Starting phenix.real_space_refine on Sun Apr 27 12:23:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ter_41198/04_2025/8ter_41198.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ter_41198/04_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_41198/04_2025/8ter_41198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ter_41198/04_2025/8ter_41198.map" model { file = "/net/cci-nas-00/data/ceres_data/8ter_41198/04_2025/8ter_41198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ter_41198/04_2025/8ter_41198.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, T Time building chain proxies: 2.88, per 1000 atoms: 0.50 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: 1.22 Conformation dependent library (CDL) restraints added in 550.4 milliseconds 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: 0.92 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: 1.65 Time building geometry restraints manager: 1.48 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' 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: 21.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.060 Find NCS groups from input model: 0.120 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:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.910 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 PHE 0.006 0.003 PHE D 288 TYR 0.016 0.006 TYR R 268 Details of bonding type rmsd hydrogen bonds : bond 0.11409 ( 174) hydrogen bonds : angle 6.48287 ( 522) covalent geometry : bond 0.00687 ( 5680) covalent geometry : angle 0.89392 ( 7680) *********************** 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 : 0.734 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: 0.9591 time to fit residues: 95.8740 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 : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 0.3980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.110533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.102980 restraints weight = 6589.757| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 0.98 r_work: 0.3450 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 5680 Z= 0.125 Angle : 0.525 3.601 7680 Z= 0.260 Chirality : 0.040 0.113 700 Planarity : 0.004 0.023 1080 Dihedral : 3.147 8.574 760 Min Nonbonded Distance : 2.691 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 7.76 % Allowed : 10.17 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.15), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.11), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE E 288 TYR 0.007 0.001 TYR H 291 Details of bonding type rmsd hydrogen bonds : bond 0.02186 ( 174) hydrogen bonds : angle 4.15969 ( 522) covalent geometry : bond 0.00286 ( 5680) covalent geometry : angle 0.52518 ( 7680) *********************** 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 137 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 92 time to evaluate : 0.689 Fit side-chains REVERT: C 293 GLN cc_start: 0.8531 (mt0) cc_final: 0.8324 (mt0) REVERT: D 266 GLN cc_start: 0.8574 (mt0) cc_final: 0.8366 (mt0) REVERT: E 293 GLN cc_start: 0.8475 (mt0) cc_final: 0.8173 (mt0) REVERT: F 266 GLN cc_start: 0.8668 (mt0) cc_final: 0.8458 (mt0) REVERT: J 293 GLN cc_start: 0.8480 (mt0) cc_final: 0.8074 (mt0) REVERT: L 293 GLN cc_start: 0.8504 (mt0) cc_final: 0.8113 (mp10) REVERT: M 293 GLN cc_start: 0.8664 (mt0) cc_final: 0.8317 (mt0) REVERT: O 293 GLN cc_start: 0.8521 (mt0) cc_final: 0.8100 (mt0) REVERT: R 297 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8670 (p) outliers start: 45 outliers final: 23 residues processed: 114 average time/residue: 0.8219 time to fit residues: 100.1458 Evaluate side-chains 113 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 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 R residue 297 SER Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 280 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 293 GLN G 293 GLN I 293 GLN K 293 GLN N 293 GLN P 293 GLN T 293 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.091457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.085574 restraints weight = 6612.550| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.73 r_work: 0.3148 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.046 5680 Z= 0.488 Angle : 0.755 5.151 7680 Z= 0.396 Chirality : 0.050 0.165 700 Planarity : 0.006 0.040 1080 Dihedral : 3.637 9.499 760 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 8.62 % Allowed : 10.00 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.15), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.005 PHE G 288 TYR 0.015 0.002 TYR C 291 Details of bonding type rmsd hydrogen bonds : bond 0.02648 ( 174) hydrogen bonds : angle 4.40596 ( 522) covalent geometry : bond 0.01082 ( 5680) covalent geometry : angle 0.75488 ( 7680) *********************** 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 142 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 92 time to evaluate : 0.622 Fit side-chains REVERT: B 266 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: D 266 GLN cc_start: 0.8720 (mt0) cc_final: 0.8497 (mt0) REVERT: F 266 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8372 (mt0) REVERT: H 266 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8512 (mt0) REVERT: I 285 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8901 (tt) REVERT: J 293 GLN cc_start: 0.8590 (mt0) cc_final: 0.8163 (mt0) REVERT: L 266 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8689 (mt0) REVERT: L 293 GLN cc_start: 0.8592 (mt0) cc_final: 0.8238 (mt0) REVERT: M 293 GLN cc_start: 0.8761 (mt0) cc_final: 0.8414 (mt0) REVERT: P 285 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8827 (tt) outliers start: 50 outliers final: 31 residues processed: 110 average time/residue: 0.7729 time to fit residues: 91.1199 Evaluate side-chains 128 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN G 293 GLN H 293 GLN I 293 GLN K 293 GLN N 293 GLN P 293 GLN T 279 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.111022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.103671 restraints weight = 6725.474| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 0.96 r_work: 0.3501 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1838 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= 0.104 Angle : 0.501 4.869 7680 Z= 0.244 Chirality : 0.038 0.113 700 Planarity : 0.004 0.025 1080 Dihedral : 3.147 8.113 760 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.83 % Allowed : 14.83 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (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 PHE 0.004 0.001 PHE G 288 TYR 0.009 0.001 TYR R 276 Details of bonding type rmsd hydrogen bonds : bond 0.01416 ( 174) hydrogen bonds : angle 3.96146 ( 522) covalent geometry : bond 0.00243 ( 5680) covalent geometry : angle 0.50057 ( 7680) *********************** 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 122 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.719 Fit side-chains REVERT: E 293 GLN cc_start: 0.8498 (mt0) cc_final: 0.8166 (mt0) REVERT: J 293 GLN cc_start: 0.8467 (mt0) cc_final: 0.8036 (mt0) REVERT: L 293 GLN cc_start: 0.8492 (mt0) cc_final: 0.8038 (mp10) REVERT: M 293 GLN cc_start: 0.8678 (mt0) cc_final: 0.8325 (mt0) outliers start: 28 outliers final: 12 residues processed: 108 average time/residue: 0.8780 time to fit residues: 100.9129 Evaluate side-chains 104 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E 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 O residue 280 THR Chi-restraints excluded: chain Q 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 55 optimal weight: 0.0570 chunk 43 optimal weight: 0.3980 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 59 optimal weight: 0.0370 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 293 GLN C 293 GLN D 266 GLN D 293 GLN F 266 GLN G 293 GLN H 293 GLN I 293 GLN K 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.090048 restraints weight = 6365.446| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 0.77 r_work: 0.3208 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1849 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= 0.160 Angle : 0.535 4.305 7680 Z= 0.263 Chirality : 0.039 0.132 700 Planarity : 0.004 0.025 1080 Dihedral : 3.124 8.290 760 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 6.72 % Allowed : 13.79 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE G 288 TYR 0.011 0.001 TYR R 276 Details of bonding type rmsd hydrogen bonds : bond 0.01474 ( 174) hydrogen bonds : angle 3.93070 ( 522) covalent geometry : bond 0.00361 ( 5680) covalent geometry : angle 0.53518 ( 7680) *********************** 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 132 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.630 Fit side-chains REVERT: B 285 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8708 (tt) REVERT: E 293 GLN cc_start: 0.8558 (mt0) cc_final: 0.8270 (mt0) REVERT: H 266 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: J 293 GLN cc_start: 0.8554 (mt0) cc_final: 0.8131 (mt0) REVERT: L 293 GLN cc_start: 0.8573 (mt0) cc_final: 0.8117 (mp10) REVERT: M 293 GLN cc_start: 0.8734 (mt0) cc_final: 0.8381 (mt0) outliers start: 39 outliers final: 22 residues processed: 106 average time/residue: 0.8252 time to fit residues: 93.4292 Evaluate side-chains 116 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 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 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 2 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 293 GLN G 293 GLN H 293 GLN I 293 GLN K 293 GLN N 293 GLN R 266 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 = 0.3348 r_free = 0.3348 target = 0.092071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086254 restraints weight = 6530.155| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 0.73 r_work: 0.3158 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.039 5680 Z= 0.406 Angle : 0.701 5.160 7680 Z= 0.361 Chirality : 0.047 0.185 700 Planarity : 0.005 0.034 1080 Dihedral : 3.539 9.338 760 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 7.93 % Allowed : 13.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 PHE 0.012 0.004 PHE J 288 TYR 0.016 0.002 TYR R 276 Details of bonding type rmsd hydrogen bonds : bond 0.02036 ( 174) hydrogen bonds : angle 4.21940 ( 522) covalent geometry : bond 0.00903 ( 5680) covalent geometry : angle 0.70121 ( 7680) *********************** 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 139 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 93 time to evaluate : 0.792 Fit side-chains REVERT: B 266 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: G 266 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8501 (mt0) REVERT: H 266 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8543 (mt0) REVERT: J 293 GLN cc_start: 0.8583 (mt0) cc_final: 0.8183 (mt0) REVERT: L 293 GLN cc_start: 0.8591 (mt0) cc_final: 0.8240 (mt0) REVERT: P 285 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8774 (tt) outliers start: 46 outliers final: 29 residues processed: 109 average time/residue: 0.8824 time to fit residues: 102.9698 Evaluate side-chains 121 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR 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 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 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 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 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 51 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN C 293 GLN D 266 GLN D 293 GLN H 293 GLN K 293 GLN M 293 GLN N 293 GLN P 293 GLN R 266 GLN S 279 GLN T 279 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.091374 restraints weight = 6352.823| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 0.83 r_work: 0.3237 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1918 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 : 0.508 5.765 7680 Z= 0.242 Chirality : 0.038 0.116 700 Planarity : 0.004 0.025 1080 Dihedral : 3.100 8.387 760 Min Nonbonded Distance : 2.681 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.83 % Allowed : 16.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (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 PHE 0.003 0.001 PHE I 288 TYR 0.010 0.001 TYR R 276 Details of bonding type rmsd hydrogen bonds : bond 0.01272 ( 174) hydrogen bonds : angle 3.86583 ( 522) covalent geometry : bond 0.00230 ( 5680) covalent geometry : angle 0.50846 ( 7680) *********************** 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 120 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.638 Fit side-chains REVERT: F 285 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8657 (tt) REVERT: J 293 GLN cc_start: 0.8540 (mt0) cc_final: 0.8123 (mt0) REVERT: L 293 GLN cc_start: 0.8542 (mt0) cc_final: 0.8053 (mp10) REVERT: R 297 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8666 (p) outliers start: 28 outliers final: 15 residues processed: 104 average time/residue: 0.9256 time to fit residues: 102.2894 Evaluate side-chains 107 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 285 LEU Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain K 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 G 293 GLN H 293 GLN I 293 GLN K 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.094758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088474 restraints weight = 6356.344| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 0.80 r_work: 0.3191 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 5680 Z= 0.210 Angle : 0.577 4.725 7680 Z= 0.284 Chirality : 0.041 0.133 700 Planarity : 0.004 0.026 1080 Dihedral : 3.225 8.592 760 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 6.38 % Allowed : 15.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE E 288 TYR 0.014 0.001 TYR R 276 Details of bonding type rmsd hydrogen bonds : bond 0.01533 ( 174) hydrogen bonds : angle 3.98447 ( 522) covalent geometry : bond 0.00470 ( 5680) covalent geometry : angle 0.57674 ( 7680) *********************** 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 129 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.716 Fit side-chains REVERT: B 266 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: J 293 GLN cc_start: 0.8559 (mt0) cc_final: 0.8150 (mt0) REVERT: L 293 GLN cc_start: 0.8564 (mt0) cc_final: 0.8209 (mt0) outliers start: 37 outliers final: 25 residues processed: 103 average time/residue: 1.0182 time to fit residues: 112.0770 Evaluate side-chains 117 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 266 GLN 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 G 293 GLN H 293 GLN I 293 GLN K 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.094950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.088902 restraints weight = 6451.738| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.76 r_work: 0.3193 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 5680 Z= 0.199 Angle : 0.574 5.249 7680 Z= 0.281 Chirality : 0.041 0.127 700 Planarity : 0.004 0.026 1080 Dihedral : 3.224 8.602 760 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.16), residues: 660 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.12), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE E 288 TYR 0.013 0.001 TYR R 276 Details of bonding type rmsd hydrogen bonds : bond 0.01488 ( 174) hydrogen bonds : angle 3.97843 ( 522) covalent geometry : bond 0.00445 ( 5680) covalent geometry : angle 0.57450 ( 7680) *********************** 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: 32 poor density : 93 time to evaluate : 0.663 Fit side-chains REVERT: B 266 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: H 266 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: J 293 GLN cc_start: 0.8561 (mt0) cc_final: 0.8152 (mt0) REVERT: L 293 GLN cc_start: 0.8559 (mt0) cc_final: 0.8091 (mt0) outliers start: 32 outliers final: 25 residues processed: 99 average time/residue: 0.9157 time to fit residues: 96.5571 Evaluate side-chains 117 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 266 GLN 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 GLN D 293 GLN G 293 GLN H 293 GLN I 293 GLN K 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.092491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.086663 restraints weight = 6629.636| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 0.73 r_work: 0.3172 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 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 : 0.008 0.033 5680 Z= 0.349 Angle : 0.670 4.801 7680 Z= 0.340 Chirality : 0.046 0.172 700 Planarity : 0.004 0.030 1080 Dihedral : 3.465 9.076 760 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.69 % Allowed : 16.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (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 PHE 0.010 0.004 PHE J 288 TYR 0.016 0.002 TYR R 276 Details of bonding type rmsd hydrogen bonds : bond 0.01841 ( 174) hydrogen bonds : angle 4.17982 ( 522) covalent geometry : bond 0.00777 ( 5680) covalent geometry : angle 0.67042 ( 7680) ********************** 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 123 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.831 Fit side-chains REVERT: B 266 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8317 (mt0) REVERT: H 266 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8548 (mt0) REVERT: J 293 GLN cc_start: 0.8576 (mt0) cc_final: 0.8171 (mt0) REVERT: L 293 GLN cc_start: 0.8587 (mt0) cc_final: 0.8233 (mt0) outliers start: 33 outliers final: 25 residues processed: 97 average time/residue: 1.1966 time to fit residues: 123.3541 Evaluate side-chains 117 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 266 GLN 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 G 293 GLN H 293 GLN K 293 GLN M 293 GLN N 293 GLN R 266 GLN T 279 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.097239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.091152 restraints weight = 6413.230| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 0.77 r_work: 0.3231 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 5680 Z= 0.110 Angle : 0.520 5.310 7680 Z= 0.247 Chirality : 0.039 0.116 700 Planarity : 0.004 0.025 1080 Dihedral : 3.112 8.281 760 Min Nonbonded Distance : 2.678 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.00 % Allowed : 17.07 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 PHE 0.004 0.001 PHE K 288 TYR 0.010 0.001 TYR R 276 Details of bonding type rmsd hydrogen bonds : bond 0.01279 ( 174) hydrogen bonds : angle 3.87570 ( 522) covalent geometry : bond 0.00253 ( 5680) covalent geometry : angle 0.51954 ( 7680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4445.84 seconds wall clock time: 78 minutes 45.34 seconds (4725.34 seconds total)