Starting phenix.real_space_refine on Mon Apr 6 19:47:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lwn_63451/04_2026/9lwn_63451.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lwn_63451/04_2026/9lwn_63451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lwn_63451/04_2026/9lwn_63451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lwn_63451/04_2026/9lwn_63451.map" model { file = "/net/cci-nas-00/data/ceres_data/9lwn_63451/04_2026/9lwn_63451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lwn_63451/04_2026/9lwn_63451.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 27 5.49 5 Mg 9 5.21 5 S 105 5.16 5 C 13547 2.51 5 N 3639 2.21 5 O 4126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21453 Number of models: 1 Model: "" Number of chains: 19 Chain: "C" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2358 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 13, 'TRANS': 285} Chain breaks: 1 Chain: "B" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2342 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain breaks: 1 Chain: "D" Number of atoms: 2368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2368 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 13, 'TRANS': 286} Chain breaks: 1 Chain: "E" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2328 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "F" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2328 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "G" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2355 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 14, 'TRANS': 284} Chain breaks: 1 Chain: "H" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2342 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 13, 'TRANS': 282} Chain breaks: 1 Chain: "I" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2333 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2301 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Chain: "J" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.07, per 1000 atoms: 0.24 Number of scatterers: 21453 At special positions: 0 Unit cell: (138.58, 133.66, 135.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 27 15.00 Mg 9 11.99 O 4126 8.00 N 3639 7.00 C 13547 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 10 sheets defined 65.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'C' and resid 43 through 61 Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.718A pdb=" N ALA C 65 " --> pdb=" O PRO C 62 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU C 66 " --> pdb=" O ALA C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 79 removed outlier: 3.730A pdb=" N SER C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 113 through 118 removed outlier: 3.773A pdb=" N TYR C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 158 through 163 removed outlier: 4.120A pdb=" N ILE C 162 " --> pdb=" O ARG C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 184 removed outlier: 3.618A pdb=" N LYS C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.233A pdb=" N PHE C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 237 through 241 removed outlier: 3.609A pdb=" N ASP C 240 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 removed outlier: 4.021A pdb=" N ARG C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 270 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.817A pdb=" N ILE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 310 Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 340 through 346 removed outlier: 3.771A pdb=" N PHE C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.874A pdb=" N GLU B 66 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 67 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.519A pdb=" N ILE B 86 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.510A pdb=" N TYR B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.820A pdb=" N GLN B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.531A pdb=" N ILE B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.252A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 282 through 290 removed outlier: 3.963A pdb=" N ILE B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 340 through 346 removed outlier: 3.910A pdb=" N PHE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 61 Processing helix chain 'D' and resid 62 through 67 removed outlier: 3.644A pdb=" N ALA D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU D 66 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL D 67 " --> pdb=" O LEU D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 67' Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.715A pdb=" N TYR D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.751A pdb=" N ILE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.387A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 237 through 241 removed outlier: 3.674A pdb=" N ASP D 240 " --> pdb=" O ARG D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.863A pdb=" N ARG D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.694A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 321 removed outlier: 5.295A pdb=" N GLU D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N TYR D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 348 removed outlier: 4.161A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 61 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.884A pdb=" N ALA E 65 " --> pdb=" O PRO E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 70 through 78 Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 107 through 113 removed outlier: 3.583A pdb=" N LEU E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 removed outlier: 4.112A pdb=" N TYR E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.706A pdb=" N GLN E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 158 through 163 removed outlier: 4.130A pdb=" N ILE E 162 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET E 163 " --> pdb=" O MET E 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 158 through 163' Processing helix chain 'E' and resid 168 through 184 removed outlier: 3.705A pdb=" N LYS E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.076A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 221 Processing helix chain 'E' and resid 242 through 248 removed outlier: 3.808A pdb=" N ARG E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 290 removed outlier: 3.933A pdb=" N ILE E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 310 Processing helix chain 'E' and resid 310 through 319 Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.804A pdb=" N PHE E 344 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 61 Processing helix chain 'F' and resid 62 through 67 removed outlier: 3.705A pdb=" N ALA F 65 " --> pdb=" O PRO F 62 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL F 67 " --> pdb=" O LEU F 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 67' Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'F' and resid 108 through 113 Processing helix chain 'F' and resid 113 through 118 removed outlier: 3.764A pdb=" N TYR F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.950A pdb=" N GLN F 124 " --> pdb=" O PRO F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 150 removed outlier: 3.515A pdb=" N SER F 150 " --> pdb=" O LEU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 163 removed outlier: 4.027A pdb=" N ILE F 162 " --> pdb=" O ARG F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.216A pdb=" N PHE F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 221 Processing helix chain 'F' and resid 237 through 241 removed outlier: 3.745A pdb=" N ASP F 240 " --> pdb=" O ARG F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 248 removed outlier: 3.874A pdb=" N ARG F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 282 through 290 removed outlier: 3.607A pdb=" N ILE F 286 " --> pdb=" O ASP F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 310 Processing helix chain 'F' and resid 310 through 319 Processing helix chain 'F' and resid 340 through 346 removed outlier: 3.842A pdb=" N PHE F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 61 Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.682A pdb=" N ALA G 65 " --> pdb=" O PRO G 62 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU G 66 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 67 " --> pdb=" O LEU G 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 67' Processing helix chain 'G' and resid 70 through 78 Processing helix chain 'G' and resid 82 through 86 removed outlier: 3.558A pdb=" N ILE G 86 " --> pdb=" O PRO G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 107 Processing helix chain 'G' and resid 108 through 113 Processing helix chain 'G' and resid 113 through 118 removed outlier: 3.691A pdb=" N TYR G 117 " --> pdb=" O MET G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 158 through 163 removed outlier: 4.008A pdb=" N ILE G 162 " --> pdb=" O ARG G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 193 through 198 removed outlier: 4.329A pdb=" N PHE G 197 " --> pdb=" O GLN G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 221 Processing helix chain 'G' and resid 242 through 248 removed outlier: 3.682A pdb=" N ARG G 248 " --> pdb=" O ALA G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 271 Processing helix chain 'G' and resid 282 through 290 removed outlier: 3.975A pdb=" N ILE G 286 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 319 removed outlier: 5.045A pdb=" N GLU G 312 " --> pdb=" O ASP G 308 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYR G 313 " --> pdb=" O ALA G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 346 removed outlier: 4.001A pdb=" N PHE G 344 " --> pdb=" O LYS G 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 61 Processing helix chain 'H' and resid 62 through 66 removed outlier: 3.508A pdb=" N ALA H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU H 66 " --> pdb=" O ALA H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 66' Processing helix chain 'H' and resid 70 through 78 Processing helix chain 'H' and resid 82 through 86 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'H' and resid 96 through 107 Processing helix chain 'H' and resid 107 through 113 Processing helix chain 'H' and resid 113 through 118 removed outlier: 3.553A pdb=" N TYR H 117 " --> pdb=" O MET H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 150 removed outlier: 3.538A pdb=" N SER H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 184 removed outlier: 3.617A pdb=" N LYS H 172 " --> pdb=" O GLY H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 198 removed outlier: 4.342A pdb=" N PHE H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 221 Processing helix chain 'H' and resid 237 through 241 removed outlier: 3.757A pdb=" N ASP H 240 " --> pdb=" O ARG H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 248 removed outlier: 3.697A pdb=" N ARG H 248 " --> pdb=" O ALA H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 271 Processing helix chain 'H' and resid 282 through 290 removed outlier: 3.723A pdb=" N ILE H 286 " --> pdb=" O ASP H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 320 removed outlier: 5.013A pdb=" N GLU H 312 " --> pdb=" O ASP H 308 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TYR H 313 " --> pdb=" O ALA H 309 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 320 " --> pdb=" O GLN H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 346 removed outlier: 3.740A pdb=" N PHE H 344 " --> pdb=" O LYS H 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 61 Processing helix chain 'I' and resid 62 through 67 removed outlier: 3.595A pdb=" N ALA I 65 " --> pdb=" O PRO I 62 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU I 66 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL I 67 " --> pdb=" O LEU I 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 67' Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 82 through 86 removed outlier: 3.509A pdb=" N ILE I 86 " --> pdb=" O PRO I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 107 Processing helix chain 'I' and resid 107 through 113 Processing helix chain 'I' and resid 120 through 124 removed outlier: 3.676A pdb=" N GLN I 124 " --> pdb=" O PRO I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 150 Processing helix chain 'I' and resid 158 through 163 removed outlier: 4.272A pdb=" N ILE I 162 " --> pdb=" O ARG I 158 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET I 163 " --> pdb=" O MET I 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 158 through 163' Processing helix chain 'I' and resid 168 through 184 Processing helix chain 'I' and resid 193 through 198 removed outlier: 4.260A pdb=" N PHE I 197 " --> pdb=" O GLN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 227 removed outlier: 3.666A pdb=" N ASP I 221 " --> pdb=" O MET I 217 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY I 222 " --> pdb=" O THR I 218 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU I 224 " --> pdb=" O TRP I 220 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN I 225 " --> pdb=" O ASP I 221 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN I 226 " --> pdb=" O GLY I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 241 removed outlier: 3.542A pdb=" N ASP I 240 " --> pdb=" O ARG I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 259 through 271 Processing helix chain 'I' and resid 282 through 290 removed outlier: 3.557A pdb=" N ILE I 286 " --> pdb=" O ASP I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 320 removed outlier: 5.039A pdb=" N GLU I 312 " --> pdb=" O ASP I 308 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR I 313 " --> pdb=" O ALA I 309 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN I 319 " --> pdb=" O LYS I 315 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 348 removed outlier: 3.908A pdb=" N PHE I 344 " --> pdb=" O LYS I 340 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS I 347 " --> pdb=" O ASP I 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 61 Processing helix chain 'A' and resid 62 through 67 removed outlier: 4.051A pdb=" N GLU A 66 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.855A pdb=" N TYR A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 6.822A pdb=" N LEU A 122 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 158 through 163 removed outlier: 4.239A pdb=" N ILE A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 158 through 163' Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.582A pdb=" N LYS A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.039A pdb=" N PHE A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.534A pdb=" N ARG A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.684A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 310 Processing helix chain 'A' and resid 310 through 319 Processing helix chain 'A' and resid 340 through 346 removed outlier: 4.026A pdb=" N PHE A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 153 through 156 removed outlier: 6.121A pdb=" N ASN C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N PHE C 190 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ASP C 192 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA C 234 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL C 129 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR C 235 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU C 131 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 153 through 157 removed outlier: 6.022A pdb=" N ASN B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE B 190 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ILE B 157 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 234 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 153 through 157 removed outlier: 4.247A pdb=" N ASP D 192 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA D 234 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 153 through 155 removed outlier: 3.704A pdb=" N ALA E 234 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 153 through 156 removed outlier: 6.226A pdb=" N ASN F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N PHE F 190 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA F 234 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU F 130 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 80 through 81 removed outlier: 3.706A pdb=" N PHE G 154 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN G 153 " --> pdb=" O ILE G 188 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N PHE G 190 " --> pdb=" O ASN G 153 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE G 155 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASP G 192 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ILE G 157 " --> pdb=" O ASP G 192 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA G 234 " --> pdb=" O ILE G 191 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL G 129 " --> pdb=" O GLY G 233 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR G 235 " --> pdb=" O VAL G 129 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU G 131 " --> pdb=" O THR G 235 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY G 128 " --> pdb=" O LYS G 251 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE G 253 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU G 130 " --> pdb=" O PHE G 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 153 through 155 removed outlier: 3.921A pdb=" N ALA H 234 " --> pdb=" O ILE H 191 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL H 129 " --> pdb=" O GLY H 233 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR H 235 " --> pdb=" O VAL H 129 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU H 131 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY H 128 " --> pdb=" O LYS H 251 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE H 253 " --> pdb=" O GLY H 128 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU H 130 " --> pdb=" O PHE H 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 153 through 155 removed outlier: 3.619A pdb=" N ILE I 232 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA I 234 " --> pdb=" O ILE I 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 153 through 155 removed outlier: 3.619A pdb=" N ILE I 232 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY I 128 " --> pdb=" O LYS I 251 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE I 253 " --> pdb=" O GLY I 128 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU I 130 " --> pdb=" O PHE I 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 153 through 156 removed outlier: 5.933A pdb=" N ASN A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N PHE A 190 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASP A 192 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS A 187 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE A 232 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 189 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA A 234 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE A 191 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE A 253 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) 1039 hydrogen bonds defined for protein. 2991 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: 4.16 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5018 1.33 - 1.45: 3960 1.45 - 1.57: 12591 1.57 - 1.70: 45 1.70 - 1.82: 183 Bond restraints: 21797 Sorted by residual: bond pdb=" C4 ATP G 401 " pdb=" C5 ATP G 401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C4 ATP F 401 " pdb=" C5 ATP F 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.74e+01 bond pdb=" C4 ATP I 401 " pdb=" C5 ATP I 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.67e+01 bond pdb=" C4 ATP H 401 " pdb=" C5 ATP H 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.60e+01 bond pdb=" C4 ATP D 401 " pdb=" C5 ATP D 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.57e+01 ... (remaining 21792 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 29101 3.68 - 7.37: 272 7.37 - 11.05: 44 11.05 - 14.74: 1 14.74 - 18.42: 14 Bond angle restraints: 29432 Sorted by residual: angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 121.45 18.42 1.00e+00 1.00e+00 3.39e+02 angle pdb=" PB ATP D 401 " pdb=" O3B ATP D 401 " pdb=" PG ATP D 401 " ideal model delta sigma weight residual 139.87 121.93 17.94 1.00e+00 1.00e+00 3.22e+02 angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 122.46 17.41 1.00e+00 1.00e+00 3.03e+02 angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 122.68 17.19 1.00e+00 1.00e+00 2.96e+02 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 122.92 16.95 1.00e+00 1.00e+00 2.87e+02 ... (remaining 29427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 11453 17.68 - 35.36: 1761 35.36 - 53.04: 385 53.04 - 70.73: 76 70.73 - 88.41: 34 Dihedral angle restraints: 13709 sinusoidal: 5864 harmonic: 7845 Sorted by residual: dihedral pdb=" CA ARG F 248 " pdb=" C ARG F 248 " pdb=" N LEU F 249 " pdb=" CA LEU F 249 " ideal model delta harmonic sigma weight residual -180.00 -154.94 -25.06 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ARG C 248 " pdb=" C ARG C 248 " pdb=" N LEU C 249 " pdb=" CA LEU C 249 " ideal model delta harmonic sigma weight residual -180.00 -157.47 -22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LEU F 184 " pdb=" C LEU F 184 " pdb=" N GLN F 185 " pdb=" CA GLN F 185 " ideal model delta harmonic sigma weight residual 180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 13706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2808 0.066 - 0.132: 511 0.132 - 0.197: 42 0.197 - 0.263: 6 0.263 - 0.329: 2 Chirality restraints: 3369 Sorted by residual: chirality pdb=" CG LEU A 52 " pdb=" CB LEU A 52 " pdb=" CD1 LEU A 52 " pdb=" CD2 LEU A 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA GLU C 149 " pdb=" N GLU C 149 " pdb=" C GLU C 149 " pdb=" CB GLU C 149 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB ILE D 314 " pdb=" CA ILE D 314 " pdb=" CG1 ILE D 314 " pdb=" CG2 ILE D 314 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3366 not shown) Planarity restraints: 3688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 113 " -0.064 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO A 114 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 246 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C LEU A 246 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU A 246 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG A 247 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 211 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" C THR G 211 " 0.043 2.00e-02 2.50e+03 pdb=" O THR G 211 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU G 212 " -0.015 2.00e-02 2.50e+03 ... (remaining 3685 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 53 2.36 - 3.00: 10652 3.00 - 3.63: 34155 3.63 - 4.27: 51769 4.27 - 4.90: 86483 Nonbonded interactions: 183112 Sorted by model distance: nonbonded pdb=" OG1 THR G 140 " pdb="MG MG G 402 " model vdw 1.731 2.170 nonbonded pdb=" OG1 THR D 140 " pdb="MG MG D 402 " model vdw 1.734 2.170 nonbonded pdb=" O3G ATP I 401 " pdb="MG MG I 402 " model vdw 1.753 2.170 nonbonded pdb=" O2G ATP G 401 " pdb="MG MG G 402 " model vdw 1.826 2.170 nonbonded pdb=" OG1 THR I 140 " pdb="MG MG I 402 " model vdw 1.839 2.170 ... (remaining 183107 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 43 through 402) selection = (chain 'B' and (resid 43 through 319 or resid 337 through 349 or resid 401 throu \ gh 402)) selection = (chain 'C' and (resid 43 through 319 or resid 337 through 349 or resid 401 throu \ gh 402)) selection = (chain 'D' and (resid 43 through 319 or resid 337 through 349 or resid 401 throu \ gh 402)) selection = (chain 'E' and (resid 43 through 319 or resid 337 through 402)) selection = (chain 'F' and (resid 43 through 319 or resid 337 through 402)) selection = (chain 'G' and (resid 43 through 319 or resid 337 through 349 or resid 401 throu \ gh 402)) selection = (chain 'H' and (resid 43 through 319 or resid 337 through 349 or resid 401 throu \ gh 402)) selection = (chain 'I' and (resid 43 through 319 or resid 337 through 349 or resid 401 throu \ gh 402)) } 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: 13.210 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: 0.020 Extract box with map and model: 1.630 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.230 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 0.083 21797 Z= 0.341 Angle : 0.956 18.422 29432 Z= 0.623 Chirality : 0.050 0.329 3369 Planarity : 0.005 0.097 3688 Dihedral : 17.663 88.407 8597 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.30 % Allowed : 22.51 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.16), residues: 2631 helix: 0.04 (0.13), residues: 1453 sheet: -0.32 (0.45), residues: 132 loop : -0.52 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 349 TYR 0.026 0.002 TYR I 313 PHE 0.030 0.002 PHE I 197 TRP 0.008 0.001 TRP F 220 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00516 (21797) covalent geometry : angle 0.95584 (29432) hydrogen bonds : bond 0.15723 ( 1035) hydrogen bonds : angle 6.15853 ( 2991) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 428 time to evaluate : 0.854 Fit side-chains REVERT: C 42 LYS cc_start: 0.6667 (pttm) cc_final: 0.6348 (mmmt) REVERT: E 284 GLN cc_start: 0.8564 (tp40) cc_final: 0.8328 (tp40) REVERT: F 291 LYS cc_start: 0.8385 (mmmt) cc_final: 0.7405 (tttm) REVERT: G 119 ASN cc_start: 0.7836 (m110) cc_final: 0.7539 (m-40) REVERT: G 308 ASP cc_start: 0.8462 (t0) cc_final: 0.7996 (t0) REVERT: G 346 LYS cc_start: 0.8648 (ptmt) cc_final: 0.8188 (ptmt) REVERT: H 156 SER cc_start: 0.9103 (t) cc_final: 0.8902 (p) REVERT: I 87 ASN cc_start: 0.6035 (p0) cc_final: 0.5759 (m-40) REVERT: I 284 GLN cc_start: 0.8752 (tp40) cc_final: 0.8480 (tp-100) REVERT: A 141 MET cc_start: 0.7817 (tpp) cc_final: 0.7602 (mmt) outliers start: 7 outliers final: 2 residues processed: 432 average time/residue: 0.1475 time to fit residues: 99.7284 Evaluate side-chains 369 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 293 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 GLN B 236 ASN D 236 ASN D 284 GLN F 236 ASN G 236 ASN H 171 ASN A 206 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.146971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112684 restraints weight = 30460.192| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.42 r_work: 0.3197 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21797 Z= 0.138 Angle : 0.585 10.452 29432 Z= 0.288 Chirality : 0.041 0.147 3369 Planarity : 0.004 0.064 3688 Dihedral : 10.952 89.658 3187 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.46 % Allowed : 22.26 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.16), residues: 2631 helix: 0.63 (0.14), residues: 1497 sheet: -0.29 (0.44), residues: 132 loop : -0.14 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 263 TYR 0.014 0.001 TYR B 264 PHE 0.021 0.002 PHE I 281 TRP 0.004 0.001 TRP C 166 HIS 0.001 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00324 (21797) covalent geometry : angle 0.58473 (29432) hydrogen bonds : bond 0.03411 ( 1035) hydrogen bonds : angle 4.73678 ( 2991) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 408 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: B 260 SER cc_start: 0.8786 (m) cc_final: 0.8460 (t) REVERT: B 264 TYR cc_start: 0.8716 (t80) cc_final: 0.8464 (t80) REVERT: D 92 ASP cc_start: 0.7768 (m-30) cc_final: 0.7394 (t0) REVERT: D 221 ASP cc_start: 0.7703 (t0) cc_final: 0.7465 (t0) REVERT: D 284 GLN cc_start: 0.8540 (tp40) cc_final: 0.8083 (tp-100) REVERT: E 275 LYS cc_start: 0.8406 (tppt) cc_final: 0.7009 (tttt) REVERT: E 284 GLN cc_start: 0.8527 (tp40) cc_final: 0.8137 (mm-40) REVERT: E 337 ARG cc_start: 0.7092 (mtp-110) cc_final: 0.6835 (ttp80) REVERT: F 291 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7225 (tmtt) REVERT: F 297 ASP cc_start: 0.8554 (m-30) cc_final: 0.8345 (m-30) REVERT: G 87 ASN cc_start: 0.7739 (p0) cc_final: 0.7449 (p0) REVERT: G 119 ASN cc_start: 0.8011 (m110) cc_final: 0.7721 (m-40) REVERT: G 284 GLN cc_start: 0.8328 (tp-100) cc_final: 0.8122 (tp40) REVERT: G 308 ASP cc_start: 0.8622 (t0) cc_final: 0.8195 (t0) REVERT: G 342 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8085 (ptpt) REVERT: H 156 SER cc_start: 0.9133 (t) cc_final: 0.8889 (p) REVERT: H 342 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8538 (ptpp) REVERT: I 284 GLN cc_start: 0.8877 (tp40) cc_final: 0.8660 (tp-100) REVERT: I 313 TYR cc_start: 0.8277 (t80) cc_final: 0.8064 (t80) REVERT: A 184 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8194 (mt) outliers start: 58 outliers final: 28 residues processed: 446 average time/residue: 0.1438 time to fit residues: 100.9410 Evaluate side-chains 403 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 373 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 342 LYS Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 184 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 90 optimal weight: 30.0000 chunk 165 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 chunk 168 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 222 optimal weight: 0.0060 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN D 236 ASN G 236 ASN I 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113398 restraints weight = 30468.352| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.41 r_work: 0.3180 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21797 Z= 0.143 Angle : 0.561 8.499 29432 Z= 0.274 Chirality : 0.041 0.160 3369 Planarity : 0.004 0.049 3688 Dihedral : 10.681 87.007 3183 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.40 % Allowed : 22.26 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.17), residues: 2631 helix: 0.86 (0.14), residues: 1497 sheet: -0.31 (0.44), residues: 132 loop : 0.02 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 349 TYR 0.012 0.001 TYR F 264 PHE 0.018 0.002 PHE I 245 TRP 0.005 0.001 TRP H 220 HIS 0.002 0.000 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00350 (21797) covalent geometry : angle 0.56095 (29432) hydrogen bonds : bond 0.03197 ( 1035) hydrogen bonds : angle 4.62044 ( 2991) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 386 time to evaluate : 0.897 Fit side-chains REVERT: B 260 SER cc_start: 0.8791 (m) cc_final: 0.8446 (t) REVERT: D 92 ASP cc_start: 0.7811 (m-30) cc_final: 0.7421 (t0) REVERT: D 262 GLN cc_start: 0.8389 (mp10) cc_final: 0.8022 (mt0) REVERT: D 284 GLN cc_start: 0.8547 (tp40) cc_final: 0.7976 (tp-100) REVERT: E 275 LYS cc_start: 0.8383 (tppt) cc_final: 0.7074 (tttt) REVERT: E 284 GLN cc_start: 0.8543 (tp40) cc_final: 0.8141 (mm-40) REVERT: E 337 ARG cc_start: 0.7055 (mtp-110) cc_final: 0.6778 (ttp80) REVERT: F 291 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7245 (tmtt) REVERT: F 297 ASP cc_start: 0.8554 (m-30) cc_final: 0.8348 (m-30) REVERT: G 87 ASN cc_start: 0.7817 (p0) cc_final: 0.7522 (p0) REVERT: G 119 ASN cc_start: 0.8041 (m110) cc_final: 0.7465 (m-40) REVERT: G 284 GLN cc_start: 0.8347 (tp-100) cc_final: 0.7802 (tp-100) REVERT: G 308 ASP cc_start: 0.8691 (t0) cc_final: 0.8282 (t0) REVERT: G 342 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8163 (ptpt) REVERT: H 156 SER cc_start: 0.9142 (t) cc_final: 0.8877 (p) REVERT: H 342 LYS cc_start: 0.8888 (ttpt) cc_final: 0.8574 (ptpp) REVERT: I 158 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7606 (ttp-170) REVERT: I 217 MET cc_start: 0.7348 (mmm) cc_final: 0.7088 (mmm) REVERT: I 245 PHE cc_start: 0.8206 (m-10) cc_final: 0.7923 (m-10) REVERT: I 284 GLN cc_start: 0.8905 (tp40) cc_final: 0.8640 (tp-100) REVERT: I 313 TYR cc_start: 0.8245 (t80) cc_final: 0.8042 (t80) REVERT: A 237 ARG cc_start: 0.7977 (ptt90) cc_final: 0.7519 (ptt90) outliers start: 80 outliers final: 41 residues processed: 439 average time/residue: 0.1428 time to fit residues: 99.2314 Evaluate side-chains 405 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 363 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 342 LYS Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 141 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 83 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN E 316 GLN F 236 ASN G 236 ASN H 284 GLN I 193 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.149323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114618 restraints weight = 30592.613| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.43 r_work: 0.3196 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21797 Z= 0.146 Angle : 0.552 8.413 29432 Z= 0.268 Chirality : 0.041 0.155 3369 Planarity : 0.004 0.038 3688 Dihedral : 10.541 87.186 3183 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.87 % Allowed : 22.18 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.17), residues: 2631 helix: 1.00 (0.14), residues: 1491 sheet: -0.32 (0.44), residues: 132 loop : 0.09 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 247 TYR 0.012 0.001 TYR E 313 PHE 0.014 0.001 PHE I 245 TRP 0.006 0.001 TRP H 220 HIS 0.002 0.000 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00358 (21797) covalent geometry : angle 0.55224 (29432) hydrogen bonds : bond 0.03033 ( 1035) hydrogen bonds : angle 4.54623 ( 2991) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 384 time to evaluate : 0.955 Fit side-chains REVERT: C 207 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: B 260 SER cc_start: 0.8779 (m) cc_final: 0.8443 (t) REVERT: B 284 GLN cc_start: 0.7894 (mp10) cc_final: 0.7584 (mp10) REVERT: D 92 ASP cc_start: 0.7765 (m-30) cc_final: 0.7347 (t0) REVERT: D 262 GLN cc_start: 0.8311 (mp10) cc_final: 0.8007 (mt0) REVERT: D 284 GLN cc_start: 0.8575 (tp40) cc_final: 0.7951 (tp-100) REVERT: E 105 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7806 (mm-30) REVERT: E 275 LYS cc_start: 0.8373 (tppt) cc_final: 0.7137 (tttt) REVERT: E 284 GLN cc_start: 0.8564 (tp40) cc_final: 0.8180 (mm-40) REVERT: E 337 ARG cc_start: 0.6991 (mtp-110) cc_final: 0.6702 (ttp80) REVERT: F 291 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7269 (tmtt) REVERT: F 297 ASP cc_start: 0.8341 (m-30) cc_final: 0.8136 (m-30) REVERT: G 80 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8518 (tt) REVERT: G 87 ASN cc_start: 0.7640 (p0) cc_final: 0.7360 (p0) REVERT: G 119 ASN cc_start: 0.7988 (m110) cc_final: 0.7458 (m-40) REVERT: G 209 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8981 (m) REVERT: G 284 GLN cc_start: 0.8368 (tp-100) cc_final: 0.7843 (tp-100) REVERT: G 308 ASP cc_start: 0.8569 (t0) cc_final: 0.8189 (t0) REVERT: H 156 SER cc_start: 0.9075 (t) cc_final: 0.8782 (p) REVERT: H 207 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8150 (pt0) REVERT: H 342 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8622 (ptpp) REVERT: I 73 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7083 (mm-30) REVERT: I 158 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7557 (mtm-85) REVERT: I 284 GLN cc_start: 0.8916 (tp40) cc_final: 0.8342 (tp-100) REVERT: I 313 TYR cc_start: 0.8216 (t80) cc_final: 0.7932 (t80) REVERT: A 85 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: A 237 ARG cc_start: 0.7977 (ptt90) cc_final: 0.7506 (ptt90) outliers start: 91 outliers final: 60 residues processed: 447 average time/residue: 0.1393 time to fit residues: 99.3146 Evaluate side-chains 424 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 359 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 293 PHE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 223 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 226 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 245 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 235 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN F 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.110982 restraints weight = 30240.919| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.41 r_work: 0.3179 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21797 Z= 0.128 Angle : 0.544 7.377 29432 Z= 0.263 Chirality : 0.041 0.226 3369 Planarity : 0.003 0.039 3688 Dihedral : 10.343 83.311 3183 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.53 % Allowed : 22.94 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.17), residues: 2631 helix: 1.11 (0.14), residues: 1483 sheet: -0.21 (0.43), residues: 140 loop : 0.11 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 349 TYR 0.013 0.001 TYR F 264 PHE 0.017 0.001 PHE I 245 TRP 0.005 0.001 TRP A 166 HIS 0.002 0.000 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00314 (21797) covalent geometry : angle 0.54359 (29432) hydrogen bonds : bond 0.02922 ( 1035) hydrogen bonds : angle 4.50357 ( 2991) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 391 time to evaluate : 1.029 Fit side-chains REVERT: C 45 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7660 (tm-30) REVERT: C 207 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: B 260 SER cc_start: 0.8768 (m) cc_final: 0.8417 (t) REVERT: B 284 GLN cc_start: 0.7940 (mp10) cc_final: 0.7597 (mp10) REVERT: D 92 ASP cc_start: 0.7805 (m-30) cc_final: 0.7340 (t0) REVERT: D 221 ASP cc_start: 0.7774 (t0) cc_final: 0.7535 (t0) REVERT: D 262 GLN cc_start: 0.8438 (mp10) cc_final: 0.8061 (mt0) REVERT: D 284 GLN cc_start: 0.8533 (tp40) cc_final: 0.8171 (tp-100) REVERT: E 105 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7935 (mm-30) REVERT: E 275 LYS cc_start: 0.8315 (tppt) cc_final: 0.7078 (tttt) REVERT: E 284 GLN cc_start: 0.8518 (tp40) cc_final: 0.8111 (mm-40) REVERT: E 337 ARG cc_start: 0.7031 (mtp-110) cc_final: 0.6725 (ttm170) REVERT: F 291 LYS cc_start: 0.8247 (mmmt) cc_final: 0.7214 (tmtt) REVERT: F 297 ASP cc_start: 0.8534 (m-30) cc_final: 0.8324 (m-30) REVERT: G 87 ASN cc_start: 0.7925 (p0) cc_final: 0.7539 (p0) REVERT: G 119 ASN cc_start: 0.8076 (m110) cc_final: 0.7499 (m-40) REVERT: G 209 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.9044 (m) REVERT: G 284 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7711 (tp-100) REVERT: G 308 ASP cc_start: 0.8671 (t0) cc_final: 0.8311 (t0) REVERT: H 156 SER cc_start: 0.9157 (t) cc_final: 0.8883 (p) REVERT: H 207 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: H 284 GLN cc_start: 0.8351 (tp40) cc_final: 0.8069 (tp-100) REVERT: H 342 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8568 (ptpp) REVERT: I 73 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7151 (mm-30) REVERT: I 245 PHE cc_start: 0.8043 (m-10) cc_final: 0.7793 (m-80) REVERT: I 248 ARG cc_start: 0.8470 (mtt90) cc_final: 0.8169 (mtt90) REVERT: I 284 GLN cc_start: 0.8855 (tp40) cc_final: 0.8233 (tp-100) REVERT: I 313 TYR cc_start: 0.8174 (t80) cc_final: 0.7943 (t80) REVERT: A 85 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: A 237 ARG cc_start: 0.7957 (ptt90) cc_final: 0.7753 (ptt90) outliers start: 83 outliers final: 59 residues processed: 449 average time/residue: 0.1395 time to fit residues: 99.6848 Evaluate side-chains 424 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 361 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 173 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 9 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 240 optimal weight: 0.0070 chunk 81 optimal weight: 0.0670 chunk 228 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 GLN C 225 ASN C 236 ASN D 124 GLN E 262 GLN E 316 GLN H 236 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112586 restraints weight = 30302.636| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.42 r_work: 0.3204 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21797 Z= 0.108 Angle : 0.540 9.817 29432 Z= 0.261 Chirality : 0.040 0.207 3369 Planarity : 0.003 0.038 3688 Dihedral : 10.102 86.832 3183 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.74 % Allowed : 23.28 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.17), residues: 2631 helix: 1.23 (0.14), residues: 1462 sheet: -0.16 (0.43), residues: 140 loop : 0.13 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 349 TYR 0.013 0.001 TYR F 264 PHE 0.018 0.001 PHE I 245 TRP 0.007 0.001 TRP F 54 HIS 0.001 0.000 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00262 (21797) covalent geometry : angle 0.54007 (29432) hydrogen bonds : bond 0.02807 ( 1035) hydrogen bonds : angle 4.45182 ( 2991) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 393 time to evaluate : 0.731 Fit side-chains REVERT: C 45 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7670 (tm-30) REVERT: C 308 ASP cc_start: 0.8687 (t0) cc_final: 0.8437 (t0) REVERT: C 347 LYS cc_start: 0.8290 (tppt) cc_final: 0.7908 (mmtm) REVERT: B 260 SER cc_start: 0.8785 (m) cc_final: 0.8440 (t) REVERT: B 284 GLN cc_start: 0.7947 (mp10) cc_final: 0.7562 (mp10) REVERT: B 343 ASP cc_start: 0.6654 (m-30) cc_final: 0.5798 (m-30) REVERT: D 92 ASP cc_start: 0.7808 (m-30) cc_final: 0.7381 (t0) REVERT: D 219 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8922 (mm) REVERT: D 221 ASP cc_start: 0.7739 (t0) cc_final: 0.7400 (t0) REVERT: D 262 GLN cc_start: 0.8410 (mp10) cc_final: 0.8080 (mt0) REVERT: D 284 GLN cc_start: 0.8608 (tp40) cc_final: 0.8252 (tp-100) REVERT: E 105 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8005 (mm-30) REVERT: E 275 LYS cc_start: 0.8284 (tppt) cc_final: 0.7076 (tttt) REVERT: E 284 GLN cc_start: 0.8560 (tp40) cc_final: 0.8171 (mm-40) REVERT: E 337 ARG cc_start: 0.6964 (mtp-110) cc_final: 0.6684 (ttm170) REVERT: F 291 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7231 (tmtt) REVERT: G 87 ASN cc_start: 0.7876 (p0) cc_final: 0.7491 (p0) REVERT: G 119 ASN cc_start: 0.8072 (m110) cc_final: 0.7729 (m-40) REVERT: G 209 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.9076 (m) REVERT: G 284 GLN cc_start: 0.8311 (tp-100) cc_final: 0.7783 (tp-100) REVERT: G 308 ASP cc_start: 0.8604 (t0) cc_final: 0.8273 (t0) REVERT: H 156 SER cc_start: 0.9141 (t) cc_final: 0.8878 (p) REVERT: H 207 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: H 284 GLN cc_start: 0.8384 (tp40) cc_final: 0.8144 (tp-100) REVERT: H 342 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8594 (ptpp) REVERT: I 73 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7153 (mm-30) REVERT: I 158 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7470 (mtm-85) REVERT: I 284 GLN cc_start: 0.8912 (tp40) cc_final: 0.8299 (tp-100) REVERT: I 313 TYR cc_start: 0.8169 (t80) cc_final: 0.7931 (t80) REVERT: A 85 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7021 (mp0) outliers start: 88 outliers final: 59 residues processed: 452 average time/residue: 0.1450 time to fit residues: 103.4248 Evaluate side-chains 434 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 371 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 224 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 171 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 236 optimal weight: 0.5980 chunk 179 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN B 236 ASN D 289 ASN ** H 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.113836 restraints weight = 30329.972| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.45 r_work: 0.3192 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21797 Z= 0.121 Angle : 0.549 9.928 29432 Z= 0.266 Chirality : 0.041 0.198 3369 Planarity : 0.004 0.060 3688 Dihedral : 10.005 85.762 3183 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.74 % Allowed : 23.70 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2631 helix: 1.23 (0.14), residues: 1468 sheet: -0.08 (0.43), residues: 140 loop : 0.16 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 248 TYR 0.012 0.001 TYR F 264 PHE 0.031 0.001 PHE I 245 TRP 0.007 0.001 TRP I 220 HIS 0.001 0.000 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00295 (21797) covalent geometry : angle 0.54933 (29432) hydrogen bonds : bond 0.02807 ( 1035) hydrogen bonds : angle 4.42775 ( 2991) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 386 time to evaluate : 0.876 Fit side-chains REVERT: C 45 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7677 (tm-30) REVERT: C 308 ASP cc_start: 0.8702 (t0) cc_final: 0.8434 (t0) REVERT: C 347 LYS cc_start: 0.8299 (tppt) cc_final: 0.7948 (mmtm) REVERT: B 284 GLN cc_start: 0.7986 (mp10) cc_final: 0.7496 (mp10) REVERT: B 343 ASP cc_start: 0.6586 (m-30) cc_final: 0.5720 (m-30) REVERT: D 92 ASP cc_start: 0.7802 (m-30) cc_final: 0.7370 (t0) REVERT: D 219 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8898 (mm) REVERT: D 221 ASP cc_start: 0.7684 (t0) cc_final: 0.7380 (t0) REVERT: D 262 GLN cc_start: 0.8430 (mp10) cc_final: 0.8064 (mt0) REVERT: D 284 GLN cc_start: 0.8623 (tp40) cc_final: 0.8255 (tp-100) REVERT: E 105 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8077 (mm-30) REVERT: E 275 LYS cc_start: 0.8267 (tppt) cc_final: 0.7092 (tttt) REVERT: E 284 GLN cc_start: 0.8561 (tp40) cc_final: 0.8179 (mm-40) REVERT: E 337 ARG cc_start: 0.6966 (mtp-110) cc_final: 0.6745 (ttp80) REVERT: F 73 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: F 291 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7210 (tmtt) REVERT: G 87 ASN cc_start: 0.7861 (p0) cc_final: 0.7486 (p0) REVERT: G 119 ASN cc_start: 0.8074 (m110) cc_final: 0.7736 (m-40) REVERT: G 209 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.9084 (m) REVERT: G 284 GLN cc_start: 0.8310 (tp-100) cc_final: 0.7775 (tp-100) REVERT: G 308 ASP cc_start: 0.8605 (t0) cc_final: 0.8292 (t0) REVERT: H 156 SER cc_start: 0.9147 (t) cc_final: 0.8883 (p) REVERT: H 207 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8244 (pt0) REVERT: H 284 GLN cc_start: 0.8381 (tp40) cc_final: 0.8161 (tp40) REVERT: H 342 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8607 (ptpp) REVERT: I 52 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7872 (tt) REVERT: I 73 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7188 (mm-30) REVERT: I 157 ILE cc_start: 0.8228 (tp) cc_final: 0.8006 (pt) REVERT: I 158 ARG cc_start: 0.7816 (ttm-80) cc_final: 0.7465 (mtm-85) REVERT: I 284 GLN cc_start: 0.8917 (tp40) cc_final: 0.8283 (tp-100) REVERT: A 85 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: A 141 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6907 (tpp) outliers start: 88 outliers final: 63 residues processed: 449 average time/residue: 0.1403 time to fit residues: 100.4737 Evaluate side-chains 440 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 370 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 293 PHE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 342 LYS Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 224 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 8 optimal weight: 5.9990 chunk 211 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN C 236 ASN B 236 ASN E 262 GLN ** H 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.148542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114289 restraints weight = 30232.752| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.38 r_work: 0.3215 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21797 Z= 0.126 Angle : 0.562 11.092 29432 Z= 0.270 Chirality : 0.041 0.192 3369 Planarity : 0.004 0.070 3688 Dihedral : 9.956 84.439 3183 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.40 % Allowed : 24.13 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2631 helix: 1.26 (0.14), residues: 1462 sheet: -0.02 (0.43), residues: 140 loop : 0.18 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 248 TYR 0.013 0.001 TYR F 264 PHE 0.010 0.001 PHE F 154 TRP 0.006 0.001 TRP F 54 HIS 0.001 0.000 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00309 (21797) covalent geometry : angle 0.56209 (29432) hydrogen bonds : bond 0.02804 ( 1035) hydrogen bonds : angle 4.41569 ( 2991) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 384 time to evaluate : 0.929 Fit side-chains REVERT: C 45 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7664 (tm-30) REVERT: C 308 ASP cc_start: 0.8699 (t0) cc_final: 0.8427 (t0) REVERT: C 347 LYS cc_start: 0.8293 (tppt) cc_final: 0.7978 (mmtm) REVERT: B 284 GLN cc_start: 0.7975 (mp10) cc_final: 0.7530 (mp10) REVERT: D 92 ASP cc_start: 0.7820 (m-30) cc_final: 0.7394 (t0) REVERT: D 219 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.8938 (mm) REVERT: D 221 ASP cc_start: 0.7685 (t0) cc_final: 0.7389 (t0) REVERT: D 262 GLN cc_start: 0.8399 (mp10) cc_final: 0.8072 (mt0) REVERT: D 284 GLN cc_start: 0.8640 (tp40) cc_final: 0.8289 (tp-100) REVERT: E 105 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8060 (mm-30) REVERT: E 275 LYS cc_start: 0.8261 (tppt) cc_final: 0.7106 (tttt) REVERT: E 284 GLN cc_start: 0.8609 (tp40) cc_final: 0.8237 (mm-40) REVERT: F 73 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: F 291 LYS cc_start: 0.8203 (mmmt) cc_final: 0.7182 (tmtt) REVERT: G 80 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8581 (tt) REVERT: G 87 ASN cc_start: 0.7833 (p0) cc_final: 0.7483 (p0) REVERT: G 119 ASN cc_start: 0.8044 (m110) cc_final: 0.7711 (m-40) REVERT: G 209 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9091 (m) REVERT: G 284 GLN cc_start: 0.8350 (tp-100) cc_final: 0.7826 (tp-100) REVERT: G 308 ASP cc_start: 0.8589 (t0) cc_final: 0.8285 (t0) REVERT: H 207 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: H 284 GLN cc_start: 0.8409 (tp40) cc_final: 0.8149 (tp40) REVERT: H 342 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8649 (ptpp) REVERT: I 52 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7850 (tt) REVERT: I 73 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7214 (mm-30) REVERT: I 284 GLN cc_start: 0.8938 (tp40) cc_final: 0.8299 (tp-100) REVERT: A 85 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: A 141 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6857 (tpp) outliers start: 80 outliers final: 64 residues processed: 439 average time/residue: 0.1409 time to fit residues: 98.3136 Evaluate side-chains 438 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 366 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 293 PHE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 342 LYS Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 224 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 180 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 134 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 GLN C 225 ASN C 236 ASN B 236 ASN E 262 GLN ** H 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.147858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114196 restraints weight = 30420.134| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.30 r_work: 0.3178 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21797 Z= 0.182 Angle : 0.602 9.566 29432 Z= 0.293 Chirality : 0.042 0.184 3369 Planarity : 0.004 0.067 3688 Dihedral : 10.084 84.558 3183 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.57 % Allowed : 23.83 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2631 helix: 1.20 (0.14), residues: 1473 sheet: -0.17 (0.43), residues: 140 loop : 0.19 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 237 TYR 0.012 0.001 TYR F 264 PHE 0.013 0.002 PHE F 154 TRP 0.011 0.001 TRP H 220 HIS 0.002 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00451 (21797) covalent geometry : angle 0.60212 (29432) hydrogen bonds : bond 0.02959 ( 1035) hydrogen bonds : angle 4.45425 ( 2991) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 365 time to evaluate : 0.863 Fit side-chains REVERT: C 45 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7735 (tm-30) REVERT: B 122 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8074 (mm) REVERT: B 260 SER cc_start: 0.8817 (m) cc_final: 0.8464 (t) REVERT: B 284 GLN cc_start: 0.8004 (mp10) cc_final: 0.7570 (mp10) REVERT: B 343 ASP cc_start: 0.6599 (m-30) cc_final: 0.5722 (m-30) REVERT: D 92 ASP cc_start: 0.7867 (m-30) cc_final: 0.7473 (t0) REVERT: D 219 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9016 (mm) REVERT: D 221 ASP cc_start: 0.7840 (t0) cc_final: 0.7498 (t0) REVERT: D 262 GLN cc_start: 0.8473 (mp10) cc_final: 0.8130 (mt0) REVERT: D 284 GLN cc_start: 0.8613 (tp40) cc_final: 0.8282 (tp-100) REVERT: E 105 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8145 (mm-30) REVERT: E 275 LYS cc_start: 0.8269 (tppt) cc_final: 0.7124 (tttt) REVERT: E 284 GLN cc_start: 0.8634 (tp40) cc_final: 0.8260 (mm-40) REVERT: F 73 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: F 291 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7221 (tmtt) REVERT: G 80 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8649 (tt) REVERT: G 87 ASN cc_start: 0.8036 (p0) cc_final: 0.7741 (p0) REVERT: G 119 ASN cc_start: 0.8105 (m110) cc_final: 0.7797 (m-40) REVERT: G 209 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.9106 (m) REVERT: G 308 ASP cc_start: 0.8624 (t0) cc_final: 0.8321 (t0) REVERT: H 207 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: H 342 LYS cc_start: 0.8963 (ttpt) cc_final: 0.8699 (ptpp) REVERT: I 73 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7173 (mm-30) REVERT: I 284 GLN cc_start: 0.8952 (tp40) cc_final: 0.8270 (tp-100) REVERT: A 85 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: A 141 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6925 (tpp) outliers start: 84 outliers final: 70 residues processed: 423 average time/residue: 0.1349 time to fit residues: 91.9230 Evaluate side-chains 434 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 356 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 293 PHE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 342 LYS Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 93 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 17 optimal weight: 0.0470 chunk 242 optimal weight: 0.8980 chunk 256 optimal weight: 0.0870 chunk 257 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 251 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 GLN C 225 ASN C 236 ASN B 236 ASN E 262 GLN ** H 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.157291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124164 restraints weight = 30461.498| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.34 r_work: 0.3294 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21797 Z= 0.112 Angle : 0.574 9.833 29432 Z= 0.278 Chirality : 0.041 0.187 3369 Planarity : 0.004 0.075 3688 Dihedral : 9.925 84.896 3183 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.89 % Allowed : 24.77 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2631 helix: 1.27 (0.14), residues: 1461 sheet: -0.13 (0.43), residues: 140 loop : 0.25 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 237 TYR 0.012 0.001 TYR F 264 PHE 0.010 0.001 PHE G 344 TRP 0.007 0.001 TRP F 220 HIS 0.001 0.000 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00271 (21797) covalent geometry : angle 0.57419 (29432) hydrogen bonds : bond 0.02792 ( 1035) hydrogen bonds : angle 4.42136 ( 2991) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 378 time to evaluate : 0.844 Fit side-chains REVERT: C 45 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7497 (tm-30) REVERT: C 308 ASP cc_start: 0.8592 (t0) cc_final: 0.8305 (t0) REVERT: C 347 LYS cc_start: 0.8361 (tppt) cc_final: 0.8041 (mmtm) REVERT: B 122 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8068 (mm) REVERT: B 284 GLN cc_start: 0.7999 (mp10) cc_final: 0.7630 (mp10) REVERT: D 92 ASP cc_start: 0.7697 (m-30) cc_final: 0.7421 (t0) REVERT: D 219 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8843 (mm) REVERT: D 221 ASP cc_start: 0.7577 (t0) cc_final: 0.7339 (t0) REVERT: D 262 GLN cc_start: 0.8291 (mp10) cc_final: 0.7958 (mt0) REVERT: D 284 GLN cc_start: 0.8638 (tp40) cc_final: 0.8332 (tp-100) REVERT: E 99 LEU cc_start: 0.8472 (tt) cc_final: 0.8189 (tp) REVERT: E 105 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7920 (mm-30) REVERT: E 275 LYS cc_start: 0.8242 (tppt) cc_final: 0.7166 (tttt) REVERT: E 284 GLN cc_start: 0.8615 (tp40) cc_final: 0.8251 (mm-40) REVERT: F 73 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: F 291 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7188 (tmtt) REVERT: G 87 ASN cc_start: 0.7768 (p0) cc_final: 0.7507 (p0) REVERT: G 119 ASN cc_start: 0.7937 (m110) cc_final: 0.7662 (m-40) REVERT: G 209 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8999 (m) REVERT: G 308 ASP cc_start: 0.8421 (t0) cc_final: 0.8143 (t0) REVERT: H 207 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8090 (pt0) REVERT: H 342 LYS cc_start: 0.8898 (ttpt) cc_final: 0.8693 (ptpp) REVERT: I 73 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7080 (mm-30) REVERT: I 205 ASP cc_start: 0.6859 (p0) cc_final: 0.6596 (p0) REVERT: I 284 GLN cc_start: 0.8978 (tp40) cc_final: 0.8355 (tp-100) REVERT: I 315 LYS cc_start: 0.8387 (tmtt) cc_final: 0.7825 (mtmm) REVERT: A 85 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: A 141 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6740 (tpp) outliers start: 68 outliers final: 54 residues processed: 428 average time/residue: 0.1359 time to fit residues: 93.8838 Evaluate side-chains 420 residues out of total 2354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 359 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 293 PHE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 342 LYS Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 177 MET Chi-restraints excluded: chain H residue 207 GLU Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 9 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 256 optimal weight: 0.0170 chunk 169 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 90 optimal weight: 0.0020 chunk 1 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 0.0770 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN C 225 ASN B 236 ASN E 262 GLN ** H 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126566 restraints weight = 30489.510| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.34 r_work: 0.3330 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21797 Z= 0.107 Angle : 0.558 9.640 29432 Z= 0.271 Chirality : 0.041 0.185 3369 Planarity : 0.004 0.069 3688 Dihedral : 9.736 89.724 3183 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.46 % Allowed : 25.28 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.17), residues: 2631 helix: 1.29 (0.14), residues: 1464 sheet: -0.02 (0.43), residues: 140 loop : 0.35 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 158 TYR 0.012 0.001 TYR F 264 PHE 0.017 0.001 PHE I 197 TRP 0.008 0.001 TRP F 220 HIS 0.002 0.000 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00255 (21797) covalent geometry : angle 0.55797 (29432) hydrogen bonds : bond 0.02714 ( 1035) hydrogen bonds : angle 4.33325 ( 2991) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7740.19 seconds wall clock time: 132 minutes 25.67 seconds (7945.67 seconds total)