Starting phenix.real_space_refine on Fri Jul 3 08:00:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dse_30832/07_2026/7dse_30832.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dse_30832/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7dse_30832/07_2026/7dse_30832.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dse_30832/07_2026/7dse_30832.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dse_30832/07_2026/7dse_30832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dse_30832/07_2026/7dse_30832.map" model { file = "/net/cci-nas-00/data/ceres_data/7dse_30832/07_2026/7dse_30832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dse_30832/07_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-6108/lib/python3.11/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 chiralities: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 1.54, per 1000 atoms: 0.12 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: 0.82 Conformation dependent library (CDL) restraints added in 392.1 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: 0.32 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: 2.28 Time building geometry restraints manager: 1.09 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: 6958 12.47 - 24.94: 617 24.94 - 37.40: 181 37.40 - 49.87: 77 49.87 - 62.34: 21 Dihedral angle restraints: 7854 sinusoidal: 3010 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 7851 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: 0.03 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: 1.280 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.640 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 : 11.837 62.341 4648 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/Z covalent geometry : bond 0.00493 / 0.24 (13265) covalent geometry : angle 0.64666 / 0.41 (17976) SS BOND : bond 0.00255 / 0.19 ( 14) SS BOND : angle 0.66592 / 0.52 ( 28) hydrogen bonds : bond 0.14221 / 9.45 ( 925) hydrogen bonds : angle 4.83422 / 3.49 ( 2775) link_NAG-ASN : bond 0.00628 / 0.41 ( 7) link_NAG-ASN : angle 3.54637 / 2.68 ( 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 : 0.479 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: 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: 0.1109 time to fit residues: 109.3116 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 : 0.311 ------------------------------------------------------------------------------- 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... 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 = 0.3687 r_free = 0.3687 target = 0.109467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077284 restraints weight = 32828.472| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.93 r_work: 0.2922 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4378 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= 0.160 Angle : 0.706 8.889 18025 Z= 0.359 Chirality : 0.039 0.127 2051 Planarity : 0.005 0.042 2212 Dihedral : 3.944 16.254 1743 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.99 % Allowed : 21.54 % Favored : 75.47 % 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: 1.40 (0.22), residues: 1575 helix: 1.71 (0.15), residues: 1239 sheet: None (None), residues: 0 loop : -2.10 (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 0.017 0.001 PHE G 212 TRP 0.006 0.001 TRP F 218 HIS 0.002 0.001 HIS G 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (13265) covalent geometry : angle 0.70205 / 0.36 (17976) SS BOND : bond 0.00301 / 0.22 ( 14) SS BOND : angle 0.63733 / 0.51 ( 28) hydrogen bonds : bond 0.05109 / 3.40 ( 925) hydrogen bonds : angle 3.81152 / 2.74 ( 2775) link_NAG-ASN : bond 0.00138 / 0.09 ( 7) link_NAG-ASN : angle 2.36379 / 1.80 ( 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 569 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 529 time to evaluate : 0.353 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 26 MET cc_start: 0.7882 (mmp) cc_final: 0.7666 (mmp) REVERT: A 47 TYR cc_start: 0.9141 (m-80) cc_final: 0.8889 (m-80) REVERT: A 49 TYR cc_start: 0.8938 (t80) cc_final: 0.8687 (t80) REVERT: A 68 TYR cc_start: 0.8827 (m-80) cc_final: 0.8585 (t80) REVERT: A 71 ASN cc_start: 0.8556 (t0) cc_final: 0.8020 (t0) REVERT: A 96 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7892 (mtt180) REVERT: A 104 GLN cc_start: 0.8953 (mt0) cc_final: 0.7701 (tp40) REVERT: A 105 ARG cc_start: 0.9342 (tpt170) cc_final: 0.8966 (mmm-85) REVERT: A 120 ASP cc_start: 0.8914 (t0) cc_final: 0.8639 (t0) REVERT: B 96 ARG cc_start: 0.8283 (mtp180) cc_final: 0.7957 (mtt180) REVERT: B 104 GLN cc_start: 0.9004 (mt0) cc_final: 0.7760 (tp40) REVERT: B 105 ARG cc_start: 0.9430 (tpt170) cc_final: 0.9169 (mmm-85) REVERT: B 120 ASP cc_start: 0.8929 (t70) cc_final: 0.8508 (t0) REVERT: B 122 LYS cc_start: 0.9394 (mmtp) cc_final: 0.9172 (mmmm) REVERT: B 152 LYS cc_start: 0.9610 (mttt) cc_final: 0.9339 (mppt) REVERT: B 179 ARG cc_start: 0.9245 (mmm-85) cc_final: 0.8832 (ttm-80) REVERT: B 233 CYS cc_start: 0.8557 (m) cc_final: 0.8274 (m) REVERT: C 96 ARG cc_start: 0.8275 (mtp180) cc_final: 0.7872 (mtt180) REVERT: C 104 GLN cc_start: 0.9029 (mt0) cc_final: 0.7972 (tp40) REVERT: C 120 ASP cc_start: 0.8977 (t70) cc_final: 0.8725 (t0) REVERT: C 142 TYR cc_start: 0.7884 (m-80) cc_final: 0.7620 (m-80) REVERT: C 152 LYS cc_start: 0.9624 (mttt) cc_final: 0.9298 (mppt) REVERT: C 201 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8229 (tpt-90) REVERT: C 216 LYS cc_start: 0.9486 (mmmm) cc_final: 0.9150 (mmtp) REVERT: C 221 TYR cc_start: 0.9169 (t80) cc_final: 0.8966 (t80) REVERT: C 225 GLU cc_start: 0.9271 (tt0) cc_final: 0.9071 (pt0) REVERT: C 226 ARG cc_start: 0.8375 (mmp-170) cc_final: 0.7820 (mmp-170) REVERT: C 233 CYS cc_start: 0.8698 (m) cc_final: 0.8389 (m) REVERT: D 32 GLN cc_start: 0.9233 (mm-40) cc_final: 0.9020 (tp40) REVERT: D 47 TYR cc_start: 0.9183 (m-80) cc_final: 0.8820 (m-80) REVERT: D 68 TYR cc_start: 0.8786 (m-80) cc_final: 0.8453 (t80) REVERT: D 71 ASN cc_start: 0.8779 (t0) cc_final: 0.8155 (t0) REVERT: D 96 ARG cc_start: 0.8330 (mtp180) cc_final: 0.8052 (mtt180) REVERT: D 104 GLN cc_start: 0.8949 (mt0) cc_final: 0.7790 (tp40) REVERT: D 105 ARG cc_start: 0.9436 (tpt170) cc_final: 0.9142 (mmm-85) REVERT: D 120 ASP cc_start: 0.8964 (t0) cc_final: 0.8596 (t0) REVERT: E 47 TYR cc_start: 0.9111 (m-80) cc_final: 0.8815 (m-80) REVERT: E 71 ASN cc_start: 0.8585 (t0) cc_final: 0.8126 (t0) REVERT: E 96 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7988 (mtt180) REVERT: E 102 MET cc_start: 0.9454 (ttm) cc_final: 0.9253 (ttm) REVERT: E 104 GLN cc_start: 0.8960 (mt0) cc_final: 0.7857 (tp40) REVERT: E 120 ASP cc_start: 0.8842 (t0) cc_final: 0.8435 (t0) REVERT: E 152 LYS cc_start: 0.9549 (mttt) cc_final: 0.9227 (mppt) REVERT: E 225 GLU cc_start: 0.9264 (tt0) cc_final: 0.9039 (pt0) REVERT: E 226 ARG cc_start: 0.8686 (mmp-170) cc_final: 0.8205 (mmp-170) REVERT: E 246 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8712 (mp10) REVERT: E 247 GLN cc_start: 0.9030 (mp10) cc_final: 0.8824 (pm20) REVERT: F 47 TYR cc_start: 0.9156 (m-80) cc_final: 0.8772 (m-80) REVERT: F 96 ARG cc_start: 0.8352 (mtp180) cc_final: 0.7995 (mtt180) REVERT: F 104 GLN cc_start: 0.8979 (mt0) cc_final: 0.7892 (tp40) REVERT: F 105 ARG cc_start: 0.9317 (tpt170) cc_final: 0.8999 (mmm-85) REVERT: F 179 ARG cc_start: 0.9222 (mmm-85) cc_final: 0.8870 (mtp85) REVERT: G 40 THR cc_start: 0.9692 (OUTLIER) cc_final: 0.9398 (p) REVERT: G 71 ASN cc_start: 0.8416 (t0) cc_final: 0.8101 (t0) REVERT: G 95 LEU cc_start: 0.9306 (mt) cc_final: 0.9071 (pt) REVERT: G 96 ARG cc_start: 0.7953 (mtp180) cc_final: 0.7489 (mtt180) REVERT: G 105 ARG cc_start: 0.9341 (tpt170) cc_final: 0.9069 (mmm-85) REVERT: G 120 ASP cc_start: 0.8919 (t0) cc_final: 0.8554 (t0) REVERT: G 148 LYS cc_start: 0.9602 (mmmt) cc_final: 0.9344 (mmmt) REVERT: G 152 LYS cc_start: 0.9585 (mttt) cc_final: 0.9290 (mppt) REVERT: G 246 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8563 (mp10) outliers start: 40 outliers final: 20 residues processed: 548 average time/residue: 0.1160 time to fit residues: 86.9096 Evaluate side-chains 488 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 467 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 74 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: 7.9990 chunk 128 optimal weight: 8.9990 chunk 104 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.109446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.076164 restraints weight = 32282.542| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.89 r_work: 0.2929 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13286 Z= 0.177 Angle : 0.676 9.080 18025 Z= 0.342 Chirality : 0.039 0.128 2051 Planarity : 0.005 0.062 2212 Dihedral : 3.835 16.826 1743 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.11 % Allowed : 24.16 % Favored : 71.73 % 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: 1.87 (0.22), residues: 1575 helix: 2.06 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -2.09 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 201 TYR 0.017 0.001 TYR G 47 PHE 0.013 0.001 PHE G 229 TRP 0.009 0.001 TRP E 62 HIS 0.002 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (13265) covalent geometry : angle 0.67105 / 0.34 (17976) SS BOND : bond 0.00312 / 0.23 ( 14) SS BOND : angle 0.58097 / 0.45 ( 28) hydrogen bonds : bond 0.04677 / 3.11 ( 925) hydrogen bonds : angle 3.77211 / 2.70 ( 2775) link_NAG-ASN : bond 0.00251 / 0.17 ( 7) link_NAG-ASN : angle 2.53727 / 1.94 ( 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 542 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 487 time to evaluate : 0.377 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 26 MET cc_start: 0.7846 (mmp) cc_final: 0.7569 (mmp) REVERT: A 47 TYR cc_start: 0.9172 (m-80) cc_final: 0.8885 (m-80) REVERT: A 68 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.8576 (t80) REVERT: A 71 ASN cc_start: 0.8554 (t0) cc_final: 0.8161 (t0) REVERT: A 96 ARG cc_start: 0.8348 (mtp180) cc_final: 0.7937 (mtt180) REVERT: A 104 GLN cc_start: 0.8944 (mt0) cc_final: 0.7854 (tp40) REVERT: A 105 ARG cc_start: 0.9406 (tpt170) cc_final: 0.9078 (mmm-85) REVERT: A 120 ASP cc_start: 0.8904 (t0) cc_final: 0.8582 (t0) REVERT: A 214 LYS cc_start: 0.9808 (mmtp) cc_final: 0.9593 (mmtt) REVERT: B 96 ARG cc_start: 0.8376 (mtp180) cc_final: 0.7990 (mtt180) REVERT: B 104 GLN cc_start: 0.9058 (mt0) cc_final: 0.7729 (tp40) REVERT: B 105 ARG cc_start: 0.9442 (tpt170) cc_final: 0.9149 (mmm-85) REVERT: B 152 LYS cc_start: 0.9601 (mttt) cc_final: 0.9362 (mppt) REVERT: B 233 CYS cc_start: 0.8673 (m) cc_final: 0.8255 (m) REVERT: C 32 GLN cc_start: 0.9280 (tp40) cc_final: 0.9018 (tp40) REVERT: C 96 ARG cc_start: 0.8440 (mtp180) cc_final: 0.8016 (mtt180) REVERT: C 104 GLN cc_start: 0.9074 (mt0) cc_final: 0.8055 (tp40) REVERT: C 142 TYR cc_start: 0.7932 (m-80) cc_final: 0.7716 (m-80) REVERT: C 152 LYS cc_start: 0.9615 (mttt) cc_final: 0.9304 (mppt) REVERT: C 201 ARG cc_start: 0.8706 (tpp80) cc_final: 0.8434 (tpt-90) REVERT: C 214 LYS cc_start: 0.9778 (mmtp) cc_final: 0.9563 (mmtt) REVERT: C 216 LYS cc_start: 0.9515 (mmmm) cc_final: 0.9105 (mmtp) REVERT: C 225 GLU cc_start: 0.9361 (tt0) cc_final: 0.9101 (pt0) REVERT: C 226 ARG cc_start: 0.8502 (mmp-170) cc_final: 0.7922 (mmp-170) REVERT: C 233 CYS cc_start: 0.8892 (m) cc_final: 0.8628 (m) REVERT: C 246 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8880 (mp10) REVERT: D 32 GLN cc_start: 0.9260 (mm-40) cc_final: 0.9043 (tp40) REVERT: D 47 TYR cc_start: 0.9210 (m-80) cc_final: 0.8835 (m-80) REVERT: D 68 TYR cc_start: 0.8853 (m-80) cc_final: 0.8419 (t80) REVERT: D 71 ASN cc_start: 0.8892 (t0) cc_final: 0.8475 (t0) REVERT: D 96 ARG cc_start: 0.8444 (mtp180) cc_final: 0.8103 (mtt180) REVERT: D 104 GLN cc_start: 0.8924 (mt0) cc_final: 0.7868 (tp40) REVERT: D 105 ARG cc_start: 0.9480 (tpt170) cc_final: 0.9064 (mmm-85) REVERT: D 108 ILE cc_start: 0.9427 (mm) cc_final: 0.9190 (mp) REVERT: D 120 ASP cc_start: 0.8947 (t0) cc_final: 0.8511 (t0) REVERT: D 246 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8655 (pp30) REVERT: E 32 GLN cc_start: 0.9237 (mt0) cc_final: 0.8824 (tt0) REVERT: E 47 TYR cc_start: 0.9187 (m-80) cc_final: 0.8866 (m-80) REVERT: E 71 ASN cc_start: 0.8564 (t0) cc_final: 0.8051 (t0) REVERT: E 96 ARG cc_start: 0.8394 (mtp180) cc_final: 0.8078 (mtt180) REVERT: E 104 GLN cc_start: 0.8987 (mt0) cc_final: 0.7959 (tm-30) REVERT: E 120 ASP cc_start: 0.8874 (t0) cc_final: 0.8387 (t0) REVERT: E 152 LYS cc_start: 0.9568 (mttt) cc_final: 0.9246 (mppt) REVERT: E 214 LYS cc_start: 0.9751 (mmtp) cc_final: 0.9533 (mmtt) REVERT: E 226 ARG cc_start: 0.8794 (mmp-170) cc_final: 0.8251 (mmp80) REVERT: E 242 LYS cc_start: 0.9668 (tppt) cc_final: 0.9446 (tppt) REVERT: E 246 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8870 (mp10) REVERT: F 96 ARG cc_start: 0.8396 (mtp180) cc_final: 0.7952 (mtt90) REVERT: F 104 GLN cc_start: 0.9031 (mt0) cc_final: 0.7971 (tp40) REVERT: F 105 ARG cc_start: 0.9388 (tpt170) cc_final: 0.9078 (mmm-85) REVERT: F 179 ARG cc_start: 0.9211 (mmm-85) cc_final: 0.8893 (mtp85) REVERT: G 40 THR cc_start: 0.9720 (OUTLIER) cc_final: 0.9410 (p) REVERT: G 71 ASN cc_start: 0.8564 (t0) cc_final: 0.8291 (t0) REVERT: G 95 LEU cc_start: 0.9369 (mt) cc_final: 0.9156 (pt) REVERT: G 96 ARG cc_start: 0.7988 (mtp180) cc_final: 0.7550 (mtt180) REVERT: G 104 GLN cc_start: 0.8935 (mt0) cc_final: 0.7637 (tp40) REVERT: G 105 ARG cc_start: 0.9409 (tpt170) cc_final: 0.9062 (mmm-85) REVERT: G 119 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8994 (mmm) REVERT: G 120 ASP cc_start: 0.8912 (t0) cc_final: 0.8530 (t0) REVERT: G 148 LYS cc_start: 0.9629 (mmmt) cc_final: 0.9402 (mmmt) REVERT: G 152 LYS cc_start: 0.9621 (mttt) cc_final: 0.9320 (mppt) REVERT: G 160 LYS cc_start: 0.9553 (ttmm) cc_final: 0.9261 (ttmm) REVERT: G 246 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8666 (mp10) outliers start: 55 outliers final: 36 residues processed: 512 average time/residue: 0.1179 time to fit residues: 82.8413 Evaluate side-chains 486 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 447 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 A residue 200 VAL 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 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 57 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 F residue 200 VAL 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 119 MET Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.110583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.077857 restraints weight = 31897.784| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.89 r_work: 0.2983 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13286 Z= 0.134 Angle : 0.646 8.843 18025 Z= 0.327 Chirality : 0.038 0.122 2051 Planarity : 0.005 0.058 2212 Dihedral : 3.743 17.436 1743 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.44 % Allowed : 24.61 % 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: 2.23 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -1.81 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 201 TYR 0.015 0.001 TYR D 217 PHE 0.014 0.001 PHE F 137 TRP 0.009 0.001 TRP E 62 HIS 0.005 0.000 HIS F 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (13265) covalent geometry : angle 0.64193 / 0.33 (17976) SS BOND : bond 0.00221 / 0.16 ( 14) SS BOND : angle 0.43517 / 0.33 ( 28) hydrogen bonds : bond 0.04231 / 2.82 ( 925) hydrogen bonds : angle 3.54569 / 2.53 ( 2775) link_NAG-ASN : bond 0.00058 / 0.03 ( 7) link_NAG-ASN : angle 2.17238 / 1.68 ( 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 515 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 469 time to evaluate : 0.380 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 44 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8761 (mm) REVERT: A 47 TYR cc_start: 0.9122 (m-80) cc_final: 0.8819 (m-80) REVERT: A 68 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8636 (t80) REVERT: A 71 ASN cc_start: 0.8509 (t0) cc_final: 0.7990 (t0) REVERT: A 96 ARG cc_start: 0.8352 (mtp180) cc_final: 0.7928 (mtt180) REVERT: A 104 GLN cc_start: 0.8893 (mt0) cc_final: 0.7683 (tp40) REVERT: A 105 ARG cc_start: 0.9389 (tpt170) cc_final: 0.9049 (mmm-85) REVERT: A 120 ASP cc_start: 0.8836 (t0) cc_final: 0.8512 (t0) REVERT: A 233 CYS cc_start: 0.8771 (m) cc_final: 0.8396 (m) REVERT: B 32 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8997 (pp30) REVERT: B 38 GLU cc_start: 0.9022 (tp30) cc_final: 0.8816 (tp30) REVERT: B 96 ARG cc_start: 0.8333 (mtp180) cc_final: 0.7959 (mtt180) REVERT: B 104 GLN cc_start: 0.9003 (mt0) cc_final: 0.7691 (tp40) REVERT: B 105 ARG cc_start: 0.9405 (tpt170) cc_final: 0.9125 (mmm-85) REVERT: B 120 ASP cc_start: 0.8924 (t0) cc_final: 0.8564 (t0) REVERT: B 152 LYS cc_start: 0.9602 (mttt) cc_final: 0.9389 (mttt) REVERT: B 220 HIS cc_start: 0.8713 (m90) cc_final: 0.8069 (m90) REVERT: B 233 CYS cc_start: 0.8770 (m) cc_final: 0.8521 (m) REVERT: C 32 GLN cc_start: 0.9230 (tp40) cc_final: 0.9006 (tp40) REVERT: C 71 ASN cc_start: 0.8455 (t0) cc_final: 0.8185 (t0) REVERT: C 96 ARG cc_start: 0.8349 (mtp180) cc_final: 0.7937 (mtt180) REVERT: C 142 TYR cc_start: 0.7947 (m-80) cc_final: 0.7735 (m-80) REVERT: C 152 LYS cc_start: 0.9613 (mttt) cc_final: 0.9349 (mttt) REVERT: C 216 LYS cc_start: 0.9520 (mmmm) cc_final: 0.9120 (mmtp) REVERT: C 226 ARG cc_start: 0.8606 (mmp-170) cc_final: 0.8296 (mmp80) REVERT: C 233 CYS cc_start: 0.8874 (m) cc_final: 0.8628 (m) REVERT: D 47 TYR cc_start: 0.9180 (m-80) cc_final: 0.8808 (m-80) REVERT: D 68 TYR cc_start: 0.8827 (m-80) cc_final: 0.8458 (t80) REVERT: D 71 ASN cc_start: 0.8779 (t0) cc_final: 0.8261 (t0) REVERT: D 96 ARG cc_start: 0.8401 (mtp180) cc_final: 0.7994 (mtt180) REVERT: D 104 GLN cc_start: 0.8885 (mt0) cc_final: 0.7782 (tp40) REVERT: D 105 ARG cc_start: 0.9450 (tpt170) cc_final: 0.9203 (mmm-85) REVERT: D 120 ASP cc_start: 0.8884 (t0) cc_final: 0.8340 (t0) REVERT: D 209 GLN cc_start: 0.9058 (pm20) cc_final: 0.8839 (pm20) REVERT: D 233 CYS cc_start: 0.8647 (m) cc_final: 0.8429 (m) REVERT: E 47 TYR cc_start: 0.9136 (m-80) cc_final: 0.8818 (m-80) REVERT: E 71 ASN cc_start: 0.8631 (t0) cc_final: 0.8251 (t0) REVERT: E 96 ARG cc_start: 0.8317 (mtp180) cc_final: 0.8016 (mtt180) REVERT: E 104 GLN cc_start: 0.8957 (mt0) cc_final: 0.7906 (tp40) REVERT: E 119 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8726 (mmm) REVERT: E 120 ASP cc_start: 0.8844 (t0) cc_final: 0.8321 (t0) REVERT: E 152 LYS cc_start: 0.9574 (mttt) cc_final: 0.9296 (mttt) REVERT: E 226 ARG cc_start: 0.8867 (mmp-170) cc_final: 0.8330 (mmp80) REVERT: E 233 CYS cc_start: 0.8882 (m) cc_final: 0.8676 (m) REVERT: F 32 GLN cc_start: 0.9328 (tp40) cc_final: 0.9014 (tt0) REVERT: F 40 THR cc_start: 0.9788 (OUTLIER) cc_final: 0.9532 (p) REVERT: F 96 ARG cc_start: 0.8353 (mtp180) cc_final: 0.7915 (mtt180) REVERT: F 104 GLN cc_start: 0.8894 (mt0) cc_final: 0.7790 (tp40) REVERT: F 105 ARG cc_start: 0.9376 (tpt170) cc_final: 0.9043 (mmm-85) REVERT: F 179 ARG cc_start: 0.9193 (mmm-85) cc_final: 0.8925 (mtp85) REVERT: G 40 THR cc_start: 0.9727 (OUTLIER) cc_final: 0.9515 (p) REVERT: G 71 ASN cc_start: 0.8490 (t0) cc_final: 0.8199 (t0) REVERT: G 96 ARG cc_start: 0.7908 (mtp180) cc_final: 0.7509 (mtt180) REVERT: G 104 GLN cc_start: 0.8901 (mt0) cc_final: 0.7575 (tp40) REVERT: G 105 ARG cc_start: 0.9395 (tpt170) cc_final: 0.9095 (mmm-85) REVERT: G 120 ASP cc_start: 0.8817 (t0) cc_final: 0.8281 (t0) REVERT: G 122 LYS cc_start: 0.9404 (mmtp) cc_final: 0.9169 (mmtp) REVERT: G 148 LYS cc_start: 0.9674 (mmmt) cc_final: 0.9417 (mmmt) REVERT: G 152 LYS cc_start: 0.9597 (mttt) cc_final: 0.9292 (mppt) REVERT: G 201 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8418 (tpp80) REVERT: G 233 CYS cc_start: 0.8561 (m) cc_final: 0.8256 (m) outliers start: 46 outliers final: 27 residues processed: 490 average time/residue: 0.1068 time to fit residues: 73.3725 Evaluate side-chains 499 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 466 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU 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 32 GLN Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 76 VAL 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 131 THR 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 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 131 THR 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: 2.9990 chunk 130 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** G 246 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 = 0.3717 r_free = 0.3717 target = 0.110726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.077928 restraints weight = 31925.555| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.84 r_work: 0.2960 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5550 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= 0.136 Angle : 0.625 8.368 18025 Z= 0.319 Chirality : 0.038 0.129 2051 Planarity : 0.005 0.055 2212 Dihedral : 3.630 16.869 1743 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.44 % Allowed : 26.10 % Favored : 70.46 % 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: 2.36 (0.22), residues: 1575 helix: 2.33 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -1.59 (0.38), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 201 TYR 0.018 0.001 TYR F 217 PHE 0.011 0.001 PHE F 124 TRP 0.011 0.001 TRP F 62 HIS 0.004 0.000 HIS F 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (13265) covalent geometry : angle 0.62066 / 0.32 (17976) SS BOND : bond 0.00239 / 0.17 ( 14) SS BOND : angle 0.44089 / 0.33 ( 28) hydrogen bonds : bond 0.04056 / 2.69 ( 925) hydrogen bonds : angle 3.47948 / 2.49 ( 2775) link_NAG-ASN : bond 0.00133 / 0.10 ( 7) link_NAG-ASN : angle 2.18934 / 1.70 ( 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 517 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 471 time to evaluate : 0.398 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 26 MET cc_start: 0.7842 (mmp) cc_final: 0.7564 (mmp) REVERT: A 47 TYR cc_start: 0.9158 (m-80) cc_final: 0.8852 (m-80) REVERT: A 68 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.8624 (t80) REVERT: A 71 ASN cc_start: 0.8539 (t0) cc_final: 0.8002 (t0) REVERT: A 96 ARG cc_start: 0.8410 (mtp180) cc_final: 0.8114 (mtt180) REVERT: A 105 ARG cc_start: 0.9397 (tpt170) cc_final: 0.9099 (mmm-85) REVERT: A 120 ASP cc_start: 0.8837 (t0) cc_final: 0.8474 (t0) REVERT: A 233 CYS cc_start: 0.8781 (m) cc_final: 0.8396 (m) REVERT: B 32 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.8964 (pp30) REVERT: B 38 GLU cc_start: 0.9003 (tp30) cc_final: 0.8775 (tp30) REVERT: B 71 ASN cc_start: 0.8817 (t0) cc_final: 0.8585 (t0) REVERT: B 96 ARG cc_start: 0.8377 (mtp180) cc_final: 0.8015 (mtt180) REVERT: B 104 GLN cc_start: 0.8991 (mt0) cc_final: 0.7743 (tp40) REVERT: B 105 ARG cc_start: 0.9423 (tpt170) cc_final: 0.9140 (mmm-85) REVERT: B 120 ASP cc_start: 0.8777 (t0) cc_final: 0.8572 (t0) REVERT: B 148 LYS cc_start: 0.9599 (mmmt) cc_final: 0.9334 (mmmt) REVERT: B 152 LYS cc_start: 0.9621 (mttt) cc_final: 0.9407 (mttt) REVERT: B 220 HIS cc_start: 0.8754 (m90) cc_final: 0.8139 (m90) REVERT: B 233 CYS cc_start: 0.8768 (m) cc_final: 0.8535 (m) REVERT: C 26 MET cc_start: 0.7930 (mmp) cc_final: 0.7687 (mmp) REVERT: C 32 GLN cc_start: 0.9239 (tp40) cc_final: 0.9035 (tp40) REVERT: C 71 ASN cc_start: 0.8628 (t0) cc_final: 0.8223 (t0) REVERT: C 96 ARG cc_start: 0.8370 (mtp180) cc_final: 0.7952 (mtt180) REVERT: C 142 TYR cc_start: 0.8008 (m-80) cc_final: 0.7776 (m-80) REVERT: C 152 LYS cc_start: 0.9625 (mttt) cc_final: 0.9364 (mttt) REVERT: C 216 LYS cc_start: 0.9521 (mmmm) cc_final: 0.9115 (mmtp) REVERT: C 226 ARG cc_start: 0.8718 (mmp-170) cc_final: 0.8380 (mmp80) REVERT: C 233 CYS cc_start: 0.8885 (m) cc_final: 0.8653 (m) REVERT: D 32 GLN cc_start: 0.9281 (mm-40) cc_final: 0.9033 (tp40) REVERT: D 47 TYR cc_start: 0.9182 (m-80) cc_final: 0.8789 (m-80) REVERT: D 68 TYR cc_start: 0.8809 (m-80) cc_final: 0.8521 (t80) REVERT: D 71 ASN cc_start: 0.8804 (t0) cc_final: 0.8323 (t0) REVERT: D 96 ARG cc_start: 0.8347 (mtp180) cc_final: 0.8016 (mtp180) REVERT: D 104 GLN cc_start: 0.8885 (mt0) cc_final: 0.7854 (tp40) REVERT: D 105 ARG cc_start: 0.9451 (tpt170) cc_final: 0.9106 (mmm-85) REVERT: D 120 ASP cc_start: 0.8797 (t0) cc_final: 0.8231 (t0) REVERT: D 209 GLN cc_start: 0.9120 (pm20) cc_final: 0.8913 (pm20) REVERT: D 233 CYS cc_start: 0.8682 (m) cc_final: 0.8482 (m) REVERT: E 32 GLN cc_start: 0.9273 (mt0) cc_final: 0.8894 (tt0) REVERT: E 38 GLU cc_start: 0.9006 (tp30) cc_final: 0.8670 (pt0) REVERT: E 47 TYR cc_start: 0.9158 (m-80) cc_final: 0.8800 (m-80) REVERT: E 71 ASN cc_start: 0.8601 (t0) cc_final: 0.8176 (t0) REVERT: E 96 ARG cc_start: 0.8390 (mtp180) cc_final: 0.8001 (mtt180) REVERT: E 104 GLN cc_start: 0.8968 (mt0) cc_final: 0.7834 (tm-30) REVERT: E 119 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8723 (mmm) REVERT: E 120 ASP cc_start: 0.8856 (t0) cc_final: 0.8240 (t0) REVERT: E 152 LYS cc_start: 0.9615 (mttt) cc_final: 0.9332 (mttt) REVERT: E 226 ARG cc_start: 0.8865 (mmp-170) cc_final: 0.8358 (mmp80) REVERT: F 40 THR cc_start: 0.9782 (OUTLIER) cc_final: 0.9567 (p) REVERT: F 96 ARG cc_start: 0.8336 (mtp180) cc_final: 0.8021 (mtp180) REVERT: F 104 GLN cc_start: 0.8906 (mt0) cc_final: 0.7786 (tp40) REVERT: F 105 ARG cc_start: 0.9388 (tpt170) cc_final: 0.9088 (mmm-85) REVERT: F 233 CYS cc_start: 0.8909 (m) cc_final: 0.8690 (m) REVERT: F 247 GLN cc_start: 0.8883 (mp10) cc_final: 0.8667 (pm20) REVERT: G 32 GLN cc_start: 0.9395 (tt0) cc_final: 0.9156 (pt0) REVERT: G 40 THR cc_start: 0.9747 (OUTLIER) cc_final: 0.9534 (p) REVERT: G 71 ASN cc_start: 0.8486 (t0) cc_final: 0.8116 (t0) REVERT: G 96 ARG cc_start: 0.8051 (mtp180) cc_final: 0.7653 (mtt180) REVERT: G 105 ARG cc_start: 0.9404 (tpt170) cc_final: 0.9104 (mmm-85) REVERT: G 119 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8922 (mmm) REVERT: G 120 ASP cc_start: 0.8836 (t0) cc_final: 0.8342 (t0) REVERT: G 148 LYS cc_start: 0.9675 (mmmt) cc_final: 0.9424 (mmmt) REVERT: G 152 LYS cc_start: 0.9593 (mttt) cc_final: 0.9279 (mppt) REVERT: G 160 LYS cc_start: 0.9535 (ttmm) cc_final: 0.9246 (ttmm) REVERT: G 201 ARG cc_start: 0.8719 (tpp80) cc_final: 0.8470 (tpp80) REVERT: G 233 CYS cc_start: 0.8590 (m) cc_final: 0.8344 (m) REVERT: G 246 GLN cc_start: 0.8443 (mp10) cc_final: 0.8118 (mp10) outliers start: 46 outliers final: 33 residues processed: 489 average time/residue: 0.1086 time to fit residues: 74.0025 Evaluate side-chains 496 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 457 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 32 GLN 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 C residue 200 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 74 ILE 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 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 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 119 MET Chi-restraints excluded: chain G residue 181 LEU 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: 2.9990 chunk 25 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 0.0170 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN G 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.111931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.078840 restraints weight = 31861.715| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.90 r_work: 0.2963 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5768 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 7.385 18025 Z= 0.320 Chirality : 0.039 0.173 2051 Planarity : 0.004 0.053 2212 Dihedral : 3.546 16.823 1743 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.37 % Allowed : 25.95 % Favored : 70.68 % 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: 2.50 (0.22), residues: 1575 helix: 2.42 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -1.50 (0.38), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 226 TYR 0.016 0.001 TYR D 217 PHE 0.013 0.001 PHE B 124 TRP 0.010 0.001 TRP E 62 HIS 0.004 0.000 HIS F 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (13265) covalent geometry : angle 0.62553 / 0.32 (17976) SS BOND : bond 0.00211 / 0.15 ( 14) SS BOND : angle 0.42021 / 0.32 ( 28) hydrogen bonds : bond 0.03871 / 2.57 ( 925) hydrogen bonds : angle 3.42394 / 2.45 ( 2775) link_NAG-ASN : bond 0.00029 / 0.02 ( 7) link_NAG-ASN : angle 1.97034 / 1.51 ( 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 531 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 486 time to evaluate : 0.313 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: A 26 MET cc_start: 0.7899 (mmp) cc_final: 0.7560 (mmp) REVERT: A 44 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8738 (mm) REVERT: A 47 TYR cc_start: 0.9197 (m-80) cc_final: 0.8890 (m-80) REVERT: A 68 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8614 (t80) REVERT: A 71 ASN cc_start: 0.8527 (t0) cc_final: 0.7965 (t0) REVERT: A 96 ARG cc_start: 0.8447 (mtp180) cc_final: 0.8124 (mtt180) REVERT: A 105 ARG cc_start: 0.9394 (tpt170) cc_final: 0.9098 (mmm-85) REVERT: A 120 ASP cc_start: 0.8874 (t0) cc_final: 0.8476 (t0) REVERT: A 233 CYS cc_start: 0.8845 (m) cc_final: 0.8485 (m) REVERT: B 32 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.8907 (pp30) REVERT: B 71 ASN cc_start: 0.8859 (t0) cc_final: 0.8602 (t0) REVERT: B 96 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7975 (mtp180) REVERT: B 104 GLN cc_start: 0.8950 (mt0) cc_final: 0.7686 (tp40) REVERT: B 105 ARG cc_start: 0.9423 (tpt170) cc_final: 0.9131 (mmm-85) REVERT: B 120 ASP cc_start: 0.8799 (t0) cc_final: 0.8416 (t0) REVERT: B 216 LYS cc_start: 0.9558 (tptt) cc_final: 0.9269 (mmtp) REVERT: B 220 HIS cc_start: 0.8734 (m90) cc_final: 0.8346 (m-70) REVERT: B 233 CYS cc_start: 0.8773 (m) cc_final: 0.8528 (m) REVERT: C 71 ASN cc_start: 0.8627 (t0) cc_final: 0.8206 (t0) REVERT: C 96 ARG cc_start: 0.8366 (mtp180) cc_final: 0.7929 (mtt180) REVERT: C 142 TYR cc_start: 0.7982 (m-80) cc_final: 0.7746 (m-80) REVERT: C 152 LYS cc_start: 0.9638 (mttt) cc_final: 0.9341 (mttt) REVERT: C 216 LYS cc_start: 0.9522 (mmmm) cc_final: 0.9086 (mmtp) REVERT: C 226 ARG cc_start: 0.8784 (mmp-170) cc_final: 0.8255 (mmp80) REVERT: C 233 CYS cc_start: 0.8997 (m) cc_final: 0.8733 (m) REVERT: D 32 GLN cc_start: 0.9273 (mm-40) cc_final: 0.9043 (tp40) REVERT: D 47 TYR cc_start: 0.9165 (m-80) cc_final: 0.8761 (m-80) REVERT: D 68 TYR cc_start: 0.8785 (m-80) cc_final: 0.8509 (t80) REVERT: D 71 ASN cc_start: 0.8880 (t0) cc_final: 0.8393 (t0) REVERT: D 96 ARG cc_start: 0.8382 (mtp180) cc_final: 0.8016 (mtp180) REVERT: D 104 GLN cc_start: 0.8993 (mt0) cc_final: 0.7948 (tp40) REVERT: D 105 ARG cc_start: 0.9519 (tpt170) cc_final: 0.9214 (mmm-85) REVERT: D 120 ASP cc_start: 0.8795 (t0) cc_final: 0.8240 (t0) REVERT: D 147 GLN cc_start: 0.9114 (pm20) cc_final: 0.8839 (tp-100) REVERT: D 233 CYS cc_start: 0.8747 (m) cc_final: 0.8537 (m) REVERT: E 32 GLN cc_start: 0.9267 (mt0) cc_final: 0.8870 (tt0) REVERT: E 38 GLU cc_start: 0.9054 (tp30) cc_final: 0.8702 (pt0) REVERT: E 47 TYR cc_start: 0.9135 (m-80) cc_final: 0.8800 (m-80) REVERT: E 71 ASN cc_start: 0.8563 (t0) cc_final: 0.8188 (t0) REVERT: E 96 ARG cc_start: 0.8319 (mtp180) cc_final: 0.7938 (mtt180) REVERT: E 104 GLN cc_start: 0.8947 (mt0) cc_final: 0.7832 (tm-30) REVERT: E 120 ASP cc_start: 0.8852 (t0) cc_final: 0.8296 (t0) REVERT: E 152 LYS cc_start: 0.9614 (mttt) cc_final: 0.9297 (mttt) REVERT: E 226 ARG cc_start: 0.8866 (mmp-170) cc_final: 0.8342 (mmp80) REVERT: F 40 THR cc_start: 0.9781 (OUTLIER) cc_final: 0.9580 (p) REVERT: F 96 ARG cc_start: 0.8382 (mtp180) cc_final: 0.7985 (mtp180) REVERT: F 105 ARG cc_start: 0.9402 (tpt170) cc_final: 0.9097 (mmm-85) REVERT: F 216 LYS cc_start: 0.9427 (mmmm) cc_final: 0.9156 (mmmm) REVERT: F 233 CYS cc_start: 0.8911 (m) cc_final: 0.8677 (m) REVERT: F 247 GLN cc_start: 0.8882 (mp10) cc_final: 0.8647 (pm20) REVERT: G 32 GLN cc_start: 0.9379 (tt0) cc_final: 0.9133 (pt0) REVERT: G 40 THR cc_start: 0.9752 (OUTLIER) cc_final: 0.9546 (p) REVERT: G 71 ASN cc_start: 0.8379 (t0) cc_final: 0.8081 (t0) REVERT: G 96 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7659 (mtt180) REVERT: G 105 ARG cc_start: 0.9392 (tpt170) cc_final: 0.9086 (mmm-85) REVERT: G 119 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8910 (mmm) REVERT: G 120 ASP cc_start: 0.8801 (t0) cc_final: 0.8303 (t0) REVERT: G 148 LYS cc_start: 0.9680 (mmmt) cc_final: 0.9445 (mmmt) REVERT: G 152 LYS cc_start: 0.9589 (mttt) cc_final: 0.9267 (mppt) REVERT: G 201 ARG cc_start: 0.8682 (tpp80) cc_final: 0.8444 (tpp80) REVERT: G 233 CYS cc_start: 0.8607 (m) cc_final: 0.8341 (m) REVERT: G 246 GLN cc_start: 0.8502 (mp10) cc_final: 0.8202 (mp10) outliers start: 45 outliers final: 36 residues processed: 506 average time/residue: 0.1021 time to fit residues: 72.9152 Evaluate side-chains 512 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 470 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU 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 28 LEU Chi-restraints excluded: chain B residue 32 GLN 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 D residue 28 LEU 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 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 131 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 40 THR 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 119 MET 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: 2.9990 chunk 5 optimal weight: 0.6980 chunk 119 optimal weight: 0.0980 chunk 46 optimal weight: 50.0000 chunk 128 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN G 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.109987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.077009 restraints weight = 32045.558| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.81 r_work: 0.2911 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13286 Z= 0.159 Angle : 0.645 6.817 18025 Z= 0.333 Chirality : 0.040 0.178 2051 Planarity : 0.005 0.054 2212 Dihedral : 3.514 16.690 1743 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.19 % Allowed : 27.15 % Favored : 68.66 % 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: 2.55 (0.22), residues: 1575 helix: 2.42 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.34 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 201 TYR 0.014 0.001 TYR C 217 PHE 0.020 0.001 PHE E 99 TRP 0.014 0.001 TRP E 62 HIS 0.003 0.001 HIS F 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (13265) covalent geometry : angle 0.64160 / 0.33 (17976) SS BOND : bond 0.00259 / 0.19 ( 14) SS BOND : angle 0.47810 / 0.37 ( 28) hydrogen bonds : bond 0.04019 / 2.66 ( 925) hydrogen bonds : angle 3.52265 / 2.51 ( 2775) link_NAG-ASN : bond 0.00151 / 0.09 ( 7) link_NAG-ASN : angle 2.12202 / 1.60 ( 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 526 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 470 time to evaluate : 0.427 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: A 26 MET cc_start: 0.7924 (mmp) cc_final: 0.7598 (mmp) REVERT: A 32 GLN cc_start: 0.9223 (tp40) cc_final: 0.8872 (pp30) REVERT: A 68 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8604 (t80) REVERT: A 71 ASN cc_start: 0.8610 (t0) cc_final: 0.8073 (t0) REVERT: A 96 ARG cc_start: 0.8428 (mtp180) cc_final: 0.8163 (mtt180) REVERT: A 104 GLN cc_start: 0.8933 (mt0) cc_final: 0.7659 (tp40) REVERT: A 105 ARG cc_start: 0.9423 (tpt170) cc_final: 0.9092 (mmm-85) REVERT: A 120 ASP cc_start: 0.8915 (t0) cc_final: 0.8521 (t0) REVERT: A 233 CYS cc_start: 0.8840 (m) cc_final: 0.8474 (m) REVERT: B 32 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.8919 (pp30) REVERT: B 71 ASN cc_start: 0.8940 (t0) cc_final: 0.8543 (t0) REVERT: B 96 ARG cc_start: 0.8387 (mtp180) cc_final: 0.8003 (mtp180) REVERT: B 104 GLN cc_start: 0.9009 (mt0) cc_final: 0.7979 (tp40) REVERT: B 105 ARG cc_start: 0.9468 (tpt170) cc_final: 0.9196 (mmm-85) REVERT: B 120 ASP cc_start: 0.8886 (t0) cc_final: 0.8354 (t0) REVERT: B 216 LYS cc_start: 0.9576 (tptt) cc_final: 0.9289 (mmmm) REVERT: B 220 HIS cc_start: 0.8802 (m90) cc_final: 0.8385 (m-70) REVERT: B 233 CYS cc_start: 0.8773 (m) cc_final: 0.8543 (m) REVERT: C 26 MET cc_start: 0.8063 (mmp) cc_final: 0.7854 (mmp) REVERT: C 71 ASN cc_start: 0.8740 (t0) cc_final: 0.8312 (t0) REVERT: C 96 ARG cc_start: 0.8345 (mtp180) cc_final: 0.7937 (mtt180) REVERT: C 104 GLN cc_start: 0.9022 (mt0) cc_final: 0.7986 (tm-30) REVERT: C 142 TYR cc_start: 0.7988 (m-80) cc_final: 0.7740 (m-80) REVERT: C 152 LYS cc_start: 0.9641 (mttt) cc_final: 0.9343 (mppt) REVERT: C 226 ARG cc_start: 0.8825 (mmp-170) cc_final: 0.8274 (mmp80) REVERT: C 233 CYS cc_start: 0.8887 (m) cc_final: 0.8659 (m) REVERT: D 68 TYR cc_start: 0.8831 (m-80) cc_final: 0.8487 (t80) REVERT: D 71 ASN cc_start: 0.8872 (t0) cc_final: 0.8380 (t0) REVERT: D 96 ARG cc_start: 0.8388 (mtp180) cc_final: 0.8043 (mtp180) REVERT: D 104 GLN cc_start: 0.9071 (mt0) cc_final: 0.7992 (tp40) REVERT: D 105 ARG cc_start: 0.9531 (tpt170) cc_final: 0.9304 (mmm-85) REVERT: D 120 ASP cc_start: 0.8887 (t0) cc_final: 0.8388 (t0) REVERT: D 147 GLN cc_start: 0.9126 (pm20) cc_final: 0.8867 (tp-100) REVERT: D 233 CYS cc_start: 0.8733 (m) cc_final: 0.8526 (m) REVERT: E 32 GLN cc_start: 0.9288 (mt0) cc_final: 0.8882 (tt0) REVERT: E 38 GLU cc_start: 0.9063 (tp30) cc_final: 0.8693 (pt0) REVERT: E 47 TYR cc_start: 0.9173 (m-80) cc_final: 0.8801 (m-80) REVERT: E 71 ASN cc_start: 0.8578 (t0) cc_final: 0.8147 (t0) REVERT: E 96 ARG cc_start: 0.8480 (mtp180) cc_final: 0.8046 (mtt180) REVERT: E 104 GLN cc_start: 0.9010 (mt0) cc_final: 0.7965 (tm-30) REVERT: E 120 ASP cc_start: 0.8870 (t0) cc_final: 0.8254 (t0) REVERT: E 152 LYS cc_start: 0.9623 (mttt) cc_final: 0.9312 (mttt) REVERT: F 40 THR cc_start: 0.9769 (OUTLIER) cc_final: 0.9551 (p) REVERT: F 96 ARG cc_start: 0.8428 (mtp180) cc_final: 0.8015 (mtp180) REVERT: F 104 GLN cc_start: 0.8925 (mt0) cc_final: 0.7817 (tp40) REVERT: F 105 ARG cc_start: 0.9407 (tpt170) cc_final: 0.9112 (mmm-85) REVERT: F 233 CYS cc_start: 0.8910 (m) cc_final: 0.8683 (m) REVERT: F 247 GLN cc_start: 0.8905 (mp10) cc_final: 0.8676 (pm20) REVERT: G 32 GLN cc_start: 0.9404 (tt0) cc_final: 0.9146 (pt0) REVERT: G 40 THR cc_start: 0.9753 (OUTLIER) cc_final: 0.9486 (p) REVERT: G 71 ASN cc_start: 0.8523 (t0) cc_final: 0.8222 (t0) REVERT: G 96 ARG cc_start: 0.8132 (mtp180) cc_final: 0.7783 (mtt180) REVERT: G 104 GLN cc_start: 0.8894 (mt0) cc_final: 0.7698 (tp40) REVERT: G 105 ARG cc_start: 0.9426 (tpt170) cc_final: 0.9115 (mmm-85) REVERT: G 119 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8945 (mmm) REVERT: G 120 ASP cc_start: 0.8912 (t0) cc_final: 0.8441 (t0) REVERT: G 148 LYS cc_start: 0.9670 (mmmt) cc_final: 0.9405 (mmmt) REVERT: G 152 LYS cc_start: 0.9607 (mttt) cc_final: 0.9301 (mppt) REVERT: G 201 ARG cc_start: 0.8766 (tpp80) cc_final: 0.8545 (tpp80) REVERT: G 233 CYS cc_start: 0.8672 (m) cc_final: 0.8404 (m) REVERT: G 246 GLN cc_start: 0.8518 (mp-120) cc_final: 0.8154 (mp10) outliers start: 56 outliers final: 40 residues processed: 495 average time/residue: 0.1089 time to fit residues: 75.7603 Evaluate side-chains 512 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 467 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 28 LEU Chi-restraints excluded: chain B residue 32 GLN 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 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 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 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 131 THR Chi-restraints excluded: chain E residue 146 SER 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 85 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 55 ILE 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 119 MET 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: 0.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 152 optimal weight: 0.0050 chunk 129 optimal weight: 0.5980 chunk 137 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.3722 r_free = 0.3722 target = 0.110748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.077743 restraints weight = 31983.862| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.81 r_work: 0.2929 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13286 Z= 0.142 Angle : 0.657 7.320 18025 Z= 0.337 Chirality : 0.040 0.202 2051 Planarity : 0.005 0.052 2212 Dihedral : 3.523 16.899 1743 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.89 % Allowed : 26.78 % 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: 2.63 (0.22), residues: 1575 helix: 2.46 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.22 (0.38), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 226 TYR 0.021 0.002 TYR D 97 PHE 0.022 0.001 PHE E 99 TRP 0.012 0.001 TRP E 62 HIS 0.003 0.001 HIS F 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (13265) covalent geometry : angle 0.65453 / 0.34 (17976) SS BOND : bond 0.00226 / 0.17 ( 14) SS BOND : angle 0.42616 / 0.33 ( 28) hydrogen bonds : bond 0.03971 / 2.64 ( 925) hydrogen bonds : angle 3.52811 / 2.52 ( 2775) link_NAG-ASN : bond 0.00081 / 0.06 ( 7) link_NAG-ASN : angle 2.02493 / 1.53 ( 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 526 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 474 time to evaluate : 0.405 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: A 32 GLN cc_start: 0.9234 (tp40) cc_final: 0.8895 (pp30) REVERT: A 68 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8601 (t80) REVERT: A 71 ASN cc_start: 0.8593 (t0) cc_final: 0.8085 (t0) REVERT: A 96 ARG cc_start: 0.8412 (mtp180) cc_final: 0.8129 (mtt180) REVERT: A 105 ARG cc_start: 0.9425 (tpt170) cc_final: 0.9145 (mmm-85) REVERT: A 120 ASP cc_start: 0.8892 (t0) cc_final: 0.8509 (t0) REVERT: A 233 CYS cc_start: 0.8883 (m) cc_final: 0.8540 (m) REVERT: B 32 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8874 (pp30) REVERT: B 71 ASN cc_start: 0.8981 (t0) cc_final: 0.8574 (t0) REVERT: B 96 ARG cc_start: 0.8388 (mtp180) cc_final: 0.7997 (mtp180) REVERT: B 104 GLN cc_start: 0.9000 (mt0) cc_final: 0.7963 (tp40) REVERT: B 105 ARG cc_start: 0.9475 (tpt170) cc_final: 0.9204 (mmm-85) REVERT: B 120 ASP cc_start: 0.8831 (t0) cc_final: 0.8330 (t0) REVERT: B 122 LYS cc_start: 0.9349 (mmmm) cc_final: 0.9071 (mtpp) REVERT: B 216 LYS cc_start: 0.9574 (tptt) cc_final: 0.9291 (mmmm) REVERT: B 220 HIS cc_start: 0.8783 (m90) cc_final: 0.8369 (m-70) REVERT: B 233 CYS cc_start: 0.8747 (m) cc_final: 0.8507 (m) REVERT: C 71 ASN cc_start: 0.8762 (t0) cc_final: 0.8310 (t0) REVERT: C 96 ARG cc_start: 0.8353 (mtp180) cc_final: 0.7939 (mtt180) REVERT: C 142 TYR cc_start: 0.7964 (m-80) cc_final: 0.7724 (m-80) REVERT: C 152 LYS cc_start: 0.9647 (mttt) cc_final: 0.9354 (mttt) REVERT: C 226 ARG cc_start: 0.8860 (mmp-170) cc_final: 0.8283 (mmp80) REVERT: C 233 CYS cc_start: 0.8979 (m) cc_final: 0.8713 (m) REVERT: D 68 TYR cc_start: 0.8829 (m-80) cc_final: 0.8480 (t80) REVERT: D 71 ASN cc_start: 0.8915 (t0) cc_final: 0.8485 (t0) REVERT: D 96 ARG cc_start: 0.8413 (mtp180) cc_final: 0.8055 (mtp180) REVERT: D 104 GLN cc_start: 0.9052 (mt0) cc_final: 0.7995 (tp40) REVERT: D 105 ARG cc_start: 0.9522 (tpt170) cc_final: 0.9295 (mmm-85) REVERT: D 120 ASP cc_start: 0.8845 (t0) cc_final: 0.8310 (t0) REVERT: E 32 GLN cc_start: 0.9289 (mt0) cc_final: 0.8874 (tt0) REVERT: E 38 GLU cc_start: 0.9058 (tp30) cc_final: 0.8625 (pt0) REVERT: E 47 TYR cc_start: 0.9167 (m-80) cc_final: 0.8780 (m-80) REVERT: E 71 ASN cc_start: 0.8762 (t0) cc_final: 0.8400 (t0) REVERT: E 96 ARG cc_start: 0.8491 (mtp180) cc_final: 0.8063 (mtt180) REVERT: E 104 GLN cc_start: 0.9005 (mt0) cc_final: 0.7953 (tm-30) REVERT: E 119 MET cc_start: 0.9024 (mmp) cc_final: 0.8723 (mmm) REVERT: E 120 ASP cc_start: 0.8880 (t0) cc_final: 0.8325 (t0) REVERT: E 152 LYS cc_start: 0.9616 (mttt) cc_final: 0.9296 (mttt) REVERT: E 223 ASP cc_start: 0.9565 (t0) cc_final: 0.9157 (t0) REVERT: F 40 THR cc_start: 0.9767 (OUTLIER) cc_final: 0.9521 (p) REVERT: F 96 ARG cc_start: 0.8410 (mtp180) cc_final: 0.8002 (mtp180) REVERT: F 104 GLN cc_start: 0.8923 (mt0) cc_final: 0.7824 (tp40) REVERT: F 105 ARG cc_start: 0.9401 (tpt170) cc_final: 0.9105 (mmm-85) REVERT: F 216 LYS cc_start: 0.9346 (mmmm) cc_final: 0.9113 (mmmm) REVERT: F 233 CYS cc_start: 0.8897 (m) cc_final: 0.8678 (m) REVERT: G 32 GLN cc_start: 0.9373 (tt0) cc_final: 0.9131 (pt0) REVERT: G 40 THR cc_start: 0.9751 (OUTLIER) cc_final: 0.9535 (p) REVERT: G 71 ASN cc_start: 0.8578 (t0) cc_final: 0.8250 (t0) REVERT: G 96 ARG cc_start: 0.8113 (mtp180) cc_final: 0.7646 (mtt180) REVERT: G 97 TYR cc_start: 0.9084 (t80) cc_final: 0.8863 (t80) REVERT: G 105 ARG cc_start: 0.9416 (tpt170) cc_final: 0.9106 (mmm-85) REVERT: G 119 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8927 (mmm) REVERT: G 120 ASP cc_start: 0.8890 (t0) cc_final: 0.8487 (t0) REVERT: G 148 LYS cc_start: 0.9655 (mmmt) cc_final: 0.9392 (mmmt) REVERT: G 152 LYS cc_start: 0.9602 (mttt) cc_final: 0.9289 (mppt) REVERT: G 201 ARG cc_start: 0.8790 (tpp80) cc_final: 0.8571 (tpp80) REVERT: G 233 CYS cc_start: 0.8691 (m) cc_final: 0.8426 (m) REVERT: G 246 GLN cc_start: 0.8459 (mp-120) cc_final: 0.8241 (mp10) outliers start: 52 outliers final: 42 residues processed: 495 average time/residue: 0.1096 time to fit residues: 75.8411 Evaluate side-chains 514 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 467 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 32 GLN 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 C residue 200 VAL 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 E residue 55 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 70 MET 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 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 85 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 55 ILE 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 119 MET Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 45 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 24 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 129 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.117237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.084104 restraints weight = 31935.088| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.94 r_work: 0.2946 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13286 Z= 0.136 Angle : 0.670 8.778 18025 Z= 0.345 Chirality : 0.041 0.218 2051 Planarity : 0.005 0.050 2212 Dihedral : 3.490 16.786 1743 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.29 % Allowed : 27.30 % Favored : 69.41 % 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: 2.51 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.18 (0.38), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 226 TYR 0.015 0.001 TYR E 49 PHE 0.021 0.001 PHE E 99 TRP 0.012 0.001 TRP F 62 HIS 0.003 0.000 HIS F 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (13265) covalent geometry : angle 0.66756 / 0.35 (17976) SS BOND : bond 0.00186 / 0.14 ( 14) SS BOND : angle 0.36801 / 0.29 ( 28) hydrogen bonds : bond 0.03800 / 2.52 ( 925) hydrogen bonds : angle 3.45960 / 2.47 ( 2775) link_NAG-ASN : bond 0.00065 / 0.05 ( 7) link_NAG-ASN : angle 1.84786 / 1.41 ( 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 527 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 483 time to evaluate : 0.333 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: A 68 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.8600 (t80) REVERT: A 71 ASN cc_start: 0.8717 (t0) cc_final: 0.8033 (t0) REVERT: A 96 ARG cc_start: 0.8371 (mtp180) cc_final: 0.8086 (mtt180) REVERT: A 105 ARG cc_start: 0.9415 (tpt170) cc_final: 0.9139 (mmm-85) REVERT: A 120 ASP cc_start: 0.8853 (t0) cc_final: 0.8449 (t0) REVERT: A 233 CYS cc_start: 0.8847 (m) cc_final: 0.8479 (m) REVERT: B 32 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.8860 (pp30) REVERT: B 71 ASN cc_start: 0.9020 (t0) cc_final: 0.8670 (t0) REVERT: B 96 ARG cc_start: 0.8365 (mtp180) cc_final: 0.7969 (mtp180) REVERT: B 104 GLN cc_start: 0.8968 (mt0) cc_final: 0.7770 (tp40) REVERT: B 105 ARG cc_start: 0.9457 (tpt170) cc_final: 0.9224 (mmm-85) REVERT: B 120 ASP cc_start: 0.8816 (t0) cc_final: 0.8339 (t0) REVERT: B 201 ARG cc_start: 0.8730 (tpp80) cc_final: 0.8230 (tpp80) REVERT: B 216 LYS cc_start: 0.9558 (tptt) cc_final: 0.9293 (mmmm) REVERT: B 220 HIS cc_start: 0.8723 (m90) cc_final: 0.8324 (m-70) REVERT: B 233 CYS cc_start: 0.8761 (m) cc_final: 0.8522 (m) REVERT: C 71 ASN cc_start: 0.8780 (t0) cc_final: 0.8327 (t0) REVERT: C 96 ARG cc_start: 0.8307 (mtp180) cc_final: 0.7898 (mtt180) REVERT: C 142 TYR cc_start: 0.7999 (m-80) cc_final: 0.7755 (m-80) REVERT: C 152 LYS cc_start: 0.9645 (mttt) cc_final: 0.9354 (mttt) REVERT: C 226 ARG cc_start: 0.8870 (mmp-170) cc_final: 0.8308 (mmp80) REVERT: C 233 CYS cc_start: 0.8970 (m) cc_final: 0.8726 (m) REVERT: D 32 GLN cc_start: 0.9352 (mt0) cc_final: 0.9012 (tt0) REVERT: D 68 TYR cc_start: 0.8805 (m-80) cc_final: 0.8504 (t80) REVERT: D 71 ASN cc_start: 0.8924 (t0) cc_final: 0.8516 (t0) REVERT: D 96 ARG cc_start: 0.8345 (mtp180) cc_final: 0.8028 (mtp180) REVERT: D 104 GLN cc_start: 0.9100 (mt0) cc_final: 0.8032 (tp40) REVERT: D 105 ARG cc_start: 0.9539 (tpt170) cc_final: 0.9313 (mmm-85) REVERT: D 120 ASP cc_start: 0.8765 (t0) cc_final: 0.8202 (t0) REVERT: D 216 LYS cc_start: 0.9313 (mmmm) cc_final: 0.8961 (mmtp) REVERT: E 32 GLN cc_start: 0.9281 (mt0) cc_final: 0.8869 (tt0) REVERT: E 38 GLU cc_start: 0.9047 (tp30) cc_final: 0.8610 (pt0) REVERT: E 71 ASN cc_start: 0.8806 (t0) cc_final: 0.8406 (t0) REVERT: E 96 ARG cc_start: 0.8380 (mtp180) cc_final: 0.8007 (mtt180) REVERT: E 104 GLN cc_start: 0.8963 (mt0) cc_final: 0.7903 (tm-30) REVERT: E 112 VAL cc_start: 0.9643 (t) cc_final: 0.9379 (p) REVERT: E 119 MET cc_start: 0.8971 (mmp) cc_final: 0.8634 (mmm) REVERT: E 120 ASP cc_start: 0.8820 (t0) cc_final: 0.8263 (t0) REVERT: E 152 LYS cc_start: 0.9627 (mttt) cc_final: 0.9303 (mttt) REVERT: E 246 GLN cc_start: 0.9048 (mm110) cc_final: 0.8802 (mp10) REVERT: F 96 ARG cc_start: 0.8363 (mtp180) cc_final: 0.7942 (mtp180) REVERT: F 105 ARG cc_start: 0.9420 (tpt170) cc_final: 0.9148 (mmm-85) REVERT: F 191 MET cc_start: 0.9584 (tpp) cc_final: 0.9290 (mmm) REVERT: F 216 LYS cc_start: 0.9322 (mmmm) cc_final: 0.9080 (mmmm) REVERT: F 233 CYS cc_start: 0.8904 (m) cc_final: 0.8683 (m) REVERT: G 32 GLN cc_start: 0.9344 (tt0) cc_final: 0.9097 (pt0) REVERT: G 40 THR cc_start: 0.9763 (OUTLIER) cc_final: 0.9517 (p) REVERT: G 71 ASN cc_start: 0.8585 (t0) cc_final: 0.8241 (t0) REVERT: G 96 ARG cc_start: 0.8088 (mtp180) cc_final: 0.7605 (mtt180) REVERT: G 105 ARG cc_start: 0.9416 (tpt170) cc_final: 0.9115 (mmm-85) REVERT: G 119 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8896 (mmm) REVERT: G 120 ASP cc_start: 0.8864 (t0) cc_final: 0.8411 (t0) REVERT: G 148 LYS cc_start: 0.9646 (mmmt) cc_final: 0.9416 (mmmt) REVERT: G 152 LYS cc_start: 0.9617 (mttt) cc_final: 0.9296 (mppt) REVERT: G 201 ARG cc_start: 0.8752 (tpp80) cc_final: 0.8505 (tpp80) REVERT: G 216 LYS cc_start: 0.9579 (tptt) cc_final: 0.9299 (mmmm) REVERT: G 233 CYS cc_start: 0.8723 (m) cc_final: 0.8469 (m) REVERT: G 246 GLN cc_start: 0.8403 (mp-120) cc_final: 0.8026 (mp10) outliers start: 44 outliers final: 33 residues processed: 499 average time/residue: 0.1079 time to fit residues: 75.3217 Evaluate side-chains 513 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 476 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 70 MET 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 32 GLN 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 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 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 119 MET 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 77 LEU 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 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 119 MET Chi-restraints excluded: chain G residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 109 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** D 246 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 = 0.3718 r_free = 0.3718 target = 0.119214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.083462 restraints weight = 31981.200| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.04 r_work: 0.2915 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13286 Z= 0.153 Angle : 0.682 9.693 18025 Z= 0.351 Chirality : 0.041 0.203 2051 Planarity : 0.005 0.048 2212 Dihedral : 3.467 16.552 1743 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.22 % Allowed : 28.12 % Favored : 68.66 % 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: 2.73 (0.22), residues: 1575 helix: 2.54 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.18 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 226 TYR 0.019 0.002 TYR D 217 PHE 0.020 0.001 PHE E 99 TRP 0.014 0.001 TRP F 62 HIS 0.003 0.000 HIS F 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.15 (13265) covalent geometry : angle 0.67909 / 0.35 (17976) SS BOND : bond 0.00229 / 0.17 ( 14) SS BOND : angle 0.45698 / 0.36 ( 28) hydrogen bonds : bond 0.03895 / 2.59 ( 925) hydrogen bonds : angle 3.53066 / 2.52 ( 2775) link_NAG-ASN : bond 0.00101 / 0.06 ( 7) link_NAG-ASN : angle 1.98197 / 1.49 ( 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 513 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 470 time to evaluate : 0.419 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: A 68 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8580 (t80) REVERT: A 71 ASN cc_start: 0.8720 (t0) cc_final: 0.8206 (t0) REVERT: A 96 ARG cc_start: 0.8389 (mtp180) cc_final: 0.8144 (mtt180) REVERT: A 105 ARG cc_start: 0.9431 (tpt170) cc_final: 0.9154 (mmm-85) REVERT: A 120 ASP cc_start: 0.8870 (t0) cc_final: 0.8492 (t0) REVERT: A 216 LYS cc_start: 0.9338 (mmmm) cc_final: 0.8999 (mmtp) REVERT: A 233 CYS cc_start: 0.8862 (m) cc_final: 0.8488 (m) REVERT: B 32 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8859 (pp30) REVERT: B 71 ASN cc_start: 0.9043 (t0) cc_final: 0.8649 (t0) REVERT: B 96 ARG cc_start: 0.8359 (mtp180) cc_final: 0.7931 (mtp180) REVERT: B 104 GLN cc_start: 0.9011 (mt0) cc_final: 0.8008 (tp40) REVERT: B 105 ARG cc_start: 0.9466 (tpt170) cc_final: 0.9240 (mmm-85) REVERT: B 120 ASP cc_start: 0.8852 (t0) cc_final: 0.8382 (t0) REVERT: B 143 GLN cc_start: 0.9200 (pm20) cc_final: 0.8941 (pm20) REVERT: B 216 LYS cc_start: 0.9550 (tptt) cc_final: 0.9288 (mmmm) REVERT: B 220 HIS cc_start: 0.8747 (m90) cc_final: 0.8336 (m-70) REVERT: B 233 CYS cc_start: 0.8753 (m) cc_final: 0.8519 (m) REVERT: C 71 ASN cc_start: 0.8759 (t0) cc_final: 0.8280 (t0) REVERT: C 96 ARG cc_start: 0.8340 (mtp180) cc_final: 0.7916 (mtt180) REVERT: C 142 TYR cc_start: 0.8033 (m-80) cc_final: 0.7773 (m-80) REVERT: C 152 LYS cc_start: 0.9652 (mttt) cc_final: 0.9362 (mttt) REVERT: C 216 LYS cc_start: 0.9338 (mmmm) cc_final: 0.9072 (mmtp) REVERT: C 226 ARG cc_start: 0.8886 (mmp-170) cc_final: 0.8318 (mmp80) REVERT: C 233 CYS cc_start: 0.8986 (m) cc_final: 0.8761 (m) REVERT: D 32 GLN cc_start: 0.9375 (mt0) cc_final: 0.9073 (tt0) REVERT: D 68 TYR cc_start: 0.8831 (m-80) cc_final: 0.8478 (t80) REVERT: D 71 ASN cc_start: 0.8953 (t0) cc_final: 0.8600 (t0) REVERT: D 96 ARG cc_start: 0.8377 (mtp180) cc_final: 0.8053 (mtp180) REVERT: D 104 GLN cc_start: 0.9122 (mt0) cc_final: 0.8056 (tp40) REVERT: D 105 ARG cc_start: 0.9545 (tpt170) cc_final: 0.9315 (mmm-85) REVERT: D 120 ASP cc_start: 0.8807 (t0) cc_final: 0.8280 (t0) REVERT: D 216 LYS cc_start: 0.9329 (mmmm) cc_final: 0.8979 (mmtp) REVERT: E 32 GLN cc_start: 0.9294 (mt0) cc_final: 0.8896 (tt0) REVERT: E 38 GLU cc_start: 0.9071 (tp30) cc_final: 0.8624 (pt0) REVERT: E 71 ASN cc_start: 0.8742 (t0) cc_final: 0.8359 (t0) REVERT: E 83 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7266 (ttt180) REVERT: E 96 ARG cc_start: 0.8409 (mtp180) cc_final: 0.8058 (mtt180) REVERT: E 104 GLN cc_start: 0.9009 (mt0) cc_final: 0.7945 (tm-30) REVERT: E 119 MET cc_start: 0.9050 (mmp) cc_final: 0.8718 (mmm) REVERT: E 120 ASP cc_start: 0.8844 (t0) cc_final: 0.8258 (t0) REVERT: E 152 LYS cc_start: 0.9619 (mttt) cc_final: 0.9312 (mttt) REVERT: E 201 ARG cc_start: 0.8707 (tpp80) cc_final: 0.8486 (tpt-90) REVERT: E 223 ASP cc_start: 0.9577 (t0) cc_final: 0.9170 (t0) REVERT: E 246 GLN cc_start: 0.9050 (mm110) cc_final: 0.8748 (mp10) REVERT: E 247 GLN cc_start: 0.9024 (mp10) cc_final: 0.8808 (pm20) REVERT: F 96 ARG cc_start: 0.8414 (mtp180) cc_final: 0.7984 (mtp180) REVERT: F 105 ARG cc_start: 0.9425 (tpt170) cc_final: 0.9200 (mmm-85) REVERT: F 216 LYS cc_start: 0.9353 (mmmm) cc_final: 0.9090 (mmmm) REVERT: F 233 CYS cc_start: 0.8854 (m) cc_final: 0.8602 (m) REVERT: G 32 GLN cc_start: 0.9331 (tt0) cc_final: 0.9108 (pt0) REVERT: G 40 THR cc_start: 0.9758 (OUTLIER) cc_final: 0.9536 (p) REVERT: G 71 ASN cc_start: 0.8644 (t0) cc_final: 0.8309 (t0) REVERT: G 96 ARG cc_start: 0.8083 (mtp180) cc_final: 0.7745 (mtt180) REVERT: G 105 ARG cc_start: 0.9457 (tpt170) cc_final: 0.9163 (mmm-85) REVERT: G 119 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8937 (mmm) REVERT: G 120 ASP cc_start: 0.8917 (t0) cc_final: 0.8455 (t0) REVERT: G 148 LYS cc_start: 0.9645 (mmmt) cc_final: 0.9418 (mmmt) REVERT: G 152 LYS cc_start: 0.9620 (mttt) cc_final: 0.9302 (mppt) REVERT: G 201 ARG cc_start: 0.8816 (tpp80) cc_final: 0.8579 (tpp80) REVERT: G 216 LYS cc_start: 0.9615 (tptt) cc_final: 0.9355 (mmmm) REVERT: G 233 CYS cc_start: 0.8726 (m) cc_final: 0.8475 (m) REVERT: G 246 GLN cc_start: 0.8414 (mp-120) cc_final: 0.8113 (mp10) outliers start: 43 outliers final: 34 residues processed: 486 average time/residue: 0.1052 time to fit residues: 71.4788 Evaluate side-chains 504 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 465 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 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 32 GLN 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 199 LEU Chi-restraints excluded: chain B residue 240 PHE 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 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 55 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 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 119 MET Chi-restraints excluded: chain G residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 62 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN G 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.119746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.084215 restraints weight = 31687.192| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 4.03 r_work: 0.2891 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13286 Z= 0.144 Angle : 0.681 9.820 18025 Z= 0.351 Chirality : 0.041 0.209 2051 Planarity : 0.005 0.047 2212 Dihedral : 3.453 16.317 1743 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.14 % Allowed : 28.35 % Favored : 68.51 % 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: 2.83 (0.22), residues: 1575 helix: 2.61 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.18 (0.38), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 226 TYR 0.018 0.001 TYR D 217 PHE 0.020 0.001 PHE E 99 TRP 0.015 0.001 TRP F 62 HIS 0.003 0.000 HIS F 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 (13265) covalent geometry : angle 0.67878 / 0.35 (17976) SS BOND : bond 0.00215 / 0.16 ( 14) SS BOND : angle 0.44388 / 0.35 ( 28) hydrogen bonds : bond 0.03842 / 2.55 ( 925) hydrogen bonds : angle 3.50417 / 2.51 ( 2775) link_NAG-ASN : bond 0.00048 / 0.03 ( 7) link_NAG-ASN : angle 1.87766 / 1.42 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.61 seconds wall clock time: 53 minutes 51.38 seconds (3231.38 seconds total)