Starting phenix.real_space_refine on Thu Mar 6 04:57:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lni_0931/03_2025/6lni_0931.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lni_0931/03_2025/6lni_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_2025/6lni_0931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lni_0931/03_2025/6lni_0931.map" model { file = "/net/cci-nas-00/data/ceres_data/6lni_0931/03_2025/6lni_0931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lni_0931/03_2025/6lni_0931.cif" } resolution = 2.702 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B, E, D, G, F, I, H, J Time building chain proxies: 2.73, per 1000 atoms: 0.55 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 C 179 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS G 179 " - pdb=" SG CYS G 214 " distance=2.03 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 179 " - pdb=" SG CYS I 214 " distance=2.03 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 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: 1.10 Conformation dependent library (CDL) restraints added in 578.9 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: 0.57 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: 1.12 Time building geometry restraints manager: 1.34 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 5.750 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.950 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.200 ------------------------------------------------------------------------------- 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 4980 Z= 0.276 Angle : 0.554 3.752 6710 Z= 0.347 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 (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: -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 HIS 0.002 0.001 HIS A 177 PHE 0.003 0.001 PHE D 175 TYR 0.011 0.001 TYR E 226 ARG 0.001 0.000 ARG A 220 *********************** 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 : 0.538 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: 0.7895 (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: 0.7746 (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: 0.7359 (tt0) REVERT: H 220 ARG cc_start: 0.7896 (ptt180) cc_final: 0.7549 (ptp-170) REVERT: H 221 GLU cc_start: 0.8262 (mp0) cc_final: 0.7751 (mp0) REVERT: I 221 GLU cc_start: 0.8052 (mp0) cc_final: 0.7754 (mp0) REVERT: J 220 ARG cc_start: 0.7873 (ptt180) cc_final: 0.6738 (mmm160) outliers start: 0 outliers final: 1 residues processed: 182 average time/residue: 1.6716 time to fit residues: 312.0265 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 : 0.594 ------------------------------------------------------------------------------- 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 50 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.123556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.105885 restraints weight = 5314.327| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.07 r_work: 0.3558 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4980 Z= 0.419 Angle : 0.617 5.779 6710 Z= 0.364 Chirality : 0.047 0.114 760 Planarity : 0.003 0.032 880 Dihedral : 6.122 40.301 652 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.45 % Favored : 86.55 % Rotamer: Outliers : 2.81 % Allowed : 19.12 % 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 (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: -5.04 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.17), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 177 PHE 0.008 0.001 PHE F 175 TYR 0.015 0.002 TYR G 226 ARG 0.008 0.001 ARG J 228 *********************** 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 170 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.574 Fit side-chains REVERT: A 228 ARG cc_start: 0.9175 (ttt-90) cc_final: 0.8906 (ttt-90) REVERT: B 221 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: D 228 ARG cc_start: 0.8991 (ttt-90) cc_final: 0.8676 (ttt-90) REVERT: G 221 GLU cc_start: 0.8435 (mp0) cc_final: 0.8162 (mp0) REVERT: G 228 ARG cc_start: 0.9001 (ttt-90) cc_final: 0.8644 (ttt-90) REVERT: H 208 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7732 (mtm180) REVERT: H 211 GLU cc_start: 0.8640 (tt0) cc_final: 0.8376 (tt0) REVERT: H 221 GLU cc_start: 0.8578 (mp0) cc_final: 0.8191 (mt-10) REVERT: I 221 GLU cc_start: 0.8493 (mp0) cc_final: 0.8206 (mp0) REVERT: J 220 ARG cc_start: 0.8414 (ptt180) cc_final: 0.6909 (mmm160) outliers start: 16 outliers final: 5 residues processed: 157 average time/residue: 1.9016 time to fit residues: 305.7134 Evaluate side-chains 152 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B residue 221 GLU 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 J residue 192 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.129907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.112095 restraints weight = 5191.702| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.10 r_work: 0.3658 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4980 Z= 0.181 Angle : 0.482 4.020 6710 Z= 0.284 Chirality : 0.043 0.115 760 Planarity : 0.002 0.038 880 Dihedral : 5.247 18.570 650 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.33 % Allowed : 21.40 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.49 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 177 PHE 0.004 0.001 PHE F 175 TYR 0.010 0.001 TYR G 226 ARG 0.008 0.001 ARG E 228 *********************** 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 171 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.582 Fit side-chains REVERT: A 220 ARG cc_start: 0.8559 (ptt-90) cc_final: 0.8305 (ptt90) REVERT: D 223 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8376 (mp10) REVERT: D 228 ARG cc_start: 0.8992 (ttt-90) cc_final: 0.8755 (ttt-90) REVERT: F 223 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8454 (mp-120) REVERT: G 228 ARG cc_start: 0.8960 (ttt-90) cc_final: 0.8433 (ttt-90) REVERT: H 211 GLU cc_start: 0.8515 (tt0) cc_final: 0.8213 (tt0) REVERT: I 221 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8221 (mp0) REVERT: J 196 GLU cc_start: 0.8568 (tt0) cc_final: 0.8019 (mp0) REVERT: J 220 ARG cc_start: 0.8303 (ptt180) cc_final: 0.6467 (mmm160) outliers start: 19 outliers final: 4 residues processed: 156 average time/residue: 2.1616 time to fit residues: 345.1946 Evaluate side-chains 153 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 I residue 213 MET 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 22 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS E 212 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.125248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.107334 restraints weight = 5269.076| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.09 r_work: 0.3585 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4980 Z= 0.373 Angle : 0.568 5.205 6710 Z= 0.336 Chirality : 0.045 0.171 760 Planarity : 0.003 0.034 880 Dihedral : 5.647 21.130 650 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.45 % Favored : 86.55 % Rotamer: Outliers : 4.56 % Allowed : 22.63 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 177 PHE 0.008 0.001 PHE F 175 TYR 0.014 0.002 TYR F 226 ARG 0.009 0.001 ARG F 228 *********************** 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 179 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.613 Fit side-chains REVERT: A 206 MET cc_start: 0.9042 (mtm) cc_final: 0.8804 (mtp) REVERT: A 228 ARG cc_start: 0.9175 (ttt-90) cc_final: 0.8877 (ttt-90) REVERT: D 205 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8393 (ttt) REVERT: D 228 ARG cc_start: 0.8996 (ttt-90) cc_final: 0.8688 (ttt-90) REVERT: F 221 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: F 223 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8524 (mp-120) REVERT: G 221 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8297 (mt-10) REVERT: G 228 ARG cc_start: 0.9042 (ttt-90) cc_final: 0.8683 (ttt-90) REVERT: H 211 GLU cc_start: 0.8555 (tt0) cc_final: 0.8273 (tt0) REVERT: J 220 ARG cc_start: 0.8395 (ptt180) cc_final: 0.6885 (mmm160) outliers start: 26 outliers final: 8 residues processed: 158 average time/residue: 2.2405 time to fit residues: 361.8360 Evaluate side-chains 159 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 F residue 223 GLN Chi-restraints excluded: chain G residue 197 ASN 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 47 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.128984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.111102 restraints weight = 5178.269| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.10 r_work: 0.3640 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4980 Z= 0.217 Angle : 0.503 4.855 6710 Z= 0.298 Chirality : 0.044 0.143 760 Planarity : 0.002 0.039 880 Dihedral : 5.315 18.558 650 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 4.74 % Allowed : 22.46 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 177 PHE 0.005 0.001 PHE F 175 TYR 0.010 0.001 TYR G 226 ARG 0.009 0.001 ARG E 228 *********************** 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: 27 poor density : 147 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 197 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8479 (m110) REVERT: A 206 MET cc_start: 0.8958 (mtm) cc_final: 0.8723 (mtp) REVERT: A 220 ARG cc_start: 0.8584 (ptt-90) cc_final: 0.8300 (ptt90) REVERT: A 228 ARG cc_start: 0.9160 (ttt-90) cc_final: 0.8895 (ttt-90) REVERT: B 221 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: D 228 ARG cc_start: 0.9016 (ttt-90) cc_final: 0.8684 (ttt-90) REVERT: F 211 GLU cc_start: 0.8395 (tt0) cc_final: 0.8111 (tt0) REVERT: F 221 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: F 223 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8500 (mp-120) REVERT: G 178 ASP cc_start: 0.8698 (m-30) cc_final: 0.8459 (m-30) REVERT: G 208 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7716 (mtm110) REVERT: G 221 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8198 (mt-10) REVERT: G 228 ARG cc_start: 0.9007 (ttt-90) cc_final: 0.8569 (ttt-90) REVERT: H 211 GLU cc_start: 0.8496 (tt0) cc_final: 0.8181 (tt0) REVERT: I 221 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8201 (mp0) REVERT: J 196 GLU cc_start: 0.8569 (tt0) cc_final: 0.8013 (mp0) REVERT: J 220 ARG cc_start: 0.8272 (ptt180) cc_final: 0.6437 (mmm160) outliers start: 27 outliers final: 10 residues processed: 159 average time/residue: 2.6689 time to fit residues: 434.7900 Evaluate side-chains 159 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 223 GLN Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 213 MET 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 16 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.128441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.110119 restraints weight = 5254.694| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.14 r_work: 0.3640 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4980 Z= 0.218 Angle : 0.507 4.353 6710 Z= 0.299 Chirality : 0.044 0.133 760 Planarity : 0.003 0.037 880 Dihedral : 5.243 18.214 650 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 4.21 % Allowed : 24.04 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 177 PHE 0.005 0.001 PHE F 175 TYR 0.011 0.001 TYR G 226 ARG 0.010 0.001 ARG E 228 *********************** 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 172 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 1.854 Fit side-chains REVERT: A 197 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8447 (m110) REVERT: A 206 MET cc_start: 0.8889 (mtm) cc_final: 0.8649 (mtp) REVERT: A 220 ARG cc_start: 0.8605 (ptt-90) cc_final: 0.8342 (ptt90) REVERT: A 228 ARG cc_start: 0.9173 (ttt-90) cc_final: 0.8938 (ttt-90) REVERT: D 228 ARG cc_start: 0.9026 (ttt-90) cc_final: 0.8717 (ttt-90) REVERT: E 220 ARG cc_start: 0.8386 (ptp90) cc_final: 0.8090 (ptp90) REVERT: F 211 GLU cc_start: 0.8452 (tt0) cc_final: 0.8181 (tt0) REVERT: F 221 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: F 223 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8505 (mp-120) REVERT: G 178 ASP cc_start: 0.8675 (m-30) cc_final: 0.8431 (m-30) REVERT: G 208 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7803 (mtm110) REVERT: G 221 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8153 (mt-10) REVERT: G 228 ARG cc_start: 0.9026 (ttt-90) cc_final: 0.8612 (ttt-90) REVERT: H 211 GLU cc_start: 0.8537 (tt0) cc_final: 0.8236 (tt0) REVERT: I 221 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8221 (mp0) REVERT: J 196 GLU cc_start: 0.8567 (tt0) cc_final: 0.8024 (mp0) REVERT: J 220 ARG cc_start: 0.8294 (ptt180) cc_final: 0.6453 (mmm160) outliers start: 24 outliers final: 9 residues processed: 160 average time/residue: 2.2976 time to fit residues: 376.7855 Evaluate side-chains 157 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 223 GLN Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 213 MET 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 51 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 174 ASN I 172 GLN J 172 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.131242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.113065 restraints weight = 5159.591| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.10 r_work: 0.3683 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4980 Z= 0.179 Angle : 0.497 5.070 6710 Z= 0.292 Chirality : 0.044 0.157 760 Planarity : 0.003 0.040 880 Dihedral : 5.126 17.699 650 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 4.39 % Allowed : 24.74 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 177 PHE 0.004 0.001 PHE F 175 TYR 0.008 0.001 TYR F 226 ARG 0.010 0.000 ARG E 228 *********************** 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 171 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.616 Fit side-chains REVERT: A 206 MET cc_start: 0.8808 (mtm) cc_final: 0.8577 (mtp) REVERT: A 228 ARG cc_start: 0.9157 (ttt-90) cc_final: 0.8885 (ttt-90) REVERT: C 221 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: D 228 ARG cc_start: 0.9026 (ttt-90) cc_final: 0.8712 (ttt-90) REVERT: E 206 MET cc_start: 0.8812 (mtp) cc_final: 0.8607 (mtp) REVERT: E 220 ARG cc_start: 0.8411 (ptp90) cc_final: 0.8068 (ptp90) REVERT: F 211 GLU cc_start: 0.8444 (tt0) cc_final: 0.8204 (tt0) REVERT: F 223 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8501 (mp-120) REVERT: G 178 ASP cc_start: 0.8656 (m-30) cc_final: 0.8410 (m-30) REVERT: G 228 ARG cc_start: 0.9008 (ttt-90) cc_final: 0.8573 (ttt-90) REVERT: H 211 GLU cc_start: 0.8507 (tt0) cc_final: 0.8199 (tt0) REVERT: H 220 ARG cc_start: 0.8356 (ptp90) cc_final: 0.8038 (ptp90) REVERT: H 221 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7944 (mp0) REVERT: J 196 GLU cc_start: 0.8562 (tt0) cc_final: 0.8026 (mp0) REVERT: J 220 ARG cc_start: 0.8261 (ptt180) cc_final: 0.6458 (mmm160) outliers start: 25 outliers final: 6 residues processed: 160 average time/residue: 2.2138 time to fit residues: 363.2945 Evaluate side-chains 152 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 223 GLN Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 213 MET 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 39 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 212 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.122688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104950 restraints weight = 5526.305| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.08 r_work: 0.3563 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 4980 Z= 0.504 Angle : 0.660 6.021 6710 Z= 0.388 Chirality : 0.049 0.200 760 Planarity : 0.003 0.035 880 Dihedral : 5.905 23.300 650 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 3.16 % Allowed : 25.79 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 177 PHE 0.010 0.002 PHE F 175 TYR 0.017 0.002 TYR G 226 ARG 0.010 0.001 ARG E 228 *********************** 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 169 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.329 Fit side-chains REVERT: A 206 MET cc_start: 0.9030 (mtm) cc_final: 0.8791 (mtp) REVERT: A 228 ARG cc_start: 0.9183 (ttt-90) cc_final: 0.8907 (ttt-90) REVERT: D 228 ARG cc_start: 0.9022 (ttt-90) cc_final: 0.8657 (ttt-90) REVERT: E 220 ARG cc_start: 0.8551 (ptp90) cc_final: 0.8247 (ptp90) REVERT: F 213 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8309 (tmm) REVERT: G 208 ARG cc_start: 0.8454 (mtp85) cc_final: 0.8038 (mtm110) REVERT: G 228 ARG cc_start: 0.9105 (ttt-90) cc_final: 0.8665 (ttt-90) REVERT: H 211 GLU cc_start: 0.8660 (tt0) cc_final: 0.8407 (tt0) REVERT: H 221 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8232 (mt-10) REVERT: I 221 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8262 (mp0) REVERT: J 220 ARG cc_start: 0.8346 (ptt180) cc_final: 0.6741 (mmm160) outliers start: 18 outliers final: 8 residues processed: 158 average time/residue: 2.0295 time to fit residues: 328.8955 Evaluate side-chains 156 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 D residue 192 THR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain G residue 197 ASN 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 7 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.129821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.111492 restraints weight = 5128.550| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.12 r_work: 0.3650 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4980 Z= 0.229 Angle : 0.568 7.093 6710 Z= 0.333 Chirality : 0.047 0.159 760 Planarity : 0.003 0.044 880 Dihedral : 5.602 22.782 650 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.81 % Allowed : 26.32 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 177 PHE 0.006 0.001 PHE F 175 TYR 0.010 0.001 TYR A 226 ARG 0.010 0.001 ARG E 228 *********************** 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: 16 poor density : 146 time to evaluate : 0.555 Fit side-chains REVERT: A 206 MET cc_start: 0.8882 (mtm) cc_final: 0.8611 (mtp) REVERT: A 228 ARG cc_start: 0.9176 (ttt-90) cc_final: 0.8853 (ttt-90) REVERT: D 228 ARG cc_start: 0.9038 (ttt-90) cc_final: 0.8717 (ttt-90) REVERT: E 220 ARG cc_start: 0.8479 (ptp90) cc_final: 0.8148 (ptp90) REVERT: F 211 GLU cc_start: 0.8366 (tt0) cc_final: 0.8074 (tt0) REVERT: G 178 ASP cc_start: 0.8664 (m-30) cc_final: 0.8404 (m-30) REVERT: G 208 ARG cc_start: 0.8335 (mtp85) cc_final: 0.7887 (mtm110) REVERT: G 228 ARG cc_start: 0.9003 (ttt-90) cc_final: 0.8440 (ttt-90) REVERT: H 211 GLU cc_start: 0.8624 (tt0) cc_final: 0.8312 (tt0) REVERT: H 221 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8054 (mp0) REVERT: I 220 ARG cc_start: 0.8504 (ptp90) cc_final: 0.8001 (ptp90) REVERT: I 221 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8139 (mp0) REVERT: I 228 ARG cc_start: 0.8753 (ttt-90) cc_final: 0.8416 (ttp80) REVERT: J 196 GLU cc_start: 0.8591 (tt0) cc_final: 0.8005 (mp0) REVERT: J 220 ARG cc_start: 0.8344 (ptt180) cc_final: 0.6307 (mmm160) outliers start: 16 outliers final: 9 residues processed: 154 average time/residue: 2.3549 time to fit residues: 371.6338 Evaluate side-chains 154 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 213 MET 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 29 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 187 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.122977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.105289 restraints weight = 5418.365| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.06 r_work: 0.3588 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 4980 Z= 0.479 Angle : 0.681 7.204 6710 Z= 0.397 Chirality : 0.050 0.187 760 Planarity : 0.003 0.026 880 Dihedral : 6.059 22.770 650 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.97 % Favored : 86.03 % Rotamer: Outliers : 2.46 % Allowed : 27.72 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 177 PHE 0.010 0.002 PHE F 175 TYR 0.016 0.002 TYR G 226 ARG 0.008 0.001 ARG F 228 ********************** 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 161 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.514 Fit side-chains REVERT: A 206 MET cc_start: 0.9046 (mtm) cc_final: 0.8801 (mtp) REVERT: A 228 ARG cc_start: 0.9156 (ttt-90) cc_final: 0.8840 (ttt-90) REVERT: C 221 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: D 205 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8478 (ttt) REVERT: D 228 ARG cc_start: 0.9031 (ttt-90) cc_final: 0.8715 (ttt-90) REVERT: E 220 ARG cc_start: 0.8418 (ptp90) cc_final: 0.8187 (ptp90) REVERT: F 211 GLU cc_start: 0.8378 (tt0) cc_final: 0.8102 (tt0) REVERT: G 208 ARG cc_start: 0.8457 (mtp85) cc_final: 0.7972 (mtm110) REVERT: G 221 GLU cc_start: 0.8417 (mp0) cc_final: 0.8173 (mp0) REVERT: G 228 ARG cc_start: 0.9104 (ttt-90) cc_final: 0.8647 (ttt-90) REVERT: H 211 GLU cc_start: 0.8690 (tt0) cc_final: 0.8377 (tt0) REVERT: H 221 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8155 (mp0) REVERT: I 221 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8219 (mp0) REVERT: I 228 ARG cc_start: 0.8838 (ttt-90) cc_final: 0.8526 (ttp80) REVERT: J 220 ARG cc_start: 0.8407 (ptt180) cc_final: 0.6605 (mmm160) outliers start: 14 outliers final: 8 residues processed: 152 average time/residue: 2.1432 time to fit residues: 333.3505 Evaluate side-chains 157 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 213 MET Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain G residue 197 ASN 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 2 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.0570 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.130764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.112756 restraints weight = 5279.687| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.12 r_work: 0.3687 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4980 Z= 0.177 Angle : 0.555 6.429 6710 Z= 0.323 Chirality : 0.046 0.164 760 Planarity : 0.003 0.030 880 Dihedral : 5.616 27.172 650 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 0.88 % Allowed : 29.47 % 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 (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: -3.91 (0.28), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 177 PHE 0.004 0.001 PHE F 175 TYR 0.011 0.001 TYR G 226 ARG 0.009 0.001 ARG E 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6673.13 seconds wall clock time: 120 minutes 0.67 seconds (7200.67 seconds total)