Starting phenix.real_space_refine on Fri Mar 6 02:40:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x0x_32928/03_2026/7x0x_32928.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x0x_32928/03_2026/7x0x_32928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x0x_32928/03_2026/7x0x_32928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x0x_32928/03_2026/7x0x_32928.map" model { file = "/net/cci-nas-00/data/ceres_data/7x0x_32928/03_2026/7x0x_32928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x0x_32928/03_2026/7x0x_32928.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.186 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14652 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 64 5.16 5 C 10096 2.51 5 N 2680 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15680 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3867 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 26, 'TRANS': 449} Chain breaks: 2 Chain: "B" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3867 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 26, 'TRANS': 449} Chain breaks: 2 Chain: "C" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3867 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 26, 'TRANS': 449} Chain breaks: 2 Chain: "A" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3867 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 26, 'TRANS': 449} Chain breaks: 2 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.28, per 1000 atoms: 0.21 Number of scatterers: 15680 At special positions: 0 Unit cell: (125.005, 127.179, 77.177, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 8 15.00 O 2832 8.00 N 2680 7.00 C 10096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 648.9 milliseconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3592 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 60.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'D' and resid 20 through 27 Processing helix chain 'D' and resid 39 through 47 removed outlier: 3.795A pdb=" N GLU D 42 " --> pdb=" O CYS D 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 43 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 44 " --> pdb=" O GLU D 41 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN D 45 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR D 47 " --> pdb=" O GLY D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 70 removed outlier: 3.661A pdb=" N ALA D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 66 " --> pdb=" O HIS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.869A pdb=" N LEU D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 3.914A pdb=" N VAL D 110 " --> pdb=" O PRO D 106 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 159 removed outlier: 3.926A pdb=" N LYS D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.568A pdb=" N LYS D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.553A pdb=" N PHE D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 274 removed outlier: 3.753A pdb=" N ILE D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 271 " --> pdb=" O MET D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 304 removed outlier: 3.529A pdb=" N LEU D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D 298 " --> pdb=" O ARG D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'D' and resid 355 through 369 Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.714A pdb=" N GLY D 377 " --> pdb=" O PRO D 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP D 383 " --> pdb=" O LYS D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 401 removed outlier: 3.608A pdb=" N SER D 401 " --> pdb=" O TRP D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 424 removed outlier: 3.600A pdb=" N TYR D 423 " --> pdb=" O GLN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 434 removed outlier: 3.512A pdb=" N TRP D 433 " --> pdb=" O TYR D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 438 removed outlier: 3.571A pdb=" N ALA D 438 " --> pdb=" O PRO D 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 435 through 438' Processing helix chain 'D' and resid 447 through 451 Processing helix chain 'D' and resid 452 through 459 Processing helix chain 'D' and resid 473 through 494 removed outlier: 3.584A pdb=" N GLU D 479 " --> pdb=" O ASP D 475 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 482 " --> pdb=" O ARG D 478 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU D 490 " --> pdb=" O SER D 486 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 493 " --> pdb=" O ARG D 489 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 27 Processing helix chain 'B' and resid 39 through 47 removed outlier: 3.795A pdb=" N GLU B 42 " --> pdb=" O CYS B 39 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 43 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 44 " --> pdb=" O GLU B 41 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR B 47 " --> pdb=" O GLY B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 70 removed outlier: 3.662A pdb=" N ALA B 61 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.869A pdb=" N LEU B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.913A pdb=" N VAL B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 117 " --> pdb=" O HIS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.926A pdb=" N LYS B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.568A pdb=" N LYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 247 through 253 removed outlier: 3.553A pdb=" N PHE B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 274 removed outlier: 3.752A pdb=" N ILE B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 271 " --> pdb=" O MET B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 304 removed outlier: 3.528A pdb=" N LEU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 Processing helix chain 'B' and resid 338 through 352 Processing helix chain 'B' and resid 355 through 369 Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.714A pdb=" N GLY B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.608A pdb=" N SER B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 424 removed outlier: 3.601A pdb=" N TYR B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.512A pdb=" N TRP B 433 " --> pdb=" O TYR B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 438 removed outlier: 3.571A pdb=" N ALA B 438 " --> pdb=" O PRO B 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 435 through 438' Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 452 through 459 Processing helix chain 'B' and resid 473 through 494 removed outlier: 3.585A pdb=" N GLU B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 482 " --> pdb=" O ARG B 478 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 493 " --> pdb=" O ARG B 489 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 27 Processing helix chain 'C' and resid 39 through 47 removed outlier: 3.795A pdb=" N GLU C 42 " --> pdb=" O CYS C 39 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 43 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 44 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN C 45 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR C 47 " --> pdb=" O GLY C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 70 removed outlier: 3.661A pdb=" N ALA C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 66 " --> pdb=" O HIS C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 94 removed outlier: 3.868A pdb=" N LEU C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 120 removed outlier: 3.914A pdb=" N VAL C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS C 116 " --> pdb=" O ASP C 112 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU C 117 " --> pdb=" O HIS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 removed outlier: 3.926A pdb=" N LYS C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.567A pdb=" N LYS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 247 through 253 removed outlier: 3.553A pdb=" N PHE C 253 " --> pdb=" O PRO C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 274 removed outlier: 3.752A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 271 " --> pdb=" O MET C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 304 removed outlier: 3.528A pdb=" N LEU C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 298 " --> pdb=" O ARG C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 334 Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'C' and resid 355 through 369 Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.714A pdb=" N GLY C 377 " --> pdb=" O PRO C 373 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP C 383 " --> pdb=" O LYS C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 401 removed outlier: 3.609A pdb=" N SER C 401 " --> pdb=" O TRP C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 424 removed outlier: 3.601A pdb=" N TYR C 423 " --> pdb=" O GLN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 434 removed outlier: 3.512A pdb=" N TRP C 433 " --> pdb=" O TYR C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 438 removed outlier: 3.572A pdb=" N ALA C 438 " --> pdb=" O PRO C 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 435 through 438' Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 452 through 459 Processing helix chain 'C' and resid 473 through 494 removed outlier: 3.585A pdb=" N GLU C 479 " --> pdb=" O ASP C 475 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU C 490 " --> pdb=" O SER C 486 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 493 " --> pdb=" O ARG C 489 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 27 Processing helix chain 'A' and resid 39 through 47 removed outlier: 3.795A pdb=" N GLU A 42 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 43 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 44 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 47 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 70 removed outlier: 3.663A pdb=" N ALA A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 66 " --> pdb=" O HIS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.869A pdb=" N LEU A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 120 removed outlier: 3.914A pdb=" N VAL A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.926A pdb=" N LYS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 213 through 228 removed outlier: 3.568A pdb=" N LYS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.553A pdb=" N PHE A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 removed outlier: 3.753A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 304 removed outlier: 3.528A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 338 through 352 Processing helix chain 'A' and resid 355 through 369 Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.715A pdb=" N GLY A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 383 " --> pdb=" O LYS A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.609A pdb=" N SER A 401 " --> pdb=" O TRP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 424 removed outlier: 3.601A pdb=" N TYR A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.512A pdb=" N TRP A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 438 removed outlier: 3.572A pdb=" N ALA A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 435 through 438' Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 473 through 494 removed outlier: 3.586A pdb=" N GLU A 479 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 75 through 78 removed outlier: 9.224A pdb=" N THR D 75 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE D 77 " --> pdb=" O PRO D 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE D 36 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE D 37 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS D 6 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL D 99 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE D 8 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N ASN D 101 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N TRP D 10 " --> pdb=" O ASN D 101 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL D 98 " --> pdb=" O GLN D 127 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N TYR D 129 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE D 100 " --> pdb=" O TYR D 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 78 removed outlier: 9.224A pdb=" N THR B 75 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE B 77 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE B 36 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE B 37 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS B 6 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL B 99 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE B 8 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ASN B 101 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N TRP B 10 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL B 98 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N TYR B 129 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE B 100 " --> pdb=" O TYR B 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 78 removed outlier: 9.225A pdb=" N THR C 75 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE C 77 " --> pdb=" O PRO C 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE C 36 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE C 37 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS C 6 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL C 99 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE C 8 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N ASN C 101 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N TRP C 10 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL C 98 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N TYR C 129 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE C 100 " --> pdb=" O TYR C 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 78 removed outlier: 9.225A pdb=" N THR A 75 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE A 77 " --> pdb=" O PRO A 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A 36 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE A 37 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS A 6 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL A 99 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE A 8 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ASN A 101 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N TRP A 10 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A 98 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N TYR A 129 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE A 100 " --> pdb=" O TYR A 129 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1956 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: 2.27 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4898 1.34 - 1.46: 3179 1.46 - 1.57: 7951 1.57 - 1.69: 12 1.69 - 1.81: 100 Bond restraints: 16140 Sorted by residual: bond pdb=" O5B FAD A 701 " pdb=" PA FAD A 701 " ideal model delta sigma weight residual 1.634 1.533 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O5B FAD C 701 " pdb=" PA FAD C 701 " ideal model delta sigma weight residual 1.634 1.533 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O5B FAD B 701 " pdb=" PA FAD B 701 " ideal model delta sigma weight residual 1.634 1.533 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O5B FAD D 701 " pdb=" PA FAD D 701 " ideal model delta sigma weight residual 1.634 1.534 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" O2P FAD C 701 " pdb=" P FAD C 701 " ideal model delta sigma weight residual 1.495 1.401 0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 16135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 21612 3.12 - 6.23: 304 6.23 - 9.35: 20 9.35 - 12.46: 12 12.46 - 15.58: 8 Bond angle restraints: 21956 Sorted by residual: angle pdb=" N LEU C 194 " pdb=" CA LEU C 194 " pdb=" C LEU C 194 " ideal model delta sigma weight residual 114.16 102.07 12.09 1.48e+00 4.57e-01 6.68e+01 angle pdb=" N LEU B 194 " pdb=" CA LEU B 194 " pdb=" C LEU B 194 " ideal model delta sigma weight residual 114.16 102.14 12.02 1.48e+00 4.57e-01 6.59e+01 angle pdb=" N LEU D 194 " pdb=" CA LEU D 194 " pdb=" C LEU D 194 " ideal model delta sigma weight residual 114.16 102.35 11.81 1.48e+00 4.57e-01 6.37e+01 angle pdb=" N LEU A 194 " pdb=" CA LEU A 194 " pdb=" C LEU A 194 " ideal model delta sigma weight residual 114.16 102.38 11.78 1.48e+00 4.57e-01 6.33e+01 angle pdb=" CA GLU B 197 " pdb=" CB GLU B 197 " pdb=" CG GLU B 197 " ideal model delta sigma weight residual 114.10 129.68 -15.58 2.00e+00 2.50e-01 6.07e+01 ... (remaining 21951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.75: 8695 20.75 - 41.50: 697 41.50 - 62.24: 159 62.24 - 82.99: 41 82.99 - 103.74: 8 Dihedral angle restraints: 9600 sinusoidal: 4052 harmonic: 5548 Sorted by residual: dihedral pdb=" CA MET D 175 " pdb=" C MET D 175 " pdb=" N PRO D 176 " pdb=" CA PRO D 176 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA MET C 175 " pdb=" C MET C 175 " pdb=" N PRO C 176 " pdb=" CA PRO C 176 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA MET A 175 " pdb=" C MET A 175 " pdb=" N PRO A 176 " pdb=" CA PRO A 176 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 9597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1536 0.054 - 0.109: 619 0.109 - 0.163: 143 0.163 - 0.218: 18 0.218 - 0.272: 12 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CB ILE A 86 " pdb=" CA ILE A 86 " pdb=" CG1 ILE A 86 " pdb=" CG2 ILE A 86 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE B 86 " pdb=" CA ILE B 86 " pdb=" CG1 ILE B 86 " pdb=" CG2 ILE B 86 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE D 86 " pdb=" CA ILE D 86 " pdb=" CG1 ILE D 86 " pdb=" CG2 ILE D 86 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2325 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 338 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PRO D 339 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 339 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 339 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 338 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO B 339 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 338 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO A 339 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " 0.034 5.00e-02 4.00e+02 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4256 2.80 - 3.33: 13028 3.33 - 3.85: 25867 3.85 - 4.38: 32264 4.38 - 4.90: 52850 Nonbonded interactions: 128265 Sorted by model distance: nonbonded pdb=" OE1 GLU A 347 " pdb=" OH TYR A 429 " model vdw 2.280 3.040 nonbonded pdb=" OE1 GLU D 347 " pdb=" OH TYR D 429 " model vdw 2.280 3.040 nonbonded pdb=" OE1 GLU B 347 " pdb=" OH TYR B 429 " model vdw 2.281 3.040 nonbonded pdb=" OE1 GLU C 347 " pdb=" OH TYR C 429 " model vdw 2.281 3.040 nonbonded pdb=" NZ LYS B 329 " pdb=" OE1 GLU A 462 " model vdw 2.363 3.120 ... (remaining 128260 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: 0.04 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'B' selection = chain 'C' selection = chain 'A' } 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.590 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:8.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.008 0.101 16140 Z= 0.370 Angle : 0.999 15.578 21956 Z= 0.536 Chirality : 0.062 0.272 2328 Planarity : 0.007 0.062 2736 Dihedral : 16.659 103.739 6008 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.15 % Allowed : 7.79 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.09 (0.14), residues: 1880 helix: -4.33 (0.06), residues: 1008 sheet: -0.78 (0.42), residues: 144 loop : -2.13 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 412 TYR 0.019 0.003 TYR C 47 PHE 0.012 0.002 PHE A 100 TRP 0.015 0.002 TRP C 321 HIS 0.007 0.002 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00841 (16140) covalent geometry : angle 0.99863 (21956) hydrogen bonds : bond 0.34319 ( 672) hydrogen bonds : angle 9.91836 ( 1956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 435 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 TRP cc_start: 0.9133 (p90) cc_final: 0.8770 (p90) REVERT: B 335 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7427 (mtm110) REVERT: C 81 ASN cc_start: 0.8461 (t0) cc_final: 0.8220 (t0) REVERT: C 113 HIS cc_start: 0.7450 (t-90) cc_final: 0.7175 (t70) REVERT: C 141 TYR cc_start: 0.7176 (m-10) cc_final: 0.6840 (m-80) REVERT: A 81 ASN cc_start: 0.8373 (t0) cc_final: 0.8137 (t0) REVERT: A 87 LEU cc_start: 0.8517 (tt) cc_final: 0.8225 (tt) REVERT: A 141 TYR cc_start: 0.7060 (m-10) cc_final: 0.6800 (m-80) outliers start: 19 outliers final: 4 residues processed: 440 average time/residue: 0.5168 time to fit residues: 253.6115 Evaluate side-chains 351 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 347 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 285 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 HIS D 356 ASN D 415 ASN B 260 HIS B 356 ASN C 356 ASN C 415 ASN A 260 HIS A 356 ASN A 415 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113625 restraints weight = 16402.932| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.07 r_work: 0.3198 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16140 Z= 0.138 Angle : 0.661 9.503 21956 Z= 0.339 Chirality : 0.045 0.151 2328 Planarity : 0.006 0.085 2736 Dihedral : 11.357 128.168 2263 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.20 % Allowed : 15.58 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.17), residues: 1880 helix: -1.89 (0.13), residues: 1040 sheet: -0.39 (0.41), residues: 144 loop : -1.35 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 274 TYR 0.017 0.002 TYR B 154 PHE 0.015 0.001 PHE B 33 TRP 0.032 0.001 TRP B 172 HIS 0.004 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00316 (16140) covalent geometry : angle 0.66110 (21956) hydrogen bonds : bond 0.05660 ( 672) hydrogen bonds : angle 5.21840 ( 1956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 368 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 GLU cc_start: 0.8287 (mp0) cc_final: 0.7895 (mp0) REVERT: D 79 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8105 (t) REVERT: D 81 ASN cc_start: 0.8175 (t0) cc_final: 0.7564 (t0) REVERT: D 127 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7978 (mt0) REVERT: D 223 GLU cc_start: 0.7730 (tt0) cc_final: 0.7528 (tt0) REVERT: D 226 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7404 (mm-30) REVERT: B 43 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6798 (mm-30) REVERT: B 81 ASN cc_start: 0.8012 (t0) cc_final: 0.7582 (t0) REVERT: B 127 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: B 172 TRP cc_start: 0.6325 (t60) cc_final: 0.5888 (t60) REVERT: B 335 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7242 (mtm110) REVERT: C 37 ILE cc_start: 0.8412 (mt) cc_final: 0.8179 (mt) REVERT: C 80 HIS cc_start: 0.7160 (m-70) cc_final: 0.6346 (m-70) REVERT: C 81 ASN cc_start: 0.7881 (t0) cc_final: 0.7310 (t0) REVERT: C 113 HIS cc_start: 0.7493 (t-90) cc_final: 0.7169 (t70) REVERT: C 141 TYR cc_start: 0.7740 (m-10) cc_final: 0.7153 (m-80) REVERT: C 226 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: C 282 GLU cc_start: 0.7871 (tp30) cc_final: 0.7543 (tp30) REVERT: A 80 HIS cc_start: 0.6939 (m-70) cc_final: 0.6469 (m-70) REVERT: A 81 ASN cc_start: 0.7943 (t0) cc_final: 0.7287 (t0) REVERT: A 113 HIS cc_start: 0.7169 (t-90) cc_final: 0.6910 (t70) REVERT: A 141 TYR cc_start: 0.7737 (m-10) cc_final: 0.7181 (m-80) REVERT: A 274 ARG cc_start: 0.6901 (mmm160) cc_final: 0.6614 (mmm160) outliers start: 53 outliers final: 9 residues processed: 378 average time/residue: 0.5146 time to fit residues: 217.1759 Evaluate side-chains 340 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 326 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain A residue 207 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 141 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN D 260 HIS ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN B 260 HIS B 315 HIS B 419 GLN C 419 GLN A 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.149570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109999 restraints weight = 16590.002| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.14 r_work: 0.3152 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16140 Z= 0.156 Angle : 0.631 7.275 21956 Z= 0.322 Chirality : 0.046 0.148 2328 Planarity : 0.005 0.079 2736 Dihedral : 10.592 93.524 2256 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.08 % Allowed : 17.75 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.19), residues: 1880 helix: -0.60 (0.15), residues: 1024 sheet: 0.00 (0.43), residues: 144 loop : -0.95 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 274 TYR 0.013 0.002 TYR C 47 PHE 0.014 0.002 PHE D 151 TRP 0.012 0.001 TRP B 172 HIS 0.005 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00373 (16140) covalent geometry : angle 0.63108 (21956) hydrogen bonds : bond 0.05441 ( 672) hydrogen bonds : angle 4.86650 ( 1956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 339 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 GLU cc_start: 0.8272 (mp0) cc_final: 0.7846 (mp0) REVERT: D 43 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6798 (mm-30) REVERT: D 79 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8155 (t) REVERT: D 81 ASN cc_start: 0.8148 (t0) cc_final: 0.7504 (t0) REVERT: D 91 ARG cc_start: 0.7440 (mpt-90) cc_final: 0.7203 (mpt-90) REVERT: D 127 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: D 149 THR cc_start: 0.8951 (p) cc_final: 0.8701 (m) REVERT: D 226 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7482 (mm-30) REVERT: D 234 LYS cc_start: 0.8090 (ptpt) cc_final: 0.7732 (ptmt) REVERT: D 422 LYS cc_start: 0.7721 (mtmt) cc_final: 0.7418 (mtpt) REVERT: B 43 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6743 (mm-30) REVERT: B 57 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7807 (ptpt) REVERT: B 81 ASN cc_start: 0.7971 (t0) cc_final: 0.7593 (t0) REVERT: B 127 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: B 172 TRP cc_start: 0.6358 (t60) cc_final: 0.5984 (t60) REVERT: B 226 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7648 (mm-30) REVERT: B 335 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7293 (mtm110) REVERT: C 43 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6729 (mm-30) REVERT: C 57 LYS cc_start: 0.8388 (ttmm) cc_final: 0.7904 (ptpt) REVERT: C 81 ASN cc_start: 0.7626 (t0) cc_final: 0.7252 (t0) REVERT: C 113 HIS cc_start: 0.7460 (t-90) cc_final: 0.7124 (t70) REVERT: C 141 TYR cc_start: 0.7761 (m-10) cc_final: 0.7145 (m-80) REVERT: C 226 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: C 234 LYS cc_start: 0.7844 (ptpt) cc_final: 0.7533 (ptpt) REVERT: A 80 HIS cc_start: 0.6903 (m-70) cc_final: 0.6480 (m-70) REVERT: A 113 HIS cc_start: 0.7179 (t-90) cc_final: 0.6919 (t70) REVERT: A 141 TYR cc_start: 0.7727 (m-10) cc_final: 0.7191 (m-80) REVERT: A 274 ARG cc_start: 0.6861 (mmm160) cc_final: 0.6631 (mmm160) REVERT: A 422 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7396 (mtpt) outliers start: 51 outliers final: 20 residues processed: 355 average time/residue: 0.5135 time to fit residues: 203.6640 Evaluate side-chains 349 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 321 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 225 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 138 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 260 HIS ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN B 260 HIS B 419 GLN C 419 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.153286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114343 restraints weight = 16532.245| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.14 r_work: 0.3215 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16140 Z= 0.104 Angle : 0.559 6.930 21956 Z= 0.283 Chirality : 0.043 0.137 2328 Planarity : 0.004 0.077 2736 Dihedral : 9.272 86.978 2256 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.66 % Allowed : 18.84 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.19), residues: 1880 helix: 0.27 (0.16), residues: 1012 sheet: 0.32 (0.44), residues: 144 loop : -0.67 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 274 TYR 0.011 0.001 TYR D 154 PHE 0.013 0.001 PHE B 33 TRP 0.008 0.001 TRP B 172 HIS 0.004 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00236 (16140) covalent geometry : angle 0.55913 (21956) hydrogen bonds : bond 0.03864 ( 672) hydrogen bonds : angle 4.61797 ( 1956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 347 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 GLU cc_start: 0.8190 (mp0) cc_final: 0.7958 (mp0) REVERT: D 43 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6745 (mm-30) REVERT: D 79 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8362 (t) REVERT: D 81 ASN cc_start: 0.8155 (t0) cc_final: 0.7540 (t0) REVERT: D 234 LYS cc_start: 0.8138 (ptpt) cc_final: 0.7795 (ptmt) REVERT: D 300 ILE cc_start: 0.7697 (pt) cc_final: 0.7469 (mm) REVERT: D 422 LYS cc_start: 0.7773 (mtmt) cc_final: 0.7424 (mtpt) REVERT: B 43 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: B 57 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7833 (ptpt) REVERT: B 81 ASN cc_start: 0.7694 (t0) cc_final: 0.7473 (t0) REVERT: B 127 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7991 (mt0) REVERT: B 149 THR cc_start: 0.8954 (p) cc_final: 0.8740 (m) REVERT: B 172 TRP cc_start: 0.6325 (t60) cc_final: 0.5892 (t60) REVERT: C 43 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: C 57 LYS cc_start: 0.8413 (ttmm) cc_final: 0.7939 (ptpt) REVERT: C 113 HIS cc_start: 0.7409 (t-90) cc_final: 0.7112 (t70) REVERT: C 141 TYR cc_start: 0.7811 (m-10) cc_final: 0.7111 (m-80) REVERT: C 234 LYS cc_start: 0.7821 (ptpt) cc_final: 0.7613 (ptpt) REVERT: C 267 MET cc_start: 0.7931 (mtp) cc_final: 0.7632 (mtt) REVERT: A 80 HIS cc_start: 0.6923 (m-70) cc_final: 0.6483 (m-70) REVERT: A 113 HIS cc_start: 0.7150 (t-90) cc_final: 0.6896 (t70) REVERT: A 141 TYR cc_start: 0.7760 (m-10) cc_final: 0.7085 (m-80) REVERT: A 274 ARG cc_start: 0.6827 (mmm160) cc_final: 0.6611 (mmm160) REVERT: A 422 LYS cc_start: 0.7753 (mtmt) cc_final: 0.7401 (mtpt) outliers start: 44 outliers final: 20 residues processed: 357 average time/residue: 0.5163 time to fit residues: 205.8043 Evaluate side-chains 338 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 313 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 11 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN B 152 ASN B 419 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 GLN A 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.147776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.107619 restraints weight = 16183.350| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.23 r_work: 0.3106 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16140 Z= 0.187 Angle : 0.648 7.491 21956 Z= 0.328 Chirality : 0.048 0.164 2328 Planarity : 0.005 0.070 2736 Dihedral : 10.103 93.410 2256 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.80 % Allowed : 18.72 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1880 helix: 0.43 (0.16), residues: 1036 sheet: 0.36 (0.44), residues: 144 loop : -0.65 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 274 TYR 0.016 0.002 TYR B 47 PHE 0.018 0.002 PHE D 151 TRP 0.009 0.001 TRP C 433 HIS 0.007 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00454 (16140) covalent geometry : angle 0.64754 (21956) hydrogen bonds : bond 0.05376 ( 672) hydrogen bonds : angle 4.70179 ( 1956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 328 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: D 57 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7760 (ptpt) REVERT: D 81 ASN cc_start: 0.8066 (t0) cc_final: 0.7391 (t0) REVERT: D 172 TRP cc_start: 0.5742 (OUTLIER) cc_final: 0.4930 (t60) REVERT: D 173 ARG cc_start: 0.7599 (tpp-160) cc_final: 0.6930 (ptp90) REVERT: D 234 LYS cc_start: 0.8148 (ptpt) cc_final: 0.7791 (ptmt) REVERT: D 422 LYS cc_start: 0.7568 (mtmt) cc_final: 0.7238 (mtpt) REVERT: D 475 ASP cc_start: 0.7904 (m-30) cc_final: 0.7290 (m-30) REVERT: B 43 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: B 57 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7738 (ptpt) REVERT: B 81 ASN cc_start: 0.7631 (t0) cc_final: 0.7418 (t0) REVERT: B 127 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: B 152 ASN cc_start: 0.7447 (p0) cc_final: 0.7014 (m110) REVERT: B 173 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7576 (mtm-85) REVERT: B 226 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: C 43 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: C 57 LYS cc_start: 0.8271 (ttmm) cc_final: 0.7745 (ptpt) REVERT: C 65 GLN cc_start: 0.6871 (tp40) cc_final: 0.6596 (tp-100) REVERT: C 81 ASN cc_start: 0.7824 (t0) cc_final: 0.7491 (t0) REVERT: C 113 HIS cc_start: 0.7135 (t-90) cc_final: 0.6878 (t70) REVERT: C 226 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7639 (mm-30) REVERT: C 234 LYS cc_start: 0.7794 (ptpt) cc_final: 0.7545 (ptpt) REVERT: A 57 LYS cc_start: 0.8378 (ttmm) cc_final: 0.7773 (pttt) REVERT: A 80 HIS cc_start: 0.6881 (m-70) cc_final: 0.6408 (m-70) REVERT: A 81 ASN cc_start: 0.7568 (t0) cc_final: 0.7062 (t0) REVERT: A 91 ARG cc_start: 0.7649 (mpt-90) cc_final: 0.7418 (mpt-90) REVERT: A 113 HIS cc_start: 0.6999 (t-90) cc_final: 0.6789 (t70) REVERT: A 274 ARG cc_start: 0.6855 (mmm160) cc_final: 0.6566 (mmm160) REVERT: A 422 LYS cc_start: 0.7530 (mtmt) cc_final: 0.7207 (mtpt) outliers start: 63 outliers final: 32 residues processed: 344 average time/residue: 0.5065 time to fit residues: 194.7252 Evaluate side-chains 351 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 312 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 172 TRP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 0 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 260 HIS ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 HIS B 419 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 GLN A 419 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.108554 restraints weight = 16062.008| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.23 r_work: 0.3121 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16140 Z= 0.158 Angle : 0.619 8.893 21956 Z= 0.312 Chirality : 0.046 0.154 2328 Planarity : 0.004 0.064 2736 Dihedral : 10.047 94.184 2256 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.44 % Allowed : 19.63 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1880 helix: 0.60 (0.16), residues: 1044 sheet: 0.31 (0.44), residues: 144 loop : -0.55 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 274 TYR 0.012 0.002 TYR B 47 PHE 0.015 0.001 PHE D 304 TRP 0.009 0.001 TRP C 433 HIS 0.005 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00383 (16140) covalent geometry : angle 0.61919 (21956) hydrogen bonds : bond 0.04830 ( 672) hydrogen bonds : angle 4.63035 ( 1956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 331 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 GLU cc_start: 0.8139 (mp0) cc_final: 0.7658 (mp0) REVERT: D 43 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: D 57 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7772 (ptpt) REVERT: D 81 ASN cc_start: 0.7776 (t0) cc_final: 0.7259 (t0) REVERT: D 152 ASN cc_start: 0.7615 (p0) cc_final: 0.7202 (m110) REVERT: D 172 TRP cc_start: 0.5748 (OUTLIER) cc_final: 0.5252 (t60) REVERT: D 173 ARG cc_start: 0.7644 (tpp-160) cc_final: 0.6927 (ptp90) REVERT: D 234 LYS cc_start: 0.8210 (ptpt) cc_final: 0.7843 (ptmt) REVERT: D 422 LYS cc_start: 0.7543 (mtmt) cc_final: 0.7233 (mtpt) REVERT: D 475 ASP cc_start: 0.7843 (m-30) cc_final: 0.7235 (m-30) REVERT: B 43 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: B 57 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7760 (ptpt) REVERT: B 76 LEU cc_start: 0.8379 (mt) cc_final: 0.7805 (mm) REVERT: B 81 ASN cc_start: 0.7635 (t0) cc_final: 0.7352 (t0) REVERT: B 127 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: B 152 ASN cc_start: 0.7409 (p0) cc_final: 0.7200 (m-40) REVERT: B 173 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7637 (mtm-85) REVERT: B 226 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7458 (mm-30) REVERT: B 422 LYS cc_start: 0.7544 (mtmt) cc_final: 0.7263 (mtpt) REVERT: C 43 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: C 57 LYS cc_start: 0.8304 (ttmm) cc_final: 0.7771 (ptpt) REVERT: C 65 GLN cc_start: 0.6880 (tp40) cc_final: 0.6515 (tp-100) REVERT: C 81 ASN cc_start: 0.7747 (t0) cc_final: 0.7486 (t0) REVERT: C 113 HIS cc_start: 0.7108 (t-90) cc_final: 0.6836 (t70) REVERT: C 234 LYS cc_start: 0.7738 (ptpt) cc_final: 0.7487 (ptpt) REVERT: C 329 LYS cc_start: 0.7670 (tttt) cc_final: 0.7190 (tttp) REVERT: A 57 LYS cc_start: 0.8419 (ttmm) cc_final: 0.7805 (pttt) REVERT: A 80 HIS cc_start: 0.6943 (m-70) cc_final: 0.6605 (m-70) REVERT: A 81 ASN cc_start: 0.7588 (t0) cc_final: 0.7095 (t0) REVERT: A 87 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7273 (tt) REVERT: A 113 HIS cc_start: 0.6991 (t-90) cc_final: 0.6744 (t70) REVERT: A 274 ARG cc_start: 0.6837 (mmm160) cc_final: 0.6609 (mmm160) REVERT: A 422 LYS cc_start: 0.7542 (mtmt) cc_final: 0.7257 (mtpt) outliers start: 57 outliers final: 23 residues processed: 354 average time/residue: 0.5107 time to fit residues: 201.9154 Evaluate side-chains 341 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 312 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 172 TRP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 103 optimal weight: 0.3980 chunk 165 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 185 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 108 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 260 HIS ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN B 260 HIS B 419 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN C 419 GLN A 152 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.151929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113635 restraints weight = 16325.134| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.21 r_work: 0.3192 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16140 Z= 0.108 Angle : 0.573 9.253 21956 Z= 0.288 Chirality : 0.043 0.133 2328 Planarity : 0.004 0.058 2736 Dihedral : 9.059 88.384 2256 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.02 % Allowed : 20.59 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1880 helix: 1.00 (0.17), residues: 1024 sheet: 0.42 (0.45), residues: 144 loop : -0.44 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 274 TYR 0.010 0.001 TYR D 154 PHE 0.015 0.001 PHE B 33 TRP 0.011 0.001 TRP B 172 HIS 0.004 0.001 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00250 (16140) covalent geometry : angle 0.57292 (21956) hydrogen bonds : bond 0.03835 ( 672) hydrogen bonds : angle 4.53412 ( 1956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 325 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: D 57 LYS cc_start: 0.8381 (ttmm) cc_final: 0.7905 (ptpt) REVERT: D 81 ASN cc_start: 0.7811 (t0) cc_final: 0.7276 (t0) REVERT: D 152 ASN cc_start: 0.7581 (p0) cc_final: 0.7229 (m-40) REVERT: D 172 TRP cc_start: 0.5823 (OUTLIER) cc_final: 0.5413 (t60) REVERT: D 173 ARG cc_start: 0.7577 (tpp-160) cc_final: 0.7064 (ptp90) REVERT: D 234 LYS cc_start: 0.8178 (ptpt) cc_final: 0.7829 (ptmt) REVERT: D 422 LYS cc_start: 0.7737 (mtmt) cc_final: 0.7438 (mtpt) REVERT: D 475 ASP cc_start: 0.7664 (m-30) cc_final: 0.7089 (m-30) REVERT: B 43 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: B 57 LYS cc_start: 0.8365 (ttmm) cc_final: 0.7851 (ptpt) REVERT: B 76 LEU cc_start: 0.8321 (mt) cc_final: 0.7766 (mm) REVERT: B 81 ASN cc_start: 0.7643 (t0) cc_final: 0.7334 (t0) REVERT: B 152 ASN cc_start: 0.7478 (p0) cc_final: 0.7069 (m-40) REVERT: B 172 TRP cc_start: 0.6207 (t60) cc_final: 0.5780 (t60) REVERT: B 226 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7492 (mm-30) REVERT: B 422 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7359 (mtpt) REVERT: C 43 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7225 (mp0) REVERT: C 57 LYS cc_start: 0.8374 (ttmm) cc_final: 0.7855 (ptpt) REVERT: C 65 GLN cc_start: 0.7042 (tp40) cc_final: 0.6710 (pt0) REVERT: C 81 ASN cc_start: 0.7823 (t0) cc_final: 0.7552 (t0) REVERT: C 113 HIS cc_start: 0.7200 (t-90) cc_final: 0.6936 (t70) REVERT: C 152 ASN cc_start: 0.7407 (p0) cc_final: 0.6992 (m-40) REVERT: C 234 LYS cc_start: 0.7731 (ptpt) cc_final: 0.7491 (ptpt) REVERT: C 329 LYS cc_start: 0.7881 (tttt) cc_final: 0.7426 (tttp) REVERT: C 422 LYS cc_start: 0.7702 (mtmt) cc_final: 0.7419 (mtpt) REVERT: A 57 LYS cc_start: 0.8437 (ttmm) cc_final: 0.7871 (pttt) REVERT: A 80 HIS cc_start: 0.6981 (m-70) cc_final: 0.6773 (m-70) REVERT: A 81 ASN cc_start: 0.7565 (t0) cc_final: 0.7086 (t0) REVERT: A 113 HIS cc_start: 0.7040 (t-90) cc_final: 0.6819 (t70) REVERT: A 152 ASN cc_start: 0.7440 (p0) cc_final: 0.6940 (m-40) REVERT: A 422 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7434 (mtpt) outliers start: 50 outliers final: 27 residues processed: 346 average time/residue: 0.5066 time to fit residues: 196.3071 Evaluate side-chains 343 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 313 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 172 TRP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 148 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN C 81 ASN C 419 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111229 restraints weight = 16475.694| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.20 r_work: 0.3157 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16140 Z= 0.146 Angle : 0.628 9.239 21956 Z= 0.314 Chirality : 0.046 0.191 2328 Planarity : 0.004 0.058 2736 Dihedral : 9.229 92.782 2256 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.32 % Allowed : 21.62 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1880 helix: 0.99 (0.16), residues: 1040 sheet: 0.36 (0.45), residues: 144 loop : -0.37 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 274 TYR 0.016 0.002 TYR A 423 PHE 0.014 0.001 PHE D 151 TRP 0.009 0.001 TRP B 172 HIS 0.004 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00352 (16140) covalent geometry : angle 0.62758 (21956) hydrogen bonds : bond 0.04624 ( 672) hydrogen bonds : angle 4.59779 ( 1956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 329 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: D 57 LYS cc_start: 0.8363 (ttmm) cc_final: 0.7885 (ptpt) REVERT: D 81 ASN cc_start: 0.7738 (t0) cc_final: 0.7207 (t0) REVERT: D 152 ASN cc_start: 0.7590 (p0) cc_final: 0.7275 (m-40) REVERT: D 172 TRP cc_start: 0.5829 (OUTLIER) cc_final: 0.5351 (t60) REVERT: D 173 ARG cc_start: 0.7562 (tpp-160) cc_final: 0.7037 (ptp90) REVERT: D 234 LYS cc_start: 0.8200 (ptpt) cc_final: 0.7847 (ptmt) REVERT: D 422 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7474 (mtpt) REVERT: D 475 ASP cc_start: 0.7714 (m-30) cc_final: 0.7129 (m-30) REVERT: B 43 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: B 57 LYS cc_start: 0.8372 (ttmm) cc_final: 0.7847 (ptpt) REVERT: B 76 LEU cc_start: 0.8394 (mt) cc_final: 0.7831 (mm) REVERT: B 81 ASN cc_start: 0.7647 (t0) cc_final: 0.7299 (t0) REVERT: B 173 ARG cc_start: 0.8129 (mtm-85) cc_final: 0.7650 (mtm-85) REVERT: B 226 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7509 (mm-30) REVERT: B 422 LYS cc_start: 0.7583 (mtmt) cc_final: 0.7269 (mtpt) REVERT: B 475 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7265 (m-30) REVERT: C 43 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7183 (mp0) REVERT: C 57 LYS cc_start: 0.8443 (ttmm) cc_final: 0.7936 (ptpt) REVERT: C 81 ASN cc_start: 0.7779 (t0) cc_final: 0.7523 (t0) REVERT: C 113 HIS cc_start: 0.7196 (t-90) cc_final: 0.6934 (t70) REVERT: C 118 LYS cc_start: 0.7522 (ttmt) cc_final: 0.7316 (ttmt) REVERT: C 152 ASN cc_start: 0.7430 (p0) cc_final: 0.7083 (m-40) REVERT: C 234 LYS cc_start: 0.7761 (ptpt) cc_final: 0.7504 (ptpt) REVERT: C 422 LYS cc_start: 0.7721 (mtmt) cc_final: 0.7410 (mtpt) REVERT: A 81 ASN cc_start: 0.7653 (t0) cc_final: 0.7159 (t0) REVERT: A 91 ARG cc_start: 0.7427 (mpt-90) cc_final: 0.7150 (mpt-90) REVERT: A 113 HIS cc_start: 0.7124 (t-90) cc_final: 0.6899 (t70) REVERT: A 152 ASN cc_start: 0.7402 (p0) cc_final: 0.7075 (m-40) REVERT: A 422 LYS cc_start: 0.7751 (mtmt) cc_final: 0.7444 (mtpt) outliers start: 55 outliers final: 31 residues processed: 345 average time/residue: 0.5061 time to fit residues: 195.3334 Evaluate side-chains 354 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 318 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 172 TRP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 100 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 181 optimal weight: 0.0670 chunk 78 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 260 HIS ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN B 260 HIS B 419 GLN C 419 GLN A 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.153126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113967 restraints weight = 16230.078| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.23 r_work: 0.3193 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16140 Z= 0.108 Angle : 0.576 9.512 21956 Z= 0.288 Chirality : 0.043 0.151 2328 Planarity : 0.004 0.056 2736 Dihedral : 8.261 84.201 2256 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.72 % Allowed : 22.10 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1880 helix: 1.34 (0.17), residues: 1024 sheet: 0.45 (0.44), residues: 144 loop : -0.27 (0.26), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 274 TYR 0.008 0.001 TYR D 154 PHE 0.011 0.001 PHE A 33 TRP 0.008 0.001 TRP B 172 HIS 0.003 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00251 (16140) covalent geometry : angle 0.57558 (21956) hydrogen bonds : bond 0.03526 ( 672) hydrogen bonds : angle 4.52543 ( 1956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 318 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 GLU cc_start: 0.8141 (mp0) cc_final: 0.7587 (mp0) REVERT: D 43 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: D 57 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7802 (ptpt) REVERT: D 76 LEU cc_start: 0.8331 (mt) cc_final: 0.7779 (mm) REVERT: D 81 ASN cc_start: 0.7646 (t0) cc_final: 0.7118 (t0) REVERT: D 152 ASN cc_start: 0.7403 (p0) cc_final: 0.7106 (m-40) REVERT: D 172 TRP cc_start: 0.5796 (OUTLIER) cc_final: 0.5525 (t60) REVERT: D 173 ARG cc_start: 0.7520 (tpp-160) cc_final: 0.6970 (ptp90) REVERT: D 234 LYS cc_start: 0.8140 (ptpt) cc_final: 0.7776 (ptmt) REVERT: D 422 LYS cc_start: 0.7646 (mtmt) cc_final: 0.7399 (mtpt) REVERT: D 475 ASP cc_start: 0.7502 (m-30) cc_final: 0.6929 (m-30) REVERT: B 43 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: B 57 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7790 (ptpt) REVERT: B 76 LEU cc_start: 0.8249 (mt) cc_final: 0.7706 (mm) REVERT: B 81 ASN cc_start: 0.7498 (t0) cc_final: 0.7153 (t0) REVERT: B 173 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7644 (mtm-85) REVERT: B 422 LYS cc_start: 0.7548 (mtmt) cc_final: 0.7272 (mtpt) REVERT: B 475 ASP cc_start: 0.7614 (m-30) cc_final: 0.7006 (m-30) REVERT: C 43 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7156 (mp0) REVERT: C 57 LYS cc_start: 0.8313 (ttmm) cc_final: 0.7809 (ptpt) REVERT: C 87 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7199 (tt) REVERT: C 113 HIS cc_start: 0.7084 (t-90) cc_final: 0.6796 (t70) REVERT: C 152 ASN cc_start: 0.7321 (p0) cc_final: 0.7001 (m-40) REVERT: C 234 LYS cc_start: 0.7684 (ptpt) cc_final: 0.7410 (ptpt) REVERT: C 391 GLU cc_start: 0.7996 (mp0) cc_final: 0.7780 (mp0) REVERT: A 57 LYS cc_start: 0.8253 (ttmm) cc_final: 0.7831 (ptpt) REVERT: A 76 LEU cc_start: 0.8213 (mt) cc_final: 0.7766 (mm) REVERT: A 91 ARG cc_start: 0.7504 (mpt-90) cc_final: 0.7254 (mpt-90) REVERT: A 113 HIS cc_start: 0.7043 (t-90) cc_final: 0.6816 (t70) REVERT: A 152 ASN cc_start: 0.7299 (p0) cc_final: 0.6998 (m-40) REVERT: A 422 LYS cc_start: 0.7659 (mtmt) cc_final: 0.7430 (mtpt) outliers start: 45 outliers final: 24 residues processed: 336 average time/residue: 0.5338 time to fit residues: 200.0772 Evaluate side-chains 333 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 305 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 172 TRP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 155 optimal weight: 0.0980 chunk 126 optimal weight: 3.9990 chunk 65 optimal weight: 0.0170 chunk 99 optimal weight: 4.9990 chunk 123 optimal weight: 0.0970 chunk 160 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 154 optimal weight: 0.4980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN B 419 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 419 GLN A 419 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117102 restraints weight = 16686.624| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.15 r_work: 0.3240 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16140 Z= 0.104 Angle : 0.573 10.257 21956 Z= 0.288 Chirality : 0.042 0.135 2328 Planarity : 0.004 0.052 2736 Dihedral : 7.806 78.708 2256 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.75 % Allowed : 23.07 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.21), residues: 1880 helix: 1.53 (0.17), residues: 1024 sheet: 0.58 (0.45), residues: 144 loop : -0.20 (0.26), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 274 TYR 0.012 0.001 TYR D 423 PHE 0.020 0.001 PHE B 304 TRP 0.008 0.001 TRP A 433 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00240 (16140) covalent geometry : angle 0.57278 (21956) hydrogen bonds : bond 0.03310 ( 672) hydrogen bonds : angle 4.48152 ( 1956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 315 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: D 57 LYS cc_start: 0.8367 (ttmm) cc_final: 0.7918 (ptpt) REVERT: D 76 LEU cc_start: 0.8433 (mt) cc_final: 0.7903 (mm) REVERT: D 122 ARG cc_start: 0.8203 (mmt-90) cc_final: 0.7933 (mmt180) REVERT: D 152 ASN cc_start: 0.7461 (p0) cc_final: 0.7242 (m-40) REVERT: D 172 TRP cc_start: 0.5843 (OUTLIER) cc_final: 0.5513 (t60) REVERT: D 173 ARG cc_start: 0.7632 (tpp-160) cc_final: 0.7015 (ptp90) REVERT: D 234 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7871 (ptmt) REVERT: D 391 GLU cc_start: 0.8080 (mp0) cc_final: 0.7811 (mp0) REVERT: D 422 LYS cc_start: 0.7798 (mtmt) cc_final: 0.7561 (mtpt) REVERT: D 475 ASP cc_start: 0.7498 (m-30) cc_final: 0.6976 (m-30) REVERT: B 43 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: B 57 LYS cc_start: 0.8440 (ttmm) cc_final: 0.7972 (ptpt) REVERT: B 76 LEU cc_start: 0.8346 (mt) cc_final: 0.7816 (mm) REVERT: B 173 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7608 (mtm-85) REVERT: B 422 LYS cc_start: 0.7686 (mtmt) cc_final: 0.7370 (mtpt) REVERT: B 475 ASP cc_start: 0.7590 (m-30) cc_final: 0.6987 (m-30) REVERT: C 43 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7268 (mp0) REVERT: C 57 LYS cc_start: 0.8371 (ttmm) cc_final: 0.7899 (ptpt) REVERT: C 113 HIS cc_start: 0.7166 (t-90) cc_final: 0.6935 (t70) REVERT: C 152 ASN cc_start: 0.7321 (p0) cc_final: 0.6961 (m-40) REVERT: C 234 LYS cc_start: 0.7839 (ptpt) cc_final: 0.7579 (ptpt) REVERT: C 391 GLU cc_start: 0.8069 (mp0) cc_final: 0.7810 (mp0) REVERT: C 422 LYS cc_start: 0.7763 (mtmt) cc_final: 0.7465 (mtpt) REVERT: A 57 LYS cc_start: 0.8418 (ttmm) cc_final: 0.7992 (ptpt) REVERT: A 76 LEU cc_start: 0.8298 (mt) cc_final: 0.7753 (mm) REVERT: A 81 ASN cc_start: 0.7980 (t0) cc_final: 0.7373 (t0) REVERT: A 113 HIS cc_start: 0.7119 (t-90) cc_final: 0.6886 (t70) REVERT: A 152 ASN cc_start: 0.7323 (p0) cc_final: 0.6871 (m-40) REVERT: A 391 GLU cc_start: 0.8044 (mp0) cc_final: 0.7771 (mp0) REVERT: A 422 LYS cc_start: 0.7814 (mtmt) cc_final: 0.7563 (mtpt) REVERT: A 457 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7506 (mtpt) outliers start: 29 outliers final: 22 residues processed: 323 average time/residue: 0.5299 time to fit residues: 190.9576 Evaluate side-chains 328 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 303 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 172 TRP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 187 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 147 optimal weight: 0.0170 chunk 45 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN B 81 ASN B 113 HIS B 419 GLN C 419 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.151678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112650 restraints weight = 16266.353| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.22 r_work: 0.3176 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16140 Z= 0.128 Angle : 0.602 9.799 21956 Z= 0.303 Chirality : 0.044 0.141 2328 Planarity : 0.004 0.052 2736 Dihedral : 7.949 83.249 2256 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.29 % Allowed : 22.77 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1880 helix: 1.44 (0.17), residues: 1024 sheet: 0.53 (0.45), residues: 144 loop : -0.19 (0.26), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 274 TYR 0.014 0.001 TYR A 296 PHE 0.011 0.001 PHE A 151 TRP 0.007 0.001 TRP D 433 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00305 (16140) covalent geometry : angle 0.60242 (21956) hydrogen bonds : bond 0.04075 ( 672) hydrogen bonds : angle 4.53905 ( 1956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6136.77 seconds wall clock time: 104 minutes 45.60 seconds (6285.60 seconds total)