Starting phenix.refine on Mon May 20 17:15:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/3fm7.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.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 strategy=individual_sites+individual_adp+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/3fm7.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/3fm7.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.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 { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1598 Classifications: {'peptide': 103} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1609 Classifications: {'peptide': 104} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 23} Chain: "D" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 24} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1381 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "F" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1380 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Time building chain proxies: 1.18, per 1000 atoms: 0.17 Number of scatterers: 6838 At special positions: 0 Unit cell: (115.79, 115.79, 90.5004, 90, 90, 120) Space group: P 62 (No. 171) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 666 8.00 N 569 7.00 C 2187 6.00 H 3394 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: 1.79 Conformation dependent library (CDL) restraints added in 253.3 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 8 helices and 4 sheets defined 28.5% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.750A pdb=" N LYS A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 19 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 53 removed outlier: 5.803A pdb=" N ASN A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR A 41 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 42 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN A 47 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS A 48 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 51 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 53 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 26 removed outlier: 4.854A pdb=" N THR B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 48 removed outlier: 4.661A pdb=" N ASN B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ASN B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 31 removed outlier: 3.637A pdb=" N GLU E 30 " --> pdb=" O THR E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 50 Processing helix chain 'F' and resid 16 through 31 removed outlier: 3.603A pdb=" N GLN F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 49 Processing sheet with id= A, first strand: chain 'A' and resid 60 through 69 removed outlier: 3.531A pdb=" N MET A 68 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 101 " --> pdb=" O MET A 68 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 59 through 69 Processing sheet with id= C, first strand: chain 'E' and resid 54 through 59 removed outlier: 6.114A pdb=" N TYR E 77 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE E 8 " --> pdb=" O TYR E 77 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 54 through 59 removed outlier: 6.889A pdb=" N TYR F 77 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE F 8 " --> pdb=" O TYR F 77 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 366 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: 1.56 Time building geometry restraints manager: 2.05 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: 3382 1.15 - 1.31: 591 1.31 - 1.48: 1393 1.48 - 1.64: 1508 1.64 - 1.81: 32 Bond restraints: 6906 Sorted by residual: bond pdb=" NE2 GLN A 33 " pdb="HE21 GLN A 33 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N ALA E 82 " pdb=" H ALA E 82 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NE2 GLN F 27 " pdb="HE21 GLN F 27 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN D 116 " pdb="HE21 GLN D 116 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N PHE F 86 " pdb=" H PHE F 86 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6901 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.50: 230 107.50 - 114.12: 8500 114.12 - 120.73: 1545 120.73 - 127.35: 2144 127.35 - 133.97: 26 Bond angle restraints: 12445 Sorted by residual: angle pdb=" C ASN F 51 " pdb=" N PRO F 52 " pdb=" CA PRO F 52 " ideal model delta sigma weight residual 119.89 122.75 -2.86 1.02e+00 9.61e-01 7.84e+00 angle pdb=" N VAL E 7 " pdb=" CA VAL E 7 " pdb=" C VAL E 7 " ideal model delta sigma weight residual 106.72 111.14 -4.42 1.59e+00 3.96e-01 7.74e+00 angle pdb=" N ASN C 119 " pdb=" CA ASN C 119 " pdb=" C ASN C 119 " ideal model delta sigma weight residual 107.61 112.16 -4.55 1.74e+00 3.30e-01 6.84e+00 angle pdb=" N ASN E 10 " pdb=" CA ASN E 10 " pdb=" C ASN E 10 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.71e+00 angle pdb=" CA GLY A 72 " pdb=" C GLY A 72 " pdb=" N ALA A 73 " ideal model delta sigma weight residual 118.67 116.19 2.48 9.80e-01 1.04e+00 6.40e+00 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.78: 2904 26.78 - 53.56: 289 53.56 - 80.34: 53 80.34 - 107.12: 5 107.12 - 133.91: 2 Dihedral angle restraints: 3253 sinusoidal: 1731 harmonic: 1522 Sorted by residual: dihedral pdb=" CA MET F 13 " pdb=" C MET F 13 " pdb=" N SER F 14 " pdb=" CA SER F 14 " ideal model delta harmonic sigma weight residual 180.00 46.09 133.91 0 5.00e+00 4.00e-02 7.17e+02 dihedral pdb=" CA ASN C 114 " pdb=" C ASN C 114 " pdb=" N VAL C 115 " pdb=" CA VAL C 115 " ideal model delta harmonic sigma weight residual 180.00 52.83 127.17 0 5.00e+00 4.00e-02 6.47e+02 dihedral pdb=" CA MET E 13 " pdb=" C MET E 13 " pdb=" N SER E 14 " pdb=" CA SER E 14 " ideal model delta harmonic sigma weight residual -180.00 -75.18 -104.82 0 5.00e+00 4.00e-02 4.39e+02 ... (remaining 3250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 437 0.022 - 0.043: 11 0.043 - 0.065: 19 0.065 - 0.087: 59 0.087 - 0.108: 13 Chirality restraints: 539 Sorted by residual: chirality pdb=" CA ASN D 114 " pdb=" N ASN D 114 " pdb=" C ASN D 114 " pdb=" CB ASN D 114 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.93e-01 chirality pdb=" CA ILE B 103 " pdb=" N ILE B 103 " pdb=" C ILE B 103 " pdb=" CB ILE B 103 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.09 2.00e-01 2.50e+01 2.10e-01 chirality pdb=" CA ILE B 23 " pdb=" N ILE B 23 " pdb=" C ILE B 23 " pdb=" CB ILE B 23 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 2.04e-01 ... (remaining 536 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 40 " -0.000 2.00e-02 2.50e+03 7.01e-04 1.97e-02 pdb=" CG TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP B 40 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 40 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP B 40 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 46 " 0.000 2.00e-02 2.50e+03 7.99e-04 1.91e-02 pdb=" CG PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE F 46 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 46 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE F 46 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE F 46 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE F 46 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 54 " -0.000 2.00e-02 2.50e+03 6.55e-04 1.72e-02 pdb=" CG TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP E 54 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP E 54 " 0.000 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 0.75 - 1.52: 46 1.52 - 2.29: 1632 2.29 - 3.06: 20346 3.06 - 3.83: 29944 3.83 - 4.60: 47504 Warning: very small nonbonded interaction distances. Nonbonded interactions: 99472 Sorted by model distance: nonbonded pdb=" HA ASN C 114 " pdb="HG23 VAL C 115 " model vdw 0.746 2.440 nonbonded pdb=" HG3 GLN C 133 " pdb=" HB3 LYS F 36 " model vdw 0.848 2.440 nonbonded pdb=" HA GLN C 116 " pdb=" HB2 ALA C 117 " model vdw 0.871 2.440 nonbonded pdb=" HG2 ARG B 94 " pdb="HH11 ARG B 94 " model vdw 0.985 2.270 nonbonded pdb=" HA MET F 13 " pdb=" HB2 SER F 14 " model vdw 1.040 2.440 ... (remaining 99467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 22 15.91 1 O 666 7.97 1 N 569 6.97 1 C 2187 5.97 1 H 3394 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: 3394 of 6838 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 6838 n_use_u_iso = 6838 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 = 6838 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6838 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 6838 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 { 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 12 through 22 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 34 through 53 helix_type = alpha pi *3_10 unknown } helix { serial_number = "3" helix_identifier = "3" selection = chain 'B' and resid 13 through 26 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'B' and resid 34 through 48 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'E' and resid 16 through 31 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'E' and resid 35 through 50 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'F' and resid 16 through 31 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'F' and resid 35 through 49 } sheet { first_strand = chain 'A' and resid 60 through 69 sheet_id = " A" strand { selection = chain 'A' and resid 100 through 109 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 109 and name N bond_start_previous = chain 'A' and resid 60 and name O } strand { selection = chain 'A' and resid 89 through 96 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 95 and name N bond_start_previous = chain 'A' and resid 102 and name O } } sheet { first_strand = chain 'B' and resid 59 through 69 sheet_id = " B" strand { selection = chain 'B' and resid 100 through 110 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 109 and name N bond_start_previous = chain 'B' and resid 60 and name O } strand { selection = chain 'B' and resid 89 through 94 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 93 and name N bond_start_previous = chain 'B' and resid 104 and name O } } sheet { first_strand = chain 'E' and resid 54 through 59 sheet_id = " C" strand { selection = chain 'E' and resid 81 through 87 sense = parallel *antiparallel unknown bond_start_current = chain 'E' and resid 86 and name N bond_start_previous = chain 'E' and resid 55 and name O } strand { selection = chain 'E' and resid 73 through 78 sense = parallel *antiparallel unknown bond_start_current = chain 'E' and resid 78 and name N bond_start_previous = chain 'E' and resid 81 and name O } strand { selection = chain 'E' and resid 6 through 12 sense = parallel *antiparallel unknown bond_start_current = chain 'E' and resid 12 and name N bond_start_previous = chain 'E' and resid 73 and name O } } sheet { first_strand = chain 'F' and resid 54 through 59 sheet_id = " D" strand { selection = chain 'F' and resid 81 through 87 sense = parallel *antiparallel unknown bond_start_current = chain 'F' and resid 86 and name N bond_start_previous = chain 'F' and resid 55 and name O } strand { selection = chain 'F' and resid 73 through 78 sense = parallel *antiparallel unknown bond_start_current = chain 'F' and resid 78 and name N bond_start_previous = chain 'F' and resid 81 and name O } strand { selection = chain 'F' and resid 6 through 12 sense = parallel *antiparallel unknown bond_start_current = chain 'F' and resid 12 and name N bond_start_previous = chain 'F' and resid 73 and name O } } } enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "3fm7_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3394 occupancy sum: 3394.00 (% of total atoms 49.68) Rotatable: count: 1005 occupancy sum: 1005.00 (% of total atoms 14.71) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 35.65 A, n_refl.=8745 (all), 9.95 % free)-------------| | | | r_work= 0.3573 r_free= 0.3825 coordinate error (max.-lik. estimate): 0.14 A | | | | normalized target function (ml) (work): 6.431057 | | target function (ml) not normalized (work): 50644.571594 | | target function (ml) not normalized (free): 5712.019596 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 35.65 - 6.35 1.00 1358 142 0.4105 0.4302 7.4385 7.4058| | 2: 6.35 - 5.05 1.00 1326 136 0.3185 0.3402 6.6863 6.7637| | 3: 5.04 - 4.41 1.00 1320 143 0.3188 0.3218 6.3284 6.4613| | 4: 4.41 - 4.01 0.99 1291 153 0.3401 0.3699 6.1277 6.4141| | 5: 4.01 - 3.72 0.99 1285 148 0.3360 0.4071 5.9732 6.2399| | 6: 3.72 - 3.50 0.99 1295 148 0.3851 0.4177 5.9746 6.1601| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 35.65 - 6.35 1358 142 0.52 50.23 0.82 0.72 437329.23| | 2: 6.35 - 5.05 1326 136 0.56 47.21 1.23 0.89 198795.77| | 3: 5.04 - 4.41 1320 143 0.78 29.03 1.38 1.01 71014.34| | 4: 4.41 - 4.01 1291 153 0.71 34.61 1.41 1.00 52577.48| | 5: 4.01 - 3.72 1285 148 0.62 42.28 1.34 0.96 45018.50| | 6: 3.72 - 3.50 1295 148 0.64 41.10 1.46 0.94 40633.46| |alpha: min = 0.72 max = 1.01 mean = 0.92| |beta: min = 40633.46 max = 437329.23 mean = 143438.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.64| |phase err.(work): min = 0.00 max = 89.98 mean = 40.81| |phase err.(test): min = 0.00 max = 89.61 mean = 40.40| |-----------------------------------------------------------------------------| ----------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 : 0.003 0.016 3512 Z= 0.194 Angle : 0.846 4.753 4762 Z= 0.586 Chirality : 0.032 0.108 539 Planarity : 0.000 0.001 601 Dihedral : 23.554 133.906 1264 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 44.73 Ramachandran Plot: Outliers : 4.77 % Allowed : 13.60 % Favored : 81.62 % Rotamer: Outliers : 25.33 % Allowed : 17.15 % Favored : 57.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 2.64 % 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: -5.75 (0.30), residues: 419 helix: -4.63 (0.19), residues: 131 sheet: -1.47 (0.57), residues: 92 loop : -4.46 (0.27), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 60 TYR 0.001 0.000 TYR F 65 PHE 0.001 0.000 PHE F 46 TRP 0.001 0.000 TRP B 40 HIS 0.000 0.000 HIS A 76 Individual atomic B min max mean iso aniso Overall: 2.00 500.00 94.66 89.80 3444 0 Protein: 2.00 500.00 94.66 89.80 3444 0 Chain A: 2.00 500.00 114.65 N/A 807 0 Chain B: 2.00 458.88 97.81 N/A 813 0 Chain C: 2.00 495.15 104.99 N/A 215 0 Chain D: 2.00 500.00 119.77 N/A 215 0 Chain E: 2.00 478.28 71.82 N/A 697 0 Chain F: 2.00 403.25 79.76 N/A 697 0 Histogram: Values Number of atoms 2.00 - 51.80 934 51.80 - 101.60 1312 101.60 - 151.40 657 151.40 - 201.20 310 201.20 - 251.00 111 251.00 - 300.80 57 300.80 - 350.60 34 350.60 - 400.40 17 400.40 - 450.20 6 450.20 - 500.00 6 |-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: 3.50 - 35.65 A, n_refl.=8745 (all), 9.95 % free)-------------| | | | r_work= 0.3573 r_free= 0.3825 coordinate error (max.-lik. estimate): 0.14 A | | | | normalized target function (ml) (work): 6.431057 | | target function (ml) not normalized (work): 50644.571594 | | target function (ml) not normalized (free): 5712.019596 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3589 0.3573 0.3825 n_refl.: 8745 re-set all scales: r(all,work,free)=0.3589 0.3573 0.3825 n_refl.: 8745 remove outliers: r(all,work,free)=0.3585 0.3571 0.3811 n_refl.: 8739 overall B=17.64 to atoms: r(all,work,free)=0.4218 0.4229 0.4187 n_refl.: 8739 bulk-solvent and scaling: r(all,work,free)=0.2240 0.2141 0.3139 n_refl.: 8739 remove outliers: r(all,work,free)=0.2235 0.2135 0.3139 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3558 1472.375 1342.545 1.239 0.973 0.325 15.490-12.512 99.01 89 11 0.2187 1306.036 1261.365 1.106 0.974 0.283 12.419-9.967 99.48 175 15 0.1814 1476.037 1437.608 1.169 0.977 0.280 9.933-7.985 99.73 337 34 0.1928 1108.226 1073.275 1.178 0.978 0.264 7.976-6.403 100.00 631 64 0.2456 609.809 575.118 1.094 0.979 0.229 6.399-5.132 99.93 1234 135 0.2161 578.066 550.281 0.973 0.981 0.174 5.129-4.115 99.81 2357 259 0.1739 559.520 545.409 0.991 0.984 0.113 4.114-3.501 98.83 2959 341 0.2478 337.971 323.299 1.036 0.987 0.037 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0046 b_overall=-0.2819 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2135 r_free=0.3139 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2135 r_free=0.3139 ========================= Local real-space refinement ========================= Before: r_work=0.2135 r_free=0.3139 270 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 174 time to evaluate : 0.291 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 46 residues processed: 96 average time/residue: 0.2146 time to fit residues: 27.0392 After: r_work=0.2273 r_free=0.3136 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.850986 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.124400 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2319 0.3237 0.0919 0.003 0.7 9.8 1.9 10.0 0 0.125 0.2281 0.3231 0.0950 0.003 0.7 9.5 1.9 10.3 0 0.250 0.2221 0.3207 0.0986 0.004 0.7 9.5 1.9 11.3 0 0.500 0.2161 0.3227 0.1066 0.004 0.7 10.3 1.9 11.3 0 1.000 0.2097 0.3249 0.1152 0.006 0.8 14.1 1.9 12.4 0 2.000 0.2047 0.3252 0.1205 0.007 0.9 15.1 1.9 13.7 0 3.000 0.2013 0.3265 0.1252 0.008 1.0 17.7 2.1 15.6 0 4.000 0.1987 0.3263 0.1276 0.009 1.0 20.1 2.1 16.9 0 5.000 0.1966 0.3254 0.1288 0.010 1.1 22.4 2.1 18.7 0 6.000 0.1947 0.3264 0.1317 0.011 1.2 24.3 2.1 19.5 0 7.000 0.1933 0.3260 0.1328 0.013 1.3 25.4 2.1 19.3 0 8.000 0.1917 0.3241 0.1325 0.013 1.3 26.8 2.4 19.5 0 9.000 0.1902 0.3243 0.1341 0.015 1.4 28.3 2.4 20.1 0 10.000 0.1918 0.3247 0.1329 0.013 1.3 26.7 2.4 19.8 0 8.925 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2221 0.3207 0.0986 0.004 0.7 9.5 1.9 11.3 0 0.500 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2221 r_free=0.3207 213 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 170 time to evaluate : 1.065 outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3255 time to fit residues: 23.1323 After: r_work=0.2312 r_free=0.3249 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.12 32.49 9.37 64.040 110.958 0.124 0.064 27.32 31.86 4.54 46.645 120.198 0.004 0.085 26.99 31.72 4.72 46.743 120.038 0.016 0.083 25.90 31.23 5.33 47.181 119.484 0.062 0.078 24.83 30.78 5.95 47.810 118.935 0.124 0.073 24.06 30.49 6.43 48.429 118.530 0.187 0.069 23.46 30.26 6.81 49.029 118.203 0.249 0.066 23.03 30.13 7.11 49.470 118.208 0.311 0.064 22.60 30.03 7.43 50.054 117.901 0.373 0.062 22.25 29.95 7.70 50.605 117.629 0.435 0.061 21.96 29.90 7.94 51.109 117.426 0.498 0.059 21.72 29.86 8.15 51.557 117.327 0.560 0.058 21.51 29.82 8.31 52.003 117.182 0.622 0.057 max suggested for this run: 22.19 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.004 Accepted refinement result: 27.32 31.86 4.54 46.645 120.198 0.004 0.085 Individual atomic B min max mean iso aniso Overall: 66.10 512.64 130.65 57.63 3444 0 Protein: 66.10 512.64 130.65 57.63 3444 0 Chain A: 78.78 512.64 152.11 N/A 807 0 Chain B: 80.90 471.52 133.54 N/A 813 0 Chain C: 75.60 507.79 144.18 N/A 215 0 Chain D: 80.63 512.64 154.98 N/A 215 0 Chain E: 66.10 490.92 106.52 N/A 697 0 Chain F: 73.08 415.89 114.87 N/A 697 0 Histogram: Values Number of atoms 66.10 - 110.75 1525 110.75 - 155.41 1241 155.41 - 200.06 390 200.06 - 244.72 142 244.72 - 289.37 61 289.37 - 334.02 36 334.02 - 378.68 26 378.68 - 423.33 14 423.33 - 467.99 3 467.99 - 512.64 6 =========================== Idealize ADP of riding H ========================== r_work=0.2732 r_free=0.3186 r_work=0.2769 r_free=0.3135 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2769 r_free= 0.3135 coordinate error (max.-lik. estimate): 0.13 A | | | | normalized target function (ls_wunit_k1) (work): 0.086953 | | target function (ls_wunit_k1) not normalized (work): 684.234343 | | target function (ls_wunit_k1) not normalized (free): 100.677462 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2804 0.2769 0.3135 n_refl.: 8738 re-set all scales: r(all,work,free)=0.5219 0.5255 0.4890 n_refl.: 8738 remove outliers: r(all,work,free)=0.5219 0.5255 0.4890 n_refl.: 8738 overall B=-30.69 to atoms: r(all,work,free)=0.4159 0.4181 0.3993 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2524 0.2477 0.2964 n_refl.: 8738 remove outliers: r(all,work,free)=0.2524 0.2477 0.2964 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3539 656.250 597.320 1.138 1.018 0.315 15.490-12.512 99.01 89 11 0.2097 582.112 559.395 1.070 1.018 0.281 12.419-9.967 99.48 175 15 0.1613 657.883 642.292 1.188 1.021 0.282 9.933-7.985 99.73 337 34 0.1844 493.946 476.149 1.195 1.022 0.287 7.976-6.403 100.00 631 64 0.2621 271.797 256.538 1.087 1.023 0.245 6.399-5.132 99.93 1234 135 0.2422 257.649 244.451 0.948 1.025 0.204 5.129-4.115 99.81 2357 259 0.2222 249.383 242.573 0.963 1.027 0.146 4.114-3.501 98.83 2959 341 0.3159 150.637 142.136 0.978 1.029 0.054 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.2877 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2477 r_free=0.2964 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 38 ASN A 85 ASN B 84 ASN Total number of N/Q/H flips: 4 r_work=0.2480 r_free=0.2961 ========================= Local real-space refinement ========================= Before: r_work=0.2480 r_free=0.2961 168 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.766 outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5187 time to fit residues: 2.8213 After: r_work=0.2478 r_free=0.2966 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 5.294630 wxc_scale = 0.022 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.034826 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2559 0.3079 0.0520 0.002 0.6 8.9 1.4 2.1 0 0.011 0.2526 0.3064 0.0537 0.002 0.6 9.2 1.4 1.8 0 0.034 0.2475 0.3040 0.0565 0.003 0.6 9.2 1.7 1.3 0 0.069 0.2444 0.3030 0.0587 0.003 0.6 9.2 1.7 1.6 0 0.103 0.2423 0.3037 0.0614 0.003 0.6 9.4 1.7 2.1 0 0.138 0.2399 0.3019 0.0619 0.003 0.6 8.7 1.7 2.4 0 0.172 0.2379 0.3025 0.0646 0.003 0.6 10.1 1.7 2.6 0 0.206 0.2364 0.3009 0.0645 0.003 0.6 10.0 1.7 2.6 0 0.241 0.2436 0.3031 0.0595 0.003 0.6 9.7 1.7 1.8 0 0.115 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2364 0.3009 0.0645 0.003 0.6 10.0 1.7 2.6 0 0.241 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2364 r_free=0.3009 174 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 164 time to evaluate : 1.075 outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2817 time to fit residues: 6.3556 After: r_work=0.2378 r_free=0.3026 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.78 30.26 6.48 45.518 111.617 0.035 5.672 29.84 32.18 2.34 33.446 127.257 0.001 5.721 28.59 31.34 2.75 33.187 126.210 0.004 5.710 25.65 29.28 3.63 34.097 123.094 0.017 5.682 23.74 28.55 4.81 36.562 120.469 0.035 5.638 22.63 28.27 5.64 38.789 118.363 0.052 5.609 22.12 28.31 6.19 40.211 117.098 0.070 5.599 21.83 28.45 6.62 41.099 115.785 0.087 5.597 21.69 28.47 6.77 41.826 115.253 0.104 5.595 21.62 28.51 6.89 42.341 114.975 0.122 5.594 21.57 28.57 7.00 42.747 114.789 0.139 5.593 21.53 28.60 7.07 43.078 114.664 0.157 5.593 21.51 28.65 7.14 43.350 114.574 0.174 5.593 max suggested for this run: 22.32 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.017 Accepted refinement result: 25.65 29.28 3.63 34.097 123.094 0.017 5.682 Individual atomic B min max mean iso aniso Overall: 35.97 476.95 122.75 37.73 3444 0 Protein: 35.97 476.95 122.75 37.73 3444 0 Chain A: 79.87 476.95 152.00 N/A 807 0 Chain B: 54.42 435.83 127.55 N/A 813 0 Chain C: 45.43 472.10 138.07 N/A 215 0 Chain D: 59.93 476.95 151.40 N/A 215 0 Chain E: 35.97 455.23 90.94 N/A 697 0 Chain F: 39.49 380.20 101.53 N/A 697 0 Histogram: Values Number of atoms 35.97 - 80.07 579 80.07 - 124.17 1442 124.17 - 168.26 982 168.26 - 212.36 283 212.36 - 256.46 76 256.46 - 300.56 35 300.56 - 344.66 24 344.66 - 388.76 14 388.76 - 432.86 3 432.86 - 476.95 6 =========================== Idealize ADP of riding H ========================== r_work=0.2565 r_free=0.2928 r_work=0.2598 r_free=0.2925 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2598 r_free= 0.2925 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.688936 | | target function (ml) not normalized (work): 44766.236238 | | target function (ml) not normalized (free): 5019.162175 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2630 0.2598 0.2925 n_refl.: 8738 re-set all scales: r(all,work,free)=0.4766 0.4807 0.4402 n_refl.: 8738 remove outliers: r(all,work,free)=0.4766 0.4807 0.4402 n_refl.: 8738 overall B=-13.57 to atoms: r(all,work,free)=0.4277 0.4312 0.3985 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2521 0.2477 0.2931 n_refl.: 8738 remove outliers: r(all,work,free)=0.2521 0.2477 0.2931 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3662 656.250 593.229 1.250 0.970 0.327 15.490-12.512 99.01 89 11 0.2037 582.112 562.268 1.175 0.970 0.295 12.419-9.967 99.48 175 15 0.1577 657.883 642.778 1.184 0.975 0.267 9.933-7.985 99.73 337 34 0.1753 493.946 479.262 1.231 0.976 0.261 7.976-6.403 100.00 631 64 0.2650 271.797 255.486 1.144 0.979 0.225 6.399-5.132 99.93 1234 135 0.2491 257.649 243.321 0.998 0.983 0.167 5.129-4.115 99.81 2357 259 0.2182 249.383 241.911 0.991 0.989 0.106 4.114-3.501 98.83 2959 341 0.3187 150.637 141.484 1.004 0.996 0.064 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.8280 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2477 r_free=0.2931 After: r_work=0.2477 r_free=0.2932 ================================== NQH flips ================================== r_work=0.2477 r_free=0.2932 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 51 ASN Total number of N/Q/H flips: 1 r_work=0.2477 r_free=0.2929 ========================= Local real-space refinement ========================= Before: r_work=0.2477 r_free=0.2929 164 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.118 outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2644 time to fit residues: 1.3784 After: r_work=0.2477 r_free=0.2929 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 5.859176 wxc_scale = 0.034 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.032908 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2485 0.2928 0.0443 0.003 0.7 11.6 1.4 0.5 0 0.020 0.2483 0.2927 0.0444 0.003 0.7 11.7 1.4 0.8 0 0.059 0.2480 0.2925 0.0445 0.003 0.7 11.6 1.4 0.8 0 0.119 0.2478 0.2926 0.0449 0.004 0.7 11.7 1.4 0.8 0 0.178 0.2474 0.2925 0.0451 0.004 0.7 11.7 1.4 0.8 0 0.237 0.2471 0.2925 0.0454 0.004 0.7 11.7 1.4 0.8 0 0.297 0.2468 0.2925 0.0457 0.004 0.7 11.7 1.4 0.8 0 0.356 0.2465 0.2926 0.0462 0.004 0.7 11.7 1.4 0.8 0 0.415 0.2477 0.2927 0.0450 0.004 0.7 11.7 1.4 0.8 0 0.198 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2485 0.2928 0.0443 0.003 0.7 11.6 1.4 0.5 0 0.020 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2485 r_free=0.2928 161 residues out of total 379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 0.506 outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1769 time to fit residues: 1.1695 After: r_work=0.2496 r_free=0.2917 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.96 29.17 4.21 32.778 121.615 0.033 5.691 30.38 31.58 1.19 27.532 130.665 0.001 5.756 29.67 31.15 1.48 26.975 130.876 0.004 5.736 26.32 29.43 3.11 29.120 127.294 0.016 5.674 24.03 28.38 4.36 31.628 122.952 0.033 5.647 23.71 28.43 4.72 32.199 122.345 0.049 5.644 23.60 28.48 4.88 32.461 122.112 0.066 5.643 23.26 28.70 5.44 32.847 122.913 0.082 5.632 23.20 28.73 5.52 33.012 122.880 0.099 5.632 23.16 28.75 5.58 33.153 122.891 0.115 5.632 23.13 28.78 5.64 33.274 122.926 0.132 5.632 23.11 28.80 5.69 33.386 122.972 0.148 5.632 23.09 28.83 5.74 33.491 123.025 0.165 5.632 max suggested for this run: 24.32 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.016 Accepted refinement result: 26.32 29.43 3.11 29.120 127.294 0.016 5.674 Individual atomic B min max mean iso aniso Overall: 50.37 458.38 120.45 33.38 3444 0 Protein: 50.37 458.38 120.45 33.38 3444 0 Chain A: 85.14 458.38 148.65 N/A 807 0 Chain B: 65.63 417.26 124.55 N/A 813 0 Chain C: 65.89 453.53 133.88 N/A 215 0 Chain D: 66.52 458.38 147.90 N/A 215 0 Chain E: 50.37 436.66 91.72 N/A 697 0 Chain F: 52.99 361.63 99.16 N/A 697 0 Histogram: Values Number of atoms 50.37 - 91.17 1035 91.17 - 131.97 1306 131.97 - 172.77 772 172.77 - 213.58 202 213.58 - 254.38 62 254.38 - 295.18 28 295.18 - 335.98 18 335.98 - 376.78 13 376.78 - 417.58 4 417.58 - 458.38 4 =========================== Idealize ADP of riding H ========================== r_work=0.2632 r_free=0.2943 r_work=0.2640 r_free=0.2951 ----------X-ray data---------- |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2640 r_free= 0.2951 coordinate error (max.-lik. estimate): 0.15 A | | | | normalized target function (ml) (work): 5.677255 | | target function (ml) not normalized (work): 44674.321562 | | target function (ml) not normalized (free): 5010.270124 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 35.65 - 6.35 1.00 1354 141 0.2402 0.2684 6.236 6.4365| | 2: 6.35 - 5.05 1.00 1326 136 0.2437 0.2936 5.8252 5.9627| | 3: 5.04 - 4.41 1.00 1320 143 0.2269 0.2461 5.6561 5.6618| | 4: 4.41 - 4.01 0.99 1291 153 0.2745 0.3074 5.5159 5.6754| | 5: 4.01 - 3.72 0.99 1285 148 0.3262 0.3370 5.3774 5.4419| | 6: 3.72 - 3.50 0.99 1293 148 0.3656 0.3973 5.4211 5.4623| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 35.65 - 6.35 1354 141 0.72 33.19 0.92 0.84 55027.49| | 2: 6.35 - 5.05 1326 136 0.71 35.03 1.02 0.90 29066.71| | 3: 5.04 - 4.41 1320 143 0.83 24.13 1.12 0.94 14060.50| | 4: 4.41 - 4.01 1291 153 0.77 29.39 1.13 0.96 11039.55| | 5: 4.01 - 3.72 1285 148 0.68 37.71 1.19 0.94 9863.65| | 6: 3.72 - 3.50 1293 148 0.67 38.57 1.25 0.91 10060.85| |alpha: min = 0.84 max = 0.96 mean = 0.92| |beta: min = 9863.65 max = 55027.49 mean = 21800.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.73| |phase err.(work): min = 0.00 max = 89.91 mean = 32.98| |phase err.(test): min = 0.00 max = 89.32 mean = 32.73| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2669 0.2638 0.2957 n_refl.: 8738 re-set all scales: r(all,work,free)=0.4915 0.4957 0.4543 n_refl.: 8738 remove outliers: r(all,work,free)=0.4915 0.4957 0.4543 n_refl.: 8738 overall B=-17.20 to atoms: r(all,work,free)=0.4303 0.4339 0.4008 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2508 0.2466 0.2893 n_refl.: 8738 remove outliers: r(all,work,free)=0.2508 0.2466 0.2893 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3699 656.250 589.341 1.211 1.011 0.336 15.490-12.512 99.01 89 11 0.2099 582.112 561.069 1.138 1.010 0.310 12.419-9.967 99.48 175 15 0.1634 657.883 642.169 1.117 1.011 0.276 9.933-7.985 99.73 337 34 0.1787 493.946 478.207 1.156 1.008 0.275 7.976-6.403 100.00 631 64 0.2653 271.797 254.622 1.059 1.005 0.229 6.399-5.132 99.93 1234 135 0.2501 257.649 243.585 0.957 0.999 0.183 5.129-4.115 99.81 2357 259 0.2159 249.383 242.827 0.986 0.989 0.123 4.114-3.501 98.83 2959 341 0.3123 150.637 142.370 1.021 0.976 0.068 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=2.2034 ================= 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 : 0.3573 0.3825 0.003 0.846 2.0 500.0 94.7 0 0.000 1_bss: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_settarget: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_updatephipsi: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_nqh: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_realsrl: 0.2273 0.3136 0.003 0.846 19.6 517.6 112.3 0 0.095 1_weight: 0.2273 0.3136 0.003 0.846 19.6 517.6 112.3 0 0.095 1_xyzrec: 0.2221 0.3207 0.004 0.745 19.6 517.6 112.3 0 0.278 1_realsrl2: 0.2312 0.3249 0.004 0.745 19.6 517.6 112.3 0 0.309 1_adp: 0.2732 0.3186 0.004 0.745 66.1 512.6 130.6 0 0.309 1_regHadp: 0.2769 0.3135 0.004 0.745 66.1 512.6 130.6 0 0.309 2_bss: 0.2477 0.2964 0.004 0.745 35.4 482.0 100.0 0 0.309 2_settarget: 0.2477 0.2964 0.004 0.745 35.4 482.0 100.0 0 0.309 2_updatephipsi: 0.2477 0.2964 0.004 0.745 35.4 482.0 100.0 0 0.309 2_updatecdl: 0.2477 0.2964 0.004 0.803 35.4 482.0 100.0 0 0.309 2_nqh: 0.2480 0.2961 0.004 0.803 35.4 482.0 100.0 0 0.315 2_realsrl: 0.2478 0.2966 0.004 0.803 35.4 482.0 100.0 0 0.314 2_weight: 0.2478 0.2966 0.004 0.803 35.4 482.0 100.0 0 0.314 2_xyzrec: 0.2364 0.3009 0.003 0.642 35.4 482.0 100.0 0 0.346 2_realsrl2: 0.2378 0.3026 0.003 0.642 35.4 482.0 100.0 0 0.349 2_adp: 0.2565 0.2928 0.003 0.642 36.0 477.0 122.7 0 0.349 2_regHadp: 0.2598 0.2925 0.003 0.642 36.0 477.0 122.7 0 0.349 3_bss: 0.2477 0.2931 0.003 0.642 22.4 463.4 109.2 0 0.349 3_settarget: 0.2477 0.2931 0.003 0.642 22.4 463.4 109.2 0 0.349 3_updatephipsi: 0.2477 0.2931 0.003 0.642 22.4 463.4 109.2 0 0.349 3_updatecdl: 0.2477 0.2931 0.003 0.670 22.4 463.4 109.2 0 0.349 3_setrh: 0.2477 0.2932 0.003 0.670 22.4 463.4 109.2 0 0.349 3_nqh: 0.2477 0.2929 0.003 0.670 22.4 463.4 109.2 0 0.350 3_realsrl: 0.2477 0.2929 0.003 0.670 22.4 463.4 109.2 0 0.350 3_weight: 0.2477 0.2929 0.003 0.670 22.4 463.4 109.2 0 0.350 3_xyzrec: 0.2485 0.2928 0.003 0.663 22.4 463.4 109.2 0 0.352 3_realsrl2: 0.2496 0.2917 0.003 0.663 22.4 463.4 109.2 0 0.354 3_adp: 0.2632 0.2943 0.003 0.663 50.4 458.4 120.5 0 0.354 3_regHadp: 0.2640 0.2951 0.003 0.663 50.4 458.4 120.5 0 0.354 end: 0.2466 0.2893 0.003 0.663 33.2 441.2 103.2 0 0.354 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/3fm7_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/3fm7_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.2200 Refinement macro-cycles (run) : 358.7300 Write final files (write_after_run_outputs) : 25.5500 Total : 389.5000 Total CPU time: 6.90 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:24 PDT -0700 (1716251664.78 s) Start R-work = 0.2135, R-free = 0.3139 Final R-work = 0.2466, R-free = 0.2893 =============================================================================== Job complete usr+sys time: 438.48 seconds wall clock time: 19 minutes 24.58 seconds (1164.58 seconds total)