Starting phenix.real_space_refine on Fri Aug 22 16:13:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ter_41198/08_2025/8ter_41198.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ter_41198/08_2025/8ter_41198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ter_41198/08_2025/8ter_41198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ter_41198/08_2025/8ter_41198.map" model { file = "/net/cci-nas-00/data/ceres_data/8ter_41198/08_2025/8ter_41198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ter_41198/08_2025/8ter_41198.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 3 Type Number sf(0) Gaussians C 3420 2.51 5 N 960 2.21 5 O 1400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5780 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 277 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "N" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "O" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "Q" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T Time building chain proxies: 0.61, per 1000 atoms: 0.11 Number of scatterers: 5780 At special positions: 0 Unit cell: (64.141, 69.531, 65.758, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1400 8.00 N 960 7.00 C 3420 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: 0.44 Conformation dependent library (CDL) restraints added in 194.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 62.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'P' and resid 266 through 273 removed outlier: 6.824A pdb=" N ILE L 270 " --> pdb=" O GLY P 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN P 271 " --> pdb=" O ILE L 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR L 272 " --> pdb=" O GLN P 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER P 273 " --> pdb=" O TYR L 272 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE H 270 " --> pdb=" O GLY L 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN L 271 " --> pdb=" O ILE H 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR H 272 " --> pdb=" O GLN L 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER L 273 " --> pdb=" O TYR H 272 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE D 270 " --> pdb=" O GLY H 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN H 271 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR D 272 " --> pdb=" O GLN H 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER H 273 " --> pdb=" O TYR D 272 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE A 270 " --> pdb=" O GLY D 269 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN D 271 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR A 272 " --> pdb=" O GLN D 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER D 273 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN A 267 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE E 270 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY A 269 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N TYR E 272 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN A 271 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN E 267 " --> pdb=" O TYR I 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE I 270 " --> pdb=" O GLN E 267 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY E 269 " --> pdb=" O ILE I 270 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N TYR I 272 " --> pdb=" O GLY E 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN E 271 " --> pdb=" O TYR I 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN I 267 " --> pdb=" O TYR M 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE M 270 " --> pdb=" O GLN I 267 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY I 269 " --> pdb=" O ILE M 270 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N TYR M 272 " --> pdb=" O GLY I 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN I 271 " --> pdb=" O TYR M 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN M 267 " --> pdb=" O TYR Q 268 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE Q 270 " --> pdb=" O GLN M 267 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLY M 269 " --> pdb=" O ILE Q 270 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N TYR Q 272 " --> pdb=" O GLY M 269 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N GLN M 271 " --> pdb=" O TYR Q 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN Q 267 " --> pdb=" O TYR T 268 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE T 270 " --> pdb=" O GLN Q 267 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLY Q 269 " --> pdb=" O ILE T 270 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N TYR T 272 " --> pdb=" O GLY Q 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN Q 271 " --> pdb=" O TYR T 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 276 through 279 removed outlier: 6.279A pdb=" N TYR L 276 " --> pdb=" O SER P 277 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLN P 279 " --> pdb=" O TYR L 276 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN L 278 " --> pdb=" O GLN P 279 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR H 276 " --> pdb=" O SER L 277 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN L 279 " --> pdb=" O TYR H 276 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN H 278 " --> pdb=" O GLN L 279 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR D 276 " --> pdb=" O SER H 277 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN H 279 " --> pdb=" O TYR D 276 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN D 278 " --> pdb=" O GLN H 279 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR A 276 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLN D 279 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN A 278 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 283 through 293 removed outlier: 6.437A pdb=" N GLN L 284 " --> pdb=" O LEU P 285 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLN P 287 " --> pdb=" O GLN L 284 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN L 286 " --> pdb=" O GLN P 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN P 289 " --> pdb=" O GLN L 286 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE L 288 " --> pdb=" O GLN P 289 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR P 291 " --> pdb=" O PHE L 288 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY L 290 " --> pdb=" O TYR P 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN P 293 " --> pdb=" O GLY L 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY L 292 " --> pdb=" O GLN P 293 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN H 284 " --> pdb=" O LEU L 285 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN L 287 " --> pdb=" O GLN H 284 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN H 286 " --> pdb=" O GLN L 287 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLN L 289 " --> pdb=" O GLN H 286 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE H 288 " --> pdb=" O GLN L 289 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR L 291 " --> pdb=" O PHE H 288 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY H 290 " --> pdb=" O TYR L 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN L 293 " --> pdb=" O GLY H 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY H 292 " --> pdb=" O GLN L 293 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN D 284 " --> pdb=" O LEU H 285 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN H 287 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN D 286 " --> pdb=" O GLN H 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN H 289 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE D 288 " --> pdb=" O GLN H 289 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR H 291 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY D 290 " --> pdb=" O TYR H 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN H 293 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY D 292 " --> pdb=" O GLN H 293 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN A 284 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLN D 287 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN A 286 " --> pdb=" O GLN D 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN D 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 288 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR D 291 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY A 290 " --> pdb=" O TYR D 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN D 293 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY A 292 " --> pdb=" O GLN D 293 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 296 through 298 removed outlier: 6.450A pdb=" N THR L 296 " --> pdb=" O SER P 297 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR H 296 " --> pdb=" O SER L 297 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR D 296 " --> pdb=" O SER H 297 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR A 296 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 266 through 273 removed outlier: 6.824A pdb=" N ILE N 270 " --> pdb=" O GLY R 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN R 271 " --> pdb=" O ILE N 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR N 272 " --> pdb=" O GLN R 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER R 273 " --> pdb=" O TYR N 272 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE J 270 " --> pdb=" O GLY N 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN N 271 " --> pdb=" O ILE J 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR J 272 " --> pdb=" O GLN N 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER N 273 " --> pdb=" O TYR J 272 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE F 270 " --> pdb=" O GLY J 269 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLN J 271 " --> pdb=" O ILE F 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR F 272 " --> pdb=" O GLN J 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER J 273 " --> pdb=" O TYR F 272 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 270 " --> pdb=" O GLY F 269 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN F 271 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR B 272 " --> pdb=" O GLN F 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER F 273 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLN B 267 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE C 270 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLY B 269 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N TYR C 272 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N GLN B 271 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN C 267 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE G 270 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY C 269 " --> pdb=" O ILE G 270 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N TYR G 272 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN C 271 " --> pdb=" O TYR G 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN G 267 " --> pdb=" O TYR K 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE K 270 " --> pdb=" O GLN G 267 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY G 269 " --> pdb=" O ILE K 270 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N TYR K 272 " --> pdb=" O GLY G 269 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N GLN G 271 " --> pdb=" O TYR K 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN K 267 " --> pdb=" O TYR O 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE O 270 " --> pdb=" O GLN K 267 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLY K 269 " --> pdb=" O ILE O 270 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N TYR O 272 " --> pdb=" O GLY K 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN K 271 " --> pdb=" O TYR O 272 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN O 267 " --> pdb=" O TYR S 268 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE S 270 " --> pdb=" O GLN O 267 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY O 269 " --> pdb=" O ILE S 270 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N TYR S 272 " --> pdb=" O GLY O 269 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLN O 271 " --> pdb=" O TYR S 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 276 through 279 removed outlier: 6.279A pdb=" N TYR N 276 " --> pdb=" O SER R 277 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN R 279 " --> pdb=" O TYR N 276 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN N 278 " --> pdb=" O GLN R 279 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR J 276 " --> pdb=" O SER N 277 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLN N 279 " --> pdb=" O TYR J 276 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN J 278 " --> pdb=" O GLN N 279 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR F 276 " --> pdb=" O SER J 277 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN J 279 " --> pdb=" O TYR F 276 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN F 278 " --> pdb=" O GLN J 279 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR B 276 " --> pdb=" O SER F 277 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN F 279 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN B 278 " --> pdb=" O GLN F 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 283 through 293 removed outlier: 6.437A pdb=" N GLN N 284 " --> pdb=" O LEU R 285 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN R 287 " --> pdb=" O GLN N 284 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN N 286 " --> pdb=" O GLN R 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN R 289 " --> pdb=" O GLN N 286 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE N 288 " --> pdb=" O GLN R 289 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR R 291 " --> pdb=" O PHE N 288 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY N 290 " --> pdb=" O TYR R 291 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N GLN R 293 " --> pdb=" O GLY N 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY N 292 " --> pdb=" O GLN R 293 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN J 284 " --> pdb=" O LEU N 285 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLN N 287 " --> pdb=" O GLN J 284 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN J 286 " --> pdb=" O GLN N 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN N 289 " --> pdb=" O GLN J 286 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE J 288 " --> pdb=" O GLN N 289 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR N 291 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY J 290 " --> pdb=" O TYR N 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN N 293 " --> pdb=" O GLY J 290 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY J 292 " --> pdb=" O GLN N 293 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN F 284 " --> pdb=" O LEU J 285 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN J 287 " --> pdb=" O GLN F 284 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN F 286 " --> pdb=" O GLN J 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN J 289 " --> pdb=" O GLN F 286 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE F 288 " --> pdb=" O GLN J 289 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR J 291 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY F 290 " --> pdb=" O TYR J 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN J 293 " --> pdb=" O GLY F 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY F 292 " --> pdb=" O GLN J 293 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 284 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN F 287 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN B 286 " --> pdb=" O GLN F 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLN F 289 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE B 288 " --> pdb=" O GLN F 289 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR F 291 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY B 290 " --> pdb=" O TYR F 291 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN F 293 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY B 292 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 296 through 298 removed outlier: 6.450A pdb=" N THR N 296 " --> pdb=" O SER R 297 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR J 296 " --> pdb=" O SER N 297 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR F 296 " --> pdb=" O SER J 297 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 296 " --> pdb=" O SER F 297 " (cutoff:3.500A) 174 hydrogen bonds defined for protein. 522 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: 0.91 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 960 1.29 - 1.35: 940 1.35 - 1.42: 759 1.42 - 1.48: 821 1.48 - 1.55: 2200 Bond restraints: 5680 Sorted by residual: bond pdb=" CG GLN J 266 " pdb=" CD GLN J 266 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.46e+00 bond pdb=" CG GLN S 266 " pdb=" CD GLN S 266 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.45e+00 bond pdb=" CG GLN Q 266 " pdb=" CD GLN Q 266 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.45e+00 bond pdb=" CG GLN E 266 " pdb=" CD GLN E 266 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CG GLN D 266 " pdb=" CD GLN D 266 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.43e+00 ... (remaining 5675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 6437 1.02 - 2.03: 882 2.03 - 3.05: 251 3.05 - 4.06: 70 4.06 - 5.08: 40 Bond angle restraints: 7680 Sorted by residual: angle pdb=" CA THR D 280 " pdb=" CB THR D 280 " pdb=" CG2 THR D 280 " ideal model delta sigma weight residual 110.50 114.37 -3.87 1.70e+00 3.46e-01 5.19e+00 angle pdb=" CA THR K 280 " pdb=" CB THR K 280 " pdb=" CG2 THR K 280 " ideal model delta sigma weight residual 110.50 114.37 -3.87 1.70e+00 3.46e-01 5.18e+00 angle pdb=" CA THR G 280 " pdb=" CB THR G 280 " pdb=" CG2 THR G 280 " ideal model delta sigma weight residual 110.50 114.37 -3.87 1.70e+00 3.46e-01 5.17e+00 angle pdb=" CA THR J 280 " pdb=" CB THR J 280 " pdb=" CG2 THR J 280 " ideal model delta sigma weight residual 110.50 114.36 -3.86 1.70e+00 3.46e-01 5.16e+00 angle pdb=" CA THR E 280 " pdb=" CB THR E 280 " pdb=" CG2 THR E 280 " ideal model delta sigma weight residual 110.50 114.36 -3.86 1.70e+00 3.46e-01 5.15e+00 ... (remaining 7675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.32: 2660 13.32 - 26.63: 420 26.63 - 39.95: 160 39.95 - 53.26: 80 53.26 - 66.58: 40 Dihedral angle restraints: 3360 sinusoidal: 1360 harmonic: 2000 Sorted by residual: dihedral pdb=" CA GLN I 266 " pdb=" CB GLN I 266 " pdb=" CG GLN I 266 " pdb=" CD GLN I 266 " ideal model delta sinusoidal sigma weight residual 180.00 134.27 45.73 3 1.50e+01 4.44e-03 8.22e+00 dihedral pdb=" CA GLN C 266 " pdb=" CB GLN C 266 " pdb=" CG GLN C 266 " pdb=" CD GLN C 266 " ideal model delta sinusoidal sigma weight residual 180.00 134.28 45.72 3 1.50e+01 4.44e-03 8.22e+00 dihedral pdb=" CA GLN Q 266 " pdb=" CB GLN Q 266 " pdb=" CG GLN Q 266 " pdb=" CD GLN Q 266 " ideal model delta sinusoidal sigma weight residual 180.00 134.28 45.72 3 1.50e+01 4.44e-03 8.22e+00 ... (remaining 3357 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.025: 254 0.025 - 0.047: 226 0.047 - 0.070: 100 0.070 - 0.093: 80 0.093 - 0.116: 40 Chirality restraints: 700 Sorted by residual: chirality pdb=" CB THR I 280 " pdb=" CA THR I 280 " pdb=" OG1 THR I 280 " pdb=" CG2 THR I 280 " both_signs ideal model delta sigma weight residual False 2.55 2.44 0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CB THR R 280 " pdb=" CA THR R 280 " pdb=" OG1 THR R 280 " pdb=" CG2 THR R 280 " both_signs ideal model delta sigma weight residual False 2.55 2.44 0.12 2.00e-01 2.50e+01 3.32e-01 chirality pdb=" CB THR S 280 " pdb=" CA THR S 280 " pdb=" OG1 THR S 280 " pdb=" CG2 THR S 280 " both_signs ideal model delta sigma weight residual False 2.55 2.44 0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 697 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 289 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" CD GLN E 289 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN E 289 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN E 289 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN S 289 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" CD GLN S 289 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN S 289 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN S 289 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN K 289 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" CD GLN K 289 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN K 289 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN K 289 " 0.013 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1566 2.81 - 3.33: 4067 3.33 - 3.86: 11742 3.86 - 4.38: 14891 4.38 - 4.90: 26124 Nonbonded interactions: 58390 Sorted by model distance: nonbonded pdb=" OG SER O 277 " pdb=" O HOH O 401 " model vdw 2.289 3.040 nonbonded pdb=" OG SER S 277 " pdb=" O HOH S 401 " model vdw 2.351 3.040 nonbonded pdb=" OG SER Q 277 " pdb=" O HOH Q 401 " model vdw 2.351 3.040 nonbonded pdb=" OG SER C 277 " pdb=" O HOH C 401 " model vdw 2.351 3.040 nonbonded pdb=" OG SER E 277 " pdb=" O HOH E 401 " model vdw 2.352 3.040 ... (remaining 58385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.310 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 5680 Z= 0.309 Angle : 0.894 5.077 7680 Z= 0.474 Chirality : 0.048 0.116 700 Planarity : 0.007 0.023 1080 Dihedral : 18.428 66.580 2120 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % 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 aren not related in a simple way. whole: -4.34 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.006 TYR R 268 PHE 0.006 0.003 PHE D 288 Details of bonding type rmsd covalent geometry : bond 0.00687 ( 5680) covalent geometry : angle 0.89392 ( 7680) hydrogen bonds : bond 0.11409 ( 174) hydrogen bonds : angle 6.48287 ( 522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.233 Fit side-chains REVERT: G 293 GLN cc_start: 0.8370 (mt0) cc_final: 0.8141 (mt0) REVERT: J 293 GLN cc_start: 0.8356 (mt0) cc_final: 0.7953 (mt0) REVERT: K 293 GLN cc_start: 0.8479 (mt0) cc_final: 0.8263 (mt0) REVERT: L 293 GLN cc_start: 0.8405 (mt0) cc_final: 0.8033 (mp10) REVERT: M 293 GLN cc_start: 0.8468 (mt0) cc_final: 0.8116 (mt0) REVERT: N 266 GLN cc_start: 0.8810 (mt0) cc_final: 0.8487 (mt0) REVERT: R 293 GLN cc_start: 0.8485 (mt0) cc_final: 0.8279 (mt0) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.3888 time to fit residues: 38.6405 Evaluate side-chains 85 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 298 GLN B 267 GLN B 298 GLN C 267 GLN C 293 GLN C 298 GLN D 267 GLN D 298 GLN E 267 GLN E 298 GLN F 267 GLN F 298 GLN G 267 GLN G 298 GLN H 267 GLN H 298 GLN I 267 GLN I 293 GLN I 298 GLN J 267 GLN J 298 GLN K 267 GLN K 298 GLN L 267 GLN L 298 GLN M 267 GLN M 298 GLN N 267 GLN N 293 GLN N 298 GLN O 267 GLN O 298 GLN P 267 GLN P 293 GLN P 298 GLN Q 267 GLN Q 298 GLN R 266 GLN R 267 GLN R 298 GLN S 267 GLN S 298 GLN T 267 GLN T 293 GLN T 298 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.108700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.100859 restraints weight = 6721.392| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.03 r_work: 0.3420 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 5680 Z= 0.185 Angle : 0.572 3.981 7680 Z= 0.288 Chirality : 0.041 0.108 700 Planarity : 0.004 0.026 1080 Dihedral : 3.310 8.387 760 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 7.59 % Allowed : 10.00 % Favored : 82.41 % 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 aren not related in a simple way. whole: -4.03 (0.15), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.11), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR H 291 PHE 0.008 0.002 PHE E 288 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 5680) covalent geometry : angle 0.57151 ( 7680) hydrogen bonds : bond 0.02493 ( 174) hydrogen bonds : angle 4.28269 ( 522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 88 time to evaluate : 0.235 Fit side-chains REVERT: D 266 GLN cc_start: 0.8628 (mt0) cc_final: 0.8403 (mt0) REVERT: E 293 GLN cc_start: 0.8514 (mt0) cc_final: 0.8176 (mt0) REVERT: I 285 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8903 (tt) REVERT: J 293 GLN cc_start: 0.8527 (mt0) cc_final: 0.8095 (mt0) REVERT: K 293 GLN cc_start: 0.8772 (mt0) cc_final: 0.8555 (mt0) REVERT: L 293 GLN cc_start: 0.8531 (mt0) cc_final: 0.8123 (mp10) REVERT: M 266 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7898 (mt0) REVERT: M 293 GLN cc_start: 0.8697 (mt0) cc_final: 0.8333 (mt0) REVERT: N 285 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8677 (tt) REVERT: O 266 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8090 (mt0) outliers start: 44 outliers final: 27 residues processed: 109 average time/residue: 0.3964 time to fit residues: 46.0763 Evaluate side-chains 116 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain O residue 266 GLN Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN D 293 GLN G 293 GLN H 293 GLN I 293 GLN N 293 GLN P 293 GLN T 293 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.108358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100601 restraints weight = 6683.300| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.03 r_work: 0.3424 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 5680 Z= 0.206 Angle : 0.570 4.741 7680 Z= 0.285 Chirality : 0.041 0.108 700 Planarity : 0.004 0.027 1080 Dihedral : 3.235 8.234 760 Min Nonbonded Distance : 2.675 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 8.62 % Allowed : 8.79 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.96 (0.15), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR R 276 PHE 0.008 0.002 PHE E 288 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 5680) covalent geometry : angle 0.57018 ( 7680) hydrogen bonds : bond 0.01974 ( 174) hydrogen bonds : angle 4.08630 ( 522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 94 time to evaluate : 0.272 Fit side-chains REVERT: B 266 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: D 266 GLN cc_start: 0.8640 (mt0) cc_final: 0.8435 (mt0) REVERT: E 293 GLN cc_start: 0.8538 (mt0) cc_final: 0.8232 (mt0) REVERT: F 266 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8512 (mt0) REVERT: H 266 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: I 285 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8917 (tt) REVERT: J 293 GLN cc_start: 0.8523 (mt0) cc_final: 0.8105 (mt0) REVERT: K 293 GLN cc_start: 0.8781 (mt0) cc_final: 0.8526 (mt0) REVERT: L 293 GLN cc_start: 0.8525 (mt0) cc_final: 0.8068 (mp10) REVERT: M 266 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: M 293 GLN cc_start: 0.8701 (mt0) cc_final: 0.8299 (mt0) REVERT: O 266 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8071 (mt0) outliers start: 50 outliers final: 32 residues processed: 112 average time/residue: 0.3972 time to fit residues: 47.4048 Evaluate side-chains 130 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain F residue 266 GLN Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 297 SER Chi-restraints excluded: chain O residue 266 GLN Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain O residue 285 LEU Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain S residue 285 LEU Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN C 293 GLN D 293 GLN G 293 GLN H 293 GLN I 293 GLN N 293 GLN P 293 GLN R 266 GLN S 279 GLN T 279 GLN T 293 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087197 restraints weight = 6456.465| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 0.72 r_work: 0.3176 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 5680 Z= 0.329 Angle : 0.647 4.537 7680 Z= 0.331 Chirality : 0.044 0.137 700 Planarity : 0.005 0.034 1080 Dihedral : 3.466 8.744 760 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 8.79 % Allowed : 10.69 % Favored : 80.52 % 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 aren not related in a simple way. whole: -3.92 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR R 276 PHE 0.010 0.004 PHE E 288 Details of bonding type rmsd covalent geometry : bond 0.00730 ( 5680) covalent geometry : angle 0.64677 ( 7680) hydrogen bonds : bond 0.02006 ( 174) hydrogen bonds : angle 4.21622 ( 522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 94 time to evaluate : 0.221 Fit side-chains REVERT: B 266 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8271 (mt0) REVERT: D 266 GLN cc_start: 0.8684 (mt0) cc_final: 0.8454 (mt0) REVERT: F 266 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: H 266 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8525 (mt0) REVERT: I 285 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8891 (tt) REVERT: J 266 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8507 (mt0) REVERT: J 293 GLN cc_start: 0.8566 (mt0) cc_final: 0.8128 (mt0) REVERT: K 293 GLN cc_start: 0.8803 (mt0) cc_final: 0.8441 (mp10) REVERT: L 293 GLN cc_start: 0.8569 (mt0) cc_final: 0.8222 (mt0) REVERT: M 266 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: M 293 GLN cc_start: 0.8764 (mt0) cc_final: 0.8411 (mt0) REVERT: O 266 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8042 (mt0) outliers start: 51 outliers final: 32 residues processed: 111 average time/residue: 0.4121 time to fit residues: 48.7360 Evaluate side-chains 131 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 266 GLN Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain J residue 266 GLN Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 297 SER Chi-restraints excluded: chain O residue 266 GLN Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain O residue 285 LEU Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain S residue 285 LEU Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN C 293 GLN D 293 GLN G 293 GLN H 293 GLN I 293 GLN N 293 GLN P 293 GLN R 266 GLN T 279 GLN T 293 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.096247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.090286 restraints weight = 6444.509| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 0.75 r_work: 0.3212 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 5680 Z= 0.163 Angle : 0.539 4.832 7680 Z= 0.267 Chirality : 0.039 0.113 700 Planarity : 0.004 0.027 1080 Dihedral : 3.215 8.301 760 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 7.76 % Allowed : 12.59 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.93 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR R 276 PHE 0.006 0.002 PHE I 288 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5680) covalent geometry : angle 0.53909 ( 7680) hydrogen bonds : bond 0.01484 ( 174) hydrogen bonds : angle 3.98490 ( 522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 94 time to evaluate : 0.240 Fit side-chains REVERT: E 293 GLN cc_start: 0.8526 (mt0) cc_final: 0.8232 (mt0) REVERT: H 266 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: I 285 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8920 (tt) REVERT: J 293 GLN cc_start: 0.8544 (mt0) cc_final: 0.8113 (mt0) REVERT: K 293 GLN cc_start: 0.8805 (mt0) cc_final: 0.8484 (mp10) REVERT: L 293 GLN cc_start: 0.8560 (mt0) cc_final: 0.8213 (mt0) REVERT: M 266 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: M 293 GLN cc_start: 0.8719 (mt0) cc_final: 0.8355 (mt0) REVERT: O 266 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8087 (mt0) outliers start: 45 outliers final: 28 residues processed: 111 average time/residue: 0.4298 time to fit residues: 50.6969 Evaluate side-chains 125 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 297 SER Chi-restraints excluded: chain O residue 266 GLN Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain O residue 285 LEU Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN D 266 GLN D 293 GLN F 266 GLN F 293 GLN G 293 GLN H 293 GLN I 293 GLN N 293 GLN P 293 GLN R 266 GLN S 279 GLN T 279 GLN T 293 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.091280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084896 restraints weight = 6641.698| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 0.81 r_work: 0.3144 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.043 5680 Z= 0.454 Angle : 0.729 5.105 7680 Z= 0.378 Chirality : 0.048 0.162 700 Planarity : 0.005 0.036 1080 Dihedral : 3.635 9.557 760 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 8.79 % Allowed : 12.41 % Favored : 78.79 % 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 aren not related in a simple way. whole: -3.88 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR C 291 PHE 0.012 0.004 PHE J 288 Details of bonding type rmsd covalent geometry : bond 0.01012 ( 5680) covalent geometry : angle 0.72853 ( 7680) hydrogen bonds : bond 0.02142 ( 174) hydrogen bonds : angle 4.31991 ( 522) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 89 time to evaluate : 0.257 Fit side-chains REVERT: B 266 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8340 (mt0) REVERT: E 266 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8599 (mt0) REVERT: G 266 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8507 (mt0) REVERT: H 266 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8528 (mt0) REVERT: I 285 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8915 (tt) REVERT: J 293 GLN cc_start: 0.8599 (mt0) cc_final: 0.8193 (mt0) REVERT: K 293 GLN cc_start: 0.8857 (mt0) cc_final: 0.8638 (mt0) REVERT: L 266 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8710 (mt0) REVERT: L 293 GLN cc_start: 0.8630 (mt0) cc_final: 0.8266 (mt0) REVERT: M 266 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8022 (mt0) REVERT: O 266 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: P 285 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8797 (tt) outliers start: 51 outliers final: 32 residues processed: 108 average time/residue: 0.4125 time to fit residues: 47.4777 Evaluate side-chains 128 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 266 GLN Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 266 GLN Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 266 GLN Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 297 SER Chi-restraints excluded: chain O residue 266 GLN Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain O residue 285 LEU Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 285 LEU Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain S residue 285 LEU Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN D 266 GLN D 293 GLN F 266 GLN G 293 GLN H 293 GLN M 293 GLN N 293 GLN T 279 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.097758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.091632 restraints weight = 6355.832| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 0.77 r_work: 0.3243 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 5680 Z= 0.099 Angle : 0.501 5.782 7680 Z= 0.242 Chirality : 0.038 0.116 700 Planarity : 0.004 0.027 1080 Dihedral : 3.151 8.075 760 Min Nonbonded Distance : 2.680 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.52 % Allowed : 16.03 % Favored : 78.45 % 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 aren not related in a simple way. whole: -3.89 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR R 276 PHE 0.003 0.001 PHE I 288 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 5680) covalent geometry : angle 0.50103 ( 7680) hydrogen bonds : bond 0.01283 ( 174) hydrogen bonds : angle 3.90561 ( 522) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.245 Fit side-chains REVERT: F 285 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8666 (tt) REVERT: J 293 GLN cc_start: 0.8537 (mt0) cc_final: 0.8137 (mt0) REVERT: K 293 GLN cc_start: 0.8785 (mt0) cc_final: 0.8585 (mt0) REVERT: L 293 GLN cc_start: 0.8533 (mt0) cc_final: 0.8075 (mt0) REVERT: R 297 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8661 (p) outliers start: 32 outliers final: 14 residues processed: 106 average time/residue: 0.4217 time to fit residues: 47.6341 Evaluate side-chains 107 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 293 GLN B 293 GLN C 293 GLN D 293 GLN F 266 GLN G 293 GLN H 293 GLN M 293 GLN N 293 GLN R 266 GLN S 279 GLN T 279 GLN T 293 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.093040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.087280 restraints weight = 6546.570| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 0.72 r_work: 0.3187 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.028 5680 Z= 0.302 Angle : 0.635 5.436 7680 Z= 0.320 Chirality : 0.045 0.253 700 Planarity : 0.004 0.030 1080 Dihedral : 3.403 9.080 760 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.90 % Allowed : 14.66 % Favored : 78.45 % 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 aren not related in a simple way. whole: -3.91 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR R 276 PHE 0.009 0.003 PHE J 288 Details of bonding type rmsd covalent geometry : bond 0.00674 ( 5680) covalent geometry : angle 0.63483 ( 7680) hydrogen bonds : bond 0.01751 ( 174) hydrogen bonds : angle 4.13371 ( 522) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.251 Fit side-chains REVERT: B 285 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8743 (tt) REVERT: H 266 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8537 (mt0) REVERT: J 293 GLN cc_start: 0.8548 (mt0) cc_final: 0.8134 (mt0) REVERT: K 293 GLN cc_start: 0.8806 (mt0) cc_final: 0.8564 (mt0) REVERT: L 293 GLN cc_start: 0.8570 (mt0) cc_final: 0.8209 (mt0) outliers start: 40 outliers final: 26 residues processed: 104 average time/residue: 0.4285 time to fit residues: 47.4294 Evaluate side-chains 117 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 297 SER Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain S residue 285 LEU Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 293 GLN C 293 GLN D 266 GLN D 293 GLN F 266 GLN G 293 GLN H 293 GLN M 293 GLN N 293 GLN R 266 GLN S 279 GLN T 279 GLN T 293 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089760 restraints weight = 6470.201| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 0.76 r_work: 0.3214 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5680 Z= 0.151 Angle : 0.548 5.761 7680 Z= 0.266 Chirality : 0.040 0.148 700 Planarity : 0.004 0.028 1080 Dihedral : 3.223 9.045 760 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.17 % Allowed : 16.72 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.93 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR R 276 PHE 0.006 0.002 PHE I 288 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5680) covalent geometry : angle 0.54785 ( 7680) hydrogen bonds : bond 0.01397 ( 174) hydrogen bonds : angle 3.95677 ( 522) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.236 Fit side-chains REVERT: J 293 GLN cc_start: 0.8563 (mt0) cc_final: 0.8159 (mt0) REVERT: K 293 GLN cc_start: 0.8804 (mt0) cc_final: 0.8588 (mt0) REVERT: L 293 GLN cc_start: 0.8555 (mt0) cc_final: 0.8096 (mt0) outliers start: 30 outliers final: 20 residues processed: 103 average time/residue: 0.4613 time to fit residues: 50.3537 Evaluate side-chains 112 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 297 SER Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 58 optimal weight: 0.4980 chunk 36 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 overall best weight: 3.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 293 GLN D 266 GLN D 293 GLN F 266 GLN G 293 GLN H 293 GLN M 293 GLN N 293 GLN P 293 GLN R 266 GLN S 279 GLN T 279 GLN T 293 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.093607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087796 restraints weight = 6631.355| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 0.74 r_work: 0.3190 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 5680 Z= 0.260 Angle : 0.612 5.559 7680 Z= 0.306 Chirality : 0.043 0.232 700 Planarity : 0.004 0.031 1080 Dihedral : 3.373 9.255 760 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 5.52 % Allowed : 16.21 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.93 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR R 276 PHE 0.008 0.003 PHE G 288 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 5680) covalent geometry : angle 0.61222 ( 7680) hydrogen bonds : bond 0.01642 ( 174) hydrogen bonds : angle 4.09957 ( 522) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.241 Fit side-chains REVERT: B 266 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8284 (mt0) REVERT: J 293 GLN cc_start: 0.8549 (mt0) cc_final: 0.8140 (mt0) REVERT: K 293 GLN cc_start: 0.8802 (mt0) cc_final: 0.8563 (mt0) REVERT: L 293 GLN cc_start: 0.8561 (mt0) cc_final: 0.8199 (mt0) outliers start: 32 outliers final: 24 residues processed: 99 average time/residue: 0.4550 time to fit residues: 47.8536 Evaluate side-chains 116 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 297 SER Chi-restraints excluded: chain O residue 280 THR Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain R residue 297 SER Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain S residue 285 LEU Chi-restraints excluded: chain T residue 280 THR Chi-restraints excluded: chain T residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN D 266 GLN D 293 GLN F 266 GLN G 293 GLN H 293 GLN M 293 GLN N 293 GLN R 266 GLN S 279 GLN T 279 GLN T 293 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.089599 restraints weight = 6376.015| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 0.79 r_work: 0.3211 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5680 Z= 0.152 Angle : 0.545 5.300 7680 Z= 0.265 Chirality : 0.040 0.151 700 Planarity : 0.004 0.027 1080 Dihedral : 3.205 8.840 760 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.69 % Allowed : 16.21 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.92 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR R 276 PHE 0.006 0.002 PHE G 288 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 5680) covalent geometry : angle 0.54537 ( 7680) hydrogen bonds : bond 0.01370 ( 174) hydrogen bonds : angle 3.93104 ( 522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1951.43 seconds wall clock time: 34 minutes 17.38 seconds (2057.38 seconds total)