Starting phenix.real_space_refine on Tue Mar 3 13:12:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lni_0931/03_2026/6lni_0931.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lni_0931/03_2026/6lni_0931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.702 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lni_0931/03_2026/6lni_0931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lni_0931/03_2026/6lni_0931.map" model { file = "/net/cci-nas-00/data/ceres_data/6lni_0931/03_2026/6lni_0931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lni_0931/03_2026/6lni_0931.cif" } resolution = 2.702 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 2990 2.51 5 N 870 2.21 5 O 1010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4920 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.51, per 1000 atoms: 0.10 Number of scatterers: 4920 At special positions: 0 Unit cell: (145.002, 122.694, 44.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1010 8.00 N 870 7.00 C 2990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 214 " distance=2.03 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 214 " distance=2.03 Simple disulfide: pdb=" SG CYS G 179 " - pdb=" SG CYS G 214 " distance=2.03 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 179 " - pdb=" SG CYS I 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 179 " - pdb=" SG CYS J 214 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 327.7 milliseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 178 Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 185 removed outlier: 6.240A pdb=" N THR A 183 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 183 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR C 183 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR D 183 " --> pdb=" O ILE E 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 192 Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 202 removed outlier: 6.356A pdb=" N ASN A 197 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU B 200 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR A 199 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP B 202 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N THR A 201 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN B 197 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N GLU C 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N THR B 199 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASP C 202 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N THR B 201 " --> pdb=" O ASP C 202 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE C 198 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR D 199 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU C 200 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN D 197 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU E 200 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR D 199 " --> pdb=" O GLU E 200 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ASP E 202 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N THR D 201 " --> pdb=" O ASP E 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 206 through 210 removed outlier: 8.802A pdb=" N GLU A 207 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N VAL B 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL A 209 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N GLU B 207 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N VAL C 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL B 209 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N GLU C 207 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 9.920A pdb=" N VAL D 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL C 209 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLU D 207 " --> pdb=" O ARG E 208 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N VAL E 210 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL D 209 " --> pdb=" O VAL E 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 223 through 225 removed outlier: 6.697A pdb=" N ALA A 224 " --> pdb=" O TYR B 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 173 through 178 Processing sheet with id=AA8, first strand: chain 'F' and resid 182 through 185 removed outlier: 6.258A pdb=" N THR F 183 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR G 183 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR H 183 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR I 183 " --> pdb=" O ILE J 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 189 through 192 Processing sheet with id=AB1, first strand: chain 'F' and resid 197 through 202 removed outlier: 6.899A pdb=" N PHE F 198 " --> pdb=" O ASN G 197 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR G 199 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU F 200 " --> pdb=" O THR G 199 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE G 198 " --> pdb=" O ASN H 197 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR H 199 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU G 200 " --> pdb=" O THR H 199 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE H 198 " --> pdb=" O ASN I 197 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR I 199 " --> pdb=" O PHE H 198 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU H 200 " --> pdb=" O THR I 199 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN I 197 " --> pdb=" O PHE J 198 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLU J 200 " --> pdb=" O ASN I 197 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N THR I 199 " --> pdb=" O GLU J 200 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP J 202 " --> pdb=" O THR I 199 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N THR I 201 " --> pdb=" O ASP J 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 206 through 210 removed outlier: 8.779A pdb=" N GLU F 207 " --> pdb=" O ARG G 208 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N VAL G 210 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL F 209 " --> pdb=" O VAL G 210 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLU G 207 " --> pdb=" O ARG H 208 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N VAL H 210 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL G 209 " --> pdb=" O VAL H 210 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N GLU H 207 " --> pdb=" O ARG I 208 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL I 210 " --> pdb=" O GLU H 207 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL H 209 " --> pdb=" O VAL I 210 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N GLU I 207 " --> pdb=" O ARG J 208 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N VAL J 210 " --> pdb=" O GLU I 207 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL I 209 " --> pdb=" O VAL J 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 79 hydrogen bonds defined for protein. 237 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: 0.50 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1700 1.34 - 1.46: 947 1.46 - 1.58: 2253 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 4980 Sorted by residual: bond pdb=" CB CYS B 214 " pdb=" SG CYS B 214 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.40e-01 bond pdb=" CB CYS I 214 " pdb=" SG CYS I 214 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.39e-01 bond pdb=" CB CYS D 214 " pdb=" SG CYS D 214 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.35e-01 bond pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.31e-01 bond pdb=" CB CYS J 214 " pdb=" SG CYS J 214 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.30e-01 ... (remaining 4975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.75: 5974 0.75 - 1.50: 601 1.50 - 2.25: 55 2.25 - 3.00: 63 3.00 - 3.75: 17 Bond angle restraints: 6710 Sorted by residual: angle pdb=" C ARG H 220 " pdb=" N GLU H 221 " pdb=" CA GLU H 221 " ideal model delta sigma weight residual 122.08 125.05 -2.97 1.47e+00 4.63e-01 4.09e+00 angle pdb=" C ARG D 220 " pdb=" N GLU D 221 " pdb=" CA GLU D 221 " ideal model delta sigma weight residual 122.08 125.05 -2.97 1.47e+00 4.63e-01 4.09e+00 angle pdb=" C ARG F 220 " pdb=" N GLU F 221 " pdb=" CA GLU F 221 " ideal model delta sigma weight residual 122.08 125.04 -2.96 1.47e+00 4.63e-01 4.07e+00 angle pdb=" C ARG J 220 " pdb=" N GLU J 221 " pdb=" CA GLU J 221 " ideal model delta sigma weight residual 122.08 125.04 -2.96 1.47e+00 4.63e-01 4.05e+00 angle pdb=" C ARG B 220 " pdb=" N GLU B 221 " pdb=" CA GLU B 221 " ideal model delta sigma weight residual 122.08 125.04 -2.96 1.47e+00 4.63e-01 4.05e+00 ... (remaining 6705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.13: 2550 13.13 - 26.26: 350 26.26 - 39.39: 100 39.39 - 52.52: 40 52.52 - 65.66: 20 Dihedral angle restraints: 3060 sinusoidal: 1280 harmonic: 1780 Sorted by residual: dihedral pdb=" CA CYS B 214 " pdb=" C CYS B 214 " pdb=" N ILE B 215 " pdb=" CA ILE B 215 " ideal model delta harmonic sigma weight residual -180.00 -161.04 -18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA CYS G 214 " pdb=" C CYS G 214 " pdb=" N ILE G 215 " pdb=" CA ILE G 215 " ideal model delta harmonic sigma weight residual 180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA CYS A 214 " pdb=" C CYS A 214 " pdb=" N ILE A 215 " pdb=" CA ILE A 215 " ideal model delta harmonic sigma weight residual 180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 3057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 353 0.024 - 0.047: 221 0.047 - 0.071: 89 0.071 - 0.095: 56 0.095 - 0.118: 41 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA ILE H 182 " pdb=" N ILE H 182 " pdb=" C ILE H 182 " pdb=" CB ILE H 182 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ILE D 182 " pdb=" N ILE D 182 " pdb=" C ILE D 182 " pdb=" CB ILE D 182 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 ... (remaining 757 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 226 " -0.007 2.00e-02 2.50e+03 4.67e-03 4.36e-01 pdb=" CG TYR E 226 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR E 226 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR E 226 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 226 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 226 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 226 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 226 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 226 " -0.007 2.00e-02 2.50e+03 4.64e-03 4.30e-01 pdb=" CG TYR A 226 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 226 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 226 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 226 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 226 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 226 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 226 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 226 " 0.007 2.00e-02 2.50e+03 4.63e-03 4.29e-01 pdb=" CG TYR F 226 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR F 226 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR F 226 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR F 226 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 226 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 226 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 226 " 0.001 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 311 2.74 - 3.28: 4447 3.28 - 3.82: 7759 3.82 - 4.36: 9521 4.36 - 4.90: 17980 Nonbonded interactions: 40018 Sorted by model distance: nonbonded pdb=" NZ LYS E 194 " pdb=" OE2 GLU J 196 " model vdw 2.200 3.120 nonbonded pdb=" NZ LYS C 194 " pdb=" OE2 GLU H 196 " model vdw 2.220 3.120 nonbonded pdb=" NZ LYS D 194 " pdb=" OE2 GLU I 196 " model vdw 2.236 3.120 nonbonded pdb=" NZ LYS B 194 " pdb=" OE2 GLU G 196 " model vdw 2.243 3.120 nonbonded pdb=" OE2 GLU C 196 " pdb=" NZ LYS G 194 " model vdw 2.267 3.120 ... (remaining 40013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4990 Z= 0.185 Angle : 0.568 3.752 6730 Z= 0.352 Chirality : 0.044 0.118 760 Planarity : 0.002 0.006 880 Dihedral : 14.813 65.656 1870 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Rotamer: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.05 (0.19), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.61 (0.14), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 220 TYR 0.011 0.001 TYR E 226 PHE 0.003 0.001 PHE D 175 HIS 0.002 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 4980) covalent geometry : angle 0.55401 ( 6710) SS BOND : bond 0.00132 ( 10) SS BOND : angle 2.34539 ( 20) hydrogen bonds : bond 0.21531 ( 79) hydrogen bonds : angle 8.80185 ( 237) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8065 (tt0) cc_final: 0.7705 (tt0) REVERT: B 208 ARG cc_start: 0.7155 (mtt180) cc_final: 0.6822 (mtm180) REVERT: B 211 GLU cc_start: 0.7950 (tt0) cc_final: 0.7719 (tt0) REVERT: B 228 ARG cc_start: 0.8476 (ttt-90) cc_final: 0.8201 (tmt170) REVERT: C 221 GLU cc_start: 0.8146 (mp0) cc_final: 0.7852 (mp0) REVERT: C 228 ARG cc_start: 0.8578 (ttt-90) cc_final: 0.8357 (ttt-90) REVERT: D 185 LYS cc_start: 0.8411 (tttm) cc_final: 0.8207 (tttt) REVERT: D 200 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7796 (mt-10) REVERT: D 228 ARG cc_start: 0.8655 (ttt-90) cc_final: 0.8362 (ttt-90) REVERT: E 200 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8049 (mt-10) REVERT: E 221 GLU cc_start: 0.8136 (mp0) cc_final: 0.7837 (mp0) REVERT: F 211 GLU cc_start: 0.8187 (tt0) cc_final: 0.7834 (tt0) REVERT: F 228 ARG cc_start: 0.8725 (ttt-90) cc_final: 0.8288 (ttt-90) REVERT: G 228 ARG cc_start: 0.8704 (ttt-90) cc_final: 0.8326 (ttt-90) REVERT: H 211 GLU cc_start: 0.7738 (tt0) cc_final: 0.7358 (tt0) REVERT: H 220 ARG cc_start: 0.7896 (ptt180) cc_final: 0.7565 (ptp-170) REVERT: H 221 GLU cc_start: 0.8262 (mp0) cc_final: 0.7765 (mp0) REVERT: J 220 ARG cc_start: 0.7873 (ptt180) cc_final: 0.6740 (mmm160) outliers start: 0 outliers final: 1 residues processed: 182 average time/residue: 0.7489 time to fit residues: 139.6456 Evaluate side-chains 150 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 174 ASN A 177 HIS A 187 HIS A 227 GLN B 173 ASN B 174 ASN B 177 HIS B 187 HIS B 217 GLN C 173 ASN C 174 ASN C 177 HIS C 187 HIS D 173 ASN D 174 ASN D 177 HIS E 173 ASN E 174 ASN E 187 HIS F 173 ASN F 174 ASN F 177 HIS F 187 HIS G 173 ASN G 174 ASN G 177 HIS G 187 HIS H 173 ASN H 174 ASN H 177 HIS I 173 ASN I 174 ASN I 177 HIS I 187 HIS J 173 ASN J 174 ASN J 187 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.123569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105854 restraints weight = 5342.132| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.09 r_work: 0.3556 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4990 Z= 0.271 Angle : 0.636 5.839 6730 Z= 0.372 Chirality : 0.047 0.114 760 Planarity : 0.003 0.033 880 Dihedral : 6.135 40.220 652 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.45 % Favored : 86.55 % Rotamer: Outliers : 3.16 % Allowed : 18.77 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.03 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 228 TYR 0.015 0.002 TYR G 226 PHE 0.007 0.001 PHE F 175 HIS 0.003 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00637 ( 4980) covalent geometry : angle 0.62074 ( 6710) SS BOND : bond 0.00159 ( 10) SS BOND : angle 2.65235 ( 20) hydrogen bonds : bond 0.04097 ( 79) hydrogen bonds : angle 5.09191 ( 237) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.194 Fit side-chains REVERT: A 228 ARG cc_start: 0.9179 (ttt-90) cc_final: 0.8910 (ttt-90) REVERT: D 228 ARG cc_start: 0.8990 (ttt-90) cc_final: 0.8674 (ttt-90) REVERT: G 228 ARG cc_start: 0.9004 (ttt-90) cc_final: 0.8648 (ttt-90) REVERT: H 208 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7742 (mtm180) REVERT: H 211 GLU cc_start: 0.8639 (tt0) cc_final: 0.8375 (tt0) REVERT: I 221 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: J 220 ARG cc_start: 0.8407 (ptt180) cc_final: 0.6895 (mmm160) outliers start: 18 outliers final: 6 residues processed: 158 average time/residue: 0.8959 time to fit residues: 144.7495 Evaluate side-chains 154 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 223 GLN Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 45 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 172 GLN I 174 ASN J 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.130329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.112466 restraints weight = 5189.239| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.11 r_work: 0.3661 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4990 Z= 0.115 Angle : 0.480 4.040 6730 Z= 0.281 Chirality : 0.043 0.115 760 Planarity : 0.002 0.038 880 Dihedral : 5.221 18.422 650 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.33 % Allowed : 21.05 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.48 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 228 TYR 0.010 0.001 TYR G 226 PHE 0.004 0.001 PHE F 175 HIS 0.002 0.000 HIS F 177 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4980) covalent geometry : angle 0.47527 ( 6710) SS BOND : bond 0.00275 ( 10) SS BOND : angle 1.30225 ( 20) hydrogen bonds : bond 0.02337 ( 79) hydrogen bonds : angle 4.67081 ( 237) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.197 Fit side-chains REVERT: A 220 ARG cc_start: 0.8565 (ptt-90) cc_final: 0.8320 (ptt90) REVERT: D 223 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8365 (mp10) REVERT: D 228 ARG cc_start: 0.8992 (ttt-90) cc_final: 0.8751 (ttt-90) REVERT: F 223 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8446 (mp-120) REVERT: G 221 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: G 228 ARG cc_start: 0.8954 (ttt-90) cc_final: 0.8433 (ttt-90) REVERT: H 211 GLU cc_start: 0.8516 (tt0) cc_final: 0.8215 (tt0) REVERT: H 221 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8125 (mt-10) REVERT: I 221 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: J 196 GLU cc_start: 0.8570 (tt0) cc_final: 0.8015 (mp0) REVERT: J 220 ARG cc_start: 0.8310 (ptt180) cc_final: 0.6462 (mmm160) outliers start: 19 outliers final: 3 residues processed: 158 average time/residue: 0.8668 time to fit residues: 140.1089 Evaluate side-chains 155 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain F residue 223 GLN Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 GLN H 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.122196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.104379 restraints weight = 5244.888| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.07 r_work: 0.3535 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 4990 Z= 0.367 Angle : 0.688 6.406 6730 Z= 0.401 Chirality : 0.049 0.187 760 Planarity : 0.003 0.030 880 Dihedral : 6.069 23.181 650 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 4.91 % Allowed : 20.88 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.44 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 228 TYR 0.018 0.003 TYR F 226 PHE 0.011 0.002 PHE F 175 HIS 0.005 0.001 HIS F 177 Details of bonding type rmsd covalent geometry : bond 0.00866 ( 4980) covalent geometry : angle 0.67005 ( 6710) SS BOND : bond 0.00206 ( 10) SS BOND : angle 2.94158 ( 20) hydrogen bonds : bond 0.03654 ( 79) hydrogen bonds : angle 4.82599 ( 237) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.295 Fit side-chains REVERT: A 228 ARG cc_start: 0.9156 (ttt-90) cc_final: 0.8824 (ttt-90) REVERT: D 205 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8531 (ttt) REVERT: D 228 ARG cc_start: 0.9009 (ttt-90) cc_final: 0.8698 (ttt-90) REVERT: F 221 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: G 228 ARG cc_start: 0.9053 (ttt-90) cc_final: 0.8694 (ttt-90) REVERT: H 211 GLU cc_start: 0.8651 (tt0) cc_final: 0.8384 (tt0) REVERT: H 221 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8269 (mp0) REVERT: I 221 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: J 220 ARG cc_start: 0.8440 (ptt180) cc_final: 0.6646 (mmm160) outliers start: 28 outliers final: 8 residues processed: 159 average time/residue: 0.8681 time to fit residues: 141.1561 Evaluate side-chains 161 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 172 GLN F 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.128301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.110417 restraints weight = 5168.448| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.09 r_work: 0.3633 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4990 Z= 0.149 Angle : 0.522 5.256 6730 Z= 0.307 Chirality : 0.044 0.152 760 Planarity : 0.003 0.040 880 Dihedral : 5.466 19.500 650 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 4.04 % Allowed : 23.68 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.10 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 228 TYR 0.010 0.001 TYR C 226 PHE 0.005 0.001 PHE F 175 HIS 0.002 0.000 HIS F 177 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4980) covalent geometry : angle 0.51654 ( 6710) SS BOND : bond 0.00254 ( 10) SS BOND : angle 1.41906 ( 20) hydrogen bonds : bond 0.02368 ( 79) hydrogen bonds : angle 4.67907 ( 237) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.175 Fit side-chains REVERT: A 220 ARG cc_start: 0.8606 (ptt-90) cc_final: 0.8357 (ptt90) REVERT: A 228 ARG cc_start: 0.9166 (ttt-90) cc_final: 0.8858 (ttt-90) REVERT: D 208 ARG cc_start: 0.7785 (mtm180) cc_final: 0.7522 (mtm110) REVERT: D 228 ARG cc_start: 0.9032 (ttt-90) cc_final: 0.8676 (ttt-90) REVERT: F 211 GLU cc_start: 0.8412 (tt0) cc_final: 0.8133 (tt0) REVERT: G 178 ASP cc_start: 0.8715 (m-30) cc_final: 0.8482 (m-30) REVERT: G 208 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7875 (mtm110) REVERT: G 228 ARG cc_start: 0.8999 (ttt-90) cc_final: 0.8535 (ttt-90) REVERT: H 211 GLU cc_start: 0.8604 (tt0) cc_final: 0.8317 (tt0) REVERT: H 221 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8190 (mp0) REVERT: I 221 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: J 196 GLU cc_start: 0.8545 (tt0) cc_final: 0.7994 (mp0) REVERT: J 220 ARG cc_start: 0.8298 (ptt180) cc_final: 0.6294 (mmm160) outliers start: 23 outliers final: 9 residues processed: 157 average time/residue: 0.8437 time to fit residues: 135.4197 Evaluate side-chains 159 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 213 MET Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 213 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.129149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.112243 restraints weight = 5571.893| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.04 r_work: 0.3674 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4990 Z= 0.122 Angle : 0.487 4.034 6730 Z= 0.286 Chirality : 0.044 0.128 760 Planarity : 0.002 0.036 880 Dihedral : 5.173 17.844 650 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 4.91 % Allowed : 24.74 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 228 TYR 0.009 0.001 TYR B 226 PHE 0.004 0.001 PHE F 175 HIS 0.002 0.000 HIS F 177 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4980) covalent geometry : angle 0.48330 ( 6710) SS BOND : bond 0.00369 ( 10) SS BOND : angle 1.15915 ( 20) hydrogen bonds : bond 0.01946 ( 79) hydrogen bonds : angle 4.48375 ( 237) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.188 Fit side-chains REVERT: A 228 ARG cc_start: 0.9143 (ttt-90) cc_final: 0.8896 (ttt-90) REVERT: D 228 ARG cc_start: 0.9012 (ttt-90) cc_final: 0.8777 (ttt-90) REVERT: F 211 GLU cc_start: 0.8399 (tt0) cc_final: 0.8128 (tt0) REVERT: F 213 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8024 (tmm) REVERT: G 178 ASP cc_start: 0.8701 (m-30) cc_final: 0.8482 (m-30) REVERT: G 208 ARG cc_start: 0.8287 (mtp85) cc_final: 0.7902 (mtm110) REVERT: G 228 ARG cc_start: 0.9018 (ttt-90) cc_final: 0.8589 (ttt-90) REVERT: H 211 GLU cc_start: 0.8498 (tt0) cc_final: 0.8234 (tt0) REVERT: I 221 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: J 196 GLU cc_start: 0.8493 (tt0) cc_final: 0.8040 (mp0) REVERT: J 220 ARG cc_start: 0.8269 (ptt180) cc_final: 0.6472 (mmm160) outliers start: 28 outliers final: 9 residues processed: 167 average time/residue: 0.7796 time to fit residues: 133.4232 Evaluate side-chains 160 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 213 MET Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 213 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 GLN F 172 GLN H 174 ASN H 212 GLN I 174 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.123018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.104902 restraints weight = 5342.547| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.10 r_work: 0.3558 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 4990 Z= 0.342 Angle : 0.698 6.332 6730 Z= 0.406 Chirality : 0.049 0.163 760 Planarity : 0.004 0.036 880 Dihedral : 6.025 22.540 650 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 3.68 % Allowed : 26.67 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 228 TYR 0.017 0.002 TYR F 226 PHE 0.010 0.002 PHE F 175 HIS 0.005 0.001 HIS F 177 Details of bonding type rmsd covalent geometry : bond 0.00809 ( 4980) covalent geometry : angle 0.68275 ( 6710) SS BOND : bond 0.00130 ( 10) SS BOND : angle 2.72082 ( 20) hydrogen bonds : bond 0.03357 ( 79) hydrogen bonds : angle 4.78598 ( 237) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.265 Fit side-chains REVERT: A 213 MET cc_start: 0.8489 (tmt) cc_final: 0.8179 (tmt) REVERT: A 228 ARG cc_start: 0.9158 (ttt-90) cc_final: 0.8840 (ttt-90) REVERT: C 221 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8219 (mt-10) REVERT: D 208 ARG cc_start: 0.8267 (mtm180) cc_final: 0.7962 (mtm110) REVERT: D 228 ARG cc_start: 0.9047 (ttt-90) cc_final: 0.8672 (ttt-90) REVERT: G 208 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8021 (mtm110) REVERT: G 221 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8242 (mp0) REVERT: G 228 ARG cc_start: 0.9115 (ttt-90) cc_final: 0.8656 (ttt-90) REVERT: H 211 GLU cc_start: 0.8712 (tt0) cc_final: 0.8440 (tt0) REVERT: I 221 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: J 220 ARG cc_start: 0.8361 (ptt180) cc_final: 0.6686 (mmm160) outliers start: 21 outliers final: 8 residues processed: 157 average time/residue: 0.8829 time to fit residues: 141.7580 Evaluate side-chains 158 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.130922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.112942 restraints weight = 5259.277| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.10 r_work: 0.3681 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4990 Z= 0.126 Angle : 0.535 6.366 6730 Z= 0.312 Chirality : 0.045 0.160 760 Planarity : 0.003 0.040 880 Dihedral : 5.432 18.353 650 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 2.63 % Allowed : 28.77 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.28), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 228 TYR 0.009 0.001 TYR B 226 PHE 0.004 0.001 PHE F 175 HIS 0.001 0.000 HIS F 177 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4980) covalent geometry : angle 0.53244 ( 6710) SS BOND : bond 0.00396 ( 10) SS BOND : angle 1.14289 ( 20) hydrogen bonds : bond 0.01961 ( 79) hydrogen bonds : angle 4.53375 ( 237) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.192 Fit side-chains REVERT: A 213 MET cc_start: 0.8288 (tmt) cc_final: 0.7844 (tmt) REVERT: A 228 ARG cc_start: 0.9153 (ttt-90) cc_final: 0.8856 (ttt-90) REVERT: D 228 ARG cc_start: 0.9057 (ttt-90) cc_final: 0.8773 (ttt-90) REVERT: E 213 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7731 (tmt) REVERT: F 211 GLU cc_start: 0.8370 (tt0) cc_final: 0.8099 (tt0) REVERT: G 178 ASP cc_start: 0.8696 (m-30) cc_final: 0.8456 (m-30) REVERT: G 208 ARG cc_start: 0.8325 (mtp85) cc_final: 0.7904 (mtm110) REVERT: G 221 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8212 (mp0) REVERT: G 228 ARG cc_start: 0.9008 (ttt-90) cc_final: 0.8431 (ttt-90) REVERT: H 211 GLU cc_start: 0.8548 (tt0) cc_final: 0.8252 (tt0) REVERT: H 221 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8158 (mp0) REVERT: I 221 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: J 196 GLU cc_start: 0.8529 (tt0) cc_final: 0.7985 (mp0) REVERT: J 220 ARG cc_start: 0.8244 (ptt180) cc_final: 0.6265 (mmm160) outliers start: 15 outliers final: 5 residues processed: 153 average time/residue: 0.8988 time to fit residues: 140.6596 Evaluate side-chains 152 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN I 172 GLN I 174 ASN J 172 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.131370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.113307 restraints weight = 5174.001| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.08 r_work: 0.3681 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4990 Z= 0.128 Angle : 0.537 5.816 6730 Z= 0.312 Chirality : 0.045 0.150 760 Planarity : 0.003 0.040 880 Dihedral : 5.312 17.618 650 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 2.28 % Allowed : 29.65 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.28), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 228 TYR 0.010 0.001 TYR F 226 PHE 0.004 0.001 PHE F 175 HIS 0.002 0.000 HIS F 177 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4980) covalent geometry : angle 0.53409 ( 6710) SS BOND : bond 0.00377 ( 10) SS BOND : angle 1.15685 ( 20) hydrogen bonds : bond 0.01870 ( 79) hydrogen bonds : angle 4.46725 ( 237) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.190 Fit side-chains REVERT: A 213 MET cc_start: 0.8310 (tmt) cc_final: 0.8098 (tmt) REVERT: A 228 ARG cc_start: 0.9134 (ttt-90) cc_final: 0.8920 (ttt-90) REVERT: C 221 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: D 228 ARG cc_start: 0.9077 (ttt-90) cc_final: 0.8838 (ttt-90) REVERT: E 206 MET cc_start: 0.8724 (mtp) cc_final: 0.8484 (mtp) REVERT: E 220 ARG cc_start: 0.8355 (ptp90) cc_final: 0.8121 (ptp90) REVERT: F 211 GLU cc_start: 0.8331 (tt0) cc_final: 0.8050 (tt0) REVERT: G 178 ASP cc_start: 0.8666 (m-30) cc_final: 0.8421 (m-30) REVERT: G 208 ARG cc_start: 0.8366 (mtp85) cc_final: 0.7927 (mtm110) REVERT: G 228 ARG cc_start: 0.9099 (ttt-90) cc_final: 0.8620 (ttt-90) REVERT: H 211 GLU cc_start: 0.8568 (tt0) cc_final: 0.8281 (tt0) REVERT: H 221 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8055 (mp0) REVERT: I 221 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: I 228 ARG cc_start: 0.8661 (ttt-90) cc_final: 0.8423 (ttp80) REVERT: J 196 GLU cc_start: 0.8524 (tt0) cc_final: 0.8011 (mp0) REVERT: J 220 ARG cc_start: 0.8226 (ptt180) cc_final: 0.6225 (mmm160) outliers start: 13 outliers final: 5 residues processed: 156 average time/residue: 0.8778 time to fit residues: 140.0197 Evaluate side-chains 152 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain I residue 213 MET Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 GLN F 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.127193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.109845 restraints weight = 5504.181| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.06 r_work: 0.3641 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4990 Z= 0.185 Angle : 0.596 5.726 6730 Z= 0.346 Chirality : 0.047 0.186 760 Planarity : 0.003 0.040 880 Dihedral : 5.686 20.696 650 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 1.40 % Allowed : 31.40 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 228 TYR 0.010 0.001 TYR C 226 PHE 0.007 0.001 PHE F 175 HIS 0.002 0.001 HIS F 177 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 4980) covalent geometry : angle 0.58981 ( 6710) SS BOND : bond 0.00229 ( 10) SS BOND : angle 1.68423 ( 20) hydrogen bonds : bond 0.02394 ( 79) hydrogen bonds : angle 4.48620 ( 237) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.199 Fit side-chains REVERT: A 228 ARG cc_start: 0.9172 (ttt-90) cc_final: 0.8932 (ttt-90) REVERT: C 221 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: D 208 ARG cc_start: 0.7984 (mtm180) cc_final: 0.7718 (mtm110) REVERT: D 228 ARG cc_start: 0.9084 (ttt-90) cc_final: 0.8775 (ttt-90) REVERT: F 211 GLU cc_start: 0.8378 (tt0) cc_final: 0.8098 (tt0) REVERT: F 213 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8100 (tmm) REVERT: G 178 ASP cc_start: 0.8681 (m-30) cc_final: 0.8441 (m-30) REVERT: G 208 ARG cc_start: 0.8378 (mtp85) cc_final: 0.7954 (mtm110) REVERT: G 228 ARG cc_start: 0.9075 (ttt-90) cc_final: 0.8683 (ttt-90) REVERT: H 211 GLU cc_start: 0.8624 (tt0) cc_final: 0.8337 (tt0) REVERT: I 221 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: J 220 ARG cc_start: 0.8274 (ptt180) cc_final: 0.6324 (mmm160) outliers start: 8 outliers final: 5 residues processed: 154 average time/residue: 0.9565 time to fit residues: 150.5364 Evaluate side-chains 154 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 221 GLU Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.129861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.111602 restraints weight = 5331.647| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.15 r_work: 0.3659 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4990 Z= 0.153 Angle : 0.591 7.887 6730 Z= 0.341 Chirality : 0.047 0.199 760 Planarity : 0.003 0.039 880 Dihedral : 5.725 26.178 650 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 2.11 % Allowed : 30.70 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.28), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 228 TYR 0.010 0.001 TYR C 226 PHE 0.005 0.001 PHE F 175 HIS 0.002 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4980) covalent geometry : angle 0.58755 ( 6710) SS BOND : bond 0.00366 ( 10) SS BOND : angle 1.30696 ( 20) hydrogen bonds : bond 0.02099 ( 79) hydrogen bonds : angle 4.32270 ( 237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2849.37 seconds wall clock time: 49 minutes 10.92 seconds (2950.92 seconds total)