06 10.714 20.797 0.470 5.526 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.003 Accepted refinement result: 18.15 21.82 3.68 5.094 20.504 0.003 5.736 Individual atomic B min max mean iso aniso Overall: 8.11 56.40 19.55 3.26 2155 0 Protein: 8.11 56.40 19.55 3.26 2155 0 Chain A: 11.00 55.34 20.05 N/A 1073 0 Chain B: 8.11 56.40 19.06 N/A 1082 0 Histogram: Values Number of atoms 8.11 - 12.94 274 12.94 - 17.76 868 17.76 - 22.59 479 22.59 - 27.42 247 27.42 - 32.25 131 32.25 - 37.08 61 37.08 - 41.91 52 41.91 - 46.74 21 46.74 - 51.57 16 51.57 - 56.40 6 =========================== Idealize ADP of riding H ========================== r_work=0.1815 r_free=0.2182 r_work=0.1831 r_free=0.2178 ----------X-ray data---------- |--(resolution: 3.10 - 36.90 A, n_refl.=5694 (all), 5.23 % free)-------------| | | | r_work= 0.1831 r_free= 0.2178 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.745754 | | target function (ml) not normalized (work): 31004.090075 | | target function (ml) not normalized (free): 1803.003977 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 36.90 - 3.91 0.97 2808 138 0.1635 0.1663 5.7733 5.9507| | 2: 3.91 - 3.10 0.94 2588 160 0.2102 0.2835 5.7158 6.1363| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 36.90 - 3.91 2808 138 0.92 12.97 0.99 1.04 11946.78| | 2: 3.91 - 3.10 2588 160 0.91 15.69 1.01 1.04 12375.66| |alpha: min = 0.90 max = 1.19 mean = 1.04| |beta: min = 3422.45 max = 19460.76 mean = 12152.48| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 90.00 mean = 14.28| |phase err.(test): min = 0.00 max = 89.32 mean = 14.51| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1849 0.1831 0.2178 n_refl.: 5694 re-set all scales: r(all,work,free)=0.3721 0.3739 0.3419 n_refl.: 5694 remove outliers: r(all,work,free)=0.3721 0.3739 0.3419 n_refl.: 5694 overall B=0.00 to atoms: r(all,work,free)=0.3721 0.3739 0.3419 n_refl.: 5694 bulk-solvent and scaling: r(all,work,free)=0.1878 0.1860 0.2210 n_refl.: 5694 remove outliers: r(all,work,free)=0.1878 0.1860 0.2210 n_refl.: 5694 ======================== 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 36.902-12.728 94.29 95 4 0.2797 377.089 353.918 1.172 1.043 0.400 12.598-9.947 96.15 96 4 0.1222 538.242 552.350 1.174 1.034 0.400 9.931-7.830 97.01 189 6 0.1381 475.633 475.863 1.218 1.032 0.420 7.826-6.174 96.81 381 14 0.1888 321.531 317.298 1.090 1.025 0.480 6.172-4.868 97.27 748 36 0.1662 361.134 354.569 0.996 1.013 0.480 4.862-3.836 96.79 1456 84 0.1606 436.971 427.454 1.028 0.993 0.390 3.836-3.102 94.30 2431 150 0.2186 310.711 295.621 1.019 0.962 0.200 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.1072 ================= 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 : 0.3522 0.3459 0.024 2.035 2.0 37.2 13.1 0 0.000 1_bss: 0.1898 0.2497 0.024 2.035 3.1 38.4 14.2 0 0.000 1_settarget: 0.1898 0.2497 0.024 2.035 3.1 38.4 14.2 0 0.000 1_weight: 0.1898 0.2497 0.024 2.035 3.1 38.4 14.2 0 0.000 1_xyzrec: 0.2038 0.2373 0.014 1.885 3.1 38.4 14.2 0 0.263 1_adp: 0.1815 0.2362 0.014 1.885 2.7 46.7 15.7 0 0.263 1_regHadp: 0.1800 0.2353 0.014 1.885 2.7 46.7 15.7 0 0.263 2_bss: 0.1793 0.2358 0.014 1.885 3.8 47.8 16.7 0 0.263 2_settarget: 0.1793 0.2358 0.014 1.885 3.8 47.8 16.7 0 0.263 2_updatecdl: 0.1793 0.2358 0.014 1.872 3.8 47.8 16.7 0 0.263 2_weight: 0.1793 0.2358 0.014 1.872 3.8 47.8 16.7 0 0.263 2_xyzrec: 0.1762 0.2354 0.014 1.884 3.8 47.8 16.7 0 0.262 2_adp: 0.1693 0.2291 0.014 1.884 2.3 61.4 18.0 0 0.262 2_regHadp: 0.1690 0.2296 0.014 1.884 2.3 61.4 18.0 0 0.262 3_bss: 0.1745 0.2306 0.014 1.884 2.3 61.4 18.0 0 0.262 3_settarget: 0.1745 0.2306 0.014 1.884 2.3 61.4 18.0 0 0.262 3_updatecdl: 0.1745 0.2306 0.014 1.882 2.3 61.4 18.0 0 0.262 3_setrh: 0.1745 0.2306 0.014 1.882 2.3 61.4 18.0 0 0.262 3_weight: 0.1745 0.2306 0.014 1.882 2.3 61.4 18.0 0 0.262 3_xyzrec: 0.1648 0.2238 0.014 1.894 2.3 61.4 18.0 0 0.273 3_adp: 0.1815 0.2182 0.014 1.894 8.1 56.4 19.6 0 0.273 3_regHadp: 0.1831 0.2178 0.014 1.894 8.1 56.4 19.6 0 0.273 end: 0.1860 0.2210 0.014 1.894 8.1 56.4 19.6 0 0.273 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2h1g_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_2h1g_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.7600 Refinement macro-cycles (run) : 125.7100 Write final files (write_after_run_outputs) : 10.0900 Total : 138.5600 Total CPU time: 2.64 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:35:55 PDT -0700 (1723221355.70 s) Start R-work = 0.1898, R-free = 0.2497 Final R-work = 0.1860, R-free = 0.2210 =============================================================================== Job complete usr+sys time: 167.03 seconds wall clock time: 4 minutes 27.31 seconds (267.31 seconds total)