Starting phenix.real_space_refine on Thu Jul 31 01:52:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dse_30832/07_2025/7dse_30832.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dse_30832/07_2025/7dse_30832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dse_30832/07_2025/7dse_30832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dse_30832/07_2025/7dse_30832.map" model { file = "/net/cci-nas-00/data/ceres_data/7dse_30832/07_2025/7dse_30832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dse_30832/07_2025/7dse_30832.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 4.76, per 1000 atoms: 0.37 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 C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 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: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.14 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: 3.55 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3630 1.33 - 1.45: 2203 1.45 - 1.57: 7278 1.57 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 13265 Sorted by residual: bond pdb=" N ALA A 93 " pdb=" CA ALA A 93 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.10e-02 8.26e+03 6.55e+00 bond pdb=" N ALA C 93 " pdb=" CA ALA C 93 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.10e-02 8.26e+03 6.44e+00 bond pdb=" N ALA E 93 " pdb=" CA ALA E 93 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.10e-02 8.26e+03 6.30e+00 bond pdb=" N ALA D 93 " pdb=" CA ALA D 93 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.10e-02 8.26e+03 6.30e+00 bond pdb=" N ALA B 93 " pdb=" CA ALA B 93 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.10e-02 8.26e+03 6.14e+00 ... (remaining 13260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 17028 1.25 - 2.51: 778 2.51 - 3.76: 121 3.76 - 5.02: 14 5.02 - 6.27: 35 Bond angle restraints: 17976 Sorted by residual: angle pdb=" N LYS C 216 " pdb=" CA LYS C 216 " pdb=" C LYS C 216 " ideal model delta sigma weight residual 111.36 105.39 5.97 1.09e+00 8.42e-01 3.00e+01 angle pdb=" N LYS A 216 " pdb=" CA LYS A 216 " pdb=" C LYS A 216 " ideal model delta sigma weight residual 111.36 105.39 5.97 1.09e+00 8.42e-01 3.00e+01 angle pdb=" N LYS E 216 " pdb=" CA LYS E 216 " pdb=" C LYS E 216 " ideal model delta sigma weight residual 111.36 105.40 5.96 1.09e+00 8.42e-01 2.99e+01 angle pdb=" N LYS D 216 " pdb=" CA LYS D 216 " pdb=" C LYS D 216 " ideal model delta sigma weight residual 111.36 105.42 5.94 1.09e+00 8.42e-01 2.97e+01 angle pdb=" N LYS F 216 " pdb=" CA LYS F 216 " pdb=" C LYS F 216 " ideal model delta sigma weight residual 111.36 105.42 5.94 1.09e+00 8.42e-01 2.97e+01 ... (remaining 17971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.47: 7077 12.47 - 24.94: 631 24.94 - 37.40: 195 37.40 - 49.87: 77 49.87 - 62.34: 21 Dihedral angle restraints: 8001 sinusoidal: 3157 harmonic: 4844 Sorted by residual: dihedral pdb=" N LYS F 82 " pdb=" CA LYS F 82 " pdb=" CB LYS F 82 " pdb=" CG LYS F 82 " ideal model delta sinusoidal sigma weight residual -180.00 -126.30 -53.70 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" N LYS D 82 " pdb=" CA LYS D 82 " pdb=" CB LYS D 82 " pdb=" CG LYS D 82 " ideal model delta sinusoidal sigma weight residual -180.00 -126.31 -53.69 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LYS G 82 " pdb=" CA LYS G 82 " pdb=" CB LYS G 82 " pdb=" CG LYS G 82 " ideal model delta sinusoidal sigma weight residual -180.00 -126.31 -53.69 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 7998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1140 0.028 - 0.055: 586 0.055 - 0.082: 196 0.082 - 0.110: 90 0.110 - 0.137: 39 Chirality restraints: 2051 Sorted by residual: chirality pdb=" CA ALA C 93 " pdb=" N ALA C 93 " pdb=" C ALA C 93 " pdb=" CB ALA C 93 " both_signs ideal model delta sigma weight residual False 2.48 2.35 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ALA E 93 " pdb=" N ALA E 93 " pdb=" C ALA E 93 " pdb=" CB ALA E 93 " both_signs ideal model delta sigma weight residual False 2.48 2.35 0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ALA G 93 " pdb=" N ALA G 93 " pdb=" C ALA G 93 " pdb=" CB ALA G 93 " both_signs ideal model delta sigma weight residual False 2.48 2.35 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 2048 not shown) Planarity restraints: 2219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 215 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C THR F 215 " -0.055 2.00e-02 2.50e+03 pdb=" O THR F 215 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS F 216 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 215 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.98e+00 pdb=" C THR B 215 " -0.055 2.00e-02 2.50e+03 pdb=" O THR B 215 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS B 216 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 215 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.98e+00 pdb=" C THR G 215 " -0.055 2.00e-02 2.50e+03 pdb=" O THR G 215 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS G 216 " 0.018 2.00e-02 2.50e+03 ... (remaining 2216 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 3776 2.82 - 3.34: 13431 3.34 - 3.86: 20754 3.86 - 4.38: 22653 4.38 - 4.90: 38774 Nonbonded interactions: 99388 Sorted by model distance: nonbonded pdb=" O LEU G 118 " pdb=" OG SER G 182 " model vdw 2.295 3.040 nonbonded pdb=" O LEU E 118 " pdb=" OG SER E 182 " model vdw 2.296 3.040 nonbonded pdb=" O LEU C 118 " pdb=" OG SER C 182 " model vdw 2.296 3.040 nonbonded pdb=" O LEU F 118 " pdb=" OG SER F 182 " model vdw 2.296 3.040 nonbonded pdb=" O LEU D 118 " pdb=" OG SER D 182 " model vdw 2.296 3.040 ... (remaining 99383 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 1.460 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: 0.510 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 27.900 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13286 Z= 0.242 Angle : 0.658 6.275 18025 Z= 0.410 Chirality : 0.041 0.137 2051 Planarity : 0.004 0.034 2212 Dihedral : 11.843 62.341 4795 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.10 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP F 62 HIS 0.002 0.001 HIS A 220 PHE 0.008 0.001 PHE G 163 TYR 0.011 0.001 TYR F 34 ARG 0.001 0.000 ARG A 226 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 7) link_NAG-ASN : angle 3.54637 ( 21) hydrogen bonds : bond 0.14221 ( 925) hydrogen bonds : angle 4.83422 ( 2775) SS BOND : bond 0.00255 ( 14) SS BOND : angle 0.66592 ( 28) covalent geometry : bond 0.00493 (13265) covalent geometry : angle 0.64666 (17976) *********************** 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 : 1.604 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: A 47 TYR cc_start: 0.8983 (m-80) cc_final: 0.8725 (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: 0.7911 (tp40) REVERT: A 105 ARG cc_start: 0.8831 (tpt170) cc_final: 0.8573 (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: 0.8368 (t0) REVERT: B 177 TYR cc_start: 0.9136 (t80) cc_final: 0.8455 (t80) REVERT: B 227 LYS cc_start: 0.9559 (tttt) cc_final: 0.9251 (ttpt) REVERT: C 47 TYR cc_start: 0.8946 (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: 0.7950 (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: 0.9270 (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: 0.8933 (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: 0.8278 (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: 0.3199 time to fit residues: 311.4131 Evaluate side-chains 484 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 484 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.107832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.075896 restraints weight = 32888.816| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.87 r_work: 0.2888 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13286 Z= 0.186 Angle : 0.716 9.280 18025 Z= 0.366 Chirality : 0.040 0.127 2051 Planarity : 0.004 0.042 2212 Dihedral : 4.709 29.775 1890 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.81 % Allowed : 21.91 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.23), residues: 1575 helix: 1.79 (0.15), residues: 1225 sheet: None (None), residues: 0 loop : -1.57 (0.40), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 218 HIS 0.003 0.001 HIS E 220 PHE 0.017 0.002 PHE F 137 TYR 0.015 0.002 TYR C 142 ARG 0.009 0.001 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 7) link_NAG-ASN : angle 2.67517 ( 21) hydrogen bonds : bond 0.05210 ( 925) hydrogen bonds : angle 3.94844 ( 2775) SS BOND : bond 0.00420 ( 14) SS BOND : angle 0.76186 ( 28) covalent geometry : bond 0.00449 (13265) covalent geometry : angle 0.71019 (17976) *********************** 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: 51 poor density : 518 time to evaluate : 1.593 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 47 TYR cc_start: 0.9197 (m-80) cc_final: 0.8900 (m-80) REVERT: A 49 TYR cc_start: 0.9026 (t80) cc_final: 0.8825 (t80) REVERT: A 68 TYR cc_start: 0.8903 (m-80) cc_final: 0.8608 (t80) REVERT: A 71 ASN cc_start: 0.8610 (t0) cc_final: 0.8198 (t0) REVERT: A 96 ARG cc_start: 0.8336 (mtp180) cc_final: 0.7962 (mtt180) REVERT: A 104 GLN cc_start: 0.8980 (mt0) cc_final: 0.7841 (tp40) REVERT: A 105 ARG cc_start: 0.9365 (tpt170) cc_final: 0.9011 (mmm-85) REVERT: A 120 ASP cc_start: 0.8937 (t0) cc_final: 0.8632 (t0) REVERT: B 40 THR cc_start: 0.9739 (OUTLIER) cc_final: 0.9461 (p) REVERT: B 96 ARG cc_start: 0.8361 (mtp180) cc_final: 0.8013 (mtt180) REVERT: B 104 GLN cc_start: 0.9046 (mt0) cc_final: 0.7863 (tp40) REVERT: B 105 ARG cc_start: 0.9456 (tpt170) cc_final: 0.9204 (mmm-85) REVERT: B 120 ASP cc_start: 0.8981 (t70) cc_final: 0.8644 (t0) REVERT: B 122 LYS cc_start: 0.9437 (mmtp) cc_final: 0.9224 (mmmm) REVERT: B 152 LYS cc_start: 0.9611 (mttt) cc_final: 0.9352 (mppt) REVERT: B 179 ARG cc_start: 0.9280 (mmm-85) cc_final: 0.8886 (ttm-80) REVERT: B 233 CYS cc_start: 0.8599 (m) cc_final: 0.8297 (m) REVERT: C 26 MET cc_start: 0.7778 (mmp) cc_final: 0.7561 (mmp) REVERT: C 96 ARG cc_start: 0.8388 (mtp180) cc_final: 0.7986 (mtt180) REVERT: C 104 GLN cc_start: 0.9076 (mt0) cc_final: 0.7961 (tp40) REVERT: C 120 ASP cc_start: 0.9030 (t70) cc_final: 0.8773 (t0) REVERT: C 142 TYR cc_start: 0.7924 (m-80) cc_final: 0.7667 (m-80) REVERT: C 225 GLU cc_start: 0.9351 (tt0) cc_final: 0.9066 (pt0) REVERT: C 226 ARG cc_start: 0.8398 (mmp-170) cc_final: 0.7854 (mmp-170) REVERT: C 233 CYS cc_start: 0.8826 (m) cc_final: 0.8560 (m) REVERT: D 47 TYR cc_start: 0.9227 (m-80) cc_final: 0.8846 (m-80) REVERT: D 68 TYR cc_start: 0.8844 (m-80) cc_final: 0.8450 (t80) REVERT: D 71 ASN cc_start: 0.8905 (t0) cc_final: 0.8323 (t0) REVERT: D 96 ARG cc_start: 0.8442 (mtp180) cc_final: 0.8197 (mtt180) REVERT: D 104 GLN cc_start: 0.9008 (mt0) cc_final: 0.7849 (tp40) REVERT: D 105 ARG cc_start: 0.9457 (tpt170) cc_final: 0.9162 (mmm-85) REVERT: D 120 ASP cc_start: 0.9003 (t0) cc_final: 0.8660 (t0) REVERT: E 47 TYR cc_start: 0.9208 (m-80) cc_final: 0.8892 (m-80) REVERT: E 68 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8574 (t80) REVERT: E 71 ASN cc_start: 0.8751 (t0) cc_final: 0.8365 (t0) REVERT: E 96 ARG cc_start: 0.8363 (mtp180) cc_final: 0.8114 (mtt180) REVERT: E 102 MET cc_start: 0.9471 (ttm) cc_final: 0.9195 (ttm) REVERT: E 104 GLN cc_start: 0.9006 (mt0) cc_final: 0.7895 (tp40) REVERT: E 120 ASP cc_start: 0.8927 (t0) cc_final: 0.8537 (t0) REVERT: E 152 LYS cc_start: 0.9559 (mttt) cc_final: 0.9277 (mppt) REVERT: E 216 LYS cc_start: 0.9531 (mmmm) cc_final: 0.9209 (mmmm) REVERT: E 225 GLU cc_start: 0.9270 (tt0) cc_final: 0.9053 (pt0) REVERT: E 226 ARG cc_start: 0.8749 (mmp-170) cc_final: 0.8256 (mmp-170) REVERT: E 246 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8680 (mp10) REVERT: E 247 GLN cc_start: 0.9032 (mp10) cc_final: 0.8822 (pm20) REVERT: F 96 ARG cc_start: 0.8374 (mtp180) cc_final: 0.7982 (mtt90) REVERT: F 104 GLN cc_start: 0.9043 (mt0) cc_final: 0.7969 (tp40) REVERT: F 105 ARG cc_start: 0.9378 (tpt170) cc_final: 0.9056 (mmm-85) REVERT: F 179 ARG cc_start: 0.9251 (mmm-85) cc_final: 0.8799 (mtp85) REVERT: F 201 ARG cc_start: 0.8934 (tpp80) cc_final: 0.8672 (tpp80) REVERT: F 216 LYS cc_start: 0.9340 (mmmm) cc_final: 0.9117 (mmtp) REVERT: G 40 THR cc_start: 0.9717 (OUTLIER) cc_final: 0.9434 (p) REVERT: G 71 ASN cc_start: 0.8582 (t0) cc_final: 0.8290 (t0) REVERT: G 95 LEU cc_start: 0.9360 (mt) cc_final: 0.9132 (pt) REVERT: G 96 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7587 (mtt180) REVERT: G 104 GLN cc_start: 0.8933 (mt0) cc_final: 0.7695 (tp40) REVERT: G 105 ARG cc_start: 0.9405 (tpt170) cc_final: 0.9123 (mmm-85) REVERT: G 120 ASP cc_start: 0.8984 (t0) cc_final: 0.8647 (t0) REVERT: G 148 LYS cc_start: 0.9617 (mmmt) cc_final: 0.9361 (mmmt) REVERT: G 152 LYS cc_start: 0.9587 (mttt) cc_final: 0.9303 (mppt) REVERT: G 246 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8490 (mp10) outliers start: 51 outliers final: 33 residues processed: 539 average time/residue: 0.3136 time to fit residues: 226.9216 Evaluate side-chains 488 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 452 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE 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 40 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain C residue 57 ILE 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 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain 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 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 57 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 203 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.109124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.076017 restraints weight = 32005.335| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.86 r_work: 0.2904 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13286 Z= 0.158 Angle : 0.670 9.077 18025 Z= 0.336 Chirality : 0.038 0.127 2051 Planarity : 0.004 0.052 2212 Dihedral : 4.247 23.534 1890 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 3.74 % Allowed : 24.46 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.23), residues: 1575 helix: 2.10 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -1.98 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 218 HIS 0.001 0.000 HIS A 236 PHE 0.015 0.001 PHE G 229 TYR 0.019 0.002 TYR G 47 ARG 0.007 0.001 ARG A 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 7) link_NAG-ASN : angle 2.62436 ( 21) hydrogen bonds : bond 0.04732 ( 925) hydrogen bonds : angle 3.74614 ( 2775) SS BOND : bond 0.00287 ( 14) SS BOND : angle 0.53627 ( 28) covalent geometry : bond 0.00382 (13265) covalent geometry : angle 0.66453 (17976) *********************** 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 531 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 481 time to evaluate : 1.609 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 26 MET cc_start: 0.7987 (mmp) cc_final: 0.7763 (mmp) REVERT: A 47 TYR cc_start: 0.9166 (m-80) cc_final: 0.8850 (m-80) REVERT: A 68 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8591 (t80) REVERT: A 71 ASN cc_start: 0.8597 (t0) cc_final: 0.8144 (t0) REVERT: A 96 ARG cc_start: 0.8346 (mtp180) cc_final: 0.7941 (mtt180) REVERT: A 104 GLN cc_start: 0.8985 (mt0) cc_final: 0.7865 (tp40) REVERT: A 105 ARG cc_start: 0.9414 (tpt170) cc_final: 0.9110 (mmm-85) REVERT: A 120 ASP cc_start: 0.8897 (t0) cc_final: 0.8615 (t0) REVERT: A 247 GLN cc_start: 0.8749 (pm20) cc_final: 0.8546 (pm20) REVERT: B 40 THR cc_start: 0.9747 (OUTLIER) cc_final: 0.9542 (p) REVERT: B 96 ARG cc_start: 0.8400 (mtp180) cc_final: 0.8004 (mtt180) REVERT: B 104 GLN cc_start: 0.9063 (mt0) cc_final: 0.7898 (tp40) REVERT: B 105 ARG cc_start: 0.9460 (tpt170) cc_final: 0.9198 (mmm-85) REVERT: B 152 LYS cc_start: 0.9603 (mttt) cc_final: 0.9359 (mppt) REVERT: B 209 GLN cc_start: 0.9153 (pm20) cc_final: 0.8922 (pm20) REVERT: B 233 CYS cc_start: 0.8726 (m) cc_final: 0.8325 (m) REVERT: C 32 GLN cc_start: 0.9265 (tp40) cc_final: 0.9010 (tp40) REVERT: C 71 ASN cc_start: 0.8639 (t0) cc_final: 0.8411 (t0) REVERT: C 96 ARG cc_start: 0.8437 (mtp180) cc_final: 0.8003 (mtt180) REVERT: C 104 GLN cc_start: 0.9088 (mt0) cc_final: 0.7924 (tp40) REVERT: C 152 LYS cc_start: 0.9618 (mttt) cc_final: 0.9313 (mppt) REVERT: C 201 ARG cc_start: 0.8714 (tpp80) cc_final: 0.8446 (tpt-90) REVERT: C 214 LYS cc_start: 0.9779 (mmtp) cc_final: 0.9565 (mmtt) REVERT: C 216 LYS cc_start: 0.9520 (mmmm) cc_final: 0.9116 (mmtp) REVERT: C 226 ARG cc_start: 0.8558 (mmp-170) cc_final: 0.8331 (mmp80) REVERT: C 233 CYS cc_start: 0.8882 (m) cc_final: 0.8648 (m) REVERT: D 47 TYR cc_start: 0.9204 (m-80) cc_final: 0.8805 (m-80) REVERT: D 68 TYR cc_start: 0.8851 (m-80) cc_final: 0.8409 (t80) REVERT: D 71 ASN cc_start: 0.8903 (t0) cc_final: 0.8481 (t0) REVERT: D 96 ARG cc_start: 0.8470 (mtp180) cc_final: 0.8124 (mtt180) REVERT: D 104 GLN cc_start: 0.8943 (mt0) cc_final: 0.7881 (tp40) REVERT: D 105 ARG cc_start: 0.9485 (tpt170) cc_final: 0.9067 (mmm-85) REVERT: D 108 ILE cc_start: 0.9435 (mm) cc_final: 0.9198 (mp) REVERT: D 120 ASP cc_start: 0.8959 (t0) cc_final: 0.8486 (t0) REVERT: D 209 GLN cc_start: 0.9071 (pm20) cc_final: 0.8864 (pm20) REVERT: D 246 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8586 (pp30) REVERT: E 32 GLN cc_start: 0.9253 (mt0) cc_final: 0.8887 (tt0) REVERT: E 47 TYR cc_start: 0.9190 (m-80) cc_final: 0.8860 (m-80) REVERT: E 71 ASN cc_start: 0.8635 (t0) cc_final: 0.8160 (t0) REVERT: E 96 ARG cc_start: 0.8411 (mtp180) cc_final: 0.8090 (mtt180) REVERT: E 104 GLN cc_start: 0.9018 (mt0) cc_final: 0.7964 (tp40) REVERT: E 120 ASP cc_start: 0.8895 (t0) cc_final: 0.8392 (t0) REVERT: E 148 LYS cc_start: 0.9633 (mmmt) cc_final: 0.9370 (mmmt) REVERT: E 152 LYS cc_start: 0.9580 (mttt) cc_final: 0.9251 (mppt) REVERT: E 214 LYS cc_start: 0.9750 (mmtp) cc_final: 0.9531 (mmtt) REVERT: E 216 LYS cc_start: 0.9548 (mmmm) cc_final: 0.9209 (mmmm) REVERT: E 226 ARG cc_start: 0.8823 (mmp-170) cc_final: 0.8298 (mmp80) REVERT: F 71 ASN cc_start: 0.8758 (t0) cc_final: 0.8546 (t0) REVERT: F 96 ARG cc_start: 0.8399 (mtp180) cc_final: 0.7939 (mtt90) REVERT: F 104 GLN cc_start: 0.9032 (mt0) cc_final: 0.7974 (tp40) REVERT: F 105 ARG cc_start: 0.9399 (tpt170) cc_final: 0.9084 (mmm-85) REVERT: F 179 ARG cc_start: 0.9203 (mmm-85) cc_final: 0.8932 (mtp85) REVERT: F 201 ARG cc_start: 0.8950 (tpp80) cc_final: 0.8688 (tpp80) REVERT: G 40 THR cc_start: 0.9736 (OUTLIER) cc_final: 0.9470 (p) REVERT: G 71 ASN cc_start: 0.8572 (t0) cc_final: 0.8291 (t0) REVERT: G 96 ARG cc_start: 0.8013 (mtp180) cc_final: 0.7582 (mtt180) REVERT: G 104 GLN cc_start: 0.8921 (mt0) cc_final: 0.7674 (tp40) REVERT: G 105 ARG cc_start: 0.9412 (tpt170) cc_final: 0.9049 (mmm-85) REVERT: G 119 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8943 (mmm) REVERT: G 120 ASP cc_start: 0.8895 (t0) cc_final: 0.8517 (t0) REVERT: G 148 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9378 (mmmt) REVERT: G 152 LYS cc_start: 0.9607 (mttt) cc_final: 0.9301 (mppt) REVERT: G 160 LYS cc_start: 0.9536 (ttmm) cc_final: 0.9237 (ttmm) REVERT: G 246 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8635 (mp10) outliers start: 50 outliers final: 34 residues processed: 504 average time/residue: 0.2930 time to fit residues: 200.3335 Evaluate side-chains 480 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 442 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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 40 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 143 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.110136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077032 restraints weight = 31541.162| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.84 r_work: 0.2932 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13286 Z= 0.137 Angle : 0.639 8.876 18025 Z= 0.323 Chirality : 0.038 0.122 2051 Planarity : 0.005 0.052 2212 Dihedral : 3.872 17.465 1890 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.96 % Allowed : 25.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.22), residues: 1575 helix: 2.22 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -1.68 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 62 HIS 0.002 0.000 HIS E 236 PHE 0.013 0.001 PHE F 137 TYR 0.015 0.001 TYR D 217 ARG 0.006 0.001 ARG G 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 7) link_NAG-ASN : angle 2.30750 ( 21) hydrogen bonds : bond 0.04312 ( 925) hydrogen bonds : angle 3.58530 ( 2775) SS BOND : bond 0.00236 ( 14) SS BOND : angle 0.43652 ( 28) covalent geometry : bond 0.00324 (13265) covalent geometry : angle 0.63432 (17976) *********************** 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 523 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 470 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8615 (t80) REVERT: A 71 ASN cc_start: 0.8607 (t0) cc_final: 0.8127 (t0) REVERT: A 96 ARG cc_start: 0.8373 (mtp180) cc_final: 0.7976 (mtt180) REVERT: A 104 GLN cc_start: 0.8953 (mt0) cc_final: 0.7728 (tp40) REVERT: A 105 ARG cc_start: 0.9404 (tpt170) cc_final: 0.9063 (mmm-85) REVERT: A 120 ASP cc_start: 0.8874 (t0) cc_final: 0.8533 (t0) REVERT: A 233 CYS cc_start: 0.8835 (m) cc_final: 0.8509 (m) REVERT: B 32 GLN cc_start: 0.9329 (tt0) cc_final: 0.9091 (tt0) REVERT: B 96 ARG cc_start: 0.8395 (mtp180) cc_final: 0.7997 (mtt180) REVERT: B 104 GLN cc_start: 0.9043 (mt0) cc_final: 0.7889 (tp40) REVERT: B 105 ARG cc_start: 0.9453 (tpt170) cc_final: 0.9175 (mmm-85) REVERT: B 120 ASP cc_start: 0.8880 (t0) cc_final: 0.8680 (t0) REVERT: B 152 LYS cc_start: 0.9618 (mttt) cc_final: 0.9396 (mttt) REVERT: B 209 GLN cc_start: 0.9161 (pm20) cc_final: 0.8941 (pm20) REVERT: B 220 HIS cc_start: 0.8727 (m90) cc_final: 0.8121 (m90) REVERT: B 233 CYS cc_start: 0.8802 (m) cc_final: 0.8554 (m) REVERT: C 26 MET cc_start: 0.7900 (mmp) cc_final: 0.7690 (mmp) REVERT: C 32 GLN cc_start: 0.9249 (tp40) cc_final: 0.9025 (tp40) REVERT: C 71 ASN cc_start: 0.8650 (t0) cc_final: 0.8233 (t0) REVERT: C 96 ARG cc_start: 0.8412 (mtp180) cc_final: 0.7972 (mtt180) REVERT: C 104 GLN cc_start: 0.9040 (mt0) cc_final: 0.8052 (tp40) REVERT: C 152 LYS cc_start: 0.9613 (mttt) cc_final: 0.9360 (mttt) REVERT: C 216 LYS cc_start: 0.9535 (mmmm) cc_final: 0.9121 (mmtp) REVERT: C 226 ARG cc_start: 0.8686 (mmp-170) cc_final: 0.8352 (mmp80) REVERT: C 233 CYS cc_start: 0.8930 (m) cc_final: 0.8679 (m) REVERT: D 47 TYR cc_start: 0.9198 (m-80) cc_final: 0.8793 (m-80) REVERT: D 68 TYR cc_start: 0.8855 (m-80) cc_final: 0.8500 (t80) REVERT: D 71 ASN cc_start: 0.8801 (t0) cc_final: 0.8282 (t0) REVERT: D 96 ARG cc_start: 0.8441 (mtp180) cc_final: 0.8107 (mtt180) REVERT: D 104 GLN cc_start: 0.8909 (mt0) cc_final: 0.7792 (tp40) REVERT: D 105 ARG cc_start: 0.9475 (tpt170) cc_final: 0.9230 (mmm-85) REVERT: D 120 ASP cc_start: 0.8880 (t0) cc_final: 0.8341 (t0) REVERT: D 209 GLN cc_start: 0.9075 (pm20) cc_final: 0.8847 (pm20) REVERT: D 246 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8561 (pp30) REVERT: E 47 TYR cc_start: 0.9183 (m-80) cc_final: 0.8852 (m-80) REVERT: E 71 ASN cc_start: 0.8702 (t0) cc_final: 0.8295 (t0) REVERT: E 96 ARG cc_start: 0.8437 (mtp180) cc_final: 0.8089 (mtt180) REVERT: E 104 GLN cc_start: 0.8979 (mt0) cc_final: 0.7942 (tp40) REVERT: E 119 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8733 (mmm) REVERT: E 120 ASP cc_start: 0.8880 (t0) cc_final: 0.8317 (t0) REVERT: E 152 LYS cc_start: 0.9599 (mttt) cc_final: 0.9321 (mttt) REVERT: E 226 ARG cc_start: 0.8861 (mmp-170) cc_final: 0.8312 (mmp80) REVERT: E 233 CYS cc_start: 0.8812 (m) cc_final: 0.8596 (m) REVERT: F 32 GLN cc_start: 0.9333 (tp40) cc_final: 0.9029 (tt0) REVERT: F 40 THR cc_start: 0.9783 (OUTLIER) cc_final: 0.9551 (p) REVERT: F 71 ASN cc_start: 0.8676 (t0) cc_final: 0.8354 (t0) REVERT: F 96 ARG cc_start: 0.8333 (mtp180) cc_final: 0.7933 (mtt180) REVERT: F 104 GLN cc_start: 0.8936 (mt0) cc_final: 0.7813 (tp40) REVERT: F 105 ARG cc_start: 0.9400 (tpt170) cc_final: 0.9088 (mmm-85) REVERT: F 179 ARG cc_start: 0.9207 (mmm-85) cc_final: 0.8941 (mtp85) REVERT: F 201 ARG cc_start: 0.8905 (tpp80) cc_final: 0.8667 (tpp80) REVERT: F 233 CYS cc_start: 0.8862 (m) cc_final: 0.8638 (m) REVERT: G 32 GLN cc_start: 0.9377 (tt0) cc_final: 0.9176 (pt0) REVERT: G 40 THR cc_start: 0.9735 (OUTLIER) cc_final: 0.9476 (p) REVERT: G 71 ASN cc_start: 0.8529 (t0) cc_final: 0.8167 (t0) REVERT: G 96 ARG cc_start: 0.8082 (mtp180) cc_final: 0.7677 (mtt180) REVERT: G 104 GLN cc_start: 0.8919 (mt0) cc_final: 0.7646 (tp40) REVERT: G 105 ARG cc_start: 0.9418 (tpt170) cc_final: 0.9118 (mmm-85) REVERT: G 119 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8929 (mmm) REVERT: G 120 ASP cc_start: 0.8843 (t0) cc_final: 0.8379 (t0) REVERT: G 148 LYS cc_start: 0.9671 (mmmt) cc_final: 0.9388 (mmmt) REVERT: G 152 LYS cc_start: 0.9606 (mttt) cc_final: 0.9290 (mppt) REVERT: G 201 ARG cc_start: 0.8738 (tpp80) cc_final: 0.8500 (tpp80) REVERT: G 233 CYS cc_start: 0.8619 (m) cc_final: 0.8296 (m) REVERT: G 246 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8770 (mp10) outliers start: 53 outliers final: 30 residues processed: 496 average time/residue: 0.2870 time to fit residues: 199.5427 Evaluate side-chains 491 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 456 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 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 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE 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 122 LYS 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 160 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 118 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.111001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.078148 restraints weight = 31939.631| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.85 r_work: 0.2943 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13286 Z= 0.127 Angle : 0.617 8.105 18025 Z= 0.314 Chirality : 0.039 0.177 2051 Planarity : 0.004 0.047 2212 Dihedral : 3.645 17.074 1890 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.14 % Allowed : 26.10 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.22), residues: 1575 helix: 2.36 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -1.47 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 62 HIS 0.002 0.000 HIS E 236 PHE 0.010 0.001 PHE F 137 TYR 0.018 0.001 TYR F 217 ARG 0.006 0.001 ARG A 226 Details of bonding type rmsd link_NAG-ASN : bond 0.00035 ( 7) link_NAG-ASN : angle 2.12233 ( 21) hydrogen bonds : bond 0.03969 ( 925) hydrogen bonds : angle 3.47476 ( 2775) SS BOND : bond 0.00212 ( 14) SS BOND : angle 0.40748 ( 28) covalent geometry : bond 0.00295 (13265) covalent geometry : angle 0.61379 (17976) *********************** 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 507 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 465 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8607 (t80) REVERT: A 71 ASN cc_start: 0.8602 (t0) cc_final: 0.8097 (t0) REVERT: A 96 ARG cc_start: 0.8351 (mtp180) cc_final: 0.8068 (mtt180) REVERT: A 105 ARG cc_start: 0.9402 (tpt170) cc_final: 0.9102 (mmm-85) REVERT: A 120 ASP cc_start: 0.8832 (t0) cc_final: 0.8448 (t0) REVERT: A 233 CYS cc_start: 0.8888 (m) cc_final: 0.8561 (m) REVERT: B 32 GLN cc_start: 0.9336 (tt0) cc_final: 0.9103 (tt0) REVERT: B 71 ASN cc_start: 0.8834 (t0) cc_final: 0.8618 (t0) REVERT: B 96 ARG cc_start: 0.8356 (mtp180) cc_final: 0.8040 (mtp180) REVERT: B 104 GLN cc_start: 0.8996 (mt0) cc_final: 0.7829 (tp40) REVERT: B 105 ARG cc_start: 0.9455 (tpt170) cc_final: 0.9173 (mmm-85) REVERT: B 120 ASP cc_start: 0.8823 (t0) cc_final: 0.8527 (t0) REVERT: B 152 LYS cc_start: 0.9623 (mttt) cc_final: 0.9365 (mppt) REVERT: B 209 GLN cc_start: 0.9166 (pm20) cc_final: 0.8942 (pm20) REVERT: B 216 LYS cc_start: 0.9559 (mmmm) cc_final: 0.9173 (mmtp) REVERT: B 220 HIS cc_start: 0.8712 (m90) cc_final: 0.8228 (m90) REVERT: B 233 CYS cc_start: 0.8769 (m) cc_final: 0.8523 (m) REVERT: C 26 MET cc_start: 0.7940 (mmp) cc_final: 0.7708 (mmp) REVERT: C 32 GLN cc_start: 0.9245 (tp40) cc_final: 0.9035 (tp40) REVERT: C 71 ASN cc_start: 0.8732 (t0) cc_final: 0.8306 (t0) REVERT: C 96 ARG cc_start: 0.8359 (mtp180) cc_final: 0.7927 (mtt180) REVERT: C 152 LYS cc_start: 0.9637 (mttt) cc_final: 0.9369 (mttt) REVERT: C 226 ARG cc_start: 0.8739 (mmp-170) cc_final: 0.8388 (mmp80) REVERT: C 233 CYS cc_start: 0.8915 (m) cc_final: 0.8656 (m) REVERT: D 47 TYR cc_start: 0.9180 (m-80) cc_final: 0.8775 (m-80) REVERT: D 68 TYR cc_start: 0.8839 (m-80) cc_final: 0.8555 (t80) REVERT: D 71 ASN cc_start: 0.8809 (t0) cc_final: 0.8340 (t0) REVERT: D 83 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7119 (ttt180) REVERT: D 96 ARG cc_start: 0.8349 (mtp180) cc_final: 0.8010 (mtp180) REVERT: D 104 GLN cc_start: 0.8894 (mt0) cc_final: 0.7898 (tp40) REVERT: D 105 ARG cc_start: 0.9461 (tpt170) cc_final: 0.9098 (mmm-85) REVERT: D 108 ILE cc_start: 0.9404 (mm) cc_final: 0.9193 (mp) REVERT: D 120 ASP cc_start: 0.8838 (t0) cc_final: 0.8265 (t0) REVERT: D 209 GLN cc_start: 0.9083 (pm20) cc_final: 0.8840 (pm20) REVERT: E 47 TYR cc_start: 0.9174 (m-80) cc_final: 0.8814 (m-80) REVERT: E 71 ASN cc_start: 0.8564 (t0) cc_final: 0.8123 (t0) REVERT: E 96 ARG cc_start: 0.8435 (mtp180) cc_final: 0.8028 (mtt180) REVERT: E 104 GLN cc_start: 0.8966 (mt0) cc_final: 0.7884 (tp40) REVERT: E 119 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8654 (mmm) REVERT: E 120 ASP cc_start: 0.8867 (t0) cc_final: 0.8343 (t0) REVERT: E 152 LYS cc_start: 0.9611 (mttt) cc_final: 0.9344 (mttt) REVERT: E 226 ARG cc_start: 0.8880 (mmp-170) cc_final: 0.8359 (mmp80) REVERT: E 233 CYS cc_start: 0.8872 (m) cc_final: 0.8655 (m) REVERT: F 40 THR cc_start: 0.9776 (OUTLIER) cc_final: 0.9567 (p) REVERT: F 71 ASN cc_start: 0.8808 (t0) cc_final: 0.8487 (t0) REVERT: F 96 ARG cc_start: 0.8387 (mtp180) cc_final: 0.8007 (mtp180) REVERT: F 104 GLN cc_start: 0.8914 (mt0) cc_final: 0.7806 (tp40) REVERT: F 105 ARG cc_start: 0.9392 (tpt170) cc_final: 0.9075 (mmm-85) REVERT: F 179 ARG cc_start: 0.9109 (mmm-85) cc_final: 0.8894 (mtp85) REVERT: F 233 CYS cc_start: 0.8931 (m) cc_final: 0.8710 (m) REVERT: G 32 GLN cc_start: 0.9403 (tt0) cc_final: 0.9181 (pt0) REVERT: G 71 ASN cc_start: 0.8437 (t0) cc_final: 0.8148 (t0) REVERT: G 96 ARG cc_start: 0.8103 (mtp180) cc_final: 0.7754 (mtt180) REVERT: G 105 ARG cc_start: 0.9412 (tpt170) cc_final: 0.9109 (mmm-85) REVERT: G 120 ASP cc_start: 0.8852 (t0) cc_final: 0.8432 (t0) REVERT: G 148 LYS cc_start: 0.9670 (mmmt) cc_final: 0.9458 (mmmt) REVERT: G 152 LYS cc_start: 0.9596 (mttt) cc_final: 0.9286 (mppt) REVERT: G 201 ARG cc_start: 0.8735 (tpp80) cc_final: 0.8477 (tpp80) REVERT: G 233 CYS cc_start: 0.8648 (m) cc_final: 0.8379 (m) outliers start: 42 outliers final: 30 residues processed: 479 average time/residue: 0.2793 time to fit residues: 187.0508 Evaluate side-chains 494 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 460 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 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 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 83 ARG Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE 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 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 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 133 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.0270 chunk 11 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.111753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079017 restraints weight = 32259.389| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.90 r_work: 0.2990 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13286 Z= 0.125 Angle : 0.608 6.757 18025 Z= 0.311 Chirality : 0.039 0.178 2051 Planarity : 0.004 0.051 2212 Dihedral : 3.468 16.520 1890 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.37 % Allowed : 25.80 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.22), residues: 1575 helix: 2.46 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.32 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 62 HIS 0.001 0.000 HIS C 236 PHE 0.008 0.001 PHE B 124 TYR 0.015 0.001 TYR D 217 ARG 0.007 0.001 ARG D 179 Details of bonding type rmsd link_NAG-ASN : bond 0.00096 ( 7) link_NAG-ASN : angle 1.95562 ( 21) hydrogen bonds : bond 0.03764 ( 925) hydrogen bonds : angle 3.40944 ( 2775) SS BOND : bond 0.00204 ( 14) SS BOND : angle 0.42618 ( 28) covalent geometry : bond 0.00295 (13265) covalent geometry : angle 0.60513 (17976) *********************** 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 523 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 478 time to evaluate : 1.420 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: A 68 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8562 (t80) REVERT: A 71 ASN cc_start: 0.8503 (t0) cc_final: 0.7922 (t0) REVERT: A 96 ARG cc_start: 0.8377 (mtp180) cc_final: 0.8086 (mtt180) REVERT: A 105 ARG cc_start: 0.9412 (tpt170) cc_final: 0.9126 (mmm-85) REVERT: A 120 ASP cc_start: 0.8829 (t0) cc_final: 0.8449 (t0) REVERT: A 233 CYS cc_start: 0.8860 (m) cc_final: 0.8508 (m) REVERT: B 71 ASN cc_start: 0.8822 (t0) cc_final: 0.8503 (t0) REVERT: B 96 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7958 (mtp180) REVERT: B 104 GLN cc_start: 0.9017 (mt0) cc_final: 0.7742 (tp40) REVERT: B 105 ARG cc_start: 0.9482 (tpt170) cc_final: 0.9183 (mmm-85) REVERT: B 120 ASP cc_start: 0.8833 (t0) cc_final: 0.8539 (t0) REVERT: B 152 LYS cc_start: 0.9617 (mttt) cc_final: 0.9364 (mttt) REVERT: B 220 HIS cc_start: 0.8747 (m90) cc_final: 0.8309 (m-70) REVERT: B 233 CYS cc_start: 0.8790 (m) cc_final: 0.8551 (m) REVERT: C 71 ASN cc_start: 0.8692 (t0) cc_final: 0.8243 (t0) REVERT: C 96 ARG cc_start: 0.8342 (mtp180) cc_final: 0.7893 (mtt180) REVERT: C 152 LYS cc_start: 0.9637 (mttt) cc_final: 0.9338 (mttt) REVERT: C 226 ARG cc_start: 0.8803 (mmp-170) cc_final: 0.8253 (mmp80) REVERT: C 233 CYS cc_start: 0.8867 (m) cc_final: 0.8618 (m) REVERT: D 68 TYR cc_start: 0.8815 (m-80) cc_final: 0.8535 (t80) REVERT: D 71 ASN cc_start: 0.8839 (t0) cc_final: 0.8341 (t0) REVERT: D 96 ARG cc_start: 0.8324 (mtp180) cc_final: 0.7961 (mtp180) REVERT: D 104 GLN cc_start: 0.8893 (mt0) cc_final: 0.7862 (tp40) REVERT: D 105 ARG cc_start: 0.9436 (tpt170) cc_final: 0.9053 (mmm-85) REVERT: D 108 ILE cc_start: 0.9397 (mm) cc_final: 0.9179 (mp) REVERT: D 120 ASP cc_start: 0.8805 (t0) cc_final: 0.8243 (t0) REVERT: D 147 GLN cc_start: 0.9120 (pm20) cc_final: 0.8854 (tp-100) REVERT: E 32 GLN cc_start: 0.9288 (mt0) cc_final: 0.8939 (tt0) REVERT: E 47 TYR cc_start: 0.9143 (m-80) cc_final: 0.8766 (m-80) REVERT: E 71 ASN cc_start: 0.8749 (t0) cc_final: 0.8342 (t0) REVERT: E 96 ARG cc_start: 0.8400 (mtp180) cc_final: 0.7968 (mtt180) REVERT: E 104 GLN cc_start: 0.8960 (mt0) cc_final: 0.7850 (tm-30) REVERT: E 112 VAL cc_start: 0.9634 (t) cc_final: 0.9370 (p) REVERT: E 119 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8645 (mmm) REVERT: E 120 ASP cc_start: 0.8800 (t0) cc_final: 0.8148 (t0) REVERT: E 152 LYS cc_start: 0.9604 (mttt) cc_final: 0.9300 (mttt) REVERT: E 226 ARG cc_start: 0.8873 (mmp-170) cc_final: 0.8370 (mmp80) REVERT: E 233 CYS cc_start: 0.8882 (m) cc_final: 0.8652 (m) REVERT: F 40 THR cc_start: 0.9768 (OUTLIER) cc_final: 0.9560 (p) REVERT: F 71 ASN cc_start: 0.8739 (t0) cc_final: 0.8397 (t0) REVERT: F 96 ARG cc_start: 0.8384 (mtp180) cc_final: 0.7974 (mtp180) REVERT: F 105 ARG cc_start: 0.9389 (tpt170) cc_final: 0.9084 (mmm-85) REVERT: F 216 LYS cc_start: 0.9448 (mmmm) cc_final: 0.8988 (mmtp) REVERT: F 233 CYS cc_start: 0.8914 (m) cc_final: 0.8688 (m) REVERT: G 32 GLN cc_start: 0.9371 (tt0) cc_final: 0.9122 (pt0) REVERT: G 71 ASN cc_start: 0.8384 (t0) cc_final: 0.8087 (t0) REVERT: G 96 ARG cc_start: 0.8066 (mtp180) cc_final: 0.7689 (mtt180) REVERT: G 105 ARG cc_start: 0.9398 (tpt170) cc_final: 0.9080 (mmm-85) REVERT: G 119 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8832 (mmm) REVERT: G 120 ASP cc_start: 0.8822 (t0) cc_final: 0.8352 (t0) REVERT: G 148 LYS cc_start: 0.9668 (mmmt) cc_final: 0.9442 (mmmt) REVERT: G 152 LYS cc_start: 0.9602 (mttt) cc_final: 0.9283 (mppt) REVERT: G 201 ARG cc_start: 0.8718 (tpp80) cc_final: 0.8492 (tpp80) REVERT: G 233 CYS cc_start: 0.8688 (m) cc_final: 0.8419 (m) outliers start: 45 outliers final: 34 residues processed: 496 average time/residue: 0.2840 time to fit residues: 195.7289 Evaluate side-chains 495 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 457 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 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 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 74 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 119 MET 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 131 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 61 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.110574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.077500 restraints weight = 32237.808| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.83 r_work: 0.2935 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.6011 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= 0.146 Angle : 0.634 7.007 18025 Z= 0.327 Chirality : 0.040 0.172 2051 Planarity : 0.005 0.049 2212 Dihedral : 3.473 16.479 1890 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.44 % Allowed : 27.82 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.22), residues: 1575 helix: 2.48 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.19 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 62 HIS 0.001 0.000 HIS D 236 PHE 0.023 0.001 PHE G 229 TYR 0.018 0.001 TYR D 97 ARG 0.011 0.001 ARG A 226 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 7) link_NAG-ASN : angle 2.01822 ( 21) hydrogen bonds : bond 0.03904 ( 925) hydrogen bonds : angle 3.52831 ( 2775) SS BOND : bond 0.00244 ( 14) SS BOND : angle 0.48299 ( 28) covalent geometry : bond 0.00355 (13265) covalent geometry : angle 0.63094 (17976) *********************** 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 511 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 465 time to evaluate : 1.366 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 32 GLN cc_start: 0.9190 (tp40) cc_final: 0.8873 (pp30) REVERT: A 71 ASN cc_start: 0.8550 (t0) cc_final: 0.8011 (t0) REVERT: A 96 ARG cc_start: 0.8416 (mtp180) cc_final: 0.8127 (mtt180) REVERT: A 104 GLN cc_start: 0.8949 (mt0) cc_final: 0.7731 (tp40) REVERT: A 105 ARG cc_start: 0.9420 (tpt170) cc_final: 0.9088 (mmm-85) REVERT: A 120 ASP cc_start: 0.8914 (t0) cc_final: 0.8515 (t0) REVERT: A 233 CYS cc_start: 0.8893 (m) cc_final: 0.8542 (m) REVERT: B 71 ASN cc_start: 0.8853 (t0) cc_final: 0.8440 (t0) REVERT: B 96 ARG cc_start: 0.8393 (mtp180) cc_final: 0.8003 (mtp180) REVERT: B 104 GLN cc_start: 0.9039 (mt0) cc_final: 0.8027 (tp40) REVERT: B 105 ARG cc_start: 0.9493 (tpt170) cc_final: 0.9256 (mmm-85) REVERT: B 120 ASP cc_start: 0.8886 (t0) cc_final: 0.8560 (t0) REVERT: B 152 LYS cc_start: 0.9626 (mttt) cc_final: 0.9398 (mttt) REVERT: B 220 HIS cc_start: 0.8703 (m90) cc_final: 0.8268 (m-70) REVERT: B 233 CYS cc_start: 0.8732 (m) cc_final: 0.8489 (m) REVERT: C 71 ASN cc_start: 0.8642 (t0) cc_final: 0.8176 (t0) REVERT: C 96 ARG cc_start: 0.8339 (mtp180) cc_final: 0.7925 (mtt180) REVERT: C 104 GLN cc_start: 0.9038 (mt0) cc_final: 0.8018 (tm-30) REVERT: C 152 LYS cc_start: 0.9648 (mttt) cc_final: 0.9357 (mttt) REVERT: C 226 ARG cc_start: 0.8858 (mmp-170) cc_final: 0.8306 (mmp80) REVERT: C 233 CYS cc_start: 0.8859 (m) cc_final: 0.8568 (m) REVERT: D 32 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8596 (tm-30) REVERT: D 68 TYR cc_start: 0.8819 (m-80) cc_final: 0.8477 (t80) REVERT: D 71 ASN cc_start: 0.8884 (t0) cc_final: 0.8386 (t0) REVERT: D 96 ARG cc_start: 0.8405 (mtp180) cc_final: 0.8021 (mtp180) REVERT: D 104 GLN cc_start: 0.8954 (mt0) cc_final: 0.7891 (tp40) REVERT: D 105 ARG cc_start: 0.9453 (tpt170) cc_final: 0.9092 (mmm-85) REVERT: D 108 ILE cc_start: 0.9415 (mm) cc_final: 0.9198 (mp) REVERT: D 120 ASP cc_start: 0.8850 (t0) cc_final: 0.8250 (t0) REVERT: D 147 GLN cc_start: 0.9124 (pm20) cc_final: 0.8882 (tp-100) REVERT: E 32 GLN cc_start: 0.9286 (mt0) cc_final: 0.8953 (tt0) REVERT: E 71 ASN cc_start: 0.8796 (t0) cc_final: 0.8450 (t0) REVERT: E 96 ARG cc_start: 0.8459 (mtp180) cc_final: 0.8011 (mtt180) REVERT: E 104 GLN cc_start: 0.8998 (mt0) cc_final: 0.7922 (tm-30) REVERT: E 120 ASP cc_start: 0.8946 (t0) cc_final: 0.8409 (t0) REVERT: E 152 LYS cc_start: 0.9616 (mttt) cc_final: 0.9308 (mttt) REVERT: E 226 ARG cc_start: 0.8930 (mmp-170) cc_final: 0.8421 (mmp-170) REVERT: F 40 THR cc_start: 0.9764 (OUTLIER) cc_final: 0.9536 (p) REVERT: F 71 ASN cc_start: 0.8849 (t0) cc_final: 0.8550 (t0) REVERT: F 96 ARG cc_start: 0.8389 (mtp180) cc_final: 0.7910 (mtt90) REVERT: F 104 GLN cc_start: 0.8916 (mt0) cc_final: 0.7813 (tp40) REVERT: F 105 ARG cc_start: 0.9390 (tpt170) cc_final: 0.9093 (mmm-85) REVERT: F 120 ASP cc_start: 0.8829 (t0) cc_final: 0.8554 (t0) REVERT: F 233 CYS cc_start: 0.8868 (m) cc_final: 0.8630 (m) REVERT: G 32 GLN cc_start: 0.9369 (tt0) cc_final: 0.9120 (pt0) REVERT: G 71 ASN cc_start: 0.8420 (t0) cc_final: 0.8097 (t0) REVERT: G 96 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7680 (mtt180) REVERT: G 97 TYR cc_start: 0.9033 (t80) cc_final: 0.8784 (t80) REVERT: G 104 GLN cc_start: 0.8856 (mt0) cc_final: 0.7677 (tp40) REVERT: G 105 ARG cc_start: 0.9423 (tpt170) cc_final: 0.9099 (mmm-85) REVERT: G 119 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8934 (mmm) REVERT: G 120 ASP cc_start: 0.8871 (t0) cc_final: 0.8382 (t0) REVERT: G 148 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9377 (mmmt) REVERT: G 152 LYS cc_start: 0.9600 (mttt) cc_final: 0.9289 (mppt) REVERT: G 201 ARG cc_start: 0.8760 (tpp80) cc_final: 0.8541 (tpp80) REVERT: G 216 LYS cc_start: 0.9592 (tptt) cc_final: 0.9303 (mmmm) REVERT: G 233 CYS cc_start: 0.8740 (m) cc_final: 0.8463 (m) REVERT: G 246 GLN cc_start: 0.8382 (mp10) cc_final: 0.7917 (mp10) outliers start: 46 outliers final: 39 residues processed: 483 average time/residue: 0.2816 time to fit residues: 189.6157 Evaluate side-chains 500 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 459 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU 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 28 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 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 55 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL 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 68 TYR 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 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 122 LYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 225 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 88 optimal weight: 6.9990 chunk 118 optimal weight: 0.1980 chunk 158 optimal weight: 20.0000 chunk 147 optimal weight: 0.6980 chunk 144 optimal weight: 0.0970 chunk 96 optimal weight: 0.6980 chunk 75 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.2376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 HIS ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.112186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.079035 restraints weight = 32204.841| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.86 r_work: 0.2989 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.6224 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= 0.134 Angle : 0.654 7.478 18025 Z= 0.336 Chirality : 0.040 0.188 2051 Planarity : 0.005 0.049 2212 Dihedral : 3.367 16.527 1890 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.62 % Allowed : 28.50 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.22), residues: 1575 helix: 2.54 (0.14), residues: 1239 sheet: None (None), residues: 0 loop : -1.09 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 62 HIS 0.005 0.000 HIS D 220 PHE 0.012 0.001 PHE A 212 TYR 0.022 0.001 TYR F 97 ARG 0.010 0.001 ARG D 226 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 7) link_NAG-ASN : angle 1.76573 ( 21) hydrogen bonds : bond 0.03585 ( 925) hydrogen bonds : angle 3.42582 ( 2775) SS BOND : bond 0.00164 ( 14) SS BOND : angle 0.41963 ( 28) covalent geometry : bond 0.00303 (13265) covalent geometry : angle 0.65226 (17976) *********************** 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 532 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 497 time to evaluate : 1.490 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 32 GLN cc_start: 0.9194 (tp40) cc_final: 0.8871 (pp30) REVERT: A 71 ASN cc_start: 0.8724 (t0) cc_final: 0.8084 (t0) REVERT: A 96 ARG cc_start: 0.8354 (mtp180) cc_final: 0.8063 (mtt180) REVERT: A 105 ARG cc_start: 0.9400 (tpt170) cc_final: 0.9105 (mmm-85) REVERT: A 120 ASP cc_start: 0.8793 (t0) cc_final: 0.8351 (t0) REVERT: A 233 CYS cc_start: 0.8871 (m) cc_final: 0.8491 (m) REVERT: B 71 ASN cc_start: 0.8901 (t0) cc_final: 0.8476 (t0) REVERT: B 96 ARG cc_start: 0.8335 (mtp180) cc_final: 0.7920 (mtp180) REVERT: B 105 ARG cc_start: 0.9476 (tpt170) cc_final: 0.9258 (mmm-85) REVERT: B 120 ASP cc_start: 0.8780 (t0) cc_final: 0.8186 (t0) REVERT: B 143 GLN cc_start: 0.9174 (pm20) cc_final: 0.8918 (pm20) REVERT: B 152 LYS cc_start: 0.9602 (mttt) cc_final: 0.9370 (mttt) REVERT: B 201 ARG cc_start: 0.8740 (tpp80) cc_final: 0.8273 (tpp80) REVERT: B 220 HIS cc_start: 0.8643 (m90) cc_final: 0.8251 (m-70) REVERT: B 233 CYS cc_start: 0.8810 (m) cc_final: 0.8574 (m) REVERT: C 71 ASN cc_start: 0.8608 (t0) cc_final: 0.8143 (t0) REVERT: C 96 ARG cc_start: 0.8280 (mtp180) cc_final: 0.7848 (mtt180) REVERT: C 152 LYS cc_start: 0.9637 (mttt) cc_final: 0.9343 (mttt) REVERT: C 226 ARG cc_start: 0.8863 (mmp-170) cc_final: 0.8301 (mmp80) REVERT: C 233 CYS cc_start: 0.8862 (m) cc_final: 0.8612 (m) REVERT: D 32 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8602 (tm-30) REVERT: D 68 TYR cc_start: 0.8769 (m-80) cc_final: 0.8534 (t80) REVERT: D 71 ASN cc_start: 0.8882 (t0) cc_final: 0.8427 (t0) REVERT: D 96 ARG cc_start: 0.8288 (mtp180) cc_final: 0.7944 (mtp180) REVERT: D 104 GLN cc_start: 0.8874 (mt0) cc_final: 0.7586 (tp40) REVERT: D 105 ARG cc_start: 0.9394 (tpt170) cc_final: 0.9100 (mmm-85) REVERT: D 120 ASP cc_start: 0.8729 (t0) cc_final: 0.8129 (t0) REVERT: E 38 GLU cc_start: 0.8999 (pt0) cc_final: 0.8314 (pp20) REVERT: E 71 ASN cc_start: 0.8832 (t0) cc_final: 0.8454 (t0) REVERT: E 96 ARG cc_start: 0.8416 (mtp180) cc_final: 0.8033 (mtt180) REVERT: E 104 GLN cc_start: 0.8964 (mt0) cc_final: 0.7832 (tm-30) REVERT: E 112 VAL cc_start: 0.9627 (t) cc_final: 0.9360 (p) REVERT: E 120 ASP cc_start: 0.8834 (t0) cc_final: 0.8282 (t0) REVERT: E 152 LYS cc_start: 0.9606 (mttt) cc_final: 0.9285 (mttt) REVERT: E 226 ARG cc_start: 0.8917 (mmp-170) cc_final: 0.8409 (mmp-170) REVERT: F 40 THR cc_start: 0.9761 (OUTLIER) cc_final: 0.9549 (p) REVERT: F 71 ASN cc_start: 0.8875 (t0) cc_final: 0.8548 (t0) REVERT: F 96 ARG cc_start: 0.8312 (mtp180) cc_final: 0.7892 (mtp180) REVERT: F 105 ARG cc_start: 0.9399 (tpt170) cc_final: 0.9120 (mmm-85) REVERT: F 120 ASP cc_start: 0.8554 (t0) cc_final: 0.8329 (t0) REVERT: F 216 LYS cc_start: 0.9331 (mmmm) cc_final: 0.9111 (mmmm) REVERT: F 233 CYS cc_start: 0.8876 (m) cc_final: 0.8632 (m) REVERT: G 32 GLN cc_start: 0.9326 (tt0) cc_final: 0.9080 (pt0) REVERT: G 71 ASN cc_start: 0.8351 (t0) cc_final: 0.8007 (t0) REVERT: G 96 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7583 (mtt180) REVERT: G 105 ARG cc_start: 0.9361 (tpt170) cc_final: 0.9053 (mmm-85) REVERT: G 119 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8767 (mmm) REVERT: G 120 ASP cc_start: 0.8728 (t0) cc_final: 0.8228 (t0) REVERT: G 148 LYS cc_start: 0.9625 (mmmt) cc_final: 0.9377 (mmmt) REVERT: G 152 LYS cc_start: 0.9594 (mttt) cc_final: 0.9259 (mppt) REVERT: G 201 ARG cc_start: 0.8715 (tpp80) cc_final: 0.8484 (tpp80) REVERT: G 216 LYS cc_start: 0.9586 (tptt) cc_final: 0.9312 (mmmm) REVERT: G 233 CYS cc_start: 0.8803 (m) cc_final: 0.8550 (m) REVERT: G 246 GLN cc_start: 0.8367 (mp-120) cc_final: 0.7976 (mp10) outliers start: 35 outliers final: 26 residues processed: 511 average time/residue: 0.2813 time to fit residues: 200.6488 Evaluate side-chains 509 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 481 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 68 TYR 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 33 MET Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL 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 181 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 225 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 121 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 92 optimal weight: 40.0000 chunk 138 optimal weight: 50.0000 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 chunk 87 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.3719 r_free = 0.3719 target = 0.116200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.082357 restraints weight = 32024.856| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.06 r_work: 0.2909 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13286 Z= 0.166 Angle : 0.667 8.254 18025 Z= 0.345 Chirality : 0.040 0.170 2051 Planarity : 0.004 0.049 2212 Dihedral : 3.433 17.227 1890 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.62 % Allowed : 29.92 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.22), residues: 1575 helix: 2.54 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.02 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 62 HIS 0.001 0.000 HIS D 236 PHE 0.025 0.001 PHE G 229 TYR 0.017 0.002 TYR D 97 ARG 0.011 0.001 ARG A 226 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 7) link_NAG-ASN : angle 2.04984 ( 21) hydrogen bonds : bond 0.03975 ( 925) hydrogen bonds : angle 3.54835 ( 2775) SS BOND : bond 0.00267 ( 14) SS BOND : angle 0.57785 ( 28) covalent geometry : bond 0.00407 (13265) covalent geometry : angle 0.66381 (17976) *********************** 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 504 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 469 time to evaluate : 1.588 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 71 ASN cc_start: 0.8708 (t0) cc_final: 0.8166 (t0) REVERT: A 96 ARG cc_start: 0.8440 (mtp180) cc_final: 0.8128 (mtt180) REVERT: A 104 GLN cc_start: 0.8963 (mt0) cc_final: 0.7798 (tp40) REVERT: A 105 ARG cc_start: 0.9408 (tpt170) cc_final: 0.9063 (mmm-85) REVERT: A 120 ASP cc_start: 0.8878 (t0) cc_final: 0.8459 (t0) REVERT: A 233 CYS cc_start: 0.8856 (m) cc_final: 0.8459 (m) REVERT: B 71 ASN cc_start: 0.8980 (t0) cc_final: 0.8529 (t0) REVERT: B 96 ARG cc_start: 0.8444 (mtp180) cc_final: 0.7992 (mtp180) REVERT: B 104 GLN cc_start: 0.9054 (mt0) cc_final: 0.8055 (tp40) REVERT: B 105 ARG cc_start: 0.9480 (tpt170) cc_final: 0.9247 (mmm-85) REVERT: B 120 ASP cc_start: 0.8925 (t0) cc_final: 0.8559 (t0) REVERT: B 143 GLN cc_start: 0.9208 (pm20) cc_final: 0.8943 (pm20) REVERT: B 152 LYS cc_start: 0.9600 (mttt) cc_final: 0.9376 (mttt) REVERT: B 220 HIS cc_start: 0.8693 (m90) cc_final: 0.8266 (m-70) REVERT: B 233 CYS cc_start: 0.8746 (m) cc_final: 0.8506 (m) REVERT: C 71 ASN cc_start: 0.8550 (t0) cc_final: 0.8040 (t0) REVERT: C 96 ARG cc_start: 0.8311 (mtp180) cc_final: 0.7905 (mtt180) REVERT: C 97 TYR cc_start: 0.9131 (t80) cc_final: 0.8885 (t80) REVERT: C 104 GLN cc_start: 0.9044 (mt0) cc_final: 0.8028 (tm-30) REVERT: C 152 LYS cc_start: 0.9639 (mttt) cc_final: 0.9346 (mttt) REVERT: C 226 ARG cc_start: 0.8930 (mmp-170) cc_final: 0.8390 (mmp80) REVERT: C 233 CYS cc_start: 0.8861 (m) cc_final: 0.8622 (m) REVERT: D 68 TYR cc_start: 0.8817 (m-80) cc_final: 0.8462 (t80) REVERT: D 71 ASN cc_start: 0.8899 (t0) cc_final: 0.8524 (t0) REVERT: D 96 ARG cc_start: 0.8368 (mtp180) cc_final: 0.8040 (mtp180) REVERT: D 104 GLN cc_start: 0.8927 (mt0) cc_final: 0.7906 (tp40) REVERT: D 105 ARG cc_start: 0.9461 (tpt170) cc_final: 0.9135 (mmm-85) REVERT: D 120 ASP cc_start: 0.8872 (t0) cc_final: 0.8319 (t0) REVERT: E 38 GLU cc_start: 0.9041 (pt0) cc_final: 0.8459 (pp20) REVERT: E 71 ASN cc_start: 0.8776 (t0) cc_final: 0.8421 (t0) REVERT: E 96 ARG cc_start: 0.8484 (mtp180) cc_final: 0.8108 (mtt180) REVERT: E 104 GLN cc_start: 0.8991 (mt0) cc_final: 0.7915 (tm-30) REVERT: E 119 MET cc_start: 0.8993 (mmp) cc_final: 0.8710 (mmm) REVERT: E 120 ASP cc_start: 0.8893 (t0) cc_final: 0.8317 (t0) REVERT: E 152 LYS cc_start: 0.9613 (mttt) cc_final: 0.9303 (mttt) REVERT: E 201 ARG cc_start: 0.8672 (tpp80) cc_final: 0.8384 (tpt-90) REVERT: E 226 ARG cc_start: 0.8926 (mmp-170) cc_final: 0.8413 (mmp-170) REVERT: F 40 THR cc_start: 0.9767 (OUTLIER) cc_final: 0.9516 (p) REVERT: F 71 ASN cc_start: 0.8872 (t0) cc_final: 0.8566 (t0) REVERT: F 96 ARG cc_start: 0.8408 (mtp180) cc_final: 0.7965 (mtp180) REVERT: F 104 GLN cc_start: 0.8886 (mt0) cc_final: 0.7811 (tp40) REVERT: F 105 ARG cc_start: 0.9438 (tpt170) cc_final: 0.9148 (mmm-85) REVERT: F 120 ASP cc_start: 0.8790 (t0) cc_final: 0.8589 (t0) REVERT: F 216 LYS cc_start: 0.9317 (mmmm) cc_final: 0.9063 (mmmm) REVERT: F 233 CYS cc_start: 0.8857 (m) cc_final: 0.8618 (m) REVERT: G 32 GLN cc_start: 0.9335 (tt0) cc_final: 0.9084 (pt0) REVERT: G 71 ASN cc_start: 0.8557 (t0) cc_final: 0.8219 (t0) REVERT: G 96 ARG cc_start: 0.8180 (mtp180) cc_final: 0.7858 (mtt180) REVERT: G 104 GLN cc_start: 0.8856 (mt0) cc_final: 0.7623 (tp40) REVERT: G 105 ARG cc_start: 0.9467 (tpt170) cc_final: 0.9158 (mmm-85) REVERT: G 119 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8924 (mmm) REVERT: G 120 ASP cc_start: 0.8841 (t0) cc_final: 0.8350 (t0) REVERT: G 148 LYS cc_start: 0.9648 (mmmt) cc_final: 0.9408 (mmmt) REVERT: G 152 LYS cc_start: 0.9608 (mttt) cc_final: 0.9283 (mppt) REVERT: G 160 LYS cc_start: 0.9564 (ttmm) cc_final: 0.9285 (ttmm) REVERT: G 201 ARG cc_start: 0.8808 (tpp80) cc_final: 0.8601 (tpp80) REVERT: G 216 LYS cc_start: 0.9615 (tptt) cc_final: 0.9362 (mmmm) REVERT: G 233 CYS cc_start: 0.8787 (m) cc_final: 0.8546 (m) REVERT: G 246 GLN cc_start: 0.8384 (mp-120) cc_final: 0.7964 (mp10) outliers start: 35 outliers final: 28 residues processed: 483 average time/residue: 0.2800 time to fit residues: 186.9585 Evaluate side-chains 491 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 461 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 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 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 E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 225 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 112 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 115 optimal weight: 30.0000 chunk 68 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.114863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.081272 restraints weight = 31768.959| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.97 r_work: 0.2867 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13286 Z= 0.223 Angle : 0.710 7.946 18025 Z= 0.371 Chirality : 0.042 0.231 2051 Planarity : 0.005 0.051 2212 Dihedral : 3.796 18.315 1890 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.62 % Allowed : 29.77 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.21), residues: 1575 helix: 2.35 (0.14), residues: 1246 sheet: None (None), residues: 0 loop : -1.00 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 62 HIS 0.002 0.001 HIS F 236 PHE 0.019 0.001 PHE C 212 TYR 0.024 0.002 TYR F 34 ARG 0.011 0.001 ARG D 226 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 7) link_NAG-ASN : angle 2.45355 ( 21) hydrogen bonds : bond 0.04627 ( 925) hydrogen bonds : angle 3.79335 ( 2775) SS BOND : bond 0.00346 ( 14) SS BOND : angle 0.65947 ( 28) covalent geometry : bond 0.00534 (13265) covalent geometry : angle 0.70530 (17976) ********************** 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 481 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 446 time to evaluate : 2.279 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 71 ASN cc_start: 0.8698 (t0) cc_final: 0.8193 (t0) REVERT: A 96 ARG cc_start: 0.8517 (mtp180) cc_final: 0.8223 (mtt180) REVERT: A 104 GLN cc_start: 0.8950 (mt0) cc_final: 0.7872 (tm-30) REVERT: A 105 ARG cc_start: 0.9446 (tpt170) cc_final: 0.9238 (mmm-85) REVERT: A 120 ASP cc_start: 0.8954 (t0) cc_final: 0.8597 (t0) REVERT: A 233 CYS cc_start: 0.8878 (m) cc_final: 0.8570 (m) REVERT: B 71 ASN cc_start: 0.9080 (t0) cc_final: 0.8717 (t0) REVERT: B 96 ARG cc_start: 0.8583 (mtp180) cc_final: 0.8132 (mtp180) REVERT: B 104 GLN cc_start: 0.9130 (mt0) cc_final: 0.8162 (tm-30) REVERT: B 105 ARG cc_start: 0.9517 (tpt170) cc_final: 0.9260 (mmm-85) REVERT: B 120 ASP cc_start: 0.9043 (t0) cc_final: 0.8721 (t0) REVERT: B 152 LYS cc_start: 0.9615 (mttt) cc_final: 0.9396 (mttt) REVERT: B 220 HIS cc_start: 0.8766 (m90) cc_final: 0.8358 (m-70) REVERT: B 233 CYS cc_start: 0.8830 (m) cc_final: 0.8598 (m) REVERT: C 71 ASN cc_start: 0.8803 (t0) cc_final: 0.8339 (t0) REVERT: C 96 ARG cc_start: 0.8421 (mtp180) cc_final: 0.8092 (mtt180) REVERT: C 104 GLN cc_start: 0.9111 (mt0) cc_final: 0.7897 (tm-30) REVERT: C 152 LYS cc_start: 0.9636 (mttt) cc_final: 0.9384 (mttt) REVERT: C 226 ARG cc_start: 0.8910 (mmp-170) cc_final: 0.8365 (mmp80) REVERT: C 233 CYS cc_start: 0.8898 (m) cc_final: 0.8664 (m) REVERT: D 68 TYR cc_start: 0.8909 (m-80) cc_final: 0.8416 (t80) REVERT: D 71 ASN cc_start: 0.8830 (t0) cc_final: 0.8492 (t0) REVERT: D 96 ARG cc_start: 0.8508 (mtp180) cc_final: 0.8156 (mtp180) REVERT: D 104 GLN cc_start: 0.9104 (mt0) cc_final: 0.8048 (tp40) REVERT: D 105 ARG cc_start: 0.9593 (tpt170) cc_final: 0.9379 (mmm-85) REVERT: D 120 ASP cc_start: 0.9046 (t0) cc_final: 0.8634 (t0) REVERT: E 71 ASN cc_start: 0.8846 (t0) cc_final: 0.8502 (t0) REVERT: E 96 ARG cc_start: 0.8597 (mtp180) cc_final: 0.8259 (mtt180) REVERT: E 104 GLN cc_start: 0.9138 (mt0) cc_final: 0.8153 (tm-30) REVERT: E 119 MET cc_start: 0.9166 (mmp) cc_final: 0.8944 (mmm) REVERT: E 120 ASP cc_start: 0.9038 (t0) cc_final: 0.8524 (t0) REVERT: E 152 LYS cc_start: 0.9636 (mttt) cc_final: 0.9298 (mppt) REVERT: E 226 ARG cc_start: 0.8930 (mmp-170) cc_final: 0.8376 (mmp-170) REVERT: F 71 ASN cc_start: 0.8963 (t0) cc_final: 0.8654 (t0) REVERT: F 96 ARG cc_start: 0.8450 (mtp180) cc_final: 0.8061 (mtp180) REVERT: F 104 GLN cc_start: 0.9008 (mt0) cc_final: 0.7906 (tp40) REVERT: F 105 ARG cc_start: 0.9489 (tpt170) cc_final: 0.9178 (mmm-85) REVERT: F 120 ASP cc_start: 0.8982 (t0) cc_final: 0.8688 (t0) REVERT: F 216 LYS cc_start: 0.9372 (mmmm) cc_final: 0.9097 (mmmm) REVERT: F 233 CYS cc_start: 0.8899 (m) cc_final: 0.8677 (m) REVERT: G 71 ASN cc_start: 0.8549 (t0) cc_final: 0.8193 (t0) REVERT: G 96 ARG cc_start: 0.8365 (mtp180) cc_final: 0.8040 (mtt180) REVERT: G 104 GLN cc_start: 0.8987 (mt0) cc_final: 0.8082 (tp40) REVERT: G 105 ARG cc_start: 0.9510 (tpt170) cc_final: 0.9211 (mmm-85) REVERT: G 119 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8987 (mmm) REVERT: G 120 ASP cc_start: 0.8974 (t0) cc_final: 0.8523 (t0) REVERT: G 148 LYS cc_start: 0.9646 (mmmt) cc_final: 0.9398 (mmmt) REVERT: G 152 LYS cc_start: 0.9638 (mttt) cc_final: 0.9350 (mppt) REVERT: G 160 LYS cc_start: 0.9551 (ttmm) cc_final: 0.9277 (ttmm) REVERT: G 201 ARG cc_start: 0.8951 (tpp80) cc_final: 0.8704 (tpp80) REVERT: G 246 GLN cc_start: 0.8326 (mp-120) cc_final: 0.7888 (mp10) outliers start: 35 outliers final: 30 residues processed: 461 average time/residue: 0.3670 time to fit residues: 233.2959 Evaluate side-chains 463 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 432 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 74 ILE 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 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 E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL 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 68 TYR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 122 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 129 optimal weight: 0.0670 chunk 123 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN D 32 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.115030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079974 restraints weight = 32107.163| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.95 r_work: 0.2890 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13286 Z= 0.143 Angle : 0.702 12.232 18025 Z= 0.363 Chirality : 0.041 0.279 2051 Planarity : 0.005 0.050 2212 Dihedral : 3.498 18.171 1890 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.39 % Allowed : 30.96 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.21), residues: 1575 helix: 2.51 (0.14), residues: 1239 sheet: None (None), residues: 0 loop : -0.90 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 62 HIS 0.001 0.000 HIS F 236 PHE 0.038 0.001 PHE C 212 TYR 0.017 0.001 TYR D 217 ARG 0.017 0.001 ARG G 226 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 7) link_NAG-ASN : angle 1.79205 ( 21) hydrogen bonds : bond 0.04072 ( 925) hydrogen bonds : angle 3.60273 ( 2775) SS BOND : bond 0.00187 ( 14) SS BOND : angle 0.48254 ( 28) covalent geometry : bond 0.00341 (13265) covalent geometry : angle 0.70005 (17976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8418.30 seconds wall clock time: 147 minutes 53.49 seconds (8873.49 seconds total)