Starting phenix.real_space_refine on Wed Mar 4 10:44:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dse_30832/03_2026/7dse_30832.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dse_30832/03_2026/7dse_30832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dse_30832/03_2026/7dse_30832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dse_30832/03_2026/7dse_30832.map" model { file = "/net/cci-nas-00/data/ceres_data/7dse_30832/03_2026/7dse_30832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dse_30832/03_2026/7dse_30832.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.057 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 105 5.16 5 C 8449 2.51 5 N 2086 2.21 5 O 2317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12957 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1837 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 1.68, per 1000 atoms: 0.13 Number of scatterers: 12957 At special positions: 0 Unit cell: (111.54, 112.554, 103.428, 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 105 16.00 O 2317 8.00 N 2086 7.00 C 8449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 159 " 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 139 " " NAG B1001 " - " ASN B 139 " " NAG C1001 " - " ASN C 139 " " NAG D1001 " - " ASN D 139 " " NAG E1001 " - " ASN E 139 " " NAG F1001 " - " ASN F 139 " " NAG G1001 " - " ASN G 139 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 592.6 milliseconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3164 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.600A pdb=" N ALA A 29 " --> pdb=" O ILE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 71 Proline residue: A 59 - end of helix removed outlier: 3.731A pdb=" N ASN A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 93 through 107 Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.644A pdb=" N LYS A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 204 Processing helix chain 'A' and resid 209 through 250 removed outlier: 3.676A pdb=" N LEU A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE A 240 " --> pdb=" O HIS A 236 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 248 " --> pdb=" O CYS A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 25 through 36 removed outlier: 3.601A pdb=" N ALA B 29 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 71 Proline residue: B 59 - end of helix removed outlier: 3.732A pdb=" N ASN B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 93 through 107 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 146 through 156 removed outlier: 3.644A pdb=" N LYS B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 204 Processing helix chain 'B' and resid 209 through 250 removed outlier: 3.677A pdb=" N LEU B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE B 240 " --> pdb=" O HIS B 236 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 248 " --> pdb=" O CYS B 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 25 through 36 removed outlier: 3.601A pdb=" N ALA C 29 " --> pdb=" O ILE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 71 Proline residue: C 59 - end of helix removed outlier: 3.732A pdb=" N ASN C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 83 Processing helix chain 'C' and resid 93 through 107 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 146 through 156 removed outlier: 3.644A pdb=" N LYS C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 204 Processing helix chain 'C' and resid 209 through 250 removed outlier: 3.676A pdb=" N LEU C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE C 240 " --> pdb=" O HIS C 236 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR C 248 " --> pdb=" O CYS C 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 25 through 36 removed outlier: 3.601A pdb=" N ALA D 29 " --> pdb=" O ILE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 71 Proline residue: D 59 - end of helix removed outlier: 3.731A pdb=" N ASN D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 83 Processing helix chain 'D' and resid 93 through 107 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 146 through 156 removed outlier: 3.643A pdb=" N LYS D 156 " --> pdb=" O LYS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 204 Processing helix chain 'D' and resid 209 through 250 removed outlier: 3.676A pdb=" N LEU D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE D 240 " --> pdb=" O HIS D 236 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR D 248 " --> pdb=" O CYS D 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 18 Processing helix chain 'E' and resid 25 through 36 removed outlier: 3.601A pdb=" N ALA E 29 " --> pdb=" O ILE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 71 Proline residue: E 59 - end of helix removed outlier: 3.732A pdb=" N ASN E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 83 Processing helix chain 'E' and resid 93 through 107 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 146 through 156 removed outlier: 3.644A pdb=" N LYS E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 204 Processing helix chain 'E' and resid 209 through 250 removed outlier: 3.676A pdb=" N LEU E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE E 240 " --> pdb=" O HIS E 236 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR E 248 " --> pdb=" O CYS E 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 18 Processing helix chain 'F' and resid 25 through 36 removed outlier: 3.601A pdb=" N ALA F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 71 Proline residue: F 59 - end of helix removed outlier: 3.731A pdb=" N ASN F 71 " --> pdb=" O GLY F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 83 Processing helix chain 'F' and resid 93 through 107 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 146 through 156 removed outlier: 3.644A pdb=" N LYS F 156 " --> pdb=" O LYS F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 204 Processing helix chain 'F' and resid 209 through 250 removed outlier: 3.676A pdb=" N LEU F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE F 240 " --> pdb=" O HIS F 236 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN F 247 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR F 248 " --> pdb=" O CYS F 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 18 Processing helix chain 'G' and resid 25 through 36 removed outlier: 3.601A pdb=" N ALA G 29 " --> pdb=" O ILE G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 71 Proline residue: G 59 - end of helix removed outlier: 3.731A pdb=" N ASN G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 83 Processing helix chain 'G' and resid 93 through 107 Processing helix chain 'G' and resid 107 through 120 Processing helix chain 'G' and resid 122 through 129 Processing helix chain 'G' and resid 146 through 156 removed outlier: 3.643A pdb=" N LYS G 156 " --> pdb=" O LYS G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 204 Processing helix chain 'G' and resid 209 through 250 removed outlier: 3.677A pdb=" N LEU G 213 " --> pdb=" O GLN G 209 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER G 239 " --> pdb=" O GLU G 235 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE G 240 " --> pdb=" O HIS G 236 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN G 247 " --> pdb=" O VAL G 243 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR G 248 " --> pdb=" O CYS G 244 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2775 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: 1.90 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3630 1.33 - 1.45: 2203 1.45 - 1.57: 7278 1.57 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 13265 Sorted by residual: bond pdb=" N ALA A 93 " pdb=" CA ALA A 93 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.10e-02 8.26e+03 6.55e+00 bond pdb=" N ALA C 93 " pdb=" CA ALA C 93 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.10e-02 8.26e+03 6.44e+00 bond pdb=" N ALA E 93 " pdb=" CA ALA E 93 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.10e-02 8.26e+03 6.30e+00 bond pdb=" N ALA D 93 " pdb=" CA ALA D 93 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.10e-02 8.26e+03 6.30e+00 bond pdb=" N ALA B 93 " pdb=" CA ALA B 93 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.10e-02 8.26e+03 6.14e+00 ... (remaining 13260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 17028 1.25 - 2.51: 778 2.51 - 3.76: 121 3.76 - 5.02: 14 5.02 - 6.27: 35 Bond angle restraints: 17976 Sorted by residual: angle pdb=" N LYS C 216 " pdb=" CA LYS C 216 " pdb=" C LYS C 216 " ideal model delta sigma weight residual 111.36 105.39 5.97 1.09e+00 8.42e-01 3.00e+01 angle pdb=" N LYS A 216 " pdb=" CA LYS A 216 " pdb=" C LYS A 216 " ideal model delta sigma weight residual 111.36 105.39 5.97 1.09e+00 8.42e-01 3.00e+01 angle pdb=" N LYS E 216 " pdb=" CA LYS E 216 " pdb=" C LYS E 216 " ideal model delta sigma weight residual 111.36 105.40 5.96 1.09e+00 8.42e-01 2.99e+01 angle pdb=" N LYS D 216 " pdb=" CA LYS D 216 " pdb=" C LYS D 216 " ideal model delta sigma weight residual 111.36 105.42 5.94 1.09e+00 8.42e-01 2.97e+01 angle pdb=" N LYS F 216 " pdb=" CA LYS F 216 " pdb=" C LYS F 216 " ideal model delta sigma weight residual 111.36 105.42 5.94 1.09e+00 8.42e-01 2.97e+01 ... (remaining 17971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.47: 7077 12.47 - 24.94: 631 24.94 - 37.40: 195 37.40 - 49.87: 77 49.87 - 62.34: 21 Dihedral angle restraints: 8001 sinusoidal: 3157 harmonic: 4844 Sorted by residual: dihedral pdb=" N LYS F 82 " pdb=" CA LYS F 82 " pdb=" CB LYS F 82 " pdb=" CG LYS F 82 " ideal model delta sinusoidal sigma weight residual -180.00 -126.30 -53.70 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" N LYS D 82 " pdb=" CA LYS D 82 " pdb=" CB LYS D 82 " pdb=" CG LYS D 82 " ideal model delta sinusoidal sigma weight residual -180.00 -126.31 -53.69 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LYS G 82 " pdb=" CA LYS G 82 " pdb=" CB LYS G 82 " pdb=" CG LYS G 82 " ideal model delta sinusoidal sigma weight residual -180.00 -126.31 -53.69 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 7998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1140 0.028 - 0.055: 586 0.055 - 0.082: 196 0.082 - 0.110: 90 0.110 - 0.137: 39 Chirality restraints: 2051 Sorted by residual: chirality pdb=" CA ALA C 93 " pdb=" N ALA C 93 " pdb=" C ALA C 93 " pdb=" CB ALA C 93 " both_signs ideal model delta sigma weight residual False 2.48 2.35 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ALA E 93 " pdb=" N ALA E 93 " pdb=" C ALA E 93 " pdb=" CB ALA E 93 " both_signs ideal model delta sigma weight residual False 2.48 2.35 0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ALA G 93 " pdb=" N ALA G 93 " pdb=" C ALA G 93 " pdb=" CB ALA G 93 " both_signs ideal model delta sigma weight residual False 2.48 2.35 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 2048 not shown) Planarity restraints: 2219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 215 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C THR F 215 " -0.055 2.00e-02 2.50e+03 pdb=" O THR F 215 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS F 216 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 215 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.98e+00 pdb=" C THR B 215 " -0.055 2.00e-02 2.50e+03 pdb=" O THR B 215 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS B 216 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 215 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.98e+00 pdb=" C THR G 215 " -0.055 2.00e-02 2.50e+03 pdb=" O THR G 215 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS G 216 " 0.018 2.00e-02 2.50e+03 ... (remaining 2216 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 3776 2.82 - 3.34: 13431 3.34 - 3.86: 20754 3.86 - 4.38: 22653 4.38 - 4.90: 38774 Nonbonded interactions: 99388 Sorted by model distance: nonbonded pdb=" O LEU G 118 " pdb=" OG SER G 182 " model vdw 2.295 3.040 nonbonded pdb=" O LEU E 118 " pdb=" OG SER E 182 " model vdw 2.296 3.040 nonbonded pdb=" O LEU C 118 " pdb=" OG SER C 182 " model vdw 2.296 3.040 nonbonded pdb=" O LEU F 118 " pdb=" OG SER F 182 " model vdw 2.296 3.040 nonbonded pdb=" O LEU D 118 " pdb=" OG SER D 182 " model vdw 2.296 3.040 ... (remaining 99383 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.250 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.720 Find NCS groups from input model: 0.110 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.005 0.040 13286 Z= 0.242 Angle : 0.658 6.275 18025 Z= 0.410 Chirality : 0.041 0.137 2051 Planarity : 0.004 0.034 2212 Dihedral : 11.843 62.341 4795 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.21), residues: 1575 helix: 0.44 (0.15), residues: 1225 sheet: None (None), residues: 0 loop : -3.31 (0.28), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 226 TYR 0.011 0.001 TYR F 34 PHE 0.008 0.001 PHE G 163 TRP 0.009 0.001 TRP F 62 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00493 (13265) covalent geometry : angle 0.64666 (17976) SS BOND : bond 0.00255 ( 14) SS BOND : angle 0.66592 ( 28) hydrogen bonds : bond 0.14221 ( 925) hydrogen bonds : angle 4.83422 ( 2775) link_NAG-ASN : bond 0.00628 ( 7) link_NAG-ASN : angle 3.54637 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 723 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.8983 (m-80) cc_final: 0.8724 (m-80) REVERT: A 49 TYR cc_start: 0.8924 (t80) cc_final: 0.8646 (t80) REVERT: A 95 LEU cc_start: 0.9332 (mt) cc_final: 0.9039 (pt) REVERT: A 96 ARG cc_start: 0.8133 (mtp180) cc_final: 0.7822 (mtt180) REVERT: A 104 GLN cc_start: 0.8984 (mt0) cc_final: 0.7912 (tp40) REVERT: A 105 ARG cc_start: 0.8831 (tpt170) cc_final: 0.8574 (mmm-85) REVERT: A 177 TYR cc_start: 0.9186 (t80) cc_final: 0.8670 (t80) REVERT: A 227 LYS cc_start: 0.9495 (tttt) cc_final: 0.9188 (ttpt) REVERT: B 95 LEU cc_start: 0.9329 (mt) cc_final: 0.9073 (pt) REVERT: B 96 ARG cc_start: 0.8148 (mtp180) cc_final: 0.7839 (mtt180) REVERT: B 104 GLN cc_start: 0.9059 (mt0) cc_final: 0.8032 (tp40) REVERT: B 105 ARG cc_start: 0.8954 (tpt170) cc_final: 0.8700 (mmm-85) REVERT: B 120 ASP cc_start: 0.8584 (t70) cc_final: 0.8361 (t0) REVERT: B 177 TYR cc_start: 0.9136 (t80) cc_final: 0.8456 (t80) REVERT: B 227 LYS cc_start: 0.9559 (tttt) cc_final: 0.9251 (ttpt) REVERT: C 47 TYR cc_start: 0.8945 (m-80) cc_final: 0.8728 (m-80) REVERT: C 95 LEU cc_start: 0.9218 (mt) cc_final: 0.9015 (pt) REVERT: C 96 ARG cc_start: 0.8082 (mtp180) cc_final: 0.7804 (mtt180) REVERT: C 104 GLN cc_start: 0.9065 (mt0) cc_final: 0.7951 (tm-30) REVERT: C 120 ASP cc_start: 0.8506 (t70) cc_final: 0.8305 (t0) REVERT: C 177 TYR cc_start: 0.9144 (t80) cc_final: 0.8374 (t80) REVERT: C 225 GLU cc_start: 0.9120 (tt0) cc_final: 0.8750 (pt0) REVERT: D 47 TYR cc_start: 0.8959 (m-80) cc_final: 0.8676 (m-80) REVERT: D 95 LEU cc_start: 0.9356 (mt) cc_final: 0.9124 (pt) REVERT: D 96 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7966 (mtt180) REVERT: D 98 MET cc_start: 0.9534 (ttp) cc_final: 0.9269 (ttp) REVERT: D 104 GLN cc_start: 0.9102 (mt0) cc_final: 0.7866 (tm-30) REVERT: D 105 ARG cc_start: 0.9030 (tpt170) cc_final: 0.8709 (mmm-85) REVERT: D 177 TYR cc_start: 0.9189 (t80) cc_final: 0.8521 (t80) REVERT: D 227 LYS cc_start: 0.9558 (tttt) cc_final: 0.9158 (ttpt) REVERT: E 47 TYR cc_start: 0.8934 (m-80) cc_final: 0.8648 (m-80) REVERT: E 95 LEU cc_start: 0.9295 (mt) cc_final: 0.9093 (pt) REVERT: E 96 ARG cc_start: 0.8183 (mtp180) cc_final: 0.7897 (mtt180) REVERT: E 98 MET cc_start: 0.9483 (ttp) cc_final: 0.9278 (ttp) REVERT: E 104 GLN cc_start: 0.8978 (mt0) cc_final: 0.7985 (tm-30) REVERT: E 177 TYR cc_start: 0.9096 (t80) cc_final: 0.8277 (t80) REVERT: E 225 GLU cc_start: 0.9195 (tt0) cc_final: 0.8935 (pt0) REVERT: F 47 TYR cc_start: 0.8944 (m-80) cc_final: 0.8641 (m-80) REVERT: F 95 LEU cc_start: 0.9316 (mt) cc_final: 0.9095 (pt) REVERT: F 96 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7876 (mtt90) REVERT: F 104 GLN cc_start: 0.9062 (mt0) cc_final: 0.8097 (tp40) REVERT: F 105 ARG cc_start: 0.8918 (tpt170) cc_final: 0.8626 (mmm-85) REVERT: F 177 TYR cc_start: 0.9185 (t80) cc_final: 0.8471 (t80) REVERT: F 215 THR cc_start: 0.9492 (t) cc_final: 0.9183 (t) REVERT: F 225 GLU cc_start: 0.9196 (tt0) cc_final: 0.8983 (pt0) REVERT: G 46 ASP cc_start: 0.9225 (m-30) cc_final: 0.9004 (m-30) REVERT: G 47 TYR cc_start: 0.8976 (m-80) cc_final: 0.8709 (m-10) REVERT: G 96 ARG cc_start: 0.7929 (mtp180) cc_final: 0.7369 (mtt90) REVERT: G 104 GLN cc_start: 0.8960 (mt0) cc_final: 0.7562 (tp40) REVERT: G 105 ARG cc_start: 0.8931 (tpt170) cc_final: 0.8517 (mmm-85) REVERT: G 142 TYR cc_start: 0.8132 (m-80) cc_final: 0.7863 (m-10) REVERT: G 177 TYR cc_start: 0.9284 (t80) cc_final: 0.8680 (t80) REVERT: G 229 PHE cc_start: 0.9292 (t80) cc_final: 0.8900 (t80) outliers start: 0 outliers final: 0 residues processed: 723 average time/residue: 0.1337 time to fit residues: 131.1427 Evaluate side-chains 486 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN D 183 GLN D 246 GLN ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.108914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077397 restraints weight = 32747.973| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.89 r_work: 0.2932 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13286 Z= 0.165 Angle : 0.711 8.787 18025 Z= 0.361 Chirality : 0.039 0.131 2051 Planarity : 0.005 0.043 2212 Dihedral : 4.561 26.928 1890 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 2.92 % Allowed : 21.69 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.22), residues: 1575 helix: 1.73 (0.15), residues: 1239 sheet: None (None), residues: 0 loop : -2.09 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 179 TYR 0.014 0.002 TYR G 49 PHE 0.016 0.001 PHE G 212 TRP 0.006 0.001 TRP F 218 HIS 0.002 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00380 (13265) covalent geometry : angle 0.70599 (17976) SS BOND : bond 0.00353 ( 14) SS BOND : angle 0.64041 ( 28) hydrogen bonds : bond 0.05058 ( 925) hydrogen bonds : angle 3.82046 ( 2775) link_NAG-ASN : bond 0.00132 ( 7) link_NAG-ASN : angle 2.48753 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 529 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.9138 (m-80) cc_final: 0.8890 (m-80) REVERT: A 49 TYR cc_start: 0.8931 (t80) cc_final: 0.8676 (t80) REVERT: A 68 TYR cc_start: 0.8823 (m-80) cc_final: 0.8586 (t80) REVERT: A 71 ASN cc_start: 0.8567 (t0) cc_final: 0.7997 (t0) REVERT: A 96 ARG cc_start: 0.8250 (mtp180) cc_final: 0.7892 (mtt180) REVERT: A 104 GLN cc_start: 0.8951 (mt0) cc_final: 0.7699 (tp40) REVERT: A 105 ARG cc_start: 0.9330 (tpt170) cc_final: 0.8951 (mmm-85) REVERT: A 120 ASP cc_start: 0.8897 (t0) cc_final: 0.8634 (t0) REVERT: B 96 ARG cc_start: 0.8285 (mtp180) cc_final: 0.7956 (mtt180) REVERT: B 104 GLN cc_start: 0.9004 (mt0) cc_final: 0.7760 (tp40) REVERT: B 105 ARG cc_start: 0.9427 (tpt170) cc_final: 0.9163 (mmm-85) REVERT: B 120 ASP cc_start: 0.8901 (t70) cc_final: 0.8552 (t0) REVERT: B 122 LYS cc_start: 0.9395 (mmtp) cc_final: 0.9190 (mmmm) REVERT: B 179 ARG cc_start: 0.9250 (mmm-85) cc_final: 0.8845 (ttm-80) REVERT: B 233 CYS cc_start: 0.8587 (m) cc_final: 0.8309 (m) REVERT: C 96 ARG cc_start: 0.8270 (mtp180) cc_final: 0.7866 (mtt180) REVERT: C 104 GLN cc_start: 0.9027 (mt0) cc_final: 0.7957 (tp40) REVERT: C 142 TYR cc_start: 0.7888 (m-80) cc_final: 0.7671 (m-80) REVERT: C 201 ARG cc_start: 0.8597 (tpp80) cc_final: 0.8254 (tpt-90) REVERT: C 221 TYR cc_start: 0.9173 (t80) cc_final: 0.8959 (t80) REVERT: C 225 GLU cc_start: 0.9272 (tt0) cc_final: 0.9050 (pt0) REVERT: C 226 ARG cc_start: 0.8298 (mmp-170) cc_final: 0.7692 (mmp-170) REVERT: C 233 CYS cc_start: 0.8725 (m) cc_final: 0.8418 (m) REVERT: D 32 GLN cc_start: 0.9228 (mm-40) cc_final: 0.9020 (tp40) REVERT: D 47 TYR cc_start: 0.9181 (m-80) cc_final: 0.8825 (m-80) REVERT: D 68 TYR cc_start: 0.8783 (m-80) cc_final: 0.8454 (t80) REVERT: D 71 ASN cc_start: 0.8780 (t0) cc_final: 0.8151 (t0) REVERT: D 96 ARG cc_start: 0.8327 (mtp180) cc_final: 0.8011 (mtt180) REVERT: D 104 GLN cc_start: 0.8949 (mt0) cc_final: 0.7791 (tp40) REVERT: D 105 ARG cc_start: 0.9433 (tpt170) cc_final: 0.9139 (mmm-85) REVERT: D 120 ASP cc_start: 0.8947 (t0) cc_final: 0.8577 (t0) REVERT: E 47 TYR cc_start: 0.9103 (m-80) cc_final: 0.8810 (m-80) REVERT: E 71 ASN cc_start: 0.8571 (t0) cc_final: 0.8115 (t0) REVERT: E 96 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7987 (mtt180) REVERT: E 104 GLN cc_start: 0.8960 (mt0) cc_final: 0.7856 (tp40) REVERT: E 120 ASP cc_start: 0.8809 (t0) cc_final: 0.8395 (t0) REVERT: E 152 LYS cc_start: 0.9548 (mttt) cc_final: 0.9275 (mptt) REVERT: E 225 GLU cc_start: 0.9274 (tt0) cc_final: 0.9025 (pt0) REVERT: E 226 ARG cc_start: 0.8652 (mmp-170) cc_final: 0.8199 (mmp-170) REVERT: E 246 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8707 (mp10) REVERT: E 247 GLN cc_start: 0.9030 (mp10) cc_final: 0.8821 (pm20) REVERT: F 47 TYR cc_start: 0.9147 (m-80) cc_final: 0.8773 (m-80) REVERT: F 96 ARG cc_start: 0.8357 (mtp180) cc_final: 0.7995 (mtt180) REVERT: F 104 GLN cc_start: 0.8985 (mt0) cc_final: 0.7901 (tp40) REVERT: F 105 ARG cc_start: 0.9307 (tpt170) cc_final: 0.8987 (mmm-85) REVERT: F 179 ARG cc_start: 0.9214 (mmm-85) cc_final: 0.8860 (mtp85) REVERT: G 40 THR cc_start: 0.9692 (OUTLIER) cc_final: 0.9411 (p) REVERT: G 47 TYR cc_start: 0.9216 (m-80) cc_final: 0.9001 (m-10) REVERT: G 71 ASN cc_start: 0.8435 (t0) cc_final: 0.8125 (t0) REVERT: G 95 LEU cc_start: 0.9317 (mt) cc_final: 0.9076 (pt) REVERT: G 96 ARG cc_start: 0.7990 (mtp180) cc_final: 0.7497 (mtt180) REVERT: G 105 ARG cc_start: 0.9335 (tpt170) cc_final: 0.9050 (mmm-85) REVERT: G 120 ASP cc_start: 0.8905 (t0) cc_final: 0.8543 (t0) REVERT: G 148 LYS cc_start: 0.9606 (mmmt) cc_final: 0.9370 (mmmt) REVERT: G 152 LYS cc_start: 0.9579 (mttt) cc_final: 0.9304 (mppt) REVERT: G 246 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8554 (mp10) outliers start: 39 outliers final: 19 residues processed: 548 average time/residue: 0.1354 time to fit residues: 100.0776 Evaluate side-chains 499 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 479 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 181 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 22 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 0.0870 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.109485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.076004 restraints weight = 32424.199| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.89 r_work: 0.2930 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13286 Z= 0.160 Angle : 0.665 9.141 18025 Z= 0.335 Chirality : 0.039 0.133 2051 Planarity : 0.005 0.051 2212 Dihedral : 4.150 22.420 1890 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 4.04 % Allowed : 23.71 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.23), residues: 1575 helix: 2.07 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -2.08 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 226 TYR 0.015 0.001 TYR B 177 PHE 0.017 0.001 PHE F 212 TRP 0.008 0.001 TRP F 218 HIS 0.001 0.000 HIS G 220 Details of bonding type rmsd covalent geometry : bond 0.00386 (13265) covalent geometry : angle 0.65967 (17976) SS BOND : bond 0.00293 ( 14) SS BOND : angle 0.56101 ( 28) hydrogen bonds : bond 0.04654 ( 925) hydrogen bonds : angle 3.71180 ( 2775) link_NAG-ASN : bond 0.00229 ( 7) link_NAG-ASN : angle 2.61981 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 495 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.9163 (m-80) cc_final: 0.8881 (m-80) REVERT: A 49 TYR cc_start: 0.9013 (t80) cc_final: 0.8771 (t80) REVERT: A 68 TYR cc_start: 0.8914 (m-80) cc_final: 0.8596 (t80) REVERT: A 71 ASN cc_start: 0.8538 (t0) cc_final: 0.8140 (t0) REVERT: A 96 ARG cc_start: 0.8333 (mtp180) cc_final: 0.7924 (mtt180) REVERT: A 104 GLN cc_start: 0.8934 (mt0) cc_final: 0.7786 (tp40) REVERT: A 105 ARG cc_start: 0.9395 (tpt170) cc_final: 0.9068 (mmm-85) REVERT: A 120 ASP cc_start: 0.8901 (t0) cc_final: 0.8606 (t0) REVERT: A 136 GLU cc_start: 0.9081 (pm20) cc_final: 0.8810 (pm20) REVERT: A 214 LYS cc_start: 0.9800 (mmtp) cc_final: 0.9587 (mmtt) REVERT: A 247 GLN cc_start: 0.8774 (pm20) cc_final: 0.8393 (pm20) REVERT: B 96 ARG cc_start: 0.8366 (mtp180) cc_final: 0.7974 (mtt180) REVERT: B 104 GLN cc_start: 0.9035 (mt0) cc_final: 0.7712 (tp40) REVERT: B 105 ARG cc_start: 0.9437 (tpt170) cc_final: 0.9144 (mmm-85) REVERT: B 152 LYS cc_start: 0.9598 (mttt) cc_final: 0.9356 (mppt) REVERT: B 220 HIS cc_start: 0.8670 (m90) cc_final: 0.8434 (m-70) REVERT: B 233 CYS cc_start: 0.8667 (m) cc_final: 0.8248 (m) REVERT: C 32 GLN cc_start: 0.9325 (mm-40) cc_final: 0.8913 (tp40) REVERT: C 96 ARG cc_start: 0.8396 (mtp180) cc_final: 0.7989 (mtt180) REVERT: C 104 GLN cc_start: 0.9033 (mt0) cc_final: 0.8038 (tp40) REVERT: C 152 LYS cc_start: 0.9618 (mttt) cc_final: 0.9313 (mppt) REVERT: C 201 ARG cc_start: 0.8672 (tpp80) cc_final: 0.8401 (tpt-90) REVERT: C 214 LYS cc_start: 0.9769 (mmtp) cc_final: 0.9555 (mmtt) REVERT: C 216 LYS cc_start: 0.9508 (mmmm) cc_final: 0.9100 (mmtp) REVERT: C 225 GLU cc_start: 0.9351 (tt0) cc_final: 0.9091 (pt0) REVERT: C 226 ARG cc_start: 0.8507 (mmp-170) cc_final: 0.7913 (mmp-170) REVERT: C 233 CYS cc_start: 0.8800 (m) cc_final: 0.8551 (m) REVERT: C 246 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8907 (mp10) REVERT: D 47 TYR cc_start: 0.9201 (m-80) cc_final: 0.8837 (m-80) REVERT: D 71 ASN cc_start: 0.8844 (t0) cc_final: 0.8395 (t0) REVERT: D 96 ARG cc_start: 0.8460 (mtp180) cc_final: 0.8109 (mtt180) REVERT: D 104 GLN cc_start: 0.8913 (mt0) cc_final: 0.7856 (tp40) REVERT: D 105 ARG cc_start: 0.9476 (tpt170) cc_final: 0.9062 (mmm-85) REVERT: D 108 ILE cc_start: 0.9407 (mm) cc_final: 0.9196 (mp) REVERT: D 120 ASP cc_start: 0.8945 (t0) cc_final: 0.8482 (t0) REVERT: D 209 GLN cc_start: 0.9101 (pm20) cc_final: 0.8839 (pm20) REVERT: E 32 GLN cc_start: 0.9244 (mt0) cc_final: 0.8818 (tt0) REVERT: E 47 TYR cc_start: 0.9169 (m-80) cc_final: 0.8858 (m-80) REVERT: E 71 ASN cc_start: 0.8609 (t0) cc_final: 0.8237 (t0) REVERT: E 96 ARG cc_start: 0.8366 (mtp180) cc_final: 0.8050 (mtt180) REVERT: E 104 GLN cc_start: 0.8970 (mt0) cc_final: 0.7962 (tp40) REVERT: E 120 ASP cc_start: 0.8864 (t0) cc_final: 0.8378 (t0) REVERT: E 152 LYS cc_start: 0.9564 (mttt) cc_final: 0.9236 (mppt) REVERT: E 214 LYS cc_start: 0.9748 (mmtp) cc_final: 0.9541 (mmtt) REVERT: E 226 ARG cc_start: 0.8822 (mmp-170) cc_final: 0.8285 (mmp80) REVERT: F 71 ASN cc_start: 0.8733 (t0) cc_final: 0.8512 (t0) REVERT: F 96 ARG cc_start: 0.8372 (mtp180) cc_final: 0.7921 (mtt90) REVERT: F 104 GLN cc_start: 0.9013 (mt0) cc_final: 0.7918 (tp40) REVERT: F 105 ARG cc_start: 0.9391 (tpt170) cc_final: 0.9067 (mmm-85) REVERT: F 179 ARG cc_start: 0.9197 (mmm-85) cc_final: 0.8975 (mtp85) REVERT: G 32 GLN cc_start: 0.9335 (tp40) cc_final: 0.9128 (tt0) REVERT: G 40 THR cc_start: 0.9725 (OUTLIER) cc_final: 0.9430 (p) REVERT: G 71 ASN cc_start: 0.8541 (t0) cc_final: 0.8258 (t0) REVERT: G 95 LEU cc_start: 0.9339 (mt) cc_final: 0.9136 (pt) REVERT: G 96 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7529 (mtt180) REVERT: G 105 ARG cc_start: 0.9370 (tpt170) cc_final: 0.9022 (mmm-85) REVERT: G 120 ASP cc_start: 0.8932 (t0) cc_final: 0.8512 (t0) REVERT: G 148 LYS cc_start: 0.9642 (mmmt) cc_final: 0.9404 (mmmt) REVERT: G 152 LYS cc_start: 0.9613 (mttt) cc_final: 0.9308 (mppt) REVERT: G 160 LYS cc_start: 0.9501 (ttmm) cc_final: 0.9196 (ttmm) REVERT: G 246 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8661 (mp10) outliers start: 54 outliers final: 36 residues processed: 521 average time/residue: 0.1311 time to fit residues: 93.2504 Evaluate side-chains 484 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 447 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 131 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 61 optimal weight: 0.0870 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.111008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.078268 restraints weight = 32055.009| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.90 r_work: 0.2954 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13286 Z= 0.130 Angle : 0.636 8.748 18025 Z= 0.322 Chirality : 0.038 0.122 2051 Planarity : 0.004 0.049 2212 Dihedral : 3.813 17.145 1890 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.77 % Allowed : 25.28 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.22), residues: 1575 helix: 2.24 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -1.85 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 201 TYR 0.019 0.001 TYR F 217 PHE 0.014 0.001 PHE F 137 TRP 0.007 0.001 TRP E 62 HIS 0.004 0.000 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00310 (13265) covalent geometry : angle 0.63178 (17976) SS BOND : bond 0.00210 ( 14) SS BOND : angle 0.42004 ( 28) hydrogen bonds : bond 0.04156 ( 925) hydrogen bonds : angle 3.51509 ( 2775) link_NAG-ASN : bond 0.00102 ( 7) link_NAG-ASN : angle 2.25370 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 474 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.9136 (m-80) cc_final: 0.8836 (m-80) REVERT: A 68 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8622 (t80) REVERT: A 71 ASN cc_start: 0.8566 (t0) cc_final: 0.8075 (t0) REVERT: A 96 ARG cc_start: 0.8379 (mtp180) cc_final: 0.7963 (mtt180) REVERT: A 105 ARG cc_start: 0.9388 (tpt170) cc_final: 0.9086 (mmm-85) REVERT: A 120 ASP cc_start: 0.8864 (t0) cc_final: 0.8481 (t0) REVERT: A 136 GLU cc_start: 0.9149 (pm20) cc_final: 0.8888 (pm20) REVERT: A 233 CYS cc_start: 0.8780 (m) cc_final: 0.8390 (m) REVERT: B 32 GLN cc_start: 0.9316 (tt0) cc_final: 0.9093 (tt0) REVERT: B 96 ARG cc_start: 0.8299 (mtp180) cc_final: 0.7920 (mtt180) REVERT: B 104 GLN cc_start: 0.9006 (mt0) cc_final: 0.7693 (tp40) REVERT: B 105 ARG cc_start: 0.9414 (tpt170) cc_final: 0.9137 (mmm-85) REVERT: B 120 ASP cc_start: 0.8917 (t0) cc_final: 0.8521 (t0) REVERT: B 152 LYS cc_start: 0.9619 (mttt) cc_final: 0.9404 (mttt) REVERT: B 220 HIS cc_start: 0.8716 (m90) cc_final: 0.8074 (m90) REVERT: B 233 CYS cc_start: 0.8769 (m) cc_final: 0.8519 (m) REVERT: C 71 ASN cc_start: 0.8512 (t0) cc_final: 0.8237 (t0) REVERT: C 96 ARG cc_start: 0.8338 (mtp180) cc_final: 0.7921 (mtt180) REVERT: C 152 LYS cc_start: 0.9622 (mttt) cc_final: 0.9362 (mttt) REVERT: C 216 LYS cc_start: 0.9526 (mmmm) cc_final: 0.9120 (mmtp) REVERT: C 226 ARG cc_start: 0.8609 (mmp-170) cc_final: 0.8307 (mmp80) REVERT: C 233 CYS cc_start: 0.8884 (m) cc_final: 0.8633 (m) REVERT: D 32 GLN cc_start: 0.9286 (mm-40) cc_final: 0.9030 (tp40) REVERT: D 47 TYR cc_start: 0.9169 (m-80) cc_final: 0.8814 (m-80) REVERT: D 68 TYR cc_start: 0.8856 (m-80) cc_final: 0.8540 (t80) REVERT: D 71 ASN cc_start: 0.8784 (t0) cc_final: 0.8265 (t0) REVERT: D 96 ARG cc_start: 0.8421 (mtp180) cc_final: 0.8015 (mtt180) REVERT: D 104 GLN cc_start: 0.8945 (mt0) cc_final: 0.7840 (tp40) REVERT: D 105 ARG cc_start: 0.9446 (tpt170) cc_final: 0.9195 (mmm-85) REVERT: D 120 ASP cc_start: 0.8835 (t0) cc_final: 0.8297 (t0) REVERT: D 209 GLN cc_start: 0.9082 (pm20) cc_final: 0.8827 (pm20) REVERT: D 216 LYS cc_start: 0.9497 (mmmm) cc_final: 0.9177 (mmmm) REVERT: E 32 GLN cc_start: 0.9276 (mt0) cc_final: 0.8858 (tt0) REVERT: E 47 TYR cc_start: 0.9145 (m-80) cc_final: 0.8834 (m-80) REVERT: E 71 ASN cc_start: 0.8563 (t0) cc_final: 0.8184 (t0) REVERT: E 96 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7983 (mtt180) REVERT: E 104 GLN cc_start: 0.8960 (mt0) cc_final: 0.7889 (tp40) REVERT: E 119 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8728 (mmm) REVERT: E 120 ASP cc_start: 0.8820 (t0) cc_final: 0.8269 (t0) REVERT: E 152 LYS cc_start: 0.9591 (mttt) cc_final: 0.9313 (mttt) REVERT: E 226 ARG cc_start: 0.8879 (mmp-170) cc_final: 0.8333 (mmp80) REVERT: E 233 CYS cc_start: 0.8885 (m) cc_final: 0.8664 (m) REVERT: F 40 THR cc_start: 0.9787 (OUTLIER) cc_final: 0.9548 (p) REVERT: F 71 ASN cc_start: 0.8709 (t0) cc_final: 0.8451 (t0) REVERT: F 96 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7908 (mtt180) REVERT: F 104 GLN cc_start: 0.8892 (mt0) cc_final: 0.7791 (tp40) REVERT: F 105 ARG cc_start: 0.9374 (tpt170) cc_final: 0.9060 (mmm-85) REVERT: F 179 ARG cc_start: 0.9197 (mmm-85) cc_final: 0.8936 (mtp85) REVERT: F 223 ASP cc_start: 0.9672 (t0) cc_final: 0.9426 (t0) REVERT: G 40 THR cc_start: 0.9728 (OUTLIER) cc_final: 0.9503 (p) REVERT: G 71 ASN cc_start: 0.8516 (t0) cc_final: 0.8224 (t0) REVERT: G 96 ARG cc_start: 0.7922 (mtp180) cc_final: 0.7546 (mtt180) REVERT: G 104 GLN cc_start: 0.8905 (mt0) cc_final: 0.7578 (tp40) REVERT: G 105 ARG cc_start: 0.9401 (tpt170) cc_final: 0.9108 (mmm-85) REVERT: G 120 ASP cc_start: 0.8874 (t0) cc_final: 0.8382 (t0) REVERT: G 148 LYS cc_start: 0.9680 (mmmt) cc_final: 0.9416 (mmmt) REVERT: G 152 LYS cc_start: 0.9609 (mttt) cc_final: 0.9292 (mppt) REVERT: G 233 CYS cc_start: 0.8571 (m) cc_final: 0.8259 (m) outliers start: 37 outliers final: 23 residues processed: 495 average time/residue: 0.1219 time to fit residues: 84.3843 Evaluate side-chains 485 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 458 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 33 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 150 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.115211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.082518 restraints weight = 31784.113| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.92 r_work: 0.2947 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13286 Z= 0.142 Angle : 0.620 8.345 18025 Z= 0.316 Chirality : 0.038 0.155 2051 Planarity : 0.004 0.048 2212 Dihedral : 3.665 17.399 1890 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.66 % Allowed : 26.10 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.22), residues: 1575 helix: 2.35 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -1.62 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 226 TYR 0.015 0.001 TYR D 217 PHE 0.011 0.001 PHE F 124 TRP 0.012 0.001 TRP E 62 HIS 0.004 0.001 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00346 (13265) covalent geometry : angle 0.61594 (17976) SS BOND : bond 0.00259 ( 14) SS BOND : angle 0.44525 ( 28) hydrogen bonds : bond 0.04069 ( 925) hydrogen bonds : angle 3.49905 ( 2775) link_NAG-ASN : bond 0.00130 ( 7) link_NAG-ASN : angle 2.20123 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 465 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.9229 (m-80) cc_final: 0.8956 (m-80) REVERT: A 68 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8598 (t80) REVERT: A 71 ASN cc_start: 0.8590 (t0) cc_final: 0.8101 (t0) REVERT: A 96 ARG cc_start: 0.8422 (mtp180) cc_final: 0.8117 (mtt180) REVERT: A 105 ARG cc_start: 0.9409 (tpt170) cc_final: 0.9122 (mmm-85) REVERT: A 120 ASP cc_start: 0.8861 (t0) cc_final: 0.8490 (t0) REVERT: A 136 GLU cc_start: 0.9135 (pm20) cc_final: 0.8870 (pm20) REVERT: A 233 CYS cc_start: 0.8807 (m) cc_final: 0.8434 (m) REVERT: B 71 ASN cc_start: 0.8850 (t0) cc_final: 0.8624 (t0) REVERT: B 96 ARG cc_start: 0.8369 (mtp180) cc_final: 0.8020 (mtp180) REVERT: B 104 GLN cc_start: 0.8998 (mt0) cc_final: 0.7731 (tp40) REVERT: B 105 ARG cc_start: 0.9432 (tpt170) cc_final: 0.9158 (mmm-85) REVERT: B 120 ASP cc_start: 0.8756 (t0) cc_final: 0.8533 (t0) REVERT: B 148 LYS cc_start: 0.9598 (mmmt) cc_final: 0.9323 (mmmt) REVERT: B 152 LYS cc_start: 0.9620 (mttt) cc_final: 0.9415 (mttt) REVERT: B 220 HIS cc_start: 0.8748 (m90) cc_final: 0.8197 (m90) REVERT: B 233 CYS cc_start: 0.8735 (m) cc_final: 0.8495 (m) REVERT: C 26 MET cc_start: 0.7952 (mmp) cc_final: 0.7709 (mmp) REVERT: C 71 ASN cc_start: 0.8653 (t0) cc_final: 0.8251 (t0) REVERT: C 96 ARG cc_start: 0.8367 (mtp180) cc_final: 0.7938 (mtt180) REVERT: C 120 ASP cc_start: 0.8827 (t0) cc_final: 0.8588 (t0) REVERT: C 152 LYS cc_start: 0.9623 (mttt) cc_final: 0.9362 (mttt) REVERT: C 216 LYS cc_start: 0.9523 (mmmm) cc_final: 0.9104 (mmtp) REVERT: C 226 ARG cc_start: 0.8718 (mmp-170) cc_final: 0.8378 (mmp80) REVERT: C 233 CYS cc_start: 0.8888 (m) cc_final: 0.8647 (m) REVERT: D 32 GLN cc_start: 0.9279 (mm-40) cc_final: 0.9070 (tp40) REVERT: D 47 TYR cc_start: 0.9198 (m-80) cc_final: 0.8809 (m-80) REVERT: D 68 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8460 (t80) REVERT: D 71 ASN cc_start: 0.8806 (t0) cc_final: 0.8348 (t0) REVERT: D 96 ARG cc_start: 0.8406 (mtp180) cc_final: 0.8063 (mtp180) REVERT: D 104 GLN cc_start: 0.8886 (mt0) cc_final: 0.7875 (tp40) REVERT: D 105 ARG cc_start: 0.9469 (tpt170) cc_final: 0.9118 (mmm-85) REVERT: D 120 ASP cc_start: 0.8829 (t0) cc_final: 0.8305 (t0) REVERT: D 209 GLN cc_start: 0.9114 (pm20) cc_final: 0.8865 (pm20) REVERT: D 246 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8712 (pp30) REVERT: E 38 GLU cc_start: 0.9022 (tp30) cc_final: 0.8688 (pt0) REVERT: E 47 TYR cc_start: 0.9168 (m-80) cc_final: 0.8830 (m-80) REVERT: E 71 ASN cc_start: 0.8446 (t0) cc_final: 0.8100 (t0) REVERT: E 96 ARG cc_start: 0.8395 (mtp180) cc_final: 0.7993 (mtt180) REVERT: E 104 GLN cc_start: 0.8986 (mt0) cc_final: 0.7850 (tm-30) REVERT: E 119 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8730 (mmm) REVERT: E 120 ASP cc_start: 0.8888 (t0) cc_final: 0.8283 (t0) REVERT: E 152 LYS cc_start: 0.9623 (mttt) cc_final: 0.9343 (mttt) REVERT: E 226 ARG cc_start: 0.8864 (mmp-170) cc_final: 0.8342 (mmp80) REVERT: E 233 CYS cc_start: 0.8872 (m) cc_final: 0.8669 (m) REVERT: F 71 ASN cc_start: 0.8662 (t0) cc_final: 0.8285 (t0) REVERT: F 96 ARG cc_start: 0.8381 (mtp180) cc_final: 0.8043 (mtp180) REVERT: F 104 GLN cc_start: 0.8919 (mt0) cc_final: 0.7797 (tp40) REVERT: F 105 ARG cc_start: 0.9402 (tpt170) cc_final: 0.9105 (mmm-85) REVERT: F 233 CYS cc_start: 0.8833 (m) cc_final: 0.8592 (m) REVERT: F 247 GLN cc_start: 0.8879 (mp10) cc_final: 0.8661 (pm20) REVERT: G 32 GLN cc_start: 0.8656 (pt0) cc_final: 0.8439 (tt0) REVERT: G 40 THR cc_start: 0.9753 (OUTLIER) cc_final: 0.9494 (p) REVERT: G 71 ASN cc_start: 0.8500 (t0) cc_final: 0.8132 (t0) REVERT: G 96 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7736 (mtt180) REVERT: G 104 GLN cc_start: 0.8866 (mt0) cc_final: 0.7656 (tp40) REVERT: G 105 ARG cc_start: 0.9428 (tpt170) cc_final: 0.9127 (mmm-85) REVERT: G 119 MET cc_start: 0.9167 (mmp) cc_final: 0.8910 (mmm) REVERT: G 120 ASP cc_start: 0.8888 (t0) cc_final: 0.8417 (t0) REVERT: G 148 LYS cc_start: 0.9680 (mmmt) cc_final: 0.9434 (mmmt) REVERT: G 152 LYS cc_start: 0.9609 (mttt) cc_final: 0.9305 (mppt) REVERT: G 160 LYS cc_start: 0.9543 (ttmm) cc_final: 0.9260 (ttmm) REVERT: G 201 ARG cc_start: 0.8750 (tpp80) cc_final: 0.8508 (tpp80) REVERT: G 233 CYS cc_start: 0.8610 (m) cc_final: 0.8354 (m) REVERT: G 246 GLN cc_start: 0.8462 (mp10) cc_final: 0.8186 (mp10) outliers start: 49 outliers final: 35 residues processed: 484 average time/residue: 0.1194 time to fit residues: 80.2530 Evaluate side-chains 491 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 452 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 203 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 153 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.115676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.082995 restraints weight = 31519.211| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.92 r_work: 0.2961 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13286 Z= 0.130 Angle : 0.618 7.380 18025 Z= 0.314 Chirality : 0.039 0.179 2051 Planarity : 0.005 0.053 2212 Dihedral : 3.509 17.709 1890 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.52 % Allowed : 25.73 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.22), residues: 1575 helix: 2.47 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -1.47 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 179 TYR 0.015 0.001 TYR D 217 PHE 0.013 0.001 PHE B 124 TRP 0.012 0.001 TRP E 62 HIS 0.003 0.000 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00315 (13265) covalent geometry : angle 0.61513 (17976) SS BOND : bond 0.00229 ( 14) SS BOND : angle 0.43847 ( 28) hydrogen bonds : bond 0.03890 ( 925) hydrogen bonds : angle 3.42113 ( 2775) link_NAG-ASN : bond 0.00060 ( 7) link_NAG-ASN : angle 2.03049 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 480 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.9210 (m-80) cc_final: 0.8922 (m-80) REVERT: A 68 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8538 (t80) REVERT: A 71 ASN cc_start: 0.8646 (t0) cc_final: 0.8148 (t0) REVERT: A 96 ARG cc_start: 0.8437 (mtp180) cc_final: 0.8125 (mtt180) REVERT: A 105 ARG cc_start: 0.9415 (tpt170) cc_final: 0.9134 (mmm-85) REVERT: A 120 ASP cc_start: 0.8865 (t0) cc_final: 0.8483 (t0) REVERT: A 136 GLU cc_start: 0.9130 (pm20) cc_final: 0.8852 (pm20) REVERT: A 233 CYS cc_start: 0.8853 (m) cc_final: 0.8495 (m) REVERT: B 71 ASN cc_start: 0.8960 (t0) cc_final: 0.8697 (t0) REVERT: B 96 ARG cc_start: 0.8317 (mtp180) cc_final: 0.7982 (mtp180) REVERT: B 104 GLN cc_start: 0.9000 (mt0) cc_final: 0.7675 (tp40) REVERT: B 105 ARG cc_start: 0.9461 (tpt170) cc_final: 0.9192 (mmm-85) REVERT: B 120 ASP cc_start: 0.8837 (t0) cc_final: 0.8438 (t0) REVERT: B 216 LYS cc_start: 0.9575 (tptt) cc_final: 0.9293 (mmtp) REVERT: B 220 HIS cc_start: 0.8806 (m90) cc_final: 0.8383 (m-70) REVERT: B 233 CYS cc_start: 0.8774 (m) cc_final: 0.8531 (m) REVERT: C 71 ASN cc_start: 0.8691 (t0) cc_final: 0.8283 (t0) REVERT: C 96 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7900 (mtt180) REVERT: C 152 LYS cc_start: 0.9649 (mttt) cc_final: 0.9355 (mppt) REVERT: C 226 ARG cc_start: 0.8791 (mmp-170) cc_final: 0.8233 (mmp80) REVERT: C 233 CYS cc_start: 0.8917 (m) cc_final: 0.8661 (m) REVERT: D 68 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8447 (t80) REVERT: D 71 ASN cc_start: 0.8808 (t0) cc_final: 0.8312 (t0) REVERT: D 96 ARG cc_start: 0.8398 (mtp180) cc_final: 0.8042 (mtp180) REVERT: D 104 GLN cc_start: 0.9077 (mt0) cc_final: 0.8084 (tp40) REVERT: D 105 ARG cc_start: 0.9544 (tpt170) cc_final: 0.9326 (mmm-85) REVERT: D 120 ASP cc_start: 0.8844 (t0) cc_final: 0.8312 (t0) REVERT: D 209 GLN cc_start: 0.9129 (pm20) cc_final: 0.8901 (pm20) REVERT: D 246 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8524 (pp30) REVERT: E 38 GLU cc_start: 0.9047 (tp30) cc_final: 0.8679 (pt0) REVERT: E 47 TYR cc_start: 0.9156 (m-80) cc_final: 0.8811 (m-80) REVERT: E 71 ASN cc_start: 0.8430 (t0) cc_final: 0.8032 (t0) REVERT: E 96 ARG cc_start: 0.8381 (mtp180) cc_final: 0.7964 (mtt180) REVERT: E 104 GLN cc_start: 0.8984 (mt0) cc_final: 0.7844 (tm-30) REVERT: E 120 ASP cc_start: 0.8870 (t0) cc_final: 0.8296 (t0) REVERT: E 152 LYS cc_start: 0.9618 (mttt) cc_final: 0.9286 (mppt) REVERT: E 226 ARG cc_start: 0.8862 (mmp-170) cc_final: 0.8335 (mmp80) REVERT: F 71 ASN cc_start: 0.8812 (t0) cc_final: 0.8517 (t0) REVERT: F 96 ARG cc_start: 0.8397 (mtp180) cc_final: 0.7994 (mtp180) REVERT: F 105 ARG cc_start: 0.9421 (tpt170) cc_final: 0.9133 (mmm-85) REVERT: F 223 ASP cc_start: 0.9671 (t0) cc_final: 0.9459 (t0) REVERT: F 233 CYS cc_start: 0.8909 (m) cc_final: 0.8685 (m) REVERT: F 247 GLN cc_start: 0.8898 (mp10) cc_final: 0.8674 (pm20) REVERT: G 32 GLN cc_start: 0.8670 (pt0) cc_final: 0.8426 (tt0) REVERT: G 40 THR cc_start: 0.9754 (OUTLIER) cc_final: 0.9539 (p) REVERT: G 71 ASN cc_start: 0.8413 (t0) cc_final: 0.8119 (t0) REVERT: G 96 ARG cc_start: 0.8105 (mtp180) cc_final: 0.7738 (mtt180) REVERT: G 105 ARG cc_start: 0.9447 (tpt170) cc_final: 0.9165 (mmm-85) REVERT: G 119 MET cc_start: 0.9151 (mmp) cc_final: 0.8899 (mmm) REVERT: G 120 ASP cc_start: 0.8869 (t0) cc_final: 0.8369 (t0) REVERT: G 148 LYS cc_start: 0.9677 (mmmt) cc_final: 0.9452 (mmmt) REVERT: G 152 LYS cc_start: 0.9605 (mttt) cc_final: 0.9293 (mppt) REVERT: G 201 ARG cc_start: 0.8778 (tpp80) cc_final: 0.8538 (tpp80) REVERT: G 233 CYS cc_start: 0.8662 (m) cc_final: 0.8401 (m) REVERT: G 246 GLN cc_start: 0.8505 (mp10) cc_final: 0.8187 (mp10) outliers start: 47 outliers final: 37 residues processed: 497 average time/residue: 0.1195 time to fit residues: 82.9367 Evaluate side-chains 503 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 463 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 74 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 50.0000 chunk 128 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 60 optimal weight: 0.0670 chunk 71 optimal weight: 4.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.110942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.078050 restraints weight = 31971.166| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.89 r_work: 0.2964 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13286 Z= 0.130 Angle : 0.629 6.918 18025 Z= 0.321 Chirality : 0.040 0.179 2051 Planarity : 0.005 0.052 2212 Dihedral : 3.397 17.290 1890 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.66 % Allowed : 27.00 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.22), residues: 1575 helix: 2.50 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.29 (0.38), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 226 TYR 0.019 0.001 TYR D 97 PHE 0.015 0.001 PHE D 124 TRP 0.011 0.001 TRP F 62 HIS 0.003 0.000 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00313 (13265) covalent geometry : angle 0.62601 (17976) SS BOND : bond 0.00213 ( 14) SS BOND : angle 0.42787 ( 28) hydrogen bonds : bond 0.03801 ( 925) hydrogen bonds : angle 3.39136 ( 2775) link_NAG-ASN : bond 0.00074 ( 7) link_NAG-ASN : angle 1.94731 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 483 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8543 (t80) REVERT: A 71 ASN cc_start: 0.8635 (t0) cc_final: 0.8141 (t0) REVERT: A 96 ARG cc_start: 0.8392 (mtp180) cc_final: 0.8114 (mtt180) REVERT: A 105 ARG cc_start: 0.9407 (tpt170) cc_final: 0.9132 (mmm-85) REVERT: A 120 ASP cc_start: 0.8854 (t0) cc_final: 0.8465 (t0) REVERT: A 136 GLU cc_start: 0.9121 (pm20) cc_final: 0.8850 (pm20) REVERT: A 233 CYS cc_start: 0.8881 (m) cc_final: 0.8541 (m) REVERT: B 71 ASN cc_start: 0.8965 (t0) cc_final: 0.8562 (t0) REVERT: B 96 ARG cc_start: 0.8353 (mtp180) cc_final: 0.7958 (mtp180) REVERT: B 104 GLN cc_start: 0.8981 (mt0) cc_final: 0.7624 (tp40) REVERT: B 105 ARG cc_start: 0.9455 (tpt170) cc_final: 0.9233 (mmm-85) REVERT: B 120 ASP cc_start: 0.8834 (t0) cc_final: 0.8391 (t0) REVERT: B 201 ARG cc_start: 0.8723 (tpp80) cc_final: 0.8483 (tpp80) REVERT: B 216 LYS cc_start: 0.9570 (tptt) cc_final: 0.9285 (mmtp) REVERT: B 220 HIS cc_start: 0.8742 (m90) cc_final: 0.8335 (m-70) REVERT: B 233 CYS cc_start: 0.8750 (m) cc_final: 0.8517 (m) REVERT: C 71 ASN cc_start: 0.8778 (t0) cc_final: 0.8351 (t0) REVERT: C 96 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7886 (mtt180) REVERT: C 152 LYS cc_start: 0.9633 (mttt) cc_final: 0.9331 (mttt) REVERT: C 226 ARG cc_start: 0.8852 (mmp-170) cc_final: 0.8291 (mmp80) REVERT: C 233 CYS cc_start: 0.8888 (m) cc_final: 0.8597 (m) REVERT: D 68 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.8436 (t80) REVERT: D 71 ASN cc_start: 0.8856 (t0) cc_final: 0.8374 (t0) REVERT: D 96 ARG cc_start: 0.8405 (mtp180) cc_final: 0.8045 (mtp180) REVERT: D 104 GLN cc_start: 0.9049 (mt0) cc_final: 0.8083 (tp40) REVERT: D 105 ARG cc_start: 0.9515 (tpt170) cc_final: 0.9263 (mmm-85) REVERT: D 120 ASP cc_start: 0.8823 (t0) cc_final: 0.8330 (t0) REVERT: D 209 GLN cc_start: 0.9184 (pm20) cc_final: 0.8949 (pm20) REVERT: E 38 GLU cc_start: 0.9072 (tp30) cc_final: 0.8689 (pt0) REVERT: E 47 TYR cc_start: 0.9129 (m-80) cc_final: 0.8772 (m-80) REVERT: E 71 ASN cc_start: 0.8351 (t0) cc_final: 0.7876 (t0) REVERT: E 96 ARG cc_start: 0.8434 (mtp180) cc_final: 0.8006 (mtt180) REVERT: E 104 GLN cc_start: 0.8999 (mt0) cc_final: 0.7844 (tm-30) REVERT: E 112 VAL cc_start: 0.9637 (t) cc_final: 0.9374 (p) REVERT: E 120 ASP cc_start: 0.8866 (t0) cc_final: 0.8303 (t0) REVERT: E 152 LYS cc_start: 0.9613 (mttt) cc_final: 0.9295 (mttt) REVERT: E 226 ARG cc_start: 0.8922 (mmp-170) cc_final: 0.8400 (mmp80) REVERT: F 71 ASN cc_start: 0.8782 (t0) cc_final: 0.8492 (t0) REVERT: F 96 ARG cc_start: 0.8382 (mtp180) cc_final: 0.7959 (mtp180) REVERT: F 105 ARG cc_start: 0.9386 (tpt170) cc_final: 0.9098 (mmm-85) REVERT: F 233 CYS cc_start: 0.8886 (m) cc_final: 0.8652 (m) REVERT: F 247 GLN cc_start: 0.8890 (mp10) cc_final: 0.8654 (pm20) REVERT: G 32 GLN cc_start: 0.8599 (pt0) cc_final: 0.8341 (tt0) REVERT: G 40 THR cc_start: 0.9757 (OUTLIER) cc_final: 0.9537 (p) REVERT: G 71 ASN cc_start: 0.8386 (t0) cc_final: 0.8086 (t0) REVERT: G 96 ARG cc_start: 0.8095 (mtp180) cc_final: 0.7695 (mtt180) REVERT: G 105 ARG cc_start: 0.9415 (tpt170) cc_final: 0.9113 (mmm-85) REVERT: G 119 MET cc_start: 0.9146 (mmp) cc_final: 0.8886 (mmm) REVERT: G 120 ASP cc_start: 0.8872 (t0) cc_final: 0.8367 (t0) REVERT: G 148 LYS cc_start: 0.9660 (mmmt) cc_final: 0.9383 (mmmt) REVERT: G 152 LYS cc_start: 0.9591 (mttt) cc_final: 0.9261 (mppt) REVERT: G 201 ARG cc_start: 0.8732 (tpp80) cc_final: 0.8503 (tpp80) REVERT: G 216 LYS cc_start: 0.9593 (tptt) cc_final: 0.9301 (mmmm) REVERT: G 233 CYS cc_start: 0.8645 (m) cc_final: 0.8390 (m) REVERT: G 246 GLN cc_start: 0.8492 (mp10) cc_final: 0.8114 (mp10) outliers start: 49 outliers final: 37 residues processed: 502 average time/residue: 0.1189 time to fit residues: 83.9180 Evaluate side-chains 510 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 470 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 129 optimal weight: 0.0570 chunk 137 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN D 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.117494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.085045 restraints weight = 31377.151| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 4.08 r_work: 0.2892 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13286 Z= 0.180 Angle : 0.649 7.073 18025 Z= 0.336 Chirality : 0.041 0.192 2051 Planarity : 0.005 0.045 2212 Dihedral : 3.557 17.518 1890 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.11 % Allowed : 26.40 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.22), residues: 1575 helix: 2.50 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.14 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 226 TYR 0.017 0.002 TYR A 49 PHE 0.014 0.001 PHE B 124 TRP 0.016 0.001 TRP F 62 HIS 0.004 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00436 (13265) covalent geometry : angle 0.64535 (17976) SS BOND : bond 0.00300 ( 14) SS BOND : angle 0.53975 ( 28) hydrogen bonds : bond 0.04142 ( 925) hydrogen bonds : angle 3.57748 ( 2775) link_NAG-ASN : bond 0.00216 ( 7) link_NAG-ASN : angle 2.18559 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 455 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8478 (t80) REVERT: A 71 ASN cc_start: 0.8673 (t0) cc_final: 0.8193 (t0) REVERT: A 96 ARG cc_start: 0.8468 (mtp180) cc_final: 0.8187 (mtt180) REVERT: A 104 GLN cc_start: 0.8974 (mt0) cc_final: 0.7752 (tp40) REVERT: A 105 ARG cc_start: 0.9447 (tpt170) cc_final: 0.9115 (mmm-85) REVERT: A 120 ASP cc_start: 0.8970 (t0) cc_final: 0.8621 (t0) REVERT: A 233 CYS cc_start: 0.8860 (m) cc_final: 0.8483 (m) REVERT: B 71 ASN cc_start: 0.9021 (t0) cc_final: 0.8654 (t0) REVERT: B 96 ARG cc_start: 0.8399 (mtp180) cc_final: 0.7971 (mtp180) REVERT: B 104 GLN cc_start: 0.9051 (mt0) cc_final: 0.8047 (tp40) REVERT: B 105 ARG cc_start: 0.9480 (tpt170) cc_final: 0.9262 (mmm-85) REVERT: B 120 ASP cc_start: 0.8961 (t0) cc_final: 0.8349 (t0) REVERT: B 122 LYS cc_start: 0.9365 (mmmm) cc_final: 0.9098 (mtpp) REVERT: B 216 LYS cc_start: 0.9583 (tptt) cc_final: 0.9310 (mmmm) REVERT: B 220 HIS cc_start: 0.8778 (m90) cc_final: 0.8344 (m-70) REVERT: B 233 CYS cc_start: 0.8754 (m) cc_final: 0.8521 (m) REVERT: B 247 GLN cc_start: 0.8668 (mp10) cc_final: 0.8396 (pm20) REVERT: C 71 ASN cc_start: 0.8724 (t0) cc_final: 0.8257 (t0) REVERT: C 96 ARG cc_start: 0.8333 (mtp180) cc_final: 0.7941 (mtt180) REVERT: C 104 GLN cc_start: 0.9054 (mt0) cc_final: 0.8035 (tm-30) REVERT: C 152 LYS cc_start: 0.9649 (mttt) cc_final: 0.9361 (mttt) REVERT: C 226 ARG cc_start: 0.8870 (mmp-170) cc_final: 0.8318 (mmp80) REVERT: C 233 CYS cc_start: 0.8813 (m) cc_final: 0.8590 (m) REVERT: D 32 GLN cc_start: 0.9368 (mt0) cc_final: 0.9049 (tt0) REVERT: D 68 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8383 (t80) REVERT: D 71 ASN cc_start: 0.8863 (t0) cc_final: 0.8434 (t0) REVERT: D 96 ARG cc_start: 0.8454 (mtp180) cc_final: 0.8115 (mtp180) REVERT: D 104 GLN cc_start: 0.9092 (mt0) cc_final: 0.8179 (tp40) REVERT: D 105 ARG cc_start: 0.9526 (tpt170) cc_final: 0.9290 (mmm-85) REVERT: D 120 ASP cc_start: 0.8947 (t0) cc_final: 0.8440 (t0) REVERT: D 209 GLN cc_start: 0.9246 (pm20) cc_final: 0.9026 (pm20) REVERT: E 38 GLU cc_start: 0.9072 (tp30) cc_final: 0.8617 (pt0) REVERT: E 47 TYR cc_start: 0.9188 (m-80) cc_final: 0.8815 (m-80) REVERT: E 71 ASN cc_start: 0.8655 (t0) cc_final: 0.8270 (t0) REVERT: E 96 ARG cc_start: 0.8480 (mtp180) cc_final: 0.8106 (mtt180) REVERT: E 104 GLN cc_start: 0.9054 (mt0) cc_final: 0.7936 (tm-30) REVERT: E 119 MET cc_start: 0.9086 (mmp) cc_final: 0.8847 (mmm) REVERT: E 120 ASP cc_start: 0.8924 (t0) cc_final: 0.8319 (t0) REVERT: E 152 LYS cc_start: 0.9631 (mttt) cc_final: 0.9315 (mttt) REVERT: E 226 ARG cc_start: 0.8920 (mmp-170) cc_final: 0.8392 (mmp-170) REVERT: F 71 ASN cc_start: 0.8895 (t0) cc_final: 0.8611 (t0) REVERT: F 96 ARG cc_start: 0.8470 (mtp180) cc_final: 0.8040 (mtp180) REVERT: F 104 GLN cc_start: 0.8944 (mt0) cc_final: 0.7770 (tp40) REVERT: F 105 ARG cc_start: 0.9421 (tpt170) cc_final: 0.9032 (mmm-85) REVERT: F 223 ASP cc_start: 0.9652 (t0) cc_final: 0.9283 (t0) REVERT: F 233 CYS cc_start: 0.8876 (m) cc_final: 0.8641 (m) REVERT: F 247 GLN cc_start: 0.8920 (mp10) cc_final: 0.8594 (pm20) REVERT: G 32 GLN cc_start: 0.8678 (pt0) cc_final: 0.8398 (tt0) REVERT: G 40 THR cc_start: 0.9760 (OUTLIER) cc_final: 0.9482 (p) REVERT: G 71 ASN cc_start: 0.8581 (t0) cc_final: 0.8263 (t0) REVERT: G 96 ARG cc_start: 0.8182 (mtp180) cc_final: 0.7817 (mtt180) REVERT: G 104 GLN cc_start: 0.8911 (mt0) cc_final: 0.7722 (tp40) REVERT: G 105 ARG cc_start: 0.9457 (tpt170) cc_final: 0.9143 (mmm-85) REVERT: G 120 ASP cc_start: 0.8985 (t0) cc_final: 0.8504 (t0) REVERT: G 148 LYS cc_start: 0.9636 (mmmt) cc_final: 0.9384 (mmmt) REVERT: G 152 LYS cc_start: 0.9623 (mttt) cc_final: 0.9308 (mppt) REVERT: G 216 LYS cc_start: 0.9591 (tptt) cc_final: 0.9303 (mmmm) REVERT: G 233 CYS cc_start: 0.8734 (m) cc_final: 0.8485 (m) outliers start: 55 outliers final: 44 residues processed: 474 average time/residue: 0.1247 time to fit residues: 81.5745 Evaluate side-chains 497 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 450 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 45 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 24 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 0.0370 chunk 109 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.111723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078650 restraints weight = 32477.053| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.92 r_work: 0.2958 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13286 Z= 0.132 Angle : 0.664 8.607 18025 Z= 0.339 Chirality : 0.040 0.215 2051 Planarity : 0.004 0.050 2212 Dihedral : 3.367 17.419 1890 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.84 % Allowed : 27.30 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.22), residues: 1575 helix: 2.60 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.13 (0.38), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 226 TYR 0.017 0.001 TYR A 49 PHE 0.013 0.001 PHE B 137 TRP 0.008 0.001 TRP E 62 HIS 0.004 0.000 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00307 (13265) covalent geometry : angle 0.66176 (17976) SS BOND : bond 0.00171 ( 14) SS BOND : angle 0.41086 ( 28) hydrogen bonds : bond 0.03715 ( 925) hydrogen bonds : angle 3.41998 ( 2775) link_NAG-ASN : bond 0.00185 ( 7) link_NAG-ASN : angle 1.72762 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 491 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8738 (t0) cc_final: 0.8166 (t0) REVERT: A 96 ARG cc_start: 0.8353 (mtp180) cc_final: 0.8062 (mtt180) REVERT: A 105 ARG cc_start: 0.9422 (tpt170) cc_final: 0.9131 (mmm-85) REVERT: A 120 ASP cc_start: 0.8862 (t0) cc_final: 0.8461 (t0) REVERT: A 147 GLN cc_start: 0.9146 (pm20) cc_final: 0.8942 (tp-100) REVERT: A 233 CYS cc_start: 0.8939 (m) cc_final: 0.8590 (m) REVERT: B 71 ASN cc_start: 0.9076 (t0) cc_final: 0.8699 (t0) REVERT: B 96 ARG cc_start: 0.8349 (mtp180) cc_final: 0.7931 (mtp180) REVERT: B 104 GLN cc_start: 0.8987 (mt0) cc_final: 0.7817 (tp40) REVERT: B 105 ARG cc_start: 0.9469 (tpt170) cc_final: 0.9230 (mmm-85) REVERT: B 120 ASP cc_start: 0.8835 (t0) cc_final: 0.8314 (t0) REVERT: B 122 LYS cc_start: 0.9332 (mmmm) cc_final: 0.9083 (mtpp) REVERT: B 143 GLN cc_start: 0.9179 (pm20) cc_final: 0.8924 (pm20) REVERT: B 201 ARG cc_start: 0.8821 (tpp80) cc_final: 0.8415 (tpp80) REVERT: B 220 HIS cc_start: 0.8750 (m90) cc_final: 0.8299 (m-70) REVERT: B 233 CYS cc_start: 0.8755 (m) cc_final: 0.8513 (m) REVERT: C 71 ASN cc_start: 0.8739 (t0) cc_final: 0.8282 (t0) REVERT: C 96 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7925 (mtt180) REVERT: C 152 LYS cc_start: 0.9616 (mttt) cc_final: 0.9325 (mttt) REVERT: C 216 LYS cc_start: 0.9351 (mmmm) cc_final: 0.9082 (mmtp) REVERT: C 226 ARG cc_start: 0.8933 (mmp-170) cc_final: 0.8367 (mmp80) REVERT: C 233 CYS cc_start: 0.8944 (m) cc_final: 0.8700 (m) REVERT: D 68 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8421 (t80) REVERT: D 71 ASN cc_start: 0.8984 (t0) cc_final: 0.8635 (t0) REVERT: D 96 ARG cc_start: 0.8457 (mtp180) cc_final: 0.8103 (mtp180) REVERT: D 104 GLN cc_start: 0.9072 (mt0) cc_final: 0.8114 (tp40) REVERT: D 105 ARG cc_start: 0.9528 (tpt170) cc_final: 0.9285 (mmm-85) REVERT: D 120 ASP cc_start: 0.8825 (t0) cc_final: 0.8329 (t0) REVERT: D 209 GLN cc_start: 0.9231 (pm20) cc_final: 0.8992 (pm20) REVERT: E 38 GLU cc_start: 0.9042 (tp30) cc_final: 0.8618 (pt0) REVERT: E 71 ASN cc_start: 0.8579 (t0) cc_final: 0.8204 (t0) REVERT: E 83 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7293 (ttt180) REVERT: E 96 ARG cc_start: 0.8381 (mtp180) cc_final: 0.8029 (mtt180) REVERT: E 104 GLN cc_start: 0.9024 (mt0) cc_final: 0.7857 (tm-30) REVERT: E 120 ASP cc_start: 0.8802 (t0) cc_final: 0.8220 (t0) REVERT: E 152 LYS cc_start: 0.9603 (mttt) cc_final: 0.9287 (mttt) REVERT: E 225 GLU cc_start: 0.9322 (tt0) cc_final: 0.9111 (pt0) REVERT: F 71 ASN cc_start: 0.8999 (t0) cc_final: 0.8700 (t0) REVERT: F 96 ARG cc_start: 0.8339 (mtp180) cc_final: 0.7942 (mtp180) REVERT: F 104 GLN cc_start: 0.8901 (mt0) cc_final: 0.7707 (tp40) REVERT: F 105 ARG cc_start: 0.9430 (tpt170) cc_final: 0.9171 (mmm-85) REVERT: F 191 MET cc_start: 0.9571 (tpp) cc_final: 0.9271 (mmm) REVERT: F 233 CYS cc_start: 0.8889 (m) cc_final: 0.8664 (m) REVERT: F 247 GLN cc_start: 0.8906 (mp10) cc_final: 0.8576 (pm20) REVERT: G 32 GLN cc_start: 0.8542 (pt0) cc_final: 0.8311 (tt0) REVERT: G 71 ASN cc_start: 0.8669 (t0) cc_final: 0.8336 (t0) REVERT: G 96 ARG cc_start: 0.8095 (mtp180) cc_final: 0.7751 (mtt180) REVERT: G 105 ARG cc_start: 0.9408 (tpt170) cc_final: 0.9093 (mmm-85) REVERT: G 120 ASP cc_start: 0.8853 (t0) cc_final: 0.8508 (t0) REVERT: G 148 LYS cc_start: 0.9617 (mmmt) cc_final: 0.9378 (mmmt) REVERT: G 152 LYS cc_start: 0.9627 (mttt) cc_final: 0.9299 (mppt) REVERT: G 179 ARG cc_start: 0.9255 (mtp85) cc_final: 0.9033 (mtp85) REVERT: G 216 LYS cc_start: 0.9610 (tptt) cc_final: 0.9340 (mmmm) REVERT: G 233 CYS cc_start: 0.8727 (m) cc_final: 0.8422 (m) REVERT: G 246 GLN cc_start: 0.8530 (mp-120) cc_final: 0.8098 (mp10) outliers start: 38 outliers final: 28 residues processed: 506 average time/residue: 0.1209 time to fit residues: 85.3117 Evaluate side-chains 509 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 479 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain C residue 33 MET Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 225 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 109 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 115 optimal weight: 70.0000 chunk 11 optimal weight: 0.2980 chunk 136 optimal weight: 9.9990 chunk 83 optimal weight: 0.0570 chunk 149 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.119914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.085612 restraints weight = 31600.959| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.95 r_work: 0.2940 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13286 Z= 0.142 Angle : 0.672 9.148 18025 Z= 0.348 Chirality : 0.041 0.236 2051 Planarity : 0.004 0.047 2212 Dihedral : 3.346 17.116 1890 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.47 % Allowed : 29.17 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.22), residues: 1575 helix: 2.63 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.15 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 226 TYR 0.018 0.002 TYR D 97 PHE 0.015 0.001 PHE D 124 TRP 0.013 0.001 TRP E 62 HIS 0.003 0.000 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00350 (13265) covalent geometry : angle 0.66986 (17976) SS BOND : bond 0.00207 ( 14) SS BOND : angle 0.49891 ( 28) hydrogen bonds : bond 0.03781 ( 925) hydrogen bonds : angle 3.44374 ( 2775) link_NAG-ASN : bond 0.00037 ( 7) link_NAG-ASN : angle 1.80803 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 474 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8830 (t0) cc_final: 0.8358 (t0) REVERT: A 96 ARG cc_start: 0.8394 (mtp180) cc_final: 0.8103 (mtt180) REVERT: A 105 ARG cc_start: 0.9416 (tpt170) cc_final: 0.9123 (mmm-85) REVERT: A 120 ASP cc_start: 0.8839 (t0) cc_final: 0.8414 (t0) REVERT: A 233 CYS cc_start: 0.8933 (m) cc_final: 0.8589 (m) REVERT: B 71 ASN cc_start: 0.9070 (t0) cc_final: 0.8707 (t0) REVERT: B 96 ARG cc_start: 0.8391 (mtp180) cc_final: 0.7956 (mtp180) REVERT: B 104 GLN cc_start: 0.9007 (mt0) cc_final: 0.7992 (tp40) REVERT: B 105 ARG cc_start: 0.9460 (tpt170) cc_final: 0.9226 (mmm-85) REVERT: B 120 ASP cc_start: 0.8883 (t0) cc_final: 0.8399 (t0) REVERT: B 143 GLN cc_start: 0.9158 (pm20) cc_final: 0.8881 (pm20) REVERT: B 220 HIS cc_start: 0.8763 (m90) cc_final: 0.8305 (m-70) REVERT: B 233 CYS cc_start: 0.8748 (m) cc_final: 0.8518 (m) REVERT: C 32 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8966 (tt0) REVERT: C 71 ASN cc_start: 0.8766 (t0) cc_final: 0.8284 (t0) REVERT: C 96 ARG cc_start: 0.8278 (mtp180) cc_final: 0.7929 (mtt180) REVERT: C 97 TYR cc_start: 0.9107 (t80) cc_final: 0.8864 (t80) REVERT: C 152 LYS cc_start: 0.9638 (mttt) cc_final: 0.9351 (mttt) REVERT: C 216 LYS cc_start: 0.9336 (mmmm) cc_final: 0.9136 (mmtp) REVERT: C 226 ARG cc_start: 0.8955 (mmp-170) cc_final: 0.8427 (mmp80) REVERT: C 233 CYS cc_start: 0.8872 (m) cc_final: 0.8654 (m) REVERT: D 68 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8439 (t80) REVERT: D 71 ASN cc_start: 0.8956 (t0) cc_final: 0.8548 (t0) REVERT: D 96 ARG cc_start: 0.8470 (mtp180) cc_final: 0.8105 (mtp180) REVERT: D 104 GLN cc_start: 0.9064 (mt0) cc_final: 0.8156 (tp40) REVERT: D 105 ARG cc_start: 0.9539 (tpt170) cc_final: 0.9302 (mmm-85) REVERT: D 120 ASP cc_start: 0.8835 (t0) cc_final: 0.8357 (t0) REVERT: D 209 GLN cc_start: 0.9246 (pm20) cc_final: 0.8987 (pm20) REVERT: E 32 GLN cc_start: 0.9310 (mm-40) cc_final: 0.8920 (tt0) REVERT: E 38 GLU cc_start: 0.9041 (tp30) cc_final: 0.8610 (pt0) REVERT: E 71 ASN cc_start: 0.8591 (t0) cc_final: 0.8208 (t0) REVERT: E 83 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7253 (ttt180) REVERT: E 96 ARG cc_start: 0.8388 (mtp180) cc_final: 0.8027 (mtt180) REVERT: E 97 TYR cc_start: 0.9083 (t80) cc_final: 0.8864 (t80) REVERT: E 104 GLN cc_start: 0.9053 (mt0) cc_final: 0.7866 (tm-30) REVERT: E 120 ASP cc_start: 0.8831 (t0) cc_final: 0.8264 (t0) REVERT: E 152 LYS cc_start: 0.9610 (mttt) cc_final: 0.9294 (mttt) REVERT: E 226 ARG cc_start: 0.8917 (mmp-170) cc_final: 0.8382 (mmp-170) REVERT: F 71 ASN cc_start: 0.8985 (t0) cc_final: 0.8675 (t0) REVERT: F 96 ARG cc_start: 0.8368 (mtp180) cc_final: 0.7977 (mtp180) REVERT: F 104 GLN cc_start: 0.8925 (mt0) cc_final: 0.7941 (tp40) REVERT: F 105 ARG cc_start: 0.9476 (tpt170) cc_final: 0.9228 (mmm-85) REVERT: F 233 CYS cc_start: 0.8866 (m) cc_final: 0.8620 (m) REVERT: F 247 GLN cc_start: 0.8913 (mp10) cc_final: 0.8584 (pm20) REVERT: G 32 GLN cc_start: 0.8563 (pt0) cc_final: 0.8336 (tt0) REVERT: G 71 ASN cc_start: 0.8638 (t0) cc_final: 0.8301 (t0) REVERT: G 96 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7782 (mtt180) REVERT: G 105 ARG cc_start: 0.9457 (tpt170) cc_final: 0.9159 (mmm-85) REVERT: G 120 ASP cc_start: 0.8941 (t0) cc_final: 0.8516 (t0) REVERT: G 148 LYS cc_start: 0.9601 (mmmt) cc_final: 0.9373 (mmmt) REVERT: G 152 LYS cc_start: 0.9635 (mttt) cc_final: 0.9311 (mppt) REVERT: G 179 ARG cc_start: 0.9253 (mtp85) cc_final: 0.9029 (mtp85) REVERT: G 216 LYS cc_start: 0.9605 (tptt) cc_final: 0.9364 (mmmm) REVERT: G 233 CYS cc_start: 0.8729 (m) cc_final: 0.8472 (m) REVERT: G 246 GLN cc_start: 0.8511 (mp-120) cc_final: 0.8117 (mp10) outliers start: 33 outliers final: 26 residues processed: 488 average time/residue: 0.1205 time to fit residues: 81.7080 Evaluate side-chains 499 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 470 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 225 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 0.0770 chunk 82 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** C 32 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 = 0.3747 r_free = 0.3747 target = 0.117498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.084527 restraints weight = 31951.505| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.98 r_work: 0.2964 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13286 Z= 0.137 Angle : 0.687 12.381 18025 Z= 0.354 Chirality : 0.041 0.284 2051 Planarity : 0.004 0.045 2212 Dihedral : 3.321 17.033 1890 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.24 % Allowed : 29.69 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.22), residues: 1575 helix: 2.65 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.15 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 226 TYR 0.019 0.002 TYR A 49 PHE 0.013 0.001 PHE D 124 TRP 0.012 0.001 TRP F 62 HIS 0.003 0.000 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00327 (13265) covalent geometry : angle 0.68499 (17976) SS BOND : bond 0.00184 ( 14) SS BOND : angle 0.45652 ( 28) hydrogen bonds : bond 0.03647 ( 925) hydrogen bonds : angle 3.40162 ( 2775) link_NAG-ASN : bond 0.00104 ( 7) link_NAG-ASN : angle 1.63177 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3626.96 seconds wall clock time: 62 minutes 34.23 seconds (3754.23 seconds total)