Starting phenix.real_space_refine on Thu Jul 24 01:52:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lni_0931/07_2025/6lni_0931.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lni_0931/07_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_0931/07_2025/6lni_0931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lni_0931/07_2025/6lni_0931.map" model { file = "/net/cci-nas-00/data/ceres_data/6lni_0931/07_2025/6lni_0931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lni_0931/07_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-5711/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: 2.48, per 1000 atoms: 0.50 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: 1.08 Conformation dependent library (CDL) restraints added in 564.0 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: 0.62 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: 1.10 Time building geometry restraints manager: 1.31 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: 0.04 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: 2.850 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.440 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.21531 ( 79) hydrogen bonds : angle 8.80185 ( 237) SS BOND : bond 0.00132 ( 10) SS BOND : angle 2.34539 ( 20) covalent geometry : bond 0.00413 ( 4980) covalent geometry : angle 0.55401 ( 6710) *********************** 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 : 0.608 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: 1.6792 time to fit residues: 313.6832 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 : 0.552 ------------------------------------------------------------------------------- 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 4990 Z= 0.268 Angle : 0.632 5.779 6730 Z= 0.370 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 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 79) hydrogen bonds : angle 5.10002 ( 237) SS BOND : bond 0.00146 ( 10) SS BOND : angle 2.62227 ( 20) covalent geometry : bond 0.00628 ( 4980) covalent geometry : angle 0.61657 ( 6710) *********************** 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 : 0.620 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: 1.9039 time to fit residues: 306.0004 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 : 0.568 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.129918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.112093 restraints weight = 5188.786| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.10 r_work: 0.3657 rms_B_bonded: 2.19 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: 0.8420 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4990 Z= 0.122 Angle : 0.488 3.995 6730 Z= 0.286 Chirality : 0.043 0.116 760 Planarity : 0.002 0.038 880 Dihedral : 5.248 18.674 650 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.49 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 (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: -4.50 (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 0.009 0.001 ARG E 228 Details of bonding type rmsd hydrogen bonds : bond 0.02397 ( 79) hydrogen bonds : angle 4.67826 ( 237) SS BOND : bond 0.00253 ( 10) SS BOND : angle 1.38339 ( 20) covalent geometry : bond 0.00270 ( 4980) covalent geometry : angle 0.48262 ( 6710) *********************** 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 : 0.579 Fit side-chains REVERT: A 220 ARG cc_start: 0.8567 (ptt-90) cc_final: 0.8321 (ptt90) REVERT: D 223 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8377 (mp10) REVERT: D 228 ARG cc_start: 0.8990 (ttt-90) cc_final: 0.8752 (ttt-90) REVERT: F 223 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8454 (mp-120) REVERT: G 228 ARG cc_start: 0.8958 (ttt-90) cc_final: 0.8434 (ttt-90) REVERT: H 211 GLU cc_start: 0.8515 (tt0) cc_final: 0.8213 (tt0) REVERT: I 221 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8222 (mp0) REVERT: J 196 GLU cc_start: 0.8566 (tt0) cc_final: 0.8021 (mp0) REVERT: J 220 ARG cc_start: 0.8310 (ptt180) cc_final: 0.6467 (mmm160) outliers start: 19 outliers final: 5 residues processed: 156 average time/residue: 1.7631 time to fit residues: 281.8756 Evaluate side-chains 153 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain J residue 213 MET 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: 3.9990 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** J 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.128180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.111095 restraints weight = 5610.501| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.05 r_work: 0.3699 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4990 Z= 0.148 Angle : 0.507 4.264 6730 Z= 0.298 Chirality : 0.044 0.156 760 Planarity : 0.003 0.036 880 Dihedral : 5.258 19.047 650 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 3.86 % Allowed : 22.98 % Favored : 73.16 % 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: -4.30 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.20), 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 F 226 ARG 0.009 0.001 ARG F 228 Details of bonding type rmsd hydrogen bonds : bond 0.02309 ( 79) hydrogen bonds : angle 4.55350 ( 237) SS BOND : bond 0.00252 ( 10) SS BOND : angle 1.46739 ( 20) covalent geometry : bond 0.00338 ( 4980) covalent geometry : angle 0.50112 ( 6710) *********************** 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 175 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.560 Fit side-chains REVERT: D 228 ARG cc_start: 0.9007 (ttt-90) cc_final: 0.8758 (ttt-90) REVERT: F 221 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: F 223 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8453 (mp-120) REVERT: G 221 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8080 (mp0) REVERT: G 223 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8327 (mt0) REVERT: G 228 ARG cc_start: 0.9051 (ttt-90) cc_final: 0.8696 (ttt-90) REVERT: H 211 GLU cc_start: 0.8452 (tt0) cc_final: 0.8196 (tt0) REVERT: H 221 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8063 (mp0) REVERT: I 221 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8120 (mp0) REVERT: J 196 GLU cc_start: 0.8496 (tt0) cc_final: 0.8064 (mp0) REVERT: J 220 ARG cc_start: 0.8328 (ptt180) cc_final: 0.6737 (mmm160) outliers start: 22 outliers final: 9 residues processed: 158 average time/residue: 3.0721 time to fit residues: 496.5657 Evaluate side-chains 162 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B 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 F residue 221 GLU Chi-restraints excluded: chain F residue 223 GLN Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 223 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.0670 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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** ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN J 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.129497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.112436 restraints weight = 5535.452| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.05 r_work: 0.3720 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4990 Z= 0.128 Angle : 0.488 4.591 6730 Z= 0.287 Chirality : 0.043 0.134 760 Planarity : 0.003 0.039 880 Dihedral : 5.118 17.692 650 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 5.61 % Allowed : 22.98 % Favored : 71.40 % 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: -4.11 (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 0.000 HIS F 177 PHE 0.004 0.001 PHE F 175 TYR 0.009 0.001 TYR G 226 ARG 0.009 0.001 ARG F 228 Details of bonding type rmsd hydrogen bonds : bond 0.02014 ( 79) hydrogen bonds : angle 4.39205 ( 237) SS BOND : bond 0.00314 ( 10) SS BOND : angle 1.23073 ( 20) covalent geometry : bond 0.00283 ( 4980) covalent geometry : angle 0.48456 ( 6710) *********************** 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 182 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.537 Fit side-chains REVERT: A 220 ARG cc_start: 0.8632 (ptt-90) cc_final: 0.8428 (ptt90) REVERT: B 221 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: D 220 ARG cc_start: 0.8463 (ptp90) cc_final: 0.8170 (ptp90) REVERT: D 228 ARG cc_start: 0.9020 (ttt-90) cc_final: 0.8743 (ttt-90) REVERT: F 211 GLU cc_start: 0.8409 (tt0) cc_final: 0.8114 (tt0) REVERT: F 223 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8473 (mp-120) REVERT: G 223 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: G 228 ARG cc_start: 0.9012 (ttt-90) cc_final: 0.8572 (ttt-90) REVERT: H 211 GLU cc_start: 0.8451 (tt0) cc_final: 0.8159 (tt0) REVERT: J 196 GLU cc_start: 0.8503 (tt0) cc_final: 0.8066 (mp0) REVERT: J 220 ARG cc_start: 0.8251 (ptt180) cc_final: 0.6363 (mmm160) outliers start: 32 outliers final: 9 residues processed: 165 average time/residue: 2.3181 time to fit residues: 391.4444 Evaluate side-chains 159 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 221 GLU 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 197 ASN Chi-restraints excluded: chain F residue 223 GLN Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 223 GLN Chi-restraints excluded: chain I residue 213 MET Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 GLN H 174 ASN ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.126070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.108986 restraints weight = 5472.056| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.03 r_work: 0.3667 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4990 Z= 0.203 Angle : 0.575 5.899 6730 Z= 0.336 Chirality : 0.046 0.142 760 Planarity : 0.003 0.036 880 Dihedral : 5.470 19.925 650 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % 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 (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: -4.08 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 177 PHE 0.007 0.001 PHE F 175 TYR 0.012 0.002 TYR G 226 ARG 0.009 0.001 ARG E 228 Details of bonding type rmsd hydrogen bonds : bond 0.02598 ( 79) hydrogen bonds : angle 4.52893 ( 237) SS BOND : bond 0.00156 ( 10) SS BOND : angle 1.85950 ( 20) covalent geometry : bond 0.00471 ( 4980) covalent geometry : angle 0.56640 ( 6710) *********************** 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: 23 poor density : 149 time to evaluate : 2.193 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8689 (ptt-90) cc_final: 0.8488 (ptt90) REVERT: A 228 ARG cc_start: 0.9168 (ttt-90) cc_final: 0.8916 (ttt-90) REVERT: D 220 ARG cc_start: 0.8462 (ptp90) cc_final: 0.8119 (ptp90) REVERT: D 228 ARG cc_start: 0.9005 (ttt-90) cc_final: 0.8721 (ttt-90) REVERT: G 221 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7981 (mp0) REVERT: G 228 ARG cc_start: 0.9091 (ttt-90) cc_final: 0.8682 (ttt-90) REVERT: H 211 GLU cc_start: 0.8525 (tt0) cc_final: 0.8250 (tt0) REVERT: J 220 ARG cc_start: 0.8294 (ptt180) cc_final: 0.6385 (mmm160) outliers start: 23 outliers final: 11 residues processed: 157 average time/residue: 2.8004 time to fit residues: 450.1358 Evaluate side-chains 158 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 205 MET Chi-restraints excluded: chain C residue 213 MET 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 H residue 221 GLU 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: 3.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 F 172 GLN ** H 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.127635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.109776 restraints weight = 5146.554| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.08 r_work: 0.3681 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4990 Z= 0.184 Angle : 0.563 5.710 6730 Z= 0.330 Chirality : 0.046 0.143 760 Planarity : 0.003 0.041 880 Dihedral : 5.483 19.351 650 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.68 % Allowed : 25.26 % 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: -3.97 (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 0.002 0.001 HIS F 177 PHE 0.007 0.001 PHE F 175 TYR 0.012 0.001 TYR G 226 ARG 0.010 0.001 ARG E 228 Details of bonding type rmsd hydrogen bonds : bond 0.02481 ( 79) hydrogen bonds : angle 4.52336 ( 237) SS BOND : bond 0.00163 ( 10) SS BOND : angle 1.69797 ( 20) covalent geometry : bond 0.00423 ( 4980) covalent geometry : angle 0.55578 ( 6710) *********************** 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 165 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.587 Fit side-chains REVERT: A 220 ARG cc_start: 0.8670 (ptt-90) cc_final: 0.8436 (ptt90) REVERT: A 228 ARG cc_start: 0.9176 (ttt-90) cc_final: 0.8866 (ttt-90) REVERT: C 221 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: D 228 ARG cc_start: 0.9026 (ttt-90) cc_final: 0.8708 (ttt-90) REVERT: F 211 GLU cc_start: 0.8411 (tt0) cc_final: 0.8122 (tt0) REVERT: F 213 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8075 (tmm) REVERT: G 178 ASP cc_start: 0.8692 (m-30) cc_final: 0.8461 (m-30) REVERT: G 208 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7815 (mtm110) REVERT: G 221 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8020 (mp0) REVERT: G 228 ARG cc_start: 0.9070 (ttt-90) cc_final: 0.8592 (ttt-90) REVERT: H 211 GLU cc_start: 0.8557 (tt0) cc_final: 0.8270 (tt0) REVERT: J 196 GLU cc_start: 0.8519 (tt0) cc_final: 0.8031 (mp0) REVERT: J 220 ARG cc_start: 0.8268 (ptt180) cc_final: 0.6516 (mmm160) outliers start: 21 outliers final: 12 residues processed: 150 average time/residue: 2.1481 time to fit residues: 330.6695 Evaluate side-chains 157 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 205 MET 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 F residue 197 ASN 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 J residue 192 THR Chi-restraints excluded: chain J residue 213 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 36 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.127983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.110859 restraints weight = 5579.204| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.07 r_work: 0.3695 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4990 Z= 0.157 Angle : 0.547 6.184 6730 Z= 0.320 Chirality : 0.045 0.178 760 Planarity : 0.003 0.038 880 Dihedral : 5.418 19.659 650 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 4.21 % Allowed : 25.61 % Favored : 70.18 % 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: -3.93 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (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 0.011 0.001 TYR G 226 ARG 0.009 0.001 ARG E 228 Details of bonding type rmsd hydrogen bonds : bond 0.02231 ( 79) hydrogen bonds : angle 4.48829 ( 237) SS BOND : bond 0.00233 ( 10) SS BOND : angle 1.46740 ( 20) covalent geometry : bond 0.00354 ( 4980) covalent geometry : angle 0.54208 ( 6710) *********************** 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: 24 poor density : 145 time to evaluate : 0.559 Fit side-chains REVERT: A 220 ARG cc_start: 0.8611 (ptt-90) cc_final: 0.8355 (ptt90) REVERT: A 228 ARG cc_start: 0.9168 (ttt-90) cc_final: 0.8888 (ttt-90) REVERT: D 228 ARG cc_start: 0.9032 (ttt-90) cc_final: 0.8730 (ttt-90) REVERT: F 211 GLU cc_start: 0.8432 (tt0) cc_final: 0.8129 (tt0) REVERT: F 213 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8047 (tmm) REVERT: G 178 ASP cc_start: 0.8679 (m-30) cc_final: 0.8457 (m-30) REVERT: G 208 ARG cc_start: 0.8281 (mtp85) cc_final: 0.7873 (mtm110) REVERT: G 221 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7982 (mp0) REVERT: G 228 ARG cc_start: 0.9075 (ttt-90) cc_final: 0.8604 (ttt-90) REVERT: H 211 GLU cc_start: 0.8489 (tt0) cc_final: 0.8202 (tt0) REVERT: J 196 GLU cc_start: 0.8489 (tt0) cc_final: 0.8057 (mp0) REVERT: J 220 ARG cc_start: 0.8272 (ptt180) cc_final: 0.6550 (mmm160) outliers start: 24 outliers final: 12 residues processed: 156 average time/residue: 2.6676 time to fit residues: 425.1726 Evaluate side-chains 158 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 205 MET 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 197 ASN Chi-restraints excluded: chain F residue 213 MET 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 Chi-restraints excluded: chain J residue 213 MET 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: 9.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** J 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.127874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.110446 restraints weight = 5193.588| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.03 r_work: 0.3670 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4990 Z= 0.144 Angle : 0.554 5.855 6730 Z= 0.322 Chirality : 0.046 0.166 760 Planarity : 0.003 0.042 880 Dihedral : 5.447 21.938 650 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 2.46 % Allowed : 27.54 % Favored : 70.00 % 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 (0.27), 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 0.005 0.001 PHE F 175 TYR 0.011 0.001 TYR G 226 ARG 0.010 0.001 ARG E 228 Details of bonding type rmsd hydrogen bonds : bond 0.02056 ( 79) hydrogen bonds : angle 4.46862 ( 237) SS BOND : bond 0.00257 ( 10) SS BOND : angle 1.33844 ( 20) covalent geometry : bond 0.00320 ( 4980) covalent geometry : angle 0.54956 ( 6710) *********************** 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 161 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.599 Fit side-chains REVERT: A 220 ARG cc_start: 0.8641 (ptt-90) cc_final: 0.8380 (ptt90) REVERT: A 228 ARG cc_start: 0.9178 (ttt-90) cc_final: 0.8833 (ttt-90) REVERT: C 221 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: D 220 ARG cc_start: 0.8297 (ptp90) cc_final: 0.8095 (ptp90) REVERT: D 228 ARG cc_start: 0.9056 (ttt-90) cc_final: 0.8725 (ttt-90) REVERT: E 220 ARG cc_start: 0.8390 (ptp90) cc_final: 0.8162 (ptp90) REVERT: F 211 GLU cc_start: 0.8409 (tt0) cc_final: 0.8088 (tt0) REVERT: F 213 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8017 (tmm) REVERT: G 178 ASP cc_start: 0.8686 (m-30) cc_final: 0.8440 (m-30) REVERT: G 208 ARG cc_start: 0.8166 (mtp85) cc_final: 0.7740 (mtm110) REVERT: G 221 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7929 (mp0) REVERT: G 228 ARG cc_start: 0.9070 (ttt-90) cc_final: 0.8570 (ttt-90) REVERT: H 206 MET cc_start: 0.8907 (mtm) cc_final: 0.8697 (mtm) REVERT: H 211 GLU cc_start: 0.8542 (tt0) cc_final: 0.8225 (tt0) REVERT: J 196 GLU cc_start: 0.8553 (tt0) cc_final: 0.7994 (mp0) REVERT: J 220 ARG cc_start: 0.8245 (ptt180) cc_final: 0.6359 (mmm160) outliers start: 14 outliers final: 10 residues processed: 154 average time/residue: 2.3381 time to fit residues: 368.5457 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 : 0.618 ------------------------------------------------------------------------------- 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 C 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 213 MET 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 Chi-restraints excluded: chain J residue 213 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 212 GLN H 212 GLN I 174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.123256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.105910 restraints weight = 5410.146| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.04 r_work: 0.3579 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2884 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= 0.326 Angle : 0.715 6.250 6730 Z= 0.414 Chirality : 0.051 0.207 760 Planarity : 0.004 0.037 880 Dihedral : 6.099 22.099 650 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.97 % Favored : 86.03 % Rotamer: Outliers : 1.93 % Allowed : 27.72 % 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 (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: -4.02 (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 0.005 0.001 HIS F 177 PHE 0.010 0.002 PHE F 175 TYR 0.016 0.002 TYR G 226 ARG 0.010 0.001 ARG E 228 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 79) hydrogen bonds : angle 4.64611 ( 237) SS BOND : bond 0.00162 ( 10) SS BOND : angle 2.72445 ( 20) covalent geometry : bond 0.00768 ( 4980) covalent geometry : angle 0.70052 ( 6710) ********************** 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: 11 poor density : 150 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8761 (ptt-90) cc_final: 0.8501 (ptt90) REVERT: A 228 ARG cc_start: 0.9172 (ttt-90) cc_final: 0.8847 (ttt-90) REVERT: B 221 GLU cc_start: 0.8544 (mp0) cc_final: 0.8184 (mp0) REVERT: C 221 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: D 220 ARG cc_start: 0.8379 (ptp90) cc_final: 0.8149 (ptt-90) REVERT: D 228 ARG cc_start: 0.9058 (ttt-90) cc_final: 0.8702 (ttt-90) REVERT: F 211 GLU cc_start: 0.8471 (tt0) cc_final: 0.8181 (tt0) REVERT: G 208 ARG cc_start: 0.8462 (mtp85) cc_final: 0.8050 (mtm110) REVERT: G 228 ARG cc_start: 0.9128 (ttt-90) cc_final: 0.8659 (ttt-90) REVERT: H 211 GLU cc_start: 0.8633 (tt0) cc_final: 0.8358 (tt0) REVERT: J 220 ARG cc_start: 0.8344 (ptt180) cc_final: 0.6807 (mmm160) outliers start: 11 outliers final: 7 residues processed: 155 average time/residue: 2.6910 time to fit residues: 427.0088 Evaluate side-chains 155 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain C residue 197 ASN 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 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: 0.8980 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.0870 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 = 0.128863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.111540 restraints weight = 5270.688| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.02 r_work: 0.3693 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4990 Z= 0.134 Angle : 0.573 7.634 6730 Z= 0.330 Chirality : 0.046 0.201 760 Planarity : 0.003 0.043 880 Dihedral : 5.677 24.614 650 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 1.23 % Allowed : 28.60 % Favored : 70.18 % 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 0.001 0.000 HIS D 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 Details of bonding type rmsd hydrogen bonds : bond 0.01965 ( 79) hydrogen bonds : angle 4.34655 ( 237) SS BOND : bond 0.00343 ( 10) SS BOND : angle 1.20756 ( 20) covalent geometry : bond 0.00286 ( 4980) covalent geometry : angle 0.57003 ( 6710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8458.31 seconds wall clock time: 155 minutes 13.60 seconds (9313.60 seconds total)