Starting phenix.real_space_refine on Fri Feb 6 01:27:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmd_62428/02_2026/9kmd_62428.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmd_62428/02_2026/9kmd_62428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kmd_62428/02_2026/9kmd_62428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmd_62428/02_2026/9kmd_62428.map" model { file = "/net/cci-nas-00/data/ceres_data/9kmd_62428/02_2026/9kmd_62428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmd_62428/02_2026/9kmd_62428.cif" } resolution = 2.99 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= 0.011 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 107 5.16 5 C 13628 2.51 5 N 3661 2.21 5 O 4140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21572 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2319 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 13, 'TRANS': 280} Chain breaks: 1 Chain: "B" Number of atoms: 2370 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 299, 2359 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 13, 'TRANS': 285} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 299, 2359 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 13, 'TRANS': 285} Chain breaks: 1 bond proxies already assigned to first conformer: 2385 Chain: "C" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2379 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} Chain breaks: 1 Chain: "D" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2375 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 13, 'TRANS': 287} Chain breaks: 1 Chain: "E" Number of atoms: 2368 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 299, 2360 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 13, 'TRANS': 285} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 299, 2360 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 13, 'TRANS': 285} Chain breaks: 1 bond proxies already assigned to first conformer: 2388 Chain: "F" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2343 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain breaks: 1 Chain: "G" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2338 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 13, 'TRANS': 282} Chain breaks: 1 Chain: "H" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2346 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain breaks: 1 Chain: "I" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2346 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain breaks: 1 Chain: "J" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 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} 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: "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: "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} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG B 74 " occ=0.57 ... (20 atoms not shown) pdb=" NH2BARG B 74 " occ=0.43 Time building chain proxies: 6.27, per 1000 atoms: 0.29 Number of scatterers: 21572 At special positions: 0 Unit cell: (152.52, 138.17, 139.4, 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 107 16.00 P 27 15.00 Mg 9 11.99 O 4140 8.00 N 3661 7.00 C 13628 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: 1.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 9 sheets defined 64.2% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 39 through 42 removed outlier: 4.108A pdb=" N LYS A 42 " --> pdb=" O LEU A 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 43 through 61 Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.980A pdb=" N GLU A 66 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.552A pdb=" N ILE A 93 " --> pdb=" O PHE A 90 " (cutoff:3.500A) 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: 3.605A pdb=" N TYR A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.734A 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 247 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 282 through 290 removed outlier: 4.006A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 319 removed outlier: 3.676A pdb=" N ALA A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 348 removed outlier: 3.919A pdb=" N PHE A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.897A pdb=" N GLU B 66 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' 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 115 through 119 removed outlier: 3.513A pdb=" N SER B 118 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN B 119 " --> pdb=" O VAL B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 115 through 119' Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 168 through 184 removed outlier: 3.511A pdb=" N LYS B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.974A 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 237 through 241 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.650A pdb=" N ARG B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 294 through 310 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.653A pdb=" N PHE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 61 Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.861A pdb=" N GLU C 66 " --> pdb=" O ALA C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 77 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.723A pdb=" N ILE C 93 " --> pdb=" O PHE C 90 " (cutoff:3.500A) 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: 3.699A pdb=" N TYR C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.869A pdb=" N GLN C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.571A pdb=" N ILE C 162 " --> pdb=" O ARG C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 184 removed outlier: 3.715A pdb=" N LYS C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.932A 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 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 294 through 310 Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 340 through 348 removed outlier: 4.497A pdb=" N LYS C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 61 Processing helix chain 'D' and resid 62 through 67 removed outlier: 3.810A pdb=" N GLU D 66 " --> pdb=" O ALA D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 77 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.524A pdb=" N ILE D 93 " --> pdb=" O PHE D 90 " (cutoff:3.500A) 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: 3.636A pdb=" N TYR D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.050A 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 Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.612A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 310 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 340 through 346 removed outlier: 3.859A 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 Processing helix chain 'E' and resid 70 through 77 Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.517A pdb=" N ILE E 93 " --> pdb=" O PHE E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.335A pdb=" N ASN E 119 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER E 120 " --> pdb=" O TYR E 117 " (cutoff:3.500A) Proline residue: E 121 - end of helix Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 158 through 163 removed outlier: 3.642A pdb=" N ILE E 162 " --> pdb=" O ARG E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.250A 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 237 through 241 Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 294 through 320 removed outlier: 5.109A pdb=" N GLU E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.603A 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 65 removed outlier: 3.639A pdb=" N ALA F 65 " --> pdb=" O PRO F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 70 through 77 Processing helix chain 'F' and resid 78 through 80 No H-bonds generated for 'chain 'F' and resid 78 through 80' 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 107 through 113 Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.630A pdb=" N LEU F 123 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN F 124 " --> pdb=" O PRO F 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 120 through 124' Processing helix chain 'F' and resid 138 through 150 Processing helix chain 'F' and resid 158 through 163 Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.166A 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 Processing helix chain 'F' and resid 242 through 248 Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 282 through 290 Processing helix chain 'F' and resid 294 through 310 Processing helix chain 'F' and resid 310 through 320 Processing helix chain 'F' and resid 340 through 348 removed outlier: 3.579A pdb=" N LYS F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 61 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 70 through 77 Processing helix chain 'G' and resid 89 through 93 Processing helix chain 'G' and resid 96 through 107 Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 120 through 124 removed outlier: 3.973A pdb=" N GLN G 124 " --> pdb=" O PRO G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 158 through 163 Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 193 through 198 removed outlier: 4.131A 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 237 through 241 Processing helix chain 'G' and resid 242 through 248 Processing helix chain 'G' and resid 259 through 271 Processing helix chain 'G' and resid 282 through 290 removed outlier: 3.907A pdb=" N ILE G 286 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 310 Processing helix chain 'G' and resid 310 through 320 Processing helix chain 'G' and resid 340 through 348 removed outlier: 3.991A pdb=" N PHE G 344 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS G 347 " --> pdb=" O ASP G 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 61 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 70 through 77 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 120 through 124 removed outlier: 3.996A pdb=" N GLN H 124 " --> pdb=" O PRO H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 150 Processing helix chain 'H' and resid 158 through 163 Processing helix chain 'H' and resid 168 through 184 Processing helix chain 'H' and resid 193 through 198 removed outlier: 4.261A 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 242 through 248 Processing helix chain 'H' and resid 259 through 271 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 294 through 310 Processing helix chain 'H' and resid 310 through 320 Processing helix chain 'H' and resid 340 through 348 removed outlier: 3.855A pdb=" N PHE H 344 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS H 347 " --> pdb=" O ASP H 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 61 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 89 through 93 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 Processing helix chain 'I' and resid 138 through 150 Processing helix chain 'I' and resid 158 through 163 removed outlier: 3.780A pdb=" N ILE I 162 " --> pdb=" O ARG I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 184 Processing helix chain 'I' and resid 193 through 198 removed outlier: 4.051A pdb=" N PHE I 197 " --> pdb=" O GLN I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 221 Processing helix chain 'I' and resid 242 through 248 Processing helix chain 'I' and resid 259 through 271 Processing helix chain 'I' and resid 283 through 290 Processing helix chain 'I' and resid 294 through 320 removed outlier: 5.189A pdb=" N GLU I 312 " --> pdb=" O ASP I 308 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TYR I 313 " --> pdb=" O ALA I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 348 removed outlier: 3.965A pdb=" N PHE I 344 " --> pdb=" O LYS I 340 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS I 347 " --> pdb=" O ASP I 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 157 removed outlier: 6.230A pdb=" N ASN A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N PHE A 190 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASP A 192 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE A 157 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS A 187 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE A 232 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE A 189 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA A 234 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE A 191 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 129 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N THR A 235 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 131 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N PHE A 253 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 153 through 156 removed outlier: 6.177A pdb=" N ASN B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N PHE B 190 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N CYS B 187 " --> pdb=" O MET B 230 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE B 232 " --> pdb=" O CYS B 187 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE B 189 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA B 234 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE B 191 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 removed outlier: 4.088A pdb=" N PHE C 154 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 234 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.904A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP D 192 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 234 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 153 through 156 removed outlier: 6.664A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 153 through 156 removed outlier: 6.247A pdb=" N ASN F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE F 190 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP F 192 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 234 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU F 130 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 80 through 81 removed outlier: 4.160A pdb=" N PHE G 154 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP G 192 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA G 234 " --> pdb=" O ILE G 191 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY G 128 " --> pdb=" O LYS G 251 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N PHE G 253 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU G 130 " --> pdb=" O PHE G 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 80 through 81 removed outlier: 4.059A pdb=" N PHE H 154 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP H 192 " --> pdb=" O ILE H 157 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA H 234 " --> pdb=" O ILE H 191 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL H 129 " --> pdb=" O GLY H 233 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR H 235 " --> pdb=" O VAL H 129 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU H 131 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY H 128 " --> pdb=" O LYS H 251 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE H 253 " --> pdb=" O GLY H 128 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU H 130 " --> pdb=" O PHE H 253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 80 through 81 removed outlier: 4.165A pdb=" N PHE I 154 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP I 192 " --> pdb=" O ILE I 157 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS I 187 " --> pdb=" O MET I 230 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE I 232 " --> pdb=" O CYS I 187 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE I 189 " --> pdb=" O ILE I 232 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA I 234 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE I 191 " --> pdb=" O ALA I 234 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY I 128 " --> pdb=" O LYS I 251 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE I 253 " --> pdb=" O GLY I 128 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU I 130 " --> pdb=" O PHE I 253 " (cutoff:3.500A) 1089 hydrogen bonds defined for protein. 3096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 2.21 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: 5592 1.33 - 1.46: 4239 1.46 - 1.58: 11859 1.58 - 1.70: 41 1.70 - 1.83: 187 Bond restraints: 21918 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 6.81e+01 bond pdb=" C4 ATP I 401 " pdb=" C5 ATP I 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.53e+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 6.51e+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 6.51e+01 bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.48e+01 ... (remaining 21913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 29365 4.28 - 8.55: 186 8.55 - 12.83: 26 12.83 - 17.11: 9 17.11 - 21.38: 7 Bond angle restraints: 29593 Sorted by residual: angle pdb=" PB ATP I 401 " pdb=" O3B ATP I 401 " pdb=" PG ATP I 401 " ideal model delta sigma weight residual 139.87 118.49 21.38 1.00e+00 1.00e+00 4.57e+02 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 120.81 19.06 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 121.15 18.72 1.00e+00 1.00e+00 3.50e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 121.95 17.92 1.00e+00 1.00e+00 3.21e+02 angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 122.25 17.62 1.00e+00 1.00e+00 3.11e+02 ... (remaining 29588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11634 17.98 - 35.96: 1598 35.96 - 53.94: 428 53.94 - 71.92: 89 71.92 - 89.90: 41 Dihedral angle restraints: 13790 sinusoidal: 5904 harmonic: 7886 Sorted by residual: dihedral pdb=" CA LEU D 184 " pdb=" C LEU D 184 " pdb=" N GLN D 185 " pdb=" CA GLN D 185 " 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 LEU G 184 " pdb=" C LEU G 184 " pdb=" N GLN G 185 " pdb=" CA GLN G 185 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LEU E 184 " pdb=" C LEU E 184 " pdb=" N GLN E 185 " pdb=" CA GLN E 185 " ideal model delta harmonic sigma weight residual 180.00 -155.27 -24.73 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 13787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2895 0.066 - 0.133: 440 0.133 - 0.199: 39 0.199 - 0.265: 9 0.265 - 0.332: 6 Chirality restraints: 3389 Sorted by residual: chirality pdb=" CA LEU F 184 " pdb=" N LEU F 184 " pdb=" C LEU F 184 " pdb=" CB LEU F 184 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA LEU H 184 " pdb=" N LEU H 184 " pdb=" C LEU H 184 " pdb=" CB LEU H 184 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ILE B 155 " pdb=" N ILE B 155 " pdb=" C ILE B 155 " pdb=" CB ILE B 155 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3386 not shown) Planarity restraints: 3706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 120 " -0.085 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO E 121 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 337 " -0.061 5.00e-02 4.00e+02 9.21e-02 1.36e+01 pdb=" N PRO D 338 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO D 338 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 338 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 184 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C LEU F 184 " 0.054 2.00e-02 2.50e+03 pdb=" O LEU F 184 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN F 185 " -0.018 2.00e-02 2.50e+03 ... (remaining 3703 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 85 2.44 - 3.06: 13391 3.06 - 3.67: 34028 3.67 - 4.29: 52247 4.29 - 4.90: 86838 Nonbonded interactions: 186589 Sorted by model distance: nonbonded pdb=" O3G ATP A 401 " pdb="MG MG A 402 " model vdw 1.827 2.170 nonbonded pdb=" O2B ATP I 401 " pdb="MG MG I 402 " model vdw 1.860 2.170 nonbonded pdb=" OG1 THR G 140 " pdb="MG MG G 402 " model vdw 1.887 2.170 nonbonded pdb=" OG1 THR D 140 " pdb="MG MG D 402 " model vdw 1.962 2.170 nonbonded pdb=" OG1 THR A 140 " pdb="MG MG A 402 " model vdw 1.964 2.170 ... (remaining 186584 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 41 through 73 or resid 75 through 402)) selection = (chain 'B' and (resid 41 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'C' and (resid 41 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'D' and (resid 41 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'E' and (resid 41 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'F' and (resid 41 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'G' and (resid 41 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'H' and (resid 41 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 402)) selection = (chain 'I' and (resid 41 through 73 or resid 75 through 319 or resid 337 through \ 349 or resid 401 through 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=0.00 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: 13.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.390 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 21.830 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 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:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.007 0.090 21918 Z= 0.374 Angle : 0.936 21.383 29593 Z= 0.615 Chirality : 0.051 0.332 3389 Planarity : 0.006 0.126 3706 Dihedral : 18.197 89.899 8654 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 1.77 % Allowed : 25.72 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 2650 helix: 0.72 (0.13), residues: 1462 sheet: -0.31 (0.35), residues: 212 loop : 0.68 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 337 TYR 0.033 0.002 TYR C 264 PHE 0.016 0.002 PHE C 154 TRP 0.012 0.001 TRP B 166 HIS 0.003 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00658 (21918) covalent geometry : angle 0.93555 (29593) hydrogen bonds : bond 0.15721 ( 1089) hydrogen bonds : angle 5.79000 ( 3096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6768 (mtt90) cc_final: 0.6431 (mtt90) REVERT: B 308 ASP cc_start: 0.7574 (t0) cc_final: 0.7322 (t0) REVERT: C 163 MET cc_start: 0.9005 (mmm) cc_final: 0.8799 (mtt) REVERT: D 47 LYS cc_start: 0.7650 (tptt) cc_final: 0.7408 (mptt) REVERT: D 86 ILE cc_start: 0.8930 (mm) cc_final: 0.8705 (mm) REVERT: D 223 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8525 (mp) REVERT: E 338 PRO cc_start: 0.7918 (Cg_exo) cc_final: 0.7655 (Cg_endo) REVERT: H 272 LYS cc_start: 0.7537 (ptmt) cc_final: 0.7284 (ptmt) REVERT: H 337 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7471 (tmm-80) REVERT: H 346 LYS cc_start: 0.8102 (mttt) cc_final: 0.7859 (mtmt) outliers start: 42 outliers final: 27 residues processed: 339 average time/residue: 0.5992 time to fit residues: 232.3803 Evaluate side-chains 301 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 273 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN D 53 GLN F 91 GLN G 289 ASN I 91 GLN I 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.163999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125613 restraints weight = 42267.916| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.80 r_work: 0.3139 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21918 Z= 0.123 Angle : 0.521 9.546 29593 Z= 0.258 Chirality : 0.040 0.153 3389 Planarity : 0.004 0.085 3706 Dihedral : 11.351 88.020 3252 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.51 % Allowed : 24.62 % Favored : 71.88 % 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: 1.59 (0.16), residues: 2650 helix: 1.48 (0.14), residues: 1459 sheet: -0.60 (0.33), residues: 228 loop : 1.07 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 337 TYR 0.015 0.001 TYR C 264 PHE 0.008 0.001 PHE A 154 TRP 0.006 0.001 TRP B 54 HIS 0.002 0.000 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00280 (21918) covalent geometry : angle 0.52148 (29593) hydrogen bonds : bond 0.03576 ( 1089) hydrogen bonds : angle 4.54961 ( 3096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 292 time to evaluate : 1.016 Fit side-chains REVERT: A 237 ARG cc_start: 0.6694 (mtt90) cc_final: 0.6176 (mtt90) REVERT: B 308 ASP cc_start: 0.7636 (t0) cc_final: 0.7337 (t0) REVERT: D 47 LYS cc_start: 0.7688 (tptt) cc_final: 0.7326 (mptt) REVERT: D 221 ASP cc_start: 0.8306 (t0) cc_final: 0.8069 (t0) REVERT: E 88 ILE cc_start: 0.8099 (mp) cc_final: 0.7898 (mm) REVERT: F 158 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7371 (mtm180) REVERT: F 200 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: F 350 MET cc_start: 0.6064 (mmt) cc_final: 0.5726 (tpp) REVERT: G 105 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: H 215 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: H 243 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7388 (t0) REVERT: H 346 LYS cc_start: 0.8086 (mttt) cc_final: 0.7803 (mtmt) REVERT: I 102 ASP cc_start: 0.7714 (t0) cc_final: 0.7513 (t0) REVERT: I 172 LYS cc_start: 0.7479 (mttp) cc_final: 0.7012 (mmtt) REVERT: I 200 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5245 (pm20) REVERT: I 347 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6447 (mppt) outliers start: 83 outliers final: 26 residues processed: 349 average time/residue: 0.6357 time to fit residues: 253.8640 Evaluate side-chains 312 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 158 ARG Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 243 ASP Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 200 GLU Chi-restraints excluded: chain I residue 236 ASN Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 347 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 55 optimal weight: 9.9990 chunk 252 optimal weight: 0.9980 chunk 245 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN C 153 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 ASN E 236 ASN F 236 ASN G 53 GLN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.159227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120255 restraints weight = 43895.490| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.89 r_work: 0.3045 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 21918 Z= 0.240 Angle : 0.584 11.294 29593 Z= 0.286 Chirality : 0.043 0.149 3389 Planarity : 0.004 0.072 3706 Dihedral : 11.294 89.725 3208 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.01 % Allowed : 24.92 % Favored : 71.07 % 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: 1.68 (0.17), residues: 2650 helix: 1.51 (0.14), residues: 1465 sheet: -0.71 (0.32), residues: 245 loop : 1.28 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 337 TYR 0.017 0.001 TYR G 167 PHE 0.012 0.002 PHE E 178 TRP 0.010 0.001 TRP E 220 HIS 0.003 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00582 (21918) covalent geometry : angle 0.58436 (29593) hydrogen bonds : bond 0.03600 ( 1089) hydrogen bonds : angle 4.51242 ( 3096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 295 time to evaluate : 0.903 Fit side-chains REVERT: A 237 ARG cc_start: 0.6688 (mtt90) cc_final: 0.6208 (mtt90) REVERT: B 308 ASP cc_start: 0.7627 (t0) cc_final: 0.7261 (m-30) REVERT: C 275 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8500 (mttp) REVERT: D 47 LYS cc_start: 0.7755 (tptt) cc_final: 0.7344 (mptt) REVERT: D 115 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8014 (mm-30) REVERT: D 223 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8604 (mp) REVERT: F 200 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: G 105 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: G 311 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7542 (ttmm) REVERT: H 215 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: H 337 ARG cc_start: 0.7867 (ttp80) cc_final: 0.7425 (ttp80) REVERT: H 346 LYS cc_start: 0.8229 (mttt) cc_final: 0.7961 (mtmt) REVERT: I 102 ASP cc_start: 0.7743 (t0) cc_final: 0.7529 (t0) REVERT: I 172 LYS cc_start: 0.7508 (mttp) cc_final: 0.7060 (mmtt) REVERT: I 200 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5358 (pm20) REVERT: I 247 ARG cc_start: 0.6962 (ttp-170) cc_final: 0.6739 (tmm160) REVERT: I 347 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6565 (mppt) outliers start: 95 outliers final: 37 residues processed: 358 average time/residue: 0.6139 time to fit residues: 252.6327 Evaluate side-chains 324 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 113 MET Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 137 CYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 200 GLU Chi-restraints excluded: chain I residue 236 ASN Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 347 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 201 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 242 optimal weight: 0.0270 chunk 56 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 240 optimal weight: 0.9980 overall best weight: 1.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 225 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN F 50 GLN F 91 GLN F 124 GLN G 53 GLN H 171 ASN H 182 ASN I 91 GLN I 289 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.161999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122160 restraints weight = 45269.889| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.79 r_work: 0.3097 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21918 Z= 0.158 Angle : 0.529 12.083 29593 Z= 0.257 Chirality : 0.041 0.144 3389 Planarity : 0.004 0.066 3706 Dihedral : 11.069 88.323 3208 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.27 % Allowed : 25.38 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.17), residues: 2650 helix: 1.73 (0.14), residues: 1458 sheet: -0.73 (0.32), residues: 235 loop : 1.25 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 247 TYR 0.010 0.001 TYR G 167 PHE 0.011 0.001 PHE I 197 TRP 0.006 0.001 TRP G 166 HIS 0.002 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00376 (21918) covalent geometry : angle 0.52909 (29593) hydrogen bonds : bond 0.03128 ( 1089) hydrogen bonds : angle 4.44413 ( 3096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 276 time to evaluate : 0.931 Fit side-chains REVERT: A 237 ARG cc_start: 0.6746 (mtt90) cc_final: 0.6298 (mtt90) REVERT: B 85 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: B 308 ASP cc_start: 0.7584 (t0) cc_final: 0.7245 (m-30) REVERT: C 275 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8488 (mttp) REVERT: D 47 LYS cc_start: 0.7767 (tptt) cc_final: 0.7336 (mptt) REVERT: D 115 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7978 (mm-30) REVERT: D 223 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8587 (mp) REVERT: F 200 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: G 105 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: H 215 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: H 243 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7434 (t0) REVERT: H 337 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7475 (ttp80) REVERT: H 346 LYS cc_start: 0.8222 (mttt) cc_final: 0.8012 (mtmt) REVERT: I 79 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8213 (t) REVERT: I 172 LYS cc_start: 0.7500 (mttp) cc_final: 0.7071 (mmtt) REVERT: I 200 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.5355 (pm20) REVERT: I 247 ARG cc_start: 0.6971 (ttp-170) cc_final: 0.6732 (tmm160) REVERT: I 252 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.6794 (mpt-90) outliers start: 101 outliers final: 38 residues processed: 346 average time/residue: 0.6187 time to fit residues: 244.8325 Evaluate side-chains 319 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 270 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 243 ASP Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 200 GLU Chi-restraints excluded: chain I residue 236 ASN Chi-restraints excluded: chain I residue 252 ARG Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 219 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 180 optimal weight: 0.4980 chunk 145 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN F 91 GLN H 182 ASN I 91 GLN I 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.161901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123911 restraints weight = 42543.924| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.76 r_work: 0.3086 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21918 Z= 0.154 Angle : 0.526 10.949 29593 Z= 0.255 Chirality : 0.040 0.143 3389 Planarity : 0.003 0.061 3706 Dihedral : 10.937 87.112 3208 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.72 % Allowed : 25.97 % Favored : 70.31 % 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: 1.99 (0.17), residues: 2650 helix: 1.81 (0.14), residues: 1459 sheet: -0.73 (0.30), residues: 261 loop : 1.42 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 263 TYR 0.019 0.001 TYR C 264 PHE 0.011 0.001 PHE I 197 TRP 0.006 0.001 TRP G 166 HIS 0.002 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00370 (21918) covalent geometry : angle 0.52560 (29593) hydrogen bonds : bond 0.03028 ( 1089) hydrogen bonds : angle 4.38918 ( 3096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 282 time to evaluate : 0.845 Fit side-chains REVERT: A 237 ARG cc_start: 0.6683 (mtt90) cc_final: 0.6259 (mtt90) REVERT: B 85 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: B 308 ASP cc_start: 0.7555 (t0) cc_final: 0.7223 (m-30) REVERT: C 74 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7932 (mtp180) REVERT: C 260 SER cc_start: 0.8406 (p) cc_final: 0.8197 (p) REVERT: C 275 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8455 (mttp) REVERT: D 115 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: F 200 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: G 105 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8165 (mm-30) REVERT: H 215 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7204 (tm-30) REVERT: H 243 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7437 (t0) REVERT: H 337 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7451 (ttp80) REVERT: I 79 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8160 (t) REVERT: I 172 LYS cc_start: 0.7454 (mttp) cc_final: 0.7031 (mmtt) REVERT: I 200 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5310 (pm20) REVERT: I 247 ARG cc_start: 0.6926 (ttp-170) cc_final: 0.6678 (tmm160) REVERT: I 252 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.6818 (mpt-90) outliers start: 88 outliers final: 45 residues processed: 341 average time/residue: 0.6123 time to fit residues: 238.0877 Evaluate side-chains 330 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 274 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 137 CYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 243 ASP Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 200 GLU Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain I residue 236 ASN Chi-restraints excluded: chain I residue 252 ARG Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 127 optimal weight: 0.0870 chunk 54 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 243 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN F 91 GLN H 182 ASN I 91 GLN I 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.162359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123948 restraints weight = 37288.050| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.40 r_work: 0.3129 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21918 Z= 0.139 Angle : 0.517 10.983 29593 Z= 0.251 Chirality : 0.040 0.143 3389 Planarity : 0.003 0.058 3706 Dihedral : 10.798 81.955 3208 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.59 % Allowed : 26.18 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.17), residues: 2650 helix: 1.94 (0.14), residues: 1439 sheet: -0.75 (0.30), residues: 266 loop : 1.45 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 263 TYR 0.016 0.001 TYR G 167 PHE 0.010 0.001 PHE I 197 TRP 0.006 0.001 TRP G 166 HIS 0.002 0.000 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00331 (21918) covalent geometry : angle 0.51666 (29593) hydrogen bonds : bond 0.02929 ( 1089) hydrogen bonds : angle 4.36010 ( 3096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 279 time to evaluate : 0.920 Fit side-chains REVERT: A 237 ARG cc_start: 0.6738 (mtt90) cc_final: 0.6325 (mtt90) REVERT: B 85 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: B 308 ASP cc_start: 0.7594 (t0) cc_final: 0.7273 (m-30) REVERT: C 74 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8047 (mtp180) REVERT: C 275 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8455 (mttp) REVERT: C 346 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8079 (mttp) REVERT: D 115 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8000 (mm-30) REVERT: D 223 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8649 (mp) REVERT: F 200 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: F 350 MET cc_start: 0.6075 (OUTLIER) cc_final: 0.5692 (tpp) REVERT: G 105 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8337 (mm-30) REVERT: H 215 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7433 (tm-30) REVERT: H 243 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7668 (t0) REVERT: H 337 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7488 (ttp80) REVERT: H 346 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7703 (mttt) REVERT: I 79 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8287 (t) REVERT: I 172 LYS cc_start: 0.7586 (mttp) cc_final: 0.7158 (mmtt) REVERT: I 200 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5297 (pm20) REVERT: I 247 ARG cc_start: 0.6959 (ttp-170) cc_final: 0.6711 (tmm160) REVERT: I 252 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.6892 (mpt-90) outliers start: 84 outliers final: 45 residues processed: 338 average time/residue: 0.6230 time to fit residues: 240.7180 Evaluate side-chains 328 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 137 CYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 243 ASP Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 200 GLU Chi-restraints excluded: chain I residue 236 ASN Chi-restraints excluded: chain I residue 252 ARG Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 7 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 ASN F 91 GLN I 91 GLN I 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.160675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119925 restraints weight = 45109.227| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.83 r_work: 0.3115 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21918 Z= 0.169 Angle : 0.537 11.251 29593 Z= 0.261 Chirality : 0.041 0.155 3389 Planarity : 0.004 0.056 3706 Dihedral : 10.726 82.765 3207 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.72 % Allowed : 26.27 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.17), residues: 2650 helix: 1.91 (0.14), residues: 1446 sheet: -0.80 (0.30), residues: 267 loop : 1.38 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 337 TYR 0.020 0.001 TYR G 167 PHE 0.011 0.001 PHE I 197 TRP 0.007 0.001 TRP G 166 HIS 0.002 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00408 (21918) covalent geometry : angle 0.53663 (29593) hydrogen bonds : bond 0.03017 ( 1089) hydrogen bonds : angle 4.37209 ( 3096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 283 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6639 (mtt90) cc_final: 0.6250 (mtt90) REVERT: B 85 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: B 308 ASP cc_start: 0.7507 (t0) cc_final: 0.7198 (m-30) REVERT: C 74 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7854 (mtp180) REVERT: C 275 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8415 (mttp) REVERT: C 346 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8032 (mttp) REVERT: D 115 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7906 (mm-30) REVERT: D 223 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8547 (mp) REVERT: D 342 LYS cc_start: 0.8356 (ttpt) cc_final: 0.7714 (ptmm) REVERT: E 163 MET cc_start: 0.7709 (mtt) cc_final: 0.7251 (mtt) REVERT: E 337 ARG cc_start: 0.8227 (tmm-80) cc_final: 0.7585 (tmt90) REVERT: F 200 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: F 350 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5730 (tpp) REVERT: G 105 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: G 350 MET cc_start: 0.6684 (mmt) cc_final: 0.6378 (mpt) REVERT: H 215 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: H 243 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7394 (t0) REVERT: H 337 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7465 (ttp80) REVERT: H 346 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7708 (mttt) REVERT: I 79 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8098 (t) REVERT: I 172 LYS cc_start: 0.7407 (mttp) cc_final: 0.6981 (mmtt) REVERT: I 200 GLU cc_start: 0.5974 (OUTLIER) cc_final: 0.5254 (pm20) REVERT: I 247 ARG cc_start: 0.6862 (ttp-170) cc_final: 0.6601 (tmm160) REVERT: I 252 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.6942 (mpt-90) outliers start: 87 outliers final: 48 residues processed: 345 average time/residue: 0.6537 time to fit residues: 258.1659 Evaluate side-chains 338 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 277 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 137 CYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain H residue 243 ASP Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 342 LYS Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 200 GLU Chi-restraints excluded: chain I residue 236 ASN Chi-restraints excluded: chain I residue 252 ARG Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 122 optimal weight: 0.0570 chunk 264 optimal weight: 10.0000 chunk 177 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 241 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN B 225 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN H 182 ASN I 91 GLN I 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.163215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122833 restraints weight = 50130.364| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.09 r_work: 0.3144 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21918 Z= 0.120 Angle : 0.510 10.910 29593 Z= 0.249 Chirality : 0.040 0.153 3389 Planarity : 0.003 0.056 3706 Dihedral : 10.568 82.688 3207 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.00 % Allowed : 27.41 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.17), residues: 2650 helix: 2.01 (0.14), residues: 1438 sheet: -0.69 (0.29), residues: 280 loop : 1.50 (0.22), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 199 TYR 0.020 0.001 TYR C 264 PHE 0.009 0.001 PHE I 197 TRP 0.005 0.001 TRP C 166 HIS 0.002 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00284 (21918) covalent geometry : angle 0.50983 (29593) hydrogen bonds : bond 0.02801 ( 1089) hydrogen bonds : angle 4.31937 ( 3096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 283 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6630 (mtt90) cc_final: 0.6248 (mtt90) REVERT: A 263 ARG cc_start: 0.5118 (mtt90) cc_final: 0.4724 (mmt180) REVERT: B 85 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: B 308 ASP cc_start: 0.7484 (t0) cc_final: 0.7175 (m-30) REVERT: C 346 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8015 (mttp) REVERT: D 115 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7863 (mm-30) REVERT: D 342 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7683 (ptmm) REVERT: E 163 MET cc_start: 0.7729 (mtt) cc_final: 0.7296 (mtt) REVERT: F 97 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: F 159 MET cc_start: 0.7679 (mmm) cc_final: 0.7477 (tpp) REVERT: F 200 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: F 221 ASP cc_start: 0.7975 (t0) cc_final: 0.7642 (t0) REVERT: G 105 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8103 (mm-30) REVERT: H 215 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: H 243 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7343 (t0) REVERT: H 337 ARG cc_start: 0.7685 (ttp80) cc_final: 0.7445 (ttp80) REVERT: H 346 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7653 (mttt) REVERT: I 172 LYS cc_start: 0.7370 (mttp) cc_final: 0.6934 (mmtt) REVERT: I 200 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5209 (pm20) REVERT: I 247 ARG cc_start: 0.6823 (ttp-170) cc_final: 0.6563 (tmm160) REVERT: I 252 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6843 (mpt-90) outliers start: 70 outliers final: 40 residues processed: 327 average time/residue: 0.6138 time to fit residues: 229.3337 Evaluate side-chains 322 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 243 ASP Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 342 LYS Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 200 GLU Chi-restraints excluded: chain I residue 236 ASN Chi-restraints excluded: chain I residue 252 ARG Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 2 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 8 optimal weight: 0.4980 chunk 19 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 216 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN E 236 ASN F 153 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 = 0.3844 r_free = 0.3844 target = 0.163256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123523 restraints weight = 39793.016| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.66 r_work: 0.3139 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21918 Z= 0.120 Angle : 0.514 10.530 29593 Z= 0.250 Chirality : 0.040 0.141 3389 Planarity : 0.003 0.056 3706 Dihedral : 10.434 84.465 3207 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.58 % Allowed : 27.79 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.17), residues: 2650 helix: 2.05 (0.14), residues: 1450 sheet: -0.66 (0.29), residues: 280 loop : 1.52 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 337 TYR 0.021 0.001 TYR I 264 PHE 0.008 0.001 PHE A 154 TRP 0.005 0.001 TRP G 166 HIS 0.002 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00284 (21918) covalent geometry : angle 0.51358 (29593) hydrogen bonds : bond 0.02747 ( 1089) hydrogen bonds : angle 4.27241 ( 3096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 283 time to evaluate : 0.774 Fit side-chains REVERT: A 237 ARG cc_start: 0.6637 (mtt90) cc_final: 0.6264 (mtt90) REVERT: A 263 ARG cc_start: 0.5155 (mtt90) cc_final: 0.4794 (mmt180) REVERT: B 85 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: B 308 ASP cc_start: 0.7455 (t0) cc_final: 0.7166 (m-30) REVERT: C 346 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8019 (mttp) REVERT: D 115 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: D 342 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7686 (ptmm) REVERT: E 163 MET cc_start: 0.7709 (mtt) cc_final: 0.7265 (mtt) REVERT: E 167 TYR cc_start: 0.8753 (t80) cc_final: 0.8515 (t80) REVERT: E 337 ARG cc_start: 0.8357 (tmm-80) cc_final: 0.7619 (tmt90) REVERT: F 97 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: F 200 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: F 221 ASP cc_start: 0.8002 (t0) cc_final: 0.7728 (t0) REVERT: G 105 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8089 (mm-30) REVERT: H 215 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: H 243 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7046 (t0) REVERT: H 337 ARG cc_start: 0.7686 (ttp80) cc_final: 0.7462 (ttp80) REVERT: H 346 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7725 (mttt) REVERT: I 79 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.8060 (t) REVERT: I 172 LYS cc_start: 0.7385 (mttp) cc_final: 0.6944 (mmtt) REVERT: I 200 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.5227 (pm20) REVERT: I 247 ARG cc_start: 0.6858 (ttp-170) cc_final: 0.6557 (tmm160) REVERT: I 252 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.6836 (mpt-90) outliers start: 60 outliers final: 40 residues processed: 322 average time/residue: 0.5317 time to fit residues: 196.6747 Evaluate side-chains 328 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 277 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 243 ASP Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 342 LYS Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 200 GLU Chi-restraints excluded: chain I residue 236 ASN Chi-restraints excluded: chain I residue 252 ARG Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 116 optimal weight: 0.0050 chunk 142 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN C 289 ASN D 289 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN I 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.163376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.123451 restraints weight = 36738.267| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.47 r_work: 0.3150 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 21918 Z= 0.196 Angle : 0.683 59.192 29593 Z= 0.380 Chirality : 0.041 0.461 3389 Planarity : 0.003 0.055 3706 Dihedral : 10.435 84.517 3207 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.36 % Allowed : 28.25 % Favored : 69.38 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.17), residues: 2650 helix: 2.04 (0.14), residues: 1450 sheet: -0.66 (0.29), residues: 280 loop : 1.53 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 248 TYR 0.013 0.001 TYR G 167 PHE 0.008 0.001 PHE A 154 TRP 0.005 0.001 TRP G 166 HIS 0.002 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00399 (21918) covalent geometry : angle 0.68281 (29593) hydrogen bonds : bond 0.02762 ( 1089) hydrogen bonds : angle 4.27124 ( 3096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 277 time to evaluate : 1.106 Fit side-chains REVERT: A 237 ARG cc_start: 0.6633 (mtt90) cc_final: 0.6262 (mtt90) REVERT: A 263 ARG cc_start: 0.5126 (mtt90) cc_final: 0.4775 (mmt180) REVERT: B 85 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: B 308 ASP cc_start: 0.7455 (t0) cc_final: 0.7168 (m-30) REVERT: C 346 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8024 (mttp) REVERT: D 115 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7843 (mm-30) REVERT: D 342 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7693 (ptmm) REVERT: E 163 MET cc_start: 0.7701 (mtt) cc_final: 0.7247 (mtt) REVERT: E 167 TYR cc_start: 0.8738 (t80) cc_final: 0.8511 (t80) REVERT: E 337 ARG cc_start: 0.8371 (tmm-80) cc_final: 0.7717 (tmt90) REVERT: F 97 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: F 200 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: F 221 ASP cc_start: 0.7996 (t0) cc_final: 0.7687 (t0) REVERT: G 105 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8092 (mm-30) REVERT: H 215 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: H 243 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7027 (t0) REVERT: H 337 ARG cc_start: 0.7698 (ttp80) cc_final: 0.7479 (ttp80) REVERT: H 346 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7726 (mttt) REVERT: I 79 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8060 (t) REVERT: I 172 LYS cc_start: 0.7385 (mttp) cc_final: 0.6945 (mmtt) REVERT: I 200 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5231 (pm20) REVERT: I 247 ARG cc_start: 0.6840 (ttp-170) cc_final: 0.6573 (tmm160) REVERT: I 252 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.6835 (mpt-90) outliers start: 55 outliers final: 39 residues processed: 310 average time/residue: 0.6321 time to fit residues: 223.7481 Evaluate side-chains 326 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 276 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 243 ASP Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 342 LYS Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 200 GLU Chi-restraints excluded: chain I residue 236 ASN Chi-restraints excluded: chain I residue 252 ARG Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 122 optimal weight: 0.1980 chunk 164 optimal weight: 0.5980 chunk 255 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 196 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN I 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.163373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125068 restraints weight = 42569.719| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.91 r_work: 0.3119 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 21918 Z= 0.196 Angle : 0.683 59.200 29593 Z= 0.380 Chirality : 0.041 0.461 3389 Planarity : 0.003 0.055 3706 Dihedral : 10.435 84.517 3207 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.15 % Allowed : 28.42 % Favored : 69.43 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.17), residues: 2650 helix: 2.04 (0.14), residues: 1450 sheet: -0.66 (0.29), residues: 280 loop : 1.53 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 248 TYR 0.013 0.001 TYR G 167 PHE 0.008 0.001 PHE A 154 TRP 0.005 0.001 TRP G 166 HIS 0.002 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00399 (21918) covalent geometry : angle 0.68278 (29593) hydrogen bonds : bond 0.02762 ( 1089) hydrogen bonds : angle 4.27124 ( 3096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10052.13 seconds wall clock time: 171 minutes 41.83 seconds (10301.83 seconds total)