Starting phenix.real_space_refine on Sun Mar 10 20:45:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lni_0931/03_2024/6lni_0931.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lni_0931/03_2024/6lni_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lni_0931/03_2024/6lni_0931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lni_0931/03_2024/6lni_0931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lni_0931/03_2024/6lni_0931.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lni_0931/03_2024/6lni_0931.pdb" } 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 Residue "A ARG 208": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "F ARG 208": "NH1" <-> "NH2" Residue "G ARG 208": "NH1" <-> "NH2" Residue "H ARG 208": "NH1" <-> "NH2" Residue "I ARG 208": "NH1" <-> "NH2" Residue "J ARG 208": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4920 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "B" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "C" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "D" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "E" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "F" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "G" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "H" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "I" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "J" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Time building chain proxies: 2.87, per 1000 atoms: 0.58 Number of scatterers: 4920 At special positions: 0 Unit cell: (145.002, 122.694, 44.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1010 8.00 N 870 7.00 C 2990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 214 " distance=2.03 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 214 " distance=2.03 Simple disulfide: pdb=" SG CYS G 179 " - pdb=" SG CYS G 214 " distance=2.03 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 179 " - pdb=" SG CYS I 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 179 " - pdb=" SG CYS J 214 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 898.4 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: 0.55 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: 1.08 Time building geometry restraints manager: 2.14 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: 100.40 - 106.56: 60 106.56 - 112.73: 2648 112.73 - 118.90: 1352 118.90 - 125.07: 2630 125.07 - 131.24: 20 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 2.520 nonbonded pdb=" NZ LYS C 194 " pdb=" OE2 GLU H 196 " model vdw 2.220 2.520 nonbonded pdb=" NZ LYS D 194 " pdb=" OE2 GLU I 196 " model vdw 2.236 2.520 nonbonded pdb=" NZ LYS B 194 " pdb=" OE2 GLU G 196 " model vdw 2.243 2.520 nonbonded pdb=" OE2 GLU C 196 " pdb=" NZ LYS G 194 " model vdw 2.267 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 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: 0.000 Extract box with map and model: 12.800 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.350 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.800 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.601 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: 1.6438 time to fit residues: 307.0759 Evaluate side-chains 150 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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: 4.9990 chunk 25 optimal weight: 0.0770 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 47 optimal weight: 0.0370 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- 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 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 J 173 ASN J 174 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4980 Z= 0.321 Angle : 0.553 4.844 6710 Z= 0.328 Chirality : 0.045 0.112 760 Planarity : 0.003 0.033 880 Dihedral : 5.822 37.849 652 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 2.98 % Allowed : 18.60 % Favored : 78.42 % 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: -5.13 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.17), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 177 PHE 0.005 0.001 PHE A 175 TYR 0.013 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 165 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: B 208 ARG cc_start: 0.7372 (mtt180) cc_final: 0.7106 (mtm180) REVERT: B 221 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: D 200 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7827 (mt-10) REVERT: D 228 ARG cc_start: 0.8693 (ttt-90) cc_final: 0.8323 (ttt-90) REVERT: G 221 GLU cc_start: 0.8063 (mp0) cc_final: 0.7594 (mp0) REVERT: G 228 ARG cc_start: 0.8647 (ttt-90) cc_final: 0.8218 (ttt-90) REVERT: H 211 GLU cc_start: 0.7813 (tt0) cc_final: 0.7397 (tt0) REVERT: H 213 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7492 (tmt) REVERT: H 220 ARG cc_start: 0.7897 (ptt180) cc_final: 0.7521 (ptp-170) REVERT: H 221 GLU cc_start: 0.8213 (mp0) cc_final: 0.7633 (mp0) REVERT: I 221 GLU cc_start: 0.8119 (mp0) cc_final: 0.7643 (mp0) REVERT: J 220 ARG cc_start: 0.7904 (ptt180) cc_final: 0.6434 (mmm160) outliers start: 17 outliers final: 8 residues processed: 152 average time/residue: 1.9150 time to fit residues: 298.2408 Evaluate side-chains 154 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 221 GLU Chi-restraints excluded: chain F residue 223 GLN Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 213 MET Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 213 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS I 174 ASN I 187 HIS ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 4980 Z= 0.505 Angle : 0.647 6.081 6710 Z= 0.382 Chirality : 0.047 0.110 760 Planarity : 0.003 0.033 880 Dihedral : 6.053 24.193 650 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Rotamer: Outliers : 3.86 % Allowed : 20.35 % Favored : 75.79 % 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: -4.70 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 177 PHE 0.010 0.002 PHE F 175 TYR 0.018 0.002 TYR D 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 166 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 0.627 Fit side-chains REVERT: A 228 ARG cc_start: 0.8915 (ttt-90) cc_final: 0.8435 (ttt-90) REVERT: B 208 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7210 (mtm180) REVERT: B 228 ARG cc_start: 0.8784 (ttt-90) cc_final: 0.8554 (tmt170) REVERT: D 200 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7908 (mt-10) REVERT: D 205 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7854 (ttt) REVERT: D 220 ARG cc_start: 0.7992 (ptp90) cc_final: 0.7621 (ptp90) REVERT: D 228 ARG cc_start: 0.8712 (ttt-90) cc_final: 0.8329 (ttt-90) REVERT: G 221 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7829 (mt-10) REVERT: G 228 ARG cc_start: 0.8732 (ttt-90) cc_final: 0.8221 (ttt-90) REVERT: H 208 ARG cc_start: 0.7368 (mtp85) cc_final: 0.7160 (mtm180) REVERT: H 211 GLU cc_start: 0.7896 (tt0) cc_final: 0.7490 (tt0) REVERT: H 221 GLU cc_start: 0.8207 (mp0) cc_final: 0.7858 (mt-10) REVERT: I 208 ARG cc_start: 0.7407 (mtm-85) cc_final: 0.7166 (mtm180) REVERT: I 221 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7901 (mp0) REVERT: J 220 ARG cc_start: 0.7922 (ptt180) cc_final: 0.6430 (mmm160) outliers start: 22 outliers final: 7 residues processed: 149 average time/residue: 1.9453 time to fit residues: 296.4707 Evaluate side-chains 150 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 197 ASN 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 G residue 197 ASN 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 41 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 0.0270 chunk 36 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 172 GLN F 177 HIS ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4980 Z= 0.408 Angle : 0.596 5.465 6710 Z= 0.353 Chirality : 0.046 0.111 760 Planarity : 0.003 0.035 880 Dihedral : 5.889 22.741 650 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 4.74 % Allowed : 22.11 % 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: -4.48 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 177 PHE 0.008 0.001 PHE F 175 TYR 0.016 0.002 TYR D 226 ARG 0.009 0.001 ARG E 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 173 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 0.637 Fit side-chains REVERT: A 220 ARG cc_start: 0.8295 (ptt-90) cc_final: 0.8034 (ptt90) REVERT: A 228 ARG cc_start: 0.8947 (ttt-90) cc_final: 0.8545 (ttt-90) REVERT: B 228 ARG cc_start: 0.8741 (ttt-90) cc_final: 0.8520 (tmt170) REVERT: C 221 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: D 200 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7880 (mt-10) REVERT: D 205 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7835 (ttt) REVERT: D 208 ARG cc_start: 0.7398 (mtm180) cc_final: 0.6953 (mtm180) REVERT: D 220 ARG cc_start: 0.7991 (ptp90) cc_final: 0.7669 (ptp90) REVERT: D 223 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: D 228 ARG cc_start: 0.8741 (ttt-90) cc_final: 0.8257 (ttt-90) REVERT: G 208 ARG cc_start: 0.7655 (mtp85) cc_final: 0.7085 (mtm110) REVERT: G 228 ARG cc_start: 0.8719 (ttt-90) cc_final: 0.8126 (ttt-90) REVERT: H 211 GLU cc_start: 0.7934 (tt0) cc_final: 0.7522 (tt0) REVERT: I 208 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.7116 (mtm180) REVERT: J 220 ARG cc_start: 0.7867 (ptt180) cc_final: 0.6245 (mmm160) outliers start: 27 outliers final: 10 residues processed: 153 average time/residue: 1.8473 time to fit residues: 289.3324 Evaluate side-chains 157 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 213 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain F residue 197 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 172 GLN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2585 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= 0.207 Angle : 0.499 4.019 6710 Z= 0.294 Chirality : 0.044 0.115 760 Planarity : 0.003 0.037 880 Dihedral : 5.379 18.759 650 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 3.68 % Allowed : 24.91 % 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: -4.19 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 177 PHE 0.005 0.001 PHE F 175 TYR 0.011 0.001 TYR D 226 ARG 0.010 0.001 ARG F 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 172 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 0.616 Fit side-chains REVERT: A 206 MET cc_start: 0.8802 (mtm) cc_final: 0.8569 (mtp) REVERT: A 220 ARG cc_start: 0.8253 (ptt-90) cc_final: 0.7931 (ptt90) REVERT: A 228 ARG cc_start: 0.8949 (ttt-90) cc_final: 0.8523 (ttt-90) REVERT: B 220 ARG cc_start: 0.7875 (ptp90) cc_final: 0.7422 (ptt-90) REVERT: B 221 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: C 220 ARG cc_start: 0.7953 (ptp90) cc_final: 0.7693 (ptp90) REVERT: D 200 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7858 (mt-10) REVERT: D 208 ARG cc_start: 0.7233 (mtm180) cc_final: 0.6811 (mtm110) REVERT: D 223 GLN cc_start: 0.8135 (mt0) cc_final: 0.7847 (mp10) REVERT: D 228 ARG cc_start: 0.8739 (ttt-90) cc_final: 0.8248 (ttt-90) REVERT: E 220 ARG cc_start: 0.8119 (ptp90) cc_final: 0.7909 (ptp90) REVERT: F 211 GLU cc_start: 0.7566 (tt0) cc_final: 0.7174 (tt0) REVERT: G 178 ASP cc_start: 0.8373 (m-30) cc_final: 0.8021 (m-30) REVERT: G 208 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7043 (mtm110) REVERT: G 228 ARG cc_start: 0.8703 (ttt-90) cc_final: 0.8134 (ttt-90) REVERT: H 211 GLU cc_start: 0.7923 (tt0) cc_final: 0.7449 (tt0) REVERT: I 221 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7660 (mp0) REVERT: J 220 ARG cc_start: 0.7840 (ptt180) cc_final: 0.5886 (mmm160) outliers start: 21 outliers final: 7 residues processed: 157 average time/residue: 1.7651 time to fit residues: 284.0415 Evaluate side-chains 152 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 204 LYS 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 14 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 HIS E 212 GLN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 HIS ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 4980 Z= 0.442 Angle : 0.619 5.627 6710 Z= 0.365 Chirality : 0.047 0.138 760 Planarity : 0.003 0.037 880 Dihedral : 5.876 22.134 650 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 4.39 % Allowed : 26.67 % Favored : 68.95 % 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: -4.15 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 177 PHE 0.009 0.002 PHE F 175 TYR 0.016 0.002 TYR G 226 ARG 0.011 0.001 ARG F 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 175 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 0.626 Fit side-chains REVERT: A 206 MET cc_start: 0.8863 (mtm) cc_final: 0.8612 (mtp) REVERT: A 228 ARG cc_start: 0.8947 (ttt-90) cc_final: 0.8534 (ttt-90) REVERT: B 228 ARG cc_start: 0.8786 (ttt-90) cc_final: 0.8541 (tmt170) REVERT: D 200 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7858 (mt-10) REVERT: D 205 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7845 (ttt) REVERT: D 223 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: D 228 ARG cc_start: 0.8754 (ttt-90) cc_final: 0.8255 (ttt-90) REVERT: E 220 ARG cc_start: 0.8036 (ptp90) cc_final: 0.7834 (ptp90) REVERT: G 206 MET cc_start: 0.8464 (mtp) cc_final: 0.8228 (mtp) REVERT: G 208 ARG cc_start: 0.7701 (mtp85) cc_final: 0.7055 (mtm110) REVERT: G 221 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7748 (mp0) REVERT: G 228 ARG cc_start: 0.8821 (ttt-90) cc_final: 0.8247 (ttt-90) REVERT: H 211 GLU cc_start: 0.8012 (tt0) cc_final: 0.7561 (tt0) REVERT: H 221 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7578 (mp0) REVERT: J 220 ARG cc_start: 0.7907 (ptt180) cc_final: 0.6233 (mmm160) outliers start: 25 outliers final: 9 residues processed: 155 average time/residue: 1.8670 time to fit residues: 296.2104 Evaluate side-chains 157 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 197 ASN 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 D residue 223 GLN Chi-restraints excluded: chain F residue 197 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.0870 chunk 48 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4980 Z= 0.242 Angle : 0.538 4.809 6710 Z= 0.316 Chirality : 0.044 0.157 760 Planarity : 0.003 0.041 880 Dihedral : 5.568 19.471 650 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 3.33 % Allowed : 29.30 % Favored : 67.37 % 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: -4.03 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (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 0.012 0.001 TYR C 226 ARG 0.010 0.001 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 fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 0.606 Fit side-chains REVERT: A 206 MET cc_start: 0.8804 (mtm) cc_final: 0.8548 (mtp) REVERT: A 220 ARG cc_start: 0.8295 (ptt-90) cc_final: 0.8076 (ptt90) REVERT: A 228 ARG cc_start: 0.8943 (ttt-90) cc_final: 0.8515 (ttt-90) REVERT: D 200 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7858 (mt-10) REVERT: D 208 ARG cc_start: 0.7256 (mtm180) cc_final: 0.6842 (mtm180) REVERT: D 220 ARG cc_start: 0.7924 (ptp90) cc_final: 0.7486 (ptp90) REVERT: D 228 ARG cc_start: 0.8763 (ttt-90) cc_final: 0.8226 (ttt-90) REVERT: E 220 ARG cc_start: 0.8036 (ptp90) cc_final: 0.7831 (ptp90) REVERT: F 211 GLU cc_start: 0.7541 (tt0) cc_final: 0.7141 (tt0) REVERT: G 206 MET cc_start: 0.8373 (mtp) cc_final: 0.8154 (mtp) REVERT: G 208 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7027 (mtm110) REVERT: G 221 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7693 (mp0) REVERT: G 228 ARG cc_start: 0.8724 (ttt-90) cc_final: 0.8113 (ttt-90) REVERT: H 211 GLU cc_start: 0.7861 (tt0) cc_final: 0.7361 (tt0) REVERT: H 221 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7676 (mp0) REVERT: I 221 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7771 (mp0) REVERT: J 220 ARG cc_start: 0.7859 (ptt180) cc_final: 0.6003 (mmm160) outliers start: 19 outliers final: 9 residues processed: 160 average time/residue: 1.8023 time to fit residues: 295.6714 Evaluate side-chains 160 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 204 LYS 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 28 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 4980 Z= 0.471 Angle : 0.648 5.885 6710 Z= 0.380 Chirality : 0.048 0.147 760 Planarity : 0.003 0.035 880 Dihedral : 5.957 21.965 650 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.97 % Favored : 86.03 % Rotamer: Outliers : 3.51 % Allowed : 29.30 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.07 (0.26), 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 0.004 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 *********************** 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 173 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 0.599 Fit side-chains REVERT: A 220 ARG cc_start: 0.8368 (ptt-90) cc_final: 0.8134 (ptt90) REVERT: A 228 ARG cc_start: 0.8919 (ttt-90) cc_final: 0.8428 (ttt-90) REVERT: B 228 ARG cc_start: 0.8787 (ttt-90) cc_final: 0.8554 (tmt170) REVERT: D 200 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7833 (mt-10) REVERT: D 220 ARG cc_start: 0.7987 (ptp90) cc_final: 0.7478 (ptp90) REVERT: D 223 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: D 228 ARG cc_start: 0.8756 (ttt-90) cc_final: 0.8289 (ttt-90) REVERT: F 211 GLU cc_start: 0.7591 (tt0) cc_final: 0.7170 (tt0) REVERT: G 206 MET cc_start: 0.8425 (mtp) cc_final: 0.8175 (mtp) REVERT: G 208 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7140 (mtm110) REVERT: G 228 ARG cc_start: 0.8827 (ttt-90) cc_final: 0.8243 (ttt-90) REVERT: H 211 GLU cc_start: 0.8017 (tt0) cc_final: 0.7581 (tt0) REVERT: H 221 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7775 (mt-10) REVERT: I 221 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7782 (mp0) REVERT: J 220 ARG cc_start: 0.7922 (ptt180) cc_final: 0.6144 (mmm160) outliers start: 20 outliers final: 9 residues processed: 160 average time/residue: 1.9453 time to fit residues: 318.8870 Evaluate side-chains 159 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 D residue 223 GLN Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 201 THR 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 48 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4980 Z= 0.251 Angle : 0.560 6.225 6710 Z= 0.328 Chirality : 0.045 0.171 760 Planarity : 0.003 0.042 880 Dihedral : 5.696 22.907 650 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.63 % Allowed : 30.18 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.99 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (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 B 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 164 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8310 (ptt-90) cc_final: 0.8047 (ptt90) REVERT: A 228 ARG cc_start: 0.8946 (ttt-90) cc_final: 0.8512 (ttt-90) REVERT: B 221 GLU cc_start: 0.8028 (mp0) cc_final: 0.7608 (mp0) REVERT: B 228 ARG cc_start: 0.8729 (ttt-90) cc_final: 0.8506 (ttt-90) REVERT: C 220 ARG cc_start: 0.7861 (ptp90) cc_final: 0.7570 (ptp90) REVERT: D 200 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7893 (mt-10) REVERT: D 208 ARG cc_start: 0.7316 (mtm180) cc_final: 0.6914 (mtm110) REVERT: D 220 ARG cc_start: 0.7884 (ptp90) cc_final: 0.7503 (ptp90) REVERT: D 228 ARG cc_start: 0.8776 (ttt-90) cc_final: 0.8249 (ttt-90) REVERT: F 211 GLU cc_start: 0.7588 (tt0) cc_final: 0.7155 (tt0) REVERT: G 208 ARG cc_start: 0.7670 (mtp85) cc_final: 0.7100 (mtm110) REVERT: G 221 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7696 (mp0) REVERT: G 228 ARG cc_start: 0.8708 (ttt-90) cc_final: 0.8116 (ttt-90) REVERT: H 211 GLU cc_start: 0.7922 (tt0) cc_final: 0.7490 (tt0) REVERT: I 221 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7724 (mp0) REVERT: J 220 ARG cc_start: 0.7812 (ptt180) cc_final: 0.5958 (mmm160) outliers start: 15 outliers final: 11 residues processed: 155 average time/residue: 1.9572 time to fit residues: 310.8960 Evaluate side-chains 160 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 213 MET 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 G residue 197 ASN Chi-restraints excluded: chain I residue 201 THR 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 4 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 4980 Z= 0.372 Angle : 0.618 5.727 6710 Z= 0.361 Chirality : 0.047 0.190 760 Planarity : 0.003 0.031 880 Dihedral : 5.906 20.711 650 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 2.63 % Allowed : 30.35 % Favored : 67.02 % 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: -4.03 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.20), 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 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 163 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8337 (ptt-90) cc_final: 0.8066 (ptt90) REVERT: A 228 ARG cc_start: 0.8910 (ttt-90) cc_final: 0.8431 (ttt-90) REVERT: B 221 GLU cc_start: 0.8015 (mp0) cc_final: 0.7514 (mp0) REVERT: B 228 ARG cc_start: 0.8781 (ttt-90) cc_final: 0.8524 (tmt170) REVERT: C 220 ARG cc_start: 0.7951 (ptp90) cc_final: 0.7672 (ptp90) REVERT: D 200 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7813 (mt-10) REVERT: D 208 ARG cc_start: 0.7437 (mtm180) cc_final: 0.7029 (mtm110) REVERT: D 220 ARG cc_start: 0.7937 (ptp90) cc_final: 0.7445 (ptp90) REVERT: D 228 ARG cc_start: 0.8749 (ttt-90) cc_final: 0.8254 (ttt-90) REVERT: E 220 ARG cc_start: 0.7981 (ptp90) cc_final: 0.7734 (ptp90) REVERT: F 211 GLU cc_start: 0.7595 (tt0) cc_final: 0.7154 (tt0) REVERT: G 208 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7149 (mtm110) REVERT: G 221 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7714 (mp0) REVERT: G 228 ARG cc_start: 0.8802 (ttt-90) cc_final: 0.8236 (ttt-90) REVERT: H 211 GLU cc_start: 0.8023 (tt0) cc_final: 0.7594 (tt0) REVERT: H 221 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7782 (mp0) REVERT: J 220 ARG cc_start: 0.7885 (ptt180) cc_final: 0.6007 (mmm160) outliers start: 15 outliers final: 11 residues processed: 154 average time/residue: 1.8821 time to fit residues: 296.7718 Evaluate side-chains 158 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 221 GLU Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 201 THR 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 48 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 172 GLN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.126921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.109474 restraints weight = 5487.662| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.04 r_work: 0.3674 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4980 Z= 0.276 Angle : 0.586 5.999 6710 Z= 0.343 Chirality : 0.046 0.195 760 Planarity : 0.003 0.035 880 Dihedral : 5.857 20.232 650 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 2.28 % Allowed : 31.93 % Favored : 65.79 % 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 : -3.06 (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 0.009 0.001 ARG E 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4261.69 seconds wall clock time: 75 minutes 28.30 seconds (4528.30 seconds total)