Starting phenix.real_space_refine on Sat Feb 7 19:58:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yin_72999/02_2026/9yin_72999.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yin_72999/02_2026/9yin_72999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yin_72999/02_2026/9yin_72999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yin_72999/02_2026/9yin_72999.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yin_72999/02_2026/9yin_72999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yin_72999/02_2026/9yin_72999.map" } resolution = 2.4 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= 0.006 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 22356 2.51 5 N 6060 2.21 5 O 6972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s 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: 35568 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2964 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 16, 'TRANS': 365} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 4.12, per 1000 atoms: 0.12 Number of scatterers: 35568 At special positions: 0 Unit cell: (165.966, 165.966, 106.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 6972 8.00 N 6060 7.00 C 22356 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: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8664 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 51.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 95 through 122 removed outlier: 3.823A pdb=" N LYS A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 234 through 256 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 281 through 299 removed outlier: 4.390A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 336 removed outlier: 4.656A pdb=" N PHE A 324 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 350 through 371 Processing helix chain 'A' and resid 371 through 386 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 52 through 63 Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 95 through 122 removed outlier: 3.823A pdb=" N LYS B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 142 through 149 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 190 through 192 No H-bonds generated for 'chain 'B' and resid 190 through 192' Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 234 through 256 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 281 through 299 removed outlier: 4.390A pdb=" N ALA B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 336 removed outlier: 4.656A pdb=" N PHE B 324 " --> pdb=" O ASP B 320 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 344 Processing helix chain 'B' and resid 350 through 371 Processing helix chain 'B' and resid 371 through 386 Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 52 through 63 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 95 through 122 removed outlier: 3.823A pdb=" N LYS C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 142 through 149 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 234 through 256 Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 281 through 299 removed outlier: 4.390A pdb=" N ALA C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 336 removed outlier: 4.656A pdb=" N PHE C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 328 " --> pdb=" O PHE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 344 Processing helix chain 'C' and resid 350 through 371 Processing helix chain 'C' and resid 371 through 386 Processing helix chain 'D' and resid 40 through 46 Processing helix chain 'D' and resid 52 through 63 Processing helix chain 'D' and resid 63 through 79 Processing helix chain 'D' and resid 95 through 122 removed outlier: 3.823A pdb=" N LYS D 107 " --> pdb=" O ASP D 103 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 142 through 149 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 223 through 227 Processing helix chain 'D' and resid 234 through 256 Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 281 through 299 removed outlier: 4.390A pdb=" N ALA D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP D 287 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 299 " --> pdb=" O MET D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 336 removed outlier: 4.656A pdb=" N PHE D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 328 " --> pdb=" O PHE D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 344 Processing helix chain 'D' and resid 350 through 371 Processing helix chain 'D' and resid 371 through 386 Processing helix chain 'E' and resid 40 through 46 Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 95 through 122 removed outlier: 3.823A pdb=" N LYS E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 142 through 149 Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 223 through 227 Processing helix chain 'E' and resid 234 through 256 Processing helix chain 'E' and resid 270 through 278 Processing helix chain 'E' and resid 281 through 299 removed outlier: 4.390A pdb=" N ALA E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP E 287 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY E 299 " --> pdb=" O MET E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 336 removed outlier: 4.656A pdb=" N PHE E 324 " --> pdb=" O ASP E 320 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 328 " --> pdb=" O PHE E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 344 Processing helix chain 'E' and resid 350 through 371 Processing helix chain 'E' and resid 371 through 386 Processing helix chain 'F' and resid 40 through 46 Processing helix chain 'F' and resid 52 through 63 Processing helix chain 'F' and resid 63 through 79 Processing helix chain 'F' and resid 95 through 122 removed outlier: 3.823A pdb=" N LYS F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 142 through 149 Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 190 through 192 No H-bonds generated for 'chain 'F' and resid 190 through 192' Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'F' and resid 223 through 227 Processing helix chain 'F' and resid 234 through 256 Processing helix chain 'F' and resid 270 through 278 Processing helix chain 'F' and resid 281 through 299 removed outlier: 4.390A pdb=" N ALA F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP F 287 " --> pdb=" O ASP F 283 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY F 299 " --> pdb=" O MET F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 336 removed outlier: 4.656A pdb=" N PHE F 324 " --> pdb=" O ASP F 320 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA F 328 " --> pdb=" O PHE F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 Processing helix chain 'F' and resid 350 through 371 Processing helix chain 'F' and resid 371 through 386 Processing helix chain 'G' and resid 40 through 46 Processing helix chain 'G' and resid 52 through 63 Processing helix chain 'G' and resid 63 through 79 Processing helix chain 'G' and resid 95 through 122 removed outlier: 3.823A pdb=" N LYS G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 142 through 149 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 190 through 192 No H-bonds generated for 'chain 'G' and resid 190 through 192' Processing helix chain 'G' and resid 208 through 210 No H-bonds generated for 'chain 'G' and resid 208 through 210' Processing helix chain 'G' and resid 223 through 227 Processing helix chain 'G' and resid 234 through 256 Processing helix chain 'G' and resid 270 through 278 Processing helix chain 'G' and resid 281 through 299 removed outlier: 4.390A pdb=" N ALA G 286 " --> pdb=" O VAL G 282 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP G 287 " --> pdb=" O ASP G 283 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY G 299 " --> pdb=" O MET G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 336 removed outlier: 4.656A pdb=" N PHE G 324 " --> pdb=" O ASP G 320 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA G 328 " --> pdb=" O PHE G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 344 Processing helix chain 'G' and resid 350 through 371 Processing helix chain 'G' and resid 371 through 386 Processing helix chain 'H' and resid 40 through 46 Processing helix chain 'H' and resid 52 through 63 Processing helix chain 'H' and resid 63 through 79 Processing helix chain 'H' and resid 95 through 122 removed outlier: 3.823A pdb=" N LYS H 107 " --> pdb=" O ASP H 103 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 142 through 149 Processing helix chain 'H' and resid 150 through 152 No H-bonds generated for 'chain 'H' and resid 150 through 152' Processing helix chain 'H' and resid 190 through 192 No H-bonds generated for 'chain 'H' and resid 190 through 192' Processing helix chain 'H' and resid 208 through 210 No H-bonds generated for 'chain 'H' and resid 208 through 210' Processing helix chain 'H' and resid 223 through 227 Processing helix chain 'H' and resid 234 through 256 Processing helix chain 'H' and resid 270 through 278 Processing helix chain 'H' and resid 281 through 299 removed outlier: 4.390A pdb=" N ALA H 286 " --> pdb=" O VAL H 282 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP H 287 " --> pdb=" O ASP H 283 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY H 299 " --> pdb=" O MET H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 336 removed outlier: 4.656A pdb=" N PHE H 324 " --> pdb=" O ASP H 320 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA H 328 " --> pdb=" O PHE H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 344 Processing helix chain 'H' and resid 350 through 371 Processing helix chain 'H' and resid 371 through 386 Processing helix chain 'I' and resid 40 through 46 Processing helix chain 'I' and resid 52 through 63 Processing helix chain 'I' and resid 63 through 79 Processing helix chain 'I' and resid 95 through 122 removed outlier: 3.823A pdb=" N LYS I 107 " --> pdb=" O ASP I 103 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 142 through 149 Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'I' and resid 190 through 192 No H-bonds generated for 'chain 'I' and resid 190 through 192' Processing helix chain 'I' and resid 208 through 210 No H-bonds generated for 'chain 'I' and resid 208 through 210' Processing helix chain 'I' and resid 223 through 227 Processing helix chain 'I' and resid 234 through 256 Processing helix chain 'I' and resid 270 through 278 Processing helix chain 'I' and resid 281 through 299 removed outlier: 4.390A pdb=" N ALA I 286 " --> pdb=" O VAL I 282 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP I 287 " --> pdb=" O ASP I 283 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY I 299 " --> pdb=" O MET I 295 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 336 removed outlier: 4.656A pdb=" N PHE I 324 " --> pdb=" O ASP I 320 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA I 328 " --> pdb=" O PHE I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 344 Processing helix chain 'I' and resid 350 through 371 Processing helix chain 'I' and resid 371 through 386 Processing helix chain 'J' and resid 40 through 46 Processing helix chain 'J' and resid 52 through 63 Processing helix chain 'J' and resid 63 through 79 Processing helix chain 'J' and resid 95 through 122 removed outlier: 3.823A pdb=" N LYS J 107 " --> pdb=" O ASP J 103 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 142 through 149 Processing helix chain 'J' and resid 150 through 152 No H-bonds generated for 'chain 'J' and resid 150 through 152' Processing helix chain 'J' and resid 190 through 192 No H-bonds generated for 'chain 'J' and resid 190 through 192' Processing helix chain 'J' and resid 208 through 210 No H-bonds generated for 'chain 'J' and resid 208 through 210' Processing helix chain 'J' and resid 223 through 227 Processing helix chain 'J' and resid 234 through 256 Processing helix chain 'J' and resid 270 through 278 Processing helix chain 'J' and resid 281 through 299 removed outlier: 4.390A pdb=" N ALA J 286 " --> pdb=" O VAL J 282 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP J 287 " --> pdb=" O ASP J 283 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY J 299 " --> pdb=" O MET J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 336 removed outlier: 4.656A pdb=" N PHE J 324 " --> pdb=" O ASP J 320 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA J 328 " --> pdb=" O PHE J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 344 Processing helix chain 'J' and resid 350 through 371 Processing helix chain 'J' and resid 371 through 386 Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'K' and resid 52 through 63 Processing helix chain 'K' and resid 63 through 79 Processing helix chain 'K' and resid 95 through 122 removed outlier: 3.823A pdb=" N LYS K 107 " --> pdb=" O ASP K 103 " (cutoff:3.500A) Proline residue: K 110 - end of helix Processing helix chain 'K' and resid 142 through 149 Processing helix chain 'K' and resid 150 through 152 No H-bonds generated for 'chain 'K' and resid 150 through 152' Processing helix chain 'K' and resid 190 through 192 No H-bonds generated for 'chain 'K' and resid 190 through 192' Processing helix chain 'K' and resid 208 through 210 No H-bonds generated for 'chain 'K' and resid 208 through 210' Processing helix chain 'K' and resid 223 through 227 Processing helix chain 'K' and resid 234 through 256 Processing helix chain 'K' and resid 270 through 278 Processing helix chain 'K' and resid 281 through 299 removed outlier: 4.390A pdb=" N ALA K 286 " --> pdb=" O VAL K 282 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP K 287 " --> pdb=" O ASP K 283 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY K 299 " --> pdb=" O MET K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 320 through 336 removed outlier: 4.656A pdb=" N PHE K 324 " --> pdb=" O ASP K 320 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA K 328 " --> pdb=" O PHE K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 344 Processing helix chain 'K' and resid 350 through 371 Processing helix chain 'K' and resid 371 through 386 Processing helix chain 'L' and resid 40 through 46 Processing helix chain 'L' and resid 52 through 63 Processing helix chain 'L' and resid 63 through 79 Processing helix chain 'L' and resid 95 through 122 removed outlier: 3.823A pdb=" N LYS L 107 " --> pdb=" O ASP L 103 " (cutoff:3.500A) Proline residue: L 110 - end of helix Processing helix chain 'L' and resid 142 through 149 Processing helix chain 'L' and resid 150 through 152 No H-bonds generated for 'chain 'L' and resid 150 through 152' Processing helix chain 'L' and resid 190 through 192 No H-bonds generated for 'chain 'L' and resid 190 through 192' Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 223 through 227 Processing helix chain 'L' and resid 234 through 256 Processing helix chain 'L' and resid 270 through 278 Processing helix chain 'L' and resid 281 through 299 removed outlier: 4.390A pdb=" N ALA L 286 " --> pdb=" O VAL L 282 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP L 287 " --> pdb=" O ASP L 283 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY L 299 " --> pdb=" O MET L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 336 removed outlier: 4.656A pdb=" N PHE L 324 " --> pdb=" O ASP L 320 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA L 328 " --> pdb=" O PHE L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 344 Processing helix chain 'L' and resid 350 through 371 Processing helix chain 'L' and resid 371 through 386 Processing sheet with id=1, first strand: chain 'A' and resid 83 through 86 Processing sheet with id=2, first strand: chain 'A' and resid 154 through 160 removed outlier: 6.854A pdb=" N GLN A 130 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE A 157 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 128 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A 126 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 165 through 170 removed outlier: 6.422A pdb=" N MET A 184 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP A 170 " --> pdb=" O PRO A 182 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 260 through 263 Processing sheet with id=5, first strand: chain 'B' and resid 83 through 86 Processing sheet with id=6, first strand: chain 'B' and resid 154 through 160 removed outlier: 6.855A pdb=" N GLN B 130 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 157 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE B 128 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA B 126 " --> pdb=" O PRO B 159 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 165 through 170 removed outlier: 6.422A pdb=" N MET B 184 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP B 170 " --> pdb=" O PRO B 182 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 260 through 263 Processing sheet with id=9, first strand: chain 'C' and resid 83 through 86 Processing sheet with id=10, first strand: chain 'C' and resid 154 through 160 removed outlier: 6.855A pdb=" N GLN C 130 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE C 157 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE C 128 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 126 " --> pdb=" O PRO C 159 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 165 through 170 removed outlier: 6.422A pdb=" N MET C 184 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP C 170 " --> pdb=" O PRO C 182 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 260 through 263 Processing sheet with id=13, first strand: chain 'D' and resid 83 through 86 Processing sheet with id=14, first strand: chain 'D' and resid 154 through 160 removed outlier: 6.854A pdb=" N GLN D 130 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE D 157 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE D 128 " --> pdb=" O PHE D 157 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA D 126 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'D' and resid 165 through 170 removed outlier: 6.422A pdb=" N MET D 184 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP D 170 " --> pdb=" O PRO D 182 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 260 through 263 Processing sheet with id=17, first strand: chain 'E' and resid 83 through 86 Processing sheet with id=18, first strand: chain 'E' and resid 154 through 160 removed outlier: 6.855A pdb=" N GLN E 130 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE E 157 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE E 128 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA E 126 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'E' and resid 165 through 170 removed outlier: 6.422A pdb=" N MET E 184 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP E 170 " --> pdb=" O PRO E 182 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'E' and resid 260 through 263 Processing sheet with id=21, first strand: chain 'F' and resid 83 through 86 Processing sheet with id=22, first strand: chain 'F' and resid 154 through 160 removed outlier: 6.855A pdb=" N GLN F 130 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE F 157 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE F 128 " --> pdb=" O PHE F 157 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA F 126 " --> pdb=" O PRO F 159 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'F' and resid 165 through 170 removed outlier: 6.422A pdb=" N MET F 184 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP F 170 " --> pdb=" O PRO F 182 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'F' and resid 260 through 263 Processing sheet with id=25, first strand: chain 'G' and resid 83 through 86 Processing sheet with id=26, first strand: chain 'G' and resid 154 through 160 removed outlier: 6.854A pdb=" N GLN G 130 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE G 157 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE G 128 " --> pdb=" O PHE G 157 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA G 126 " --> pdb=" O PRO G 159 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'G' and resid 165 through 170 removed outlier: 6.422A pdb=" N MET G 184 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP G 170 " --> pdb=" O PRO G 182 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'G' and resid 260 through 263 Processing sheet with id=29, first strand: chain 'H' and resid 83 through 86 Processing sheet with id=30, first strand: chain 'H' and resid 154 through 160 removed outlier: 6.855A pdb=" N GLN H 130 " --> pdb=" O VAL H 155 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE H 157 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE H 128 " --> pdb=" O PHE H 157 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA H 126 " --> pdb=" O PRO H 159 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'H' and resid 165 through 170 removed outlier: 6.422A pdb=" N MET H 184 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP H 170 " --> pdb=" O PRO H 182 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'H' and resid 260 through 263 Processing sheet with id=33, first strand: chain 'I' and resid 83 through 86 Processing sheet with id=34, first strand: chain 'I' and resid 154 through 160 removed outlier: 6.855A pdb=" N GLN I 130 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE I 157 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE I 128 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA I 126 " --> pdb=" O PRO I 159 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'I' and resid 165 through 170 removed outlier: 6.422A pdb=" N MET I 184 " --> pdb=" O SER I 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP I 170 " --> pdb=" O PRO I 182 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'I' and resid 260 through 263 Processing sheet with id=37, first strand: chain 'J' and resid 83 through 86 Processing sheet with id=38, first strand: chain 'J' and resid 154 through 160 removed outlier: 6.854A pdb=" N GLN J 130 " --> pdb=" O VAL J 155 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE J 157 " --> pdb=" O ILE J 128 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE J 128 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA J 126 " --> pdb=" O PRO J 159 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'J' and resid 165 through 170 removed outlier: 6.422A pdb=" N MET J 184 " --> pdb=" O SER J 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP J 170 " --> pdb=" O PRO J 182 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'J' and resid 260 through 263 Processing sheet with id=41, first strand: chain 'K' and resid 83 through 86 Processing sheet with id=42, first strand: chain 'K' and resid 154 through 160 removed outlier: 6.855A pdb=" N GLN K 130 " --> pdb=" O VAL K 155 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE K 157 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE K 128 " --> pdb=" O PHE K 157 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA K 126 " --> pdb=" O PRO K 159 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'K' and resid 165 through 170 removed outlier: 6.422A pdb=" N MET K 184 " --> pdb=" O SER K 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP K 170 " --> pdb=" O PRO K 182 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'K' and resid 260 through 263 Processing sheet with id=45, first strand: chain 'L' and resid 83 through 86 Processing sheet with id=46, first strand: chain 'L' and resid 154 through 160 removed outlier: 6.855A pdb=" N GLN L 130 " --> pdb=" O VAL L 155 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE L 157 " --> pdb=" O ILE L 128 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE L 128 " --> pdb=" O PHE L 157 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA L 126 " --> pdb=" O PRO L 159 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'L' and resid 165 through 170 removed outlier: 6.422A pdb=" N MET L 184 " --> pdb=" O SER L 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP L 170 " --> pdb=" O PRO L 182 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'L' and resid 260 through 263 1788 hydrogen bonds defined for protein. 5184 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: 7.35 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12060 1.34 - 1.46: 8116 1.46 - 1.58: 15788 1.58 - 1.70: 0 1.70 - 1.81: 324 Bond restraints: 36288 Sorted by residual: bond pdb=" CA VAL A 280 " pdb=" CB VAL A 280 " ideal model delta sigma weight residual 1.547 1.538 0.009 1.10e-02 8.26e+03 6.20e-01 bond pdb=" CA VAL J 280 " pdb=" CB VAL J 280 " ideal model delta sigma weight residual 1.547 1.538 0.009 1.10e-02 8.26e+03 6.20e-01 bond pdb=" CA VAL G 280 " pdb=" CB VAL G 280 " ideal model delta sigma weight residual 1.547 1.538 0.009 1.10e-02 8.26e+03 6.20e-01 bond pdb=" CA VAL D 280 " pdb=" CB VAL D 280 " ideal model delta sigma weight residual 1.547 1.538 0.009 1.10e-02 8.26e+03 6.20e-01 bond pdb=" CA VAL K 280 " pdb=" CB VAL K 280 " ideal model delta sigma weight residual 1.547 1.538 0.009 1.10e-02 8.26e+03 6.16e-01 ... (remaining 36283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 48296 1.66 - 3.31: 700 3.31 - 4.97: 192 4.97 - 6.63: 0 6.63 - 8.28: 12 Bond angle restraints: 49200 Sorted by residual: angle pdb=" CB MET L 362 " pdb=" CG MET L 362 " pdb=" SD MET L 362 " ideal model delta sigma weight residual 112.70 120.98 -8.28 3.00e+00 1.11e-01 7.63e+00 angle pdb=" CB MET C 362 " pdb=" CG MET C 362 " pdb=" SD MET C 362 " ideal model delta sigma weight residual 112.70 120.98 -8.28 3.00e+00 1.11e-01 7.63e+00 angle pdb=" CB MET I 362 " pdb=" CG MET I 362 " pdb=" SD MET I 362 " ideal model delta sigma weight residual 112.70 120.98 -8.28 3.00e+00 1.11e-01 7.63e+00 angle pdb=" CB MET F 362 " pdb=" CG MET F 362 " pdb=" SD MET F 362 " ideal model delta sigma weight residual 112.70 120.98 -8.28 3.00e+00 1.11e-01 7.63e+00 angle pdb=" CB MET J 362 " pdb=" CG MET J 362 " pdb=" SD MET J 362 " ideal model delta sigma weight residual 112.70 120.97 -8.27 3.00e+00 1.11e-01 7.61e+00 ... (remaining 49195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 19004 17.24 - 34.48: 2024 34.48 - 51.73: 764 51.73 - 68.97: 132 68.97 - 86.21: 48 Dihedral angle restraints: 21972 sinusoidal: 8604 harmonic: 13368 Sorted by residual: dihedral pdb=" CA ILE F 149 " pdb=" C ILE F 149 " pdb=" N LYS F 150 " pdb=" CA LYS F 150 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ILE C 149 " pdb=" C ILE C 149 " pdb=" N LYS C 150 " pdb=" CA LYS C 150 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ILE I 149 " pdb=" C ILE I 149 " pdb=" N LYS I 150 " pdb=" CA LYS I 150 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 21969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2856 0.025 - 0.050: 1394 0.050 - 0.075: 710 0.075 - 0.099: 244 0.099 - 0.124: 148 Chirality restraints: 5352 Sorted by residual: chirality pdb=" CA LEU F 109 " pdb=" N LEU F 109 " pdb=" C LEU F 109 " pdb=" CB LEU F 109 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA LEU L 109 " pdb=" N LEU L 109 " pdb=" C LEU L 109 " pdb=" CB LEU L 109 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA LEU C 109 " pdb=" N LEU C 109 " pdb=" C LEU C 109 " pdb=" CB LEU C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 5349 not shown) Planarity restraints: 6516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS K 208 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO K 209 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO K 209 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO K 209 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 208 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO E 209 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 209 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 209 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS H 208 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO H 209 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 209 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 209 " -0.024 5.00e-02 4.00e+02 ... (remaining 6513 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.02: 24 2.02 - 2.74: 3554 2.74 - 3.46: 50694 3.46 - 4.18: 91549 4.18 - 4.90: 161491 Nonbonded interactions: 307312 Sorted by model distance: nonbonded pdb=" OD2 ASP G 301 " pdb=" NZ LYS K 37 " model vdw 1.306 3.120 nonbonded pdb=" NZ LYS B 37 " pdb=" OD2 ASP J 301 " model vdw 1.306 3.120 nonbonded pdb=" OD2 ASP A 301 " pdb=" NZ LYS E 37 " model vdw 1.306 3.120 nonbonded pdb=" OD2 ASP D 301 " pdb=" NZ LYS H 37 " model vdw 1.306 3.120 nonbonded pdb=" NZ LYS D 37 " pdb=" OD2 ASP L 301 " model vdw 1.306 3.120 ... (remaining 307307 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 28.340 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.003 0.023 36288 Z= 0.132 Angle : 0.535 8.284 49200 Z= 0.286 Chirality : 0.040 0.124 5352 Planarity : 0.004 0.043 6516 Dihedral : 16.886 86.212 13308 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.59 % Allowed : 17.88 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.13), residues: 4560 helix: 2.02 (0.11), residues: 2136 sheet: -1.17 (0.20), residues: 624 loop : 0.95 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 148 TYR 0.006 0.001 TYR B 187 PHE 0.009 0.001 PHE D 111 TRP 0.006 0.001 TRP B 161 HIS 0.001 0.000 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00302 (36288) covalent geometry : angle 0.53496 (49200) hydrogen bonds : bond 0.12785 ( 1788) hydrogen bonds : angle 5.46172 ( 5184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 810 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7637 (mtm110) cc_final: 0.7372 (ttp-110) REVERT: B 145 LYS cc_start: 0.8340 (tppt) cc_final: 0.7485 (tptm) REVERT: B 148 ARG cc_start: 0.7672 (mtm110) cc_final: 0.7325 (ttp-110) REVERT: B 272 GLN cc_start: 0.8517 (tp40) cc_final: 0.8210 (tm-30) REVERT: B 276 GLN cc_start: 0.8763 (tt0) cc_final: 0.8248 (tp40) REVERT: B 341 ASN cc_start: 0.8145 (m-40) cc_final: 0.7665 (m110) REVERT: C 145 LYS cc_start: 0.8324 (tppt) cc_final: 0.7554 (tptm) REVERT: C 173 ASP cc_start: 0.7478 (t0) cc_final: 0.7060 (t0) REVERT: D 145 LYS cc_start: 0.7964 (tppt) cc_final: 0.7486 (tptm) REVERT: E 145 LYS cc_start: 0.7591 (tppt) cc_final: 0.7355 (tptm) REVERT: E 391 LYS cc_start: 0.8175 (ptmt) cc_final: 0.7802 (pmtt) REVERT: F 310 ASP cc_start: 0.6279 (m-30) cc_final: 0.5932 (m-30) REVERT: F 391 LYS cc_start: 0.7954 (ptmt) cc_final: 0.7716 (pmtt) REVERT: H 362 MET cc_start: 0.7407 (tpp) cc_final: 0.7032 (mmm) REVERT: H 403 ASP cc_start: 0.6821 (t70) cc_final: 0.6540 (t70) REVERT: I 98 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7037 (mt-10) REVERT: I 326 TYR cc_start: 0.6703 (t80) cc_final: 0.6499 (t80) REVERT: I 331 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7234 (mm-40) REVERT: I 374 TYR cc_start: 0.7589 (m-80) cc_final: 0.7383 (m-10) REVERT: I 403 ASP cc_start: 0.7273 (t70) cc_final: 0.6958 (t70) REVERT: J 76 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7608 (mppt) REVERT: J 398 TYR cc_start: 0.7924 (p90) cc_final: 0.7669 (p90) REVERT: J 403 ASP cc_start: 0.7579 (t70) cc_final: 0.7376 (t70) REVERT: K 318 MET cc_start: 0.8791 (mtp) cc_final: 0.8543 (mtt) REVERT: L 196 ASP cc_start: 0.7769 (t70) cc_final: 0.7369 (t70) REVERT: L 318 MET cc_start: 0.9195 (mtp) cc_final: 0.8919 (mtp) outliers start: 60 outliers final: 12 residues processed: 855 average time/residue: 0.7789 time to fit residues: 788.4077 Evaluate side-chains 542 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 530 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain J residue 263 SER Chi-restraints excluded: chain K residue 263 SER Chi-restraints excluded: chain K residue 402 ASN Chi-restraints excluded: chain L residue 263 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 3.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN B 366 GLN B 402 ASN C 366 GLN D 171 ASN D 276 GLN D 341 ASN D 366 GLN E 119 ASN E 164 GLN E 208 HIS E 402 ASN F 33 ASN F 119 ASN F 164 GLN F 206 GLN F 208 HIS G 102 ASN G 119 ASN G 164 GLN G 208 HIS G 366 GLN H 102 ASN H 119 ASN H 164 GLN H 366 GLN H 402 ASN I 102 ASN I 119 ASN I 164 GLN I 358 GLN I 366 GLN I 402 ASN J 102 ASN J 119 ASN J 164 GLN J 366 GLN J 402 ASN K 52 ASN K 102 ASN K 164 GLN L 119 ASN L 164 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.090123 restraints weight = 45611.601| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.02 r_work: 0.2946 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 36288 Z= 0.170 Angle : 0.586 6.981 49200 Z= 0.314 Chirality : 0.044 0.174 5352 Planarity : 0.004 0.044 6516 Dihedral : 4.721 38.190 4940 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.26 % Allowed : 17.49 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.12), residues: 4560 helix: 1.61 (0.11), residues: 2148 sheet: -1.07 (0.19), residues: 696 loop : 0.66 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 148 TYR 0.018 0.002 TYR J 397 PHE 0.020 0.002 PHE G 307 TRP 0.011 0.001 TRP I 401 HIS 0.007 0.002 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00374 (36288) covalent geometry : angle 0.58607 (49200) hydrogen bonds : bond 0.04489 ( 1788) hydrogen bonds : angle 4.65099 ( 5184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 567 time to evaluate : 1.475 Fit side-chains REVERT: A 294 GLU cc_start: 0.5679 (OUTLIER) cc_final: 0.4776 (tp30) REVERT: B 272 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8244 (tm-30) REVERT: B 276 GLN cc_start: 0.8679 (tt0) cc_final: 0.8082 (tp40) REVERT: B 294 GLU cc_start: 0.5430 (OUTLIER) cc_final: 0.4533 (tp30) REVERT: C 113 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8367 (ttt-90) REVERT: C 272 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8013 (tp40) REVERT: D 40 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7797 (mtp-110) REVERT: D 188 GLN cc_start: 0.8692 (tt0) cc_final: 0.7969 (tm-30) REVERT: D 278 MET cc_start: 0.8156 (mtp) cc_final: 0.7926 (mtp) REVERT: D 279 GLN cc_start: 0.8790 (mt0) cc_final: 0.8512 (mp10) REVERT: E 40 ARG cc_start: 0.8257 (mtp180) cc_final: 0.8000 (mtp85) REVERT: E 50 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8515 (mm-30) REVERT: E 76 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7999 (mmmt) REVERT: E 188 GLN cc_start: 0.8529 (tp40) cc_final: 0.8004 (tm-30) REVERT: E 276 GLN cc_start: 0.8317 (tt0) cc_final: 0.8061 (tm-30) REVERT: E 294 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.4628 (tm-30) REVERT: E 362 MET cc_start: 0.8418 (mmm) cc_final: 0.8174 (mmp) REVERT: E 402 ASN cc_start: 0.7118 (m110) cc_final: 0.6473 (p0) REVERT: F 174 GLU cc_start: 0.7862 (mp0) cc_final: 0.7631 (mp0) REVERT: F 177 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7447 (mt-10) REVERT: F 179 TYR cc_start: 0.8758 (t80) cc_final: 0.8518 (t80) REVERT: F 184 MET cc_start: 0.9196 (tpp) cc_final: 0.8852 (tpp) REVERT: F 188 GLN cc_start: 0.8293 (mt0) cc_final: 0.7909 (tm-30) REVERT: F 318 MET cc_start: 0.9027 (mtp) cc_final: 0.8772 (mtp) REVERT: F 369 ASP cc_start: 0.7947 (m-30) cc_final: 0.7722 (m-30) REVERT: G 40 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7611 (mtp-110) REVERT: G 173 ASP cc_start: 0.7719 (m-30) cc_final: 0.6962 (t0) REVERT: G 188 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7827 (tp40) REVERT: G 358 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7667 (mm-40) REVERT: H 40 ARG cc_start: 0.8074 (ttm170) cc_final: 0.7662 (mtp-110) REVERT: H 144 THR cc_start: 0.7671 (OUTLIER) cc_final: 0.7396 (p) REVERT: H 147 ARG cc_start: 0.7075 (ttm110) cc_final: 0.6603 (ttp80) REVERT: H 173 ASP cc_start: 0.7807 (m-30) cc_final: 0.7197 (t0) REVERT: H 188 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: H 294 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.4269 (tm-30) REVERT: H 403 ASP cc_start: 0.7050 (t70) cc_final: 0.6750 (t70) REVERT: I 147 ARG cc_start: 0.7107 (ttm110) cc_final: 0.6745 (ttp80) REVERT: I 184 MET cc_start: 0.9048 (tpp) cc_final: 0.8686 (tpp) REVERT: I 294 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5011 (tm-30) REVERT: I 403 ASP cc_start: 0.7269 (t70) cc_final: 0.6982 (t70) REVERT: J 147 ARG cc_start: 0.7308 (ttm110) cc_final: 0.6946 (ttp80) REVERT: J 294 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5318 (tm-30) REVERT: K 294 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.5052 (tp30) REVERT: L 99 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7608 (mtpt) REVERT: L 154 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8266 (mt) REVERT: L 174 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: L 196 ASP cc_start: 0.7738 (t70) cc_final: 0.7301 (t70) REVERT: L 294 GLU cc_start: 0.5862 (OUTLIER) cc_final: 0.4994 (tp30) outliers start: 161 outliers final: 33 residues processed: 664 average time/residue: 0.8111 time to fit residues: 630.8077 Evaluate side-chains 508 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 457 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 188 GLN Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 263 SER Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 378 SER Chi-restraints excluded: chain I residue 402 ASN Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain J residue 402 ASN Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 294 GLU Chi-restraints excluded: chain K residue 315 SER Chi-restraints excluded: chain L residue 99 LYS Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 174 GLU Chi-restraints excluded: chain L residue 294 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 204 optimal weight: 0.0270 chunk 189 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 223 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 overall best weight: 2.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN B 366 GLN C 164 GLN C 366 GLN D 164 GLN D 366 GLN E 366 GLN F 33 ASN F 366 GLN G 38 HIS G 366 GLN G 402 ASN H 52 ASN H 331 GLN H 358 GLN H 366 GLN H 402 ASN I 119 ASN J 38 HIS J 366 GLN L 119 ASN L 402 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.080500 restraints weight = 45660.168| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.97 r_work: 0.2801 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36288 Z= 0.185 Angle : 0.549 5.217 49200 Z= 0.286 Chirality : 0.043 0.200 5352 Planarity : 0.004 0.052 6516 Dihedral : 4.501 22.891 4921 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.36 % Allowed : 18.04 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.12), residues: 4560 helix: 1.57 (0.10), residues: 2160 sheet: -1.00 (0.19), residues: 696 loop : 0.93 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 118 TYR 0.015 0.002 TYR L 397 PHE 0.015 0.001 PHE D 111 TRP 0.008 0.001 TRP G 401 HIS 0.004 0.001 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00437 (36288) covalent geometry : angle 0.54870 (49200) hydrogen bonds : bond 0.05075 ( 1788) hydrogen bonds : angle 4.67937 ( 5184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 491 time to evaluate : 1.364 Fit side-chains REVERT: A 154 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8488 (mt) REVERT: A 294 GLU cc_start: 0.5996 (OUTLIER) cc_final: 0.4948 (tp30) REVERT: B 276 GLN cc_start: 0.8563 (tt0) cc_final: 0.7984 (tp40) REVERT: B 294 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.4594 (tm-30) REVERT: B 402 ASN cc_start: 0.8624 (p0) cc_final: 0.8414 (p0) REVERT: C 113 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8139 (ttt180) REVERT: C 196 ASP cc_start: 0.8124 (t70) cc_final: 0.7691 (t0) REVERT: C 291 GLU cc_start: 0.8246 (tt0) cc_final: 0.8001 (tt0) REVERT: C 294 GLU cc_start: 0.5554 (OUTLIER) cc_final: 0.4885 (tp30) REVERT: D 40 ARG cc_start: 0.8453 (mtp85) cc_final: 0.8134 (mtp-110) REVERT: D 279 GLN cc_start: 0.8978 (mt0) cc_final: 0.8747 (mp10) REVERT: D 294 GLU cc_start: 0.8651 (tm-30) cc_final: 0.7184 (tp30) REVERT: D 403 ASP cc_start: 0.8060 (t70) cc_final: 0.7817 (t70) REVERT: E 92 GLU cc_start: 0.5647 (pt0) cc_final: 0.5325 (pp20) REVERT: E 113 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7831 (ttt180) REVERT: E 144 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8059 (p) REVERT: E 188 GLN cc_start: 0.8637 (tp40) cc_final: 0.8337 (tt0) REVERT: E 276 GLN cc_start: 0.8621 (tt0) cc_final: 0.8115 (tp40) REVERT: E 294 GLU cc_start: 0.6088 (mm-30) cc_final: 0.5038 (tm-30) REVERT: E 402 ASN cc_start: 0.7606 (m110) cc_final: 0.7013 (p0) REVERT: F 113 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8060 (ttt180) REVERT: F 179 TYR cc_start: 0.8953 (t80) cc_final: 0.8693 (t80) REVERT: F 190 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8201 (p) REVERT: F 276 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7979 (tm130) REVERT: F 279 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8647 (mp10) REVERT: F 294 GLU cc_start: 0.8661 (tm-30) cc_final: 0.7074 (tp30) REVERT: G 40 ARG cc_start: 0.8307 (ttm170) cc_final: 0.7835 (mtp-110) REVERT: G 173 ASP cc_start: 0.7768 (m-30) cc_final: 0.7425 (t0) REVERT: G 279 GLN cc_start: 0.9002 (mt0) cc_final: 0.8680 (mp10) REVERT: G 294 GLU cc_start: 0.8760 (tm-30) cc_final: 0.7176 (tp30) REVERT: H 40 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7864 (mtp-110) REVERT: H 113 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7941 (ttt180) REVERT: H 173 ASP cc_start: 0.7600 (m-30) cc_final: 0.7317 (t0) REVERT: H 279 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8457 (mp10) REVERT: H 294 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.4437 (tm-30) REVERT: H 403 ASP cc_start: 0.7634 (t70) cc_final: 0.7403 (t70) REVERT: I 294 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.5141 (tm-30) REVERT: I 402 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8108 (p0) REVERT: J 113 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8188 (ttp-170) REVERT: J 278 MET cc_start: 0.8770 (mtp) cc_final: 0.8499 (mtp) REVERT: J 294 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.5239 (tm-30) REVERT: J 315 SER cc_start: 0.8982 (m) cc_final: 0.8770 (t) REVERT: J 402 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.7948 (p0) REVERT: K 113 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7935 (ttt180) REVERT: K 294 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5071 (tp30) REVERT: L 81 MET cc_start: 0.9288 (mmt) cc_final: 0.9066 (mmt) REVERT: L 174 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: L 196 ASP cc_start: 0.7897 (t70) cc_final: 0.7404 (t0) REVERT: L 272 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8062 (tp40) REVERT: L 294 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5025 (tp30) outliers start: 127 outliers final: 40 residues processed: 570 average time/residue: 0.9031 time to fit residues: 595.3359 Evaluate side-chains 522 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 458 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 113 ARG Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 363 MET Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 188 GLN Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 363 MET Chi-restraints excluded: chain H residue 400 LYS Chi-restraints excluded: chain H residue 402 ASN Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 378 SER Chi-restraints excluded: chain I residue 402 ASN Chi-restraints excluded: chain J residue 113 ARG Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain J residue 378 SER Chi-restraints excluded: chain J residue 402 ASN Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 188 GLN Chi-restraints excluded: chain K residue 294 GLU Chi-restraints excluded: chain K residue 378 SER Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 174 GLU Chi-restraints excluded: chain L residue 188 GLN Chi-restraints excluded: chain L residue 272 GLN Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 0 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 chunk 285 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 365 optimal weight: 8.9990 chunk 431 optimal weight: 7.9990 chunk 222 optimal weight: 0.5980 chunk 407 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 234 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN E 119 ASN F 119 ASN F 366 GLN G 119 ASN G 402 ASN H 119 ASN H 402 ASN I 402 ASN J 402 ASN K 402 ASN L 119 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.081462 restraints weight = 45652.425| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.97 r_work: 0.2819 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36288 Z= 0.133 Angle : 0.504 8.702 49200 Z= 0.261 Chirality : 0.042 0.224 5352 Planarity : 0.004 0.051 6516 Dihedral : 4.315 20.930 4920 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.04 % Allowed : 18.20 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.12), residues: 4560 helix: 1.55 (0.10), residues: 2220 sheet: -0.98 (0.19), residues: 696 loop : 0.88 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 113 TYR 0.018 0.001 TYR F 397 PHE 0.010 0.001 PHE G 111 TRP 0.008 0.001 TRP G 401 HIS 0.002 0.000 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00310 (36288) covalent geometry : angle 0.50440 (49200) hydrogen bonds : bond 0.04341 ( 1788) hydrogen bonds : angle 4.52927 ( 5184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 475 time to evaluate : 1.385 Fit side-chains REVERT: A 154 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8443 (mt) REVERT: A 294 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.4911 (tp30) REVERT: B 276 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7959 (tp40) REVERT: B 294 GLU cc_start: 0.5851 (OUTLIER) cc_final: 0.4808 (tp30) REVERT: C 113 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8214 (ttt180) REVERT: C 196 ASP cc_start: 0.8042 (t70) cc_final: 0.7582 (t0) REVERT: C 272 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8206 (tp40) REVERT: C 291 GLU cc_start: 0.8202 (tt0) cc_final: 0.7808 (mt-10) REVERT: D 40 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8161 (mtp-110) REVERT: D 92 GLU cc_start: 0.6017 (pt0) cc_final: 0.5752 (pp20) REVERT: D 188 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: D 205 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8734 (p) REVERT: D 272 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7876 (tp40) REVERT: D 279 GLN cc_start: 0.8967 (mt0) cc_final: 0.8747 (mp10) REVERT: D 291 GLU cc_start: 0.8018 (tt0) cc_final: 0.7734 (tt0) REVERT: D 294 GLU cc_start: 0.8605 (tm-30) cc_final: 0.7166 (tp30) REVERT: E 76 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8457 (mmmt) REVERT: E 92 GLU cc_start: 0.5759 (OUTLIER) cc_final: 0.5350 (pp20) REVERT: E 113 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7891 (ttt180) REVERT: E 188 GLN cc_start: 0.8597 (tp40) cc_final: 0.8393 (tt0) REVERT: E 276 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8095 (tp40) REVERT: E 294 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.5283 (tm-30) REVERT: E 402 ASN cc_start: 0.7687 (m110) cc_final: 0.7032 (p0) REVERT: F 81 MET cc_start: 0.9319 (mmt) cc_final: 0.9050 (mmm) REVERT: F 190 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8385 (p) REVERT: F 276 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8105 (tp40) REVERT: F 279 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8735 (mp10) REVERT: F 294 GLU cc_start: 0.8582 (tm-30) cc_final: 0.7020 (tp30) REVERT: G 40 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7818 (mtp-110) REVERT: G 173 ASP cc_start: 0.7749 (m-30) cc_final: 0.7448 (t0) REVERT: G 278 MET cc_start: 0.8614 (mtp) cc_final: 0.8391 (mtp) REVERT: G 279 GLN cc_start: 0.9038 (mt0) cc_final: 0.8710 (mp10) REVERT: G 294 GLU cc_start: 0.8705 (tm-30) cc_final: 0.7221 (tp30) REVERT: G 358 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: H 40 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7881 (mtp-110) REVERT: H 279 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8522 (mp10) REVERT: H 294 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.4464 (tm-30) REVERT: H 315 SER cc_start: 0.8872 (m) cc_final: 0.8651 (t) REVERT: H 403 ASP cc_start: 0.7705 (t70) cc_final: 0.7449 (t70) REVERT: I 196 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7683 (t0) REVERT: I 294 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.5138 (tm-30) REVERT: I 315 SER cc_start: 0.8778 (m) cc_final: 0.8531 (t) REVERT: J 99 LYS cc_start: 0.8104 (tppp) cc_final: 0.7880 (mttt) REVERT: J 278 MET cc_start: 0.8736 (mtp) cc_final: 0.8492 (mtp) REVERT: J 294 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.5308 (tm-30) REVERT: K 113 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7983 (ttt180) REVERT: K 294 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.4903 (tm-30) REVERT: L 81 MET cc_start: 0.9312 (mmt) cc_final: 0.9010 (mmt) REVERT: L 154 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8342 (mt) REVERT: L 156 ARG cc_start: 0.8546 (mtm-85) cc_final: 0.8321 (ptp90) REVERT: L 166 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7559 (ptt-90) REVERT: L 174 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: L 196 ASP cc_start: 0.7881 (t70) cc_final: 0.7404 (t0) REVERT: L 294 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5269 (tp30) outliers start: 115 outliers final: 45 residues processed: 544 average time/residue: 0.9518 time to fit residues: 596.1604 Evaluate side-chains 528 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 455 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 113 ARG Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain G residue 40 ARG Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 188 GLN Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 358 GLN Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 363 MET Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain J residue 378 SER Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 151 ASP Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 294 GLU Chi-restraints excluded: chain K residue 378 SER Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 174 GLU Chi-restraints excluded: chain L residue 188 GLN Chi-restraints excluded: chain L residue 294 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 274 optimal weight: 0.8980 chunk 344 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 423 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 412 optimal weight: 20.0000 chunk 443 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 362 optimal weight: 0.6980 chunk 371 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN F 119 ASN G 119 ASN G 366 GLN G 402 ASN H 119 ASN H 402 ASN J 402 ASN K 366 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.082715 restraints weight = 45694.023| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.97 r_work: 0.2841 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 36288 Z= 0.109 Angle : 0.485 7.448 49200 Z= 0.251 Chirality : 0.041 0.202 5352 Planarity : 0.004 0.054 6516 Dihedral : 4.165 19.931 4920 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.49 % Allowed : 18.36 % Favored : 79.15 % 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: 1.36 (0.13), residues: 4560 helix: 1.70 (0.11), residues: 2220 sheet: -0.96 (0.20), residues: 696 loop : 0.89 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 148 TYR 0.021 0.001 TYR F 397 PHE 0.007 0.001 PHE G 111 TRP 0.007 0.001 TRP G 401 HIS 0.002 0.000 HIS K 79 Details of bonding type rmsd covalent geometry : bond 0.00247 (36288) covalent geometry : angle 0.48466 (49200) hydrogen bonds : bond 0.04006 ( 1788) hydrogen bonds : angle 4.43618 ( 5184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 475 time to evaluate : 1.400 Fit side-chains REVERT: A 294 GLU cc_start: 0.5887 (OUTLIER) cc_final: 0.4899 (tp30) REVERT: B 196 ASP cc_start: 0.8146 (t70) cc_final: 0.7654 (t70) REVERT: B 276 GLN cc_start: 0.8517 (tm-30) cc_final: 0.7953 (tp40) REVERT: B 294 GLU cc_start: 0.5745 (OUTLIER) cc_final: 0.4784 (tp30) REVERT: C 113 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8173 (ttt180) REVERT: C 196 ASP cc_start: 0.7996 (t70) cc_final: 0.7536 (t0) REVERT: C 272 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8195 (tp40) REVERT: D 40 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8147 (mtp-110) REVERT: D 154 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8353 (mt) REVERT: D 205 VAL cc_start: 0.8933 (m) cc_final: 0.8683 (p) REVERT: D 279 GLN cc_start: 0.8955 (mt0) cc_final: 0.8705 (mp10) REVERT: D 291 GLU cc_start: 0.8018 (tt0) cc_final: 0.7665 (mt-10) REVERT: D 294 GLU cc_start: 0.8615 (tm-30) cc_final: 0.7174 (tp30) REVERT: E 76 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8444 (mmmt) REVERT: E 92 GLU cc_start: 0.5742 (OUTLIER) cc_final: 0.5331 (pp20) REVERT: E 276 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8064 (tp40) REVERT: E 291 GLU cc_start: 0.8179 (tt0) cc_final: 0.7633 (mt-10) REVERT: E 294 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5270 (tm-30) REVERT: E 402 ASN cc_start: 0.7730 (m110) cc_final: 0.7077 (p0) REVERT: F 147 ARG cc_start: 0.7481 (ttm110) cc_final: 0.7231 (ttm110) REVERT: F 190 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8442 (p) REVERT: F 272 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8115 (tp40) REVERT: F 276 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8147 (tp40) REVERT: F 279 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8695 (mp10) REVERT: F 294 GLU cc_start: 0.8598 (tm-30) cc_final: 0.7058 (tp30) REVERT: G 40 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7838 (mtp-110) REVERT: G 113 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8418 (ttt180) REVERT: G 173 ASP cc_start: 0.7732 (m-30) cc_final: 0.7510 (t0) REVERT: G 278 MET cc_start: 0.8619 (mtp) cc_final: 0.8390 (mtp) REVERT: G 279 GLN cc_start: 0.9033 (mt0) cc_final: 0.8714 (mp10) REVERT: G 294 GLU cc_start: 0.8686 (tm-30) cc_final: 0.7208 (tp30) REVERT: G 315 SER cc_start: 0.8822 (m) cc_final: 0.8608 (t) REVERT: H 40 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7872 (mtp-110) REVERT: H 113 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7960 (ttt180) REVERT: H 272 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7825 (tp40) REVERT: H 279 GLN cc_start: 0.8962 (mt0) cc_final: 0.8557 (mp10) REVERT: H 294 GLU cc_start: 0.5918 (OUTLIER) cc_final: 0.4536 (tm-30) REVERT: H 403 ASP cc_start: 0.7727 (t70) cc_final: 0.7496 (t70) REVERT: I 81 MET cc_start: 0.9323 (mmt) cc_final: 0.9090 (mmm) REVERT: I 196 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7686 (t0) REVERT: I 294 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5170 (tm-30) REVERT: I 315 SER cc_start: 0.8690 (m) cc_final: 0.8460 (t) REVERT: J 99 LYS cc_start: 0.8102 (tppp) cc_final: 0.7860 (mttt) REVERT: J 196 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7626 (t70) REVERT: J 294 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.5383 (tm-30) REVERT: K 113 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7997 (ttt180) REVERT: K 154 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8504 (mt) REVERT: K 294 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.4876 (tm-30) REVERT: L 81 MET cc_start: 0.9317 (mmt) cc_final: 0.9083 (mmt) REVERT: L 154 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8359 (mt) REVERT: L 166 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7548 (ptt-90) REVERT: L 174 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: L 196 ASP cc_start: 0.7841 (t70) cc_final: 0.7377 (t0) REVERT: L 272 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8043 (tp40) REVERT: L 294 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5291 (tp30) outliers start: 94 outliers final: 34 residues processed: 533 average time/residue: 0.9540 time to fit residues: 586.1078 Evaluate side-chains 507 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 444 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain G residue 40 ARG Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 363 MET Chi-restraints excluded: chain H residue 400 LYS Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 188 GLN Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain J residue 378 SER Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 188 GLN Chi-restraints excluded: chain K residue 294 GLU Chi-restraints excluded: chain K residue 378 SER Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 174 GLU Chi-restraints excluded: chain L residue 272 GLN Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 422 optimal weight: 7.9990 chunk 401 optimal weight: 5.9990 chunk 419 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 374 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 326 optimal weight: 6.9990 chunk 399 optimal weight: 0.0770 chunk 288 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN F 119 ASN G 402 ASN H 119 ASN H 358 GLN H 402 ASN I 402 ASN J 402 ASN L 366 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.079552 restraints weight = 45825.440| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.96 r_work: 0.2789 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 36288 Z= 0.170 Angle : 0.524 7.086 49200 Z= 0.269 Chirality : 0.042 0.176 5352 Planarity : 0.004 0.057 6516 Dihedral : 4.368 21.123 4920 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.88 % Allowed : 18.20 % Favored : 78.92 % 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: 1.39 (0.12), residues: 4560 helix: 1.73 (0.11), residues: 2160 sheet: -1.04 (0.19), residues: 696 loop : 0.99 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 148 TYR 0.013 0.001 TYR J 397 PHE 0.013 0.001 PHE E 111 TRP 0.008 0.001 TRP G 401 HIS 0.002 0.000 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00408 (36288) covalent geometry : angle 0.52355 (49200) hydrogen bonds : bond 0.04650 ( 1788) hydrogen bonds : angle 4.56784 ( 5184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 458 time to evaluate : 1.264 Fit side-chains REVERT: A 154 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8419 (mt) REVERT: A 294 GLU cc_start: 0.6147 (OUTLIER) cc_final: 0.4621 (tm-30) REVERT: B 276 GLN cc_start: 0.8542 (tm-30) cc_final: 0.7973 (tp40) REVERT: B 294 GLU cc_start: 0.5808 (OUTLIER) cc_final: 0.4632 (tp30) REVERT: B 404 LEU cc_start: 0.8072 (mt) cc_final: 0.7824 (mt) REVERT: C 113 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8232 (ttt180) REVERT: C 174 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: C 196 ASP cc_start: 0.8070 (t70) cc_final: 0.7551 (t0) REVERT: C 272 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8150 (tp40) REVERT: C 291 GLU cc_start: 0.8136 (tt0) cc_final: 0.7711 (mt-10) REVERT: D 40 ARG cc_start: 0.8479 (mtp85) cc_final: 0.8151 (mtp-110) REVERT: D 279 GLN cc_start: 0.8982 (mt0) cc_final: 0.8706 (mp10) REVERT: D 291 GLU cc_start: 0.8092 (tt0) cc_final: 0.7815 (tt0) REVERT: D 294 GLU cc_start: 0.8667 (tm-30) cc_final: 0.7287 (tp30) REVERT: E 76 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8472 (mmmt) REVERT: E 92 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5412 (pp20) REVERT: E 276 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8031 (tp40) REVERT: E 291 GLU cc_start: 0.8222 (tt0) cc_final: 0.7709 (mt-10) REVERT: E 294 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5084 (tm-30) REVERT: E 402 ASN cc_start: 0.7787 (m110) cc_final: 0.7087 (p0) REVERT: F 147 ARG cc_start: 0.7498 (ttm110) cc_final: 0.7234 (ttm110) REVERT: F 190 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8482 (p) REVERT: F 272 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8137 (tp40) REVERT: F 276 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8287 (tm-30) REVERT: F 279 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8707 (mp10) REVERT: F 294 GLU cc_start: 0.8631 (tm-30) cc_final: 0.7161 (tp30) REVERT: G 40 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7928 (mtp-110) REVERT: G 173 ASP cc_start: 0.7729 (m-30) cc_final: 0.7511 (t0) REVERT: G 190 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8446 (p) REVERT: G 278 MET cc_start: 0.8710 (mtp) cc_final: 0.8496 (mtp) REVERT: G 279 GLN cc_start: 0.9064 (mt0) cc_final: 0.8748 (mp10) REVERT: G 294 GLU cc_start: 0.8712 (tm-30) cc_final: 0.7283 (tp30) REVERT: G 358 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: H 40 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7894 (mtp-110) REVERT: H 113 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7892 (ttt180) REVERT: H 190 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8495 (p) REVERT: H 279 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8588 (mp10) REVERT: H 294 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.4453 (tm-30) REVERT: H 403 ASP cc_start: 0.7835 (t70) cc_final: 0.7625 (t70) REVERT: I 81 MET cc_start: 0.9320 (mmt) cc_final: 0.9050 (mmm) REVERT: I 196 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7678 (t0) REVERT: I 294 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.5091 (tm-30) REVERT: J 99 LYS cc_start: 0.8153 (tppp) cc_final: 0.7913 (mttt) REVERT: J 113 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8240 (ttp-170) REVERT: J 294 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5163 (tm-30) REVERT: K 50 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8659 (mm-30) REVERT: K 113 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7871 (ttt180) REVERT: K 294 GLU cc_start: 0.6115 (OUTLIER) cc_final: 0.4824 (tm-30) REVERT: L 154 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8365 (mt) REVERT: L 166 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7573 (ptt-90) REVERT: L 174 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: L 196 ASP cc_start: 0.7960 (t70) cc_final: 0.7447 (t0) REVERT: L 272 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8065 (tp40) REVERT: L 294 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.4689 (tm-30) outliers start: 109 outliers final: 51 residues processed: 522 average time/residue: 0.8803 time to fit residues: 531.2395 Evaluate side-chains 527 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 445 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 358 GLN Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain G residue 40 ARG Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 188 GLN Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 358 GLN Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 363 MET Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain H residue 400 LYS Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 188 GLN Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain J residue 113 ARG Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 188 GLN Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain J residue 378 SER Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 188 GLN Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 294 GLU Chi-restraints excluded: chain K residue 378 SER Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 174 GLU Chi-restraints excluded: chain L residue 188 GLN Chi-restraints excluded: chain L residue 272 GLN Chi-restraints excluded: chain L residue 294 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 2 optimal weight: 1.9990 chunk 279 optimal weight: 8.9990 chunk 313 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 398 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 336 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 ASN E 119 ASN F 119 ASN G 119 ASN G 402 ASN H 119 ASN H 402 ASN I 402 ASN J 402 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.079455 restraints weight = 45748.117| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.96 r_work: 0.2785 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 36288 Z= 0.164 Angle : 0.520 7.319 49200 Z= 0.267 Chirality : 0.042 0.195 5352 Planarity : 0.004 0.057 6516 Dihedral : 4.385 21.419 4920 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.72 % Allowed : 18.15 % Favored : 79.13 % 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: 1.37 (0.12), residues: 4560 helix: 1.70 (0.10), residues: 2160 sheet: -1.08 (0.20), residues: 696 loop : 1.01 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 148 TYR 0.019 0.001 TYR F 397 PHE 0.012 0.001 PHE E 111 TRP 0.007 0.001 TRP G 401 HIS 0.002 0.000 HIS K 79 Details of bonding type rmsd covalent geometry : bond 0.00392 (36288) covalent geometry : angle 0.51979 (49200) hydrogen bonds : bond 0.04597 ( 1788) hydrogen bonds : angle 4.56984 ( 5184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 453 time to evaluate : 1.482 Fit side-chains REVERT: A 154 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8392 (mt) REVERT: A 294 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.4670 (tm-30) REVERT: B 276 GLN cc_start: 0.8523 (tm-30) cc_final: 0.7946 (tp40) REVERT: B 294 GLU cc_start: 0.5894 (OUTLIER) cc_final: 0.4474 (tm-30) REVERT: B 404 LEU cc_start: 0.8062 (mt) cc_final: 0.7841 (mt) REVERT: C 113 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8243 (ttt180) REVERT: C 174 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: C 196 ASP cc_start: 0.8066 (t70) cc_final: 0.7533 (t0) REVERT: C 272 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8135 (tp40) REVERT: C 291 GLU cc_start: 0.8144 (tt0) cc_final: 0.7726 (mt-10) REVERT: D 40 ARG cc_start: 0.8481 (mtp85) cc_final: 0.8171 (mtp-110) REVERT: D 279 GLN cc_start: 0.8975 (mt0) cc_final: 0.8708 (mp10) REVERT: D 291 GLU cc_start: 0.8094 (tt0) cc_final: 0.7787 (mt-10) REVERT: D 294 GLU cc_start: 0.8662 (tm-30) cc_final: 0.7290 (tp30) REVERT: D 358 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: D 369 ASP cc_start: 0.8206 (m-30) cc_final: 0.7920 (m-30) REVERT: E 76 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8482 (mmmt) REVERT: E 92 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.5460 (pp20) REVERT: E 205 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8748 (p) REVERT: E 276 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8017 (tp40) REVERT: E 291 GLU cc_start: 0.8217 (tt0) cc_final: 0.7728 (mt-10) REVERT: E 294 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5153 (tm-30) REVERT: E 402 ASN cc_start: 0.7783 (m110) cc_final: 0.7078 (p0) REVERT: F 147 ARG cc_start: 0.7452 (ttm110) cc_final: 0.7245 (ttm110) REVERT: F 190 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8512 (p) REVERT: F 272 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8154 (tp40) REVERT: F 276 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8301 (tm-30) REVERT: F 279 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8679 (mp10) REVERT: F 294 GLU cc_start: 0.8612 (tm-30) cc_final: 0.7133 (tp30) REVERT: G 40 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7922 (mtp-110) REVERT: G 173 ASP cc_start: 0.7754 (m-30) cc_final: 0.7546 (t0) REVERT: G 190 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8538 (p) REVERT: G 278 MET cc_start: 0.8730 (mtp) cc_final: 0.8518 (mtp) REVERT: G 279 GLN cc_start: 0.9037 (mt0) cc_final: 0.8723 (mp10) REVERT: G 294 GLU cc_start: 0.8654 (tm-30) cc_final: 0.7260 (tp30) REVERT: G 358 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: G 369 ASP cc_start: 0.8233 (m-30) cc_final: 0.7945 (m-30) REVERT: H 40 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7884 (mtp-110) REVERT: H 113 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7934 (ttt180) REVERT: H 279 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8580 (mp10) REVERT: H 294 GLU cc_start: 0.5959 (OUTLIER) cc_final: 0.4474 (tm-30) REVERT: I 81 MET cc_start: 0.9327 (mmt) cc_final: 0.9066 (mmm) REVERT: I 92 GLU cc_start: 0.5369 (OUTLIER) cc_final: 0.4863 (pt0) REVERT: I 113 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8305 (ttt180) REVERT: I 196 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7685 (t0) REVERT: I 294 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.5096 (tm-30) REVERT: J 113 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8248 (ttp-170) REVERT: J 294 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5099 (tm-30) REVERT: K 50 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8653 (mm-30) REVERT: K 113 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7881 (ttt180) REVERT: K 154 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8556 (mt) REVERT: K 294 GLU cc_start: 0.6112 (OUTLIER) cc_final: 0.4812 (tm-30) REVERT: L 154 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8322 (mt) REVERT: L 166 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7575 (ptt-90) REVERT: L 174 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: L 196 ASP cc_start: 0.7967 (t70) cc_final: 0.7426 (t0) REVERT: L 272 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8092 (tp40) REVERT: L 294 GLU cc_start: 0.6111 (OUTLIER) cc_final: 0.4624 (tm-30) outliers start: 103 outliers final: 44 residues processed: 515 average time/residue: 0.8982 time to fit residues: 534.8350 Evaluate side-chains 523 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 444 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 358 GLN Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 358 GLN Chi-restraints excluded: chain G residue 40 ARG Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 188 GLN Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 358 GLN Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 315 SER Chi-restraints excluded: chain H residue 363 MET Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain H residue 400 LYS Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 188 GLN Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain J residue 113 ARG Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 188 GLN Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 294 GLU Chi-restraints excluded: chain K residue 315 SER Chi-restraints excluded: chain K residue 378 SER Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 174 GLU Chi-restraints excluded: chain L residue 188 GLN Chi-restraints excluded: chain L residue 272 GLN Chi-restraints excluded: chain L residue 294 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 217 optimal weight: 0.0030 chunk 33 optimal weight: 9.9990 chunk 306 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 300 optimal weight: 3.9990 chunk 281 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 379 optimal weight: 5.9990 chunk 338 optimal weight: 6.9990 chunk 397 optimal weight: 0.7980 chunk 307 optimal weight: 3.9990 overall best weight: 2.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 119 ASN F 119 ASN G 119 ASN G 402 ASN H 119 ASN H 402 ASN I 402 ASN J 402 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.078682 restraints weight = 45929.601| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.96 r_work: 0.2773 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 36288 Z= 0.181 Angle : 0.531 7.805 49200 Z= 0.273 Chirality : 0.042 0.188 5352 Planarity : 0.004 0.058 6516 Dihedral : 4.455 22.344 4920 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.96 % Allowed : 18.07 % Favored : 78.97 % 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: 1.33 (0.12), residues: 4560 helix: 1.64 (0.10), residues: 2160 sheet: -1.10 (0.20), residues: 696 loop : 1.03 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 148 TYR 0.021 0.002 TYR I 397 PHE 0.013 0.001 PHE F 111 TRP 0.007 0.001 TRP G 401 HIS 0.003 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00434 (36288) covalent geometry : angle 0.53131 (49200) hydrogen bonds : bond 0.04760 ( 1788) hydrogen bonds : angle 4.61276 ( 5184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 463 time to evaluate : 1.457 Fit side-chains REVERT: A 154 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8394 (mt) REVERT: A 272 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8024 (tp40) REVERT: A 294 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.4723 (tm-30) REVERT: B 113 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8153 (ttt180) REVERT: B 276 GLN cc_start: 0.8532 (tm-30) cc_final: 0.7954 (tp40) REVERT: B 294 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.4495 (tm-30) REVERT: C 113 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8258 (ttt180) REVERT: C 174 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: C 196 ASP cc_start: 0.8079 (t70) cc_final: 0.7496 (t0) REVERT: C 272 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8147 (tp40) REVERT: C 291 GLU cc_start: 0.8149 (tt0) cc_final: 0.7751 (mt-10) REVERT: D 40 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8186 (mtp-110) REVERT: D 279 GLN cc_start: 0.8974 (mt0) cc_final: 0.8699 (mp10) REVERT: D 291 GLU cc_start: 0.8098 (tt0) cc_final: 0.7784 (mt-10) REVERT: D 294 GLU cc_start: 0.8668 (tm-30) cc_final: 0.7291 (tp30) REVERT: D 358 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: D 369 ASP cc_start: 0.8231 (m-30) cc_final: 0.7945 (m-30) REVERT: E 76 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8511 (mmmt) REVERT: E 92 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5474 (pp20) REVERT: E 205 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8755 (p) REVERT: E 276 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8024 (tp40) REVERT: E 291 GLU cc_start: 0.8264 (tt0) cc_final: 0.7765 (mt-10) REVERT: E 294 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5075 (tm-30) REVERT: F 174 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: F 190 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8543 (p) REVERT: F 272 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8158 (tp40) REVERT: F 279 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8688 (mp10) REVERT: F 294 GLU cc_start: 0.8615 (tm-30) cc_final: 0.7145 (tp30) REVERT: F 358 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8314 (tp-100) REVERT: G 40 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7879 (mtp-110) REVERT: G 113 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8462 (ttt180) REVERT: G 147 ARG cc_start: 0.7598 (ttm110) cc_final: 0.7259 (ttp80) REVERT: G 173 ASP cc_start: 0.7761 (m-30) cc_final: 0.7544 (t0) REVERT: G 190 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8523 (p) REVERT: G 278 MET cc_start: 0.8760 (mtp) cc_final: 0.8537 (mtp) REVERT: G 279 GLN cc_start: 0.9021 (mt0) cc_final: 0.8701 (mp10) REVERT: G 294 GLU cc_start: 0.8639 (tm-30) cc_final: 0.7303 (tp30) REVERT: G 358 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: H 40 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7889 (mtp-110) REVERT: H 113 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7890 (ttt180) REVERT: H 279 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8562 (mp10) REVERT: H 294 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.4424 (tm-30) REVERT: I 81 MET cc_start: 0.9326 (mmt) cc_final: 0.9066 (mmm) REVERT: I 92 GLU cc_start: 0.5190 (OUTLIER) cc_final: 0.4714 (pt0) REVERT: I 113 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8289 (ttt90) REVERT: I 174 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: I 196 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7682 (t0) REVERT: I 294 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.5077 (tm-30) REVERT: J 113 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8361 (ttt180) REVERT: J 294 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5176 (tm-30) REVERT: K 50 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8658 (mm-30) REVERT: K 99 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7663 (mttt) REVERT: K 113 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7845 (ttt180) REVERT: K 154 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8545 (mp) REVERT: K 294 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.4656 (tm-30) REVERT: L 81 MET cc_start: 0.9285 (mmt) cc_final: 0.8963 (mmt) REVERT: L 154 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8338 (mt) REVERT: L 166 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7550 (ptt-90) REVERT: L 174 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: L 196 ASP cc_start: 0.8007 (t70) cc_final: 0.7448 (t0) REVERT: L 272 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8092 (tp40) REVERT: L 294 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.4624 (tm-30) outliers start: 112 outliers final: 45 residues processed: 526 average time/residue: 0.9195 time to fit residues: 558.4713 Evaluate side-chains 542 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 455 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 358 GLN Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 358 GLN Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 358 GLN Chi-restraints excluded: chain G residue 40 ARG Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 188 GLN Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 358 GLN Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 315 SER Chi-restraints excluded: chain H residue 363 MET Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain H residue 400 LYS Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 174 GLU Chi-restraints excluded: chain I residue 188 GLN Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain J residue 113 ARG Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain K residue 99 LYS Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 294 GLU Chi-restraints excluded: chain K residue 315 SER Chi-restraints excluded: chain K residue 378 SER Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 174 GLU Chi-restraints excluded: chain L residue 188 GLN Chi-restraints excluded: chain L residue 272 GLN Chi-restraints excluded: chain L residue 294 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 82 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 268 optimal weight: 4.9990 chunk 447 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 361 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 119 ASN E 402 ASN F 119 ASN G 119 ASN G 402 ASN H 119 ASN H 402 ASN I 402 ASN J 402 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.100899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.078838 restraints weight = 45607.323| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.95 r_work: 0.2775 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 36288 Z= 0.173 Angle : 0.532 9.821 49200 Z= 0.273 Chirality : 0.042 0.217 5352 Planarity : 0.004 0.059 6516 Dihedral : 4.455 22.247 4920 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.70 % Allowed : 18.57 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.12), residues: 4560 helix: 1.65 (0.10), residues: 2160 sheet: -1.10 (0.20), residues: 696 loop : 1.01 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 148 TYR 0.020 0.001 TYR F 397 PHE 0.012 0.001 PHE E 111 TRP 0.007 0.001 TRP G 401 HIS 0.003 0.001 HIS K 79 Details of bonding type rmsd covalent geometry : bond 0.00415 (36288) covalent geometry : angle 0.53226 (49200) hydrogen bonds : bond 0.04701 ( 1788) hydrogen bonds : angle 4.60522 ( 5184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 457 time to evaluate : 1.378 Fit side-chains REVERT: A 154 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8386 (mt) REVERT: A 272 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8013 (tp40) REVERT: A 294 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.4699 (tm-30) REVERT: B 113 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8148 (ttt180) REVERT: B 276 GLN cc_start: 0.8535 (tm-30) cc_final: 0.7962 (tp40) REVERT: B 294 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.4491 (tm-30) REVERT: C 113 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8251 (ttt180) REVERT: C 174 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: C 196 ASP cc_start: 0.8065 (t70) cc_final: 0.7486 (t0) REVERT: C 272 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8128 (tp40) REVERT: C 291 GLU cc_start: 0.8135 (tt0) cc_final: 0.7742 (mt-10) REVERT: C 294 GLU cc_start: 0.5415 (OUTLIER) cc_final: 0.4026 (tt0) REVERT: D 40 ARG cc_start: 0.8491 (mtp85) cc_final: 0.8203 (mtp-110) REVERT: D 279 GLN cc_start: 0.8968 (mt0) cc_final: 0.8694 (mp10) REVERT: D 291 GLU cc_start: 0.8107 (tt0) cc_final: 0.7803 (mt-10) REVERT: D 294 GLU cc_start: 0.8664 (tm-30) cc_final: 0.7291 (tp30) REVERT: D 358 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: E 76 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8509 (mmmt) REVERT: E 92 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5503 (pp20) REVERT: E 118 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7407 (mtt-85) REVERT: E 205 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8756 (p) REVERT: E 276 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8001 (tp40) REVERT: E 291 GLU cc_start: 0.8257 (tt0) cc_final: 0.7757 (mt-10) REVERT: E 294 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5105 (tm-30) REVERT: E 402 ASN cc_start: 0.7970 (m110) cc_final: 0.7179 (p0) REVERT: F 190 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8544 (p) REVERT: F 272 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8147 (tp40) REVERT: F 279 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8659 (mp10) REVERT: F 294 GLU cc_start: 0.8612 (tm-30) cc_final: 0.7147 (tp30) REVERT: G 40 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7871 (mtp-110) REVERT: G 113 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8453 (ttt180) REVERT: G 147 ARG cc_start: 0.7589 (ttm110) cc_final: 0.7242 (ttp80) REVERT: G 278 MET cc_start: 0.8755 (mtp) cc_final: 0.8545 (mtp) REVERT: G 279 GLN cc_start: 0.9028 (mt0) cc_final: 0.8689 (mp10) REVERT: G 291 GLU cc_start: 0.8087 (tt0) cc_final: 0.7666 (mt-10) REVERT: G 294 GLU cc_start: 0.8623 (tm-30) cc_final: 0.7251 (tp30) REVERT: G 358 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: G 369 ASP cc_start: 0.8219 (m-30) cc_final: 0.7932 (m-30) REVERT: H 40 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7887 (mtp-110) REVERT: H 113 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7893 (ttt180) REVERT: H 174 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: H 279 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8575 (mp10) REVERT: H 294 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.4418 (tm-30) REVERT: I 81 MET cc_start: 0.9331 (mmt) cc_final: 0.9077 (mmm) REVERT: I 92 GLU cc_start: 0.5198 (OUTLIER) cc_final: 0.4713 (pt0) REVERT: I 113 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8296 (ttt90) REVERT: I 196 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7662 (t0) REVERT: I 294 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.5052 (tm-30) REVERT: I 381 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8466 (mm-30) REVERT: J 113 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8238 (ttp-170) REVERT: J 294 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.5173 (tm-30) REVERT: K 50 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8642 (mm-30) REVERT: K 99 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7654 (mttt) REVERT: K 113 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7849 (ttt180) REVERT: K 154 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8547 (mp) REVERT: K 294 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.4666 (tm-30) REVERT: L 154 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8337 (mt) REVERT: L 166 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7559 (ptt-90) REVERT: L 174 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: L 196 ASP cc_start: 0.8012 (t70) cc_final: 0.7458 (t0) REVERT: L 272 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8097 (tp40) REVERT: L 294 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.4625 (tm-30) outliers start: 102 outliers final: 43 residues processed: 516 average time/residue: 0.9140 time to fit residues: 544.1086 Evaluate side-chains 533 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 449 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 358 GLN Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 358 GLN Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 358 GLN Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain G residue 40 ARG Chi-restraints excluded: chain G residue 113 ARG Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 188 GLN Chi-restraints excluded: chain G residue 358 GLN Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 174 GLU Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 315 SER Chi-restraints excluded: chain H residue 363 MET Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain H residue 400 LYS Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 113 ARG Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain J residue 113 ARG Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 151 ASP Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain K residue 99 LYS Chi-restraints excluded: chain K residue 113 ARG Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 294 GLU Chi-restraints excluded: chain K residue 315 SER Chi-restraints excluded: chain K residue 378 SER Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 174 GLU Chi-restraints excluded: chain L residue 188 GLN Chi-restraints excluded: chain L residue 272 GLN Chi-restraints excluded: chain L residue 294 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 98 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 377 optimal weight: 7.9990 chunk 234 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 96 optimal weight: 0.0040 chunk 187 optimal weight: 0.9990 chunk 330 optimal weight: 5.9990 chunk 128 optimal weight: 0.4980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 119 ASN G 402 ASN H 402 ASN I 402 ASN J 402 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.082760 restraints weight = 45975.596| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.97 r_work: 0.2839 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 36288 Z= 0.100 Angle : 0.488 9.418 49200 Z= 0.251 Chirality : 0.041 0.239 5352 Planarity : 0.004 0.057 6516 Dihedral : 4.104 18.951 4920 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.88 % Allowed : 19.52 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.13), residues: 4560 helix: 1.76 (0.11), residues: 2220 sheet: -1.05 (0.20), residues: 696 loop : 0.99 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 148 TYR 0.016 0.001 TYR E 397 PHE 0.006 0.001 PHE G 111 TRP 0.007 0.001 TRP L 401 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00221 (36288) covalent geometry : angle 0.48835 (49200) hydrogen bonds : bond 0.03781 ( 1788) hydrogen bonds : angle 4.40249 ( 5184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 460 time to evaluate : 1.372 Fit side-chains REVERT: A 154 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8336 (mt) REVERT: A 272 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7942 (tp40) REVERT: A 294 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5074 (tp30) REVERT: B 276 GLN cc_start: 0.8528 (tm-30) cc_final: 0.7963 (tp40) REVERT: B 294 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.4529 (tm-30) REVERT: C 113 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8185 (ttt180) REVERT: C 174 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: C 196 ASP cc_start: 0.8033 (t70) cc_final: 0.7494 (t0) REVERT: C 291 GLU cc_start: 0.8134 (tt0) cc_final: 0.7758 (mt-10) REVERT: D 40 ARG cc_start: 0.8483 (mtp85) cc_final: 0.8153 (mtp-110) REVERT: D 279 GLN cc_start: 0.8962 (mt0) cc_final: 0.8675 (mp10) REVERT: D 291 GLU cc_start: 0.8059 (tt0) cc_final: 0.7746 (mt-10) REVERT: D 294 GLU cc_start: 0.8618 (tm-30) cc_final: 0.7217 (tp30) REVERT: E 92 GLU cc_start: 0.5956 (OUTLIER) cc_final: 0.5502 (pp20) REVERT: E 118 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7352 (mtt-85) REVERT: E 205 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8725 (p) REVERT: E 276 GLN cc_start: 0.8524 (tm-30) cc_final: 0.7999 (tp40) REVERT: E 291 GLU cc_start: 0.8184 (tt0) cc_final: 0.7675 (mt-10) REVERT: E 294 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5280 (tm-30) REVERT: F 190 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8604 (p) REVERT: F 196 ASP cc_start: 0.8254 (t70) cc_final: 0.7592 (t0) REVERT: F 279 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8645 (mp10) REVERT: F 294 GLU cc_start: 0.8604 (tm-30) cc_final: 0.7154 (tp30) REVERT: F 358 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8299 (tp-100) REVERT: G 40 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7738 (mtp-110) REVERT: G 279 GLN cc_start: 0.9039 (mt0) cc_final: 0.8703 (mp10) REVERT: G 294 GLU cc_start: 0.8598 (tm-30) cc_final: 0.7234 (tp30) REVERT: G 358 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: G 402 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7328 (p0) REVERT: H 40 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7838 (mtp-110) REVERT: H 99 LYS cc_start: 0.7907 (tppp) cc_final: 0.7697 (mttt) REVERT: H 279 GLN cc_start: 0.8975 (mt0) cc_final: 0.8602 (mp10) REVERT: H 294 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.4548 (tm-30) REVERT: I 92 GLU cc_start: 0.5239 (OUTLIER) cc_final: 0.4785 (pt0) REVERT: I 196 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7629 (t0) REVERT: I 294 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5110 (tm-30) REVERT: I 381 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8331 (mm-30) REVERT: J 294 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.5786 (tp30) REVERT: K 99 LYS cc_start: 0.7841 (tppp) cc_final: 0.7601 (mttt) REVERT: K 294 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.4803 (tm-30) REVERT: L 166 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7515 (ptt-90) REVERT: L 174 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: L 196 ASP cc_start: 0.7940 (t70) cc_final: 0.7438 (t0) REVERT: L 272 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: L 294 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5418 (tp30) outliers start: 71 outliers final: 21 residues processed: 499 average time/residue: 0.8768 time to fit residues: 505.6127 Evaluate side-chains 491 residues out of total 3936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 443 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 294 GLU Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 358 GLN Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain G residue 40 ARG Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 358 GLN Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain H residue 40 ARG Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 363 MET Chi-restraints excluded: chain H residue 400 LYS Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 294 GLU Chi-restraints excluded: chain K residue 294 GLU Chi-restraints excluded: chain K residue 315 SER Chi-restraints excluded: chain K residue 378 SER Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 174 GLU Chi-restraints excluded: chain L residue 272 GLN Chi-restraints excluded: chain L residue 294 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 135 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 413 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 315 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 0.0670 chunk 234 optimal weight: 0.9980 chunk 450 optimal weight: 9.9990 chunk 331 optimal weight: 2.9990 chunk 382 optimal weight: 3.9990 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 119 ASN G 402 ASN H 402 ASN I 402 ASN J 402 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.102642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.080598 restraints weight = 45628.452| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.96 r_work: 0.2805 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36288 Z= 0.137 Angle : 0.514 9.019 49200 Z= 0.263 Chirality : 0.041 0.218 5352 Planarity : 0.004 0.058 6516 Dihedral : 4.198 19.564 4920 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.75 % Allowed : 19.84 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.13), residues: 4560 helix: 1.88 (0.11), residues: 2160 sheet: -1.05 (0.20), residues: 696 loop : 0.99 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 113 TYR 0.018 0.001 TYR C 397 PHE 0.010 0.001 PHE G 111 TRP 0.015 0.001 TRP G 401 HIS 0.003 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00323 (36288) covalent geometry : angle 0.51389 (49200) hydrogen bonds : bond 0.04256 ( 1788) hydrogen bonds : angle 4.46949 ( 5184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14541.02 seconds wall clock time: 247 minutes 45.23 seconds (14865.23 seconds total)