Starting phenix.real_space_refine on Sun Feb 8 03:52:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2l_17369/02_2026/8p2l_17369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2l_17369/02_2026/8p2l_17369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p2l_17369/02_2026/8p2l_17369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2l_17369/02_2026/8p2l_17369.map" model { file = "/net/cci-nas-00/data/ceres_data/8p2l_17369/02_2026/8p2l_17369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2l_17369/02_2026/8p2l_17369.cif" } resolution = 2.68 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= 0.004 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 176 5.16 5 C 25672 2.51 5 N 7328 2.21 5 O 7584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 419 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40776 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "B" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "C" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "D" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "E" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "F" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "G" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "H" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3845 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 17, 'TRANS': 478} Chain: "J" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "I" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "K" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "L" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "M" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "N" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "O" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "P" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1208 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.84, per 1000 atoms: 0.22 Number of scatterers: 40776 At special positions: 0 Unit cell: (210.84, 210.84, 87.36, 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 176 16.00 P 16 15.00 O 7584 8.00 N 7328 7.00 C 25672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.7 seconds 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9632 Finding SS restraints... Secondary structure from input PDB file: 368 helices and 8 sheets defined 75.6% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 57 through 81 Proline residue: A 70 - end of helix removed outlier: 3.943A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 105 Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.757A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 137 through 150 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.806A pdb=" N ILE A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.505A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.690A pdb=" N VAL A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 237 Processing helix chain 'A' and resid 237 through 248 removed outlier: 3.791A pdb=" N VAL A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 263 through 279 Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 291 through 294 Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 305 through 312 removed outlier: 4.626A pdb=" N ALA A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.661A pdb=" N LEU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 360 Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.984A pdb=" N ASP A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.765A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 496 through 500 removed outlier: 4.089A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 545 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'B' and resid 57 through 81 Proline residue: B 70 - end of helix removed outlier: 3.943A pdb=" N GLN B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 105 Processing helix chain 'B' and resid 108 through 123 removed outlier: 3.759A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 137 through 150 Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.806A pdb=" N ILE B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 193 removed outlier: 3.506A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.691A pdb=" N VAL B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 237 Processing helix chain 'B' and resid 237 through 248 removed outlier: 3.791A pdb=" N VAL B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 263 through 279 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 291 through 294 Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 305 through 312 removed outlier: 4.628A pdb=" N ALA B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.659A pdb=" N LEU B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 360 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.983A pdb=" N ASP B 367 " --> pdb=" O LYS B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.766A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 459 through 477 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 500 removed outlier: 4.088A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 508 Processing helix chain 'B' and resid 514 through 518 Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 545 Processing helix chain 'B' and resid 546 through 548 No H-bonds generated for 'chain 'B' and resid 546 through 548' Processing helix chain 'C' and resid 57 through 81 Proline residue: C 70 - end of helix removed outlier: 3.944A pdb=" N GLN C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 105 Processing helix chain 'C' and resid 108 through 123 removed outlier: 3.757A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 133 Processing helix chain 'C' and resid 137 through 150 Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.805A pdb=" N ILE C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 193 removed outlier: 3.505A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.691A pdb=" N VAL C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 237 Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.791A pdb=" N VAL C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 263 through 279 Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 291 through 294 Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 305 through 312 removed outlier: 4.627A pdb=" N ALA C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 329 Processing helix chain 'C' and resid 330 through 336 removed outlier: 3.660A pdb=" N LEU C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 360 Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.985A pdb=" N ASP C 367 " --> pdb=" O LYS C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.765A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 424 Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 459 through 477 Processing helix chain 'C' and resid 486 through 495 Processing helix chain 'C' and resid 496 through 500 removed outlier: 4.090A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 508 Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 through 545 Processing helix chain 'C' and resid 546 through 548 No H-bonds generated for 'chain 'C' and resid 546 through 548' Processing helix chain 'D' and resid 57 through 81 Proline residue: D 70 - end of helix removed outlier: 3.944A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 105 Processing helix chain 'D' and resid 108 through 123 removed outlier: 3.758A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 Processing helix chain 'D' and resid 137 through 150 Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.806A pdb=" N ILE D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 193 removed outlier: 3.505A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 206 through 215 removed outlier: 3.693A pdb=" N VAL D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 237 Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.791A pdb=" N VAL D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 254 through 259 Processing helix chain 'D' and resid 263 through 279 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 291 through 294 Processing helix chain 'D' and resid 295 through 303 Processing helix chain 'D' and resid 305 through 312 removed outlier: 4.628A pdb=" N ALA D 309 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 329 Processing helix chain 'D' and resid 330 through 336 removed outlier: 3.660A pdb=" N LEU D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 360 Processing helix chain 'D' and resid 363 through 368 removed outlier: 3.986A pdb=" N ASP D 367 " --> pdb=" O LYS D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.766A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 424 Processing helix chain 'D' and resid 426 through 428 No H-bonds generated for 'chain 'D' and resid 426 through 428' Processing helix chain 'D' and resid 429 through 436 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 459 through 477 Processing helix chain 'D' and resid 486 through 495 Processing helix chain 'D' and resid 496 through 500 removed outlier: 4.087A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 508 Processing helix chain 'D' and resid 514 through 518 Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 545 Processing helix chain 'D' and resid 546 through 548 No H-bonds generated for 'chain 'D' and resid 546 through 548' Processing helix chain 'E' and resid 57 through 81 Proline residue: E 70 - end of helix removed outlier: 3.945A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 105 Processing helix chain 'E' and resid 108 through 123 removed outlier: 3.760A pdb=" N VAL E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 137 through 150 Processing helix chain 'E' and resid 153 through 161 Processing helix chain 'E' and resid 164 through 172 removed outlier: 3.806A pdb=" N ILE E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 193 removed outlier: 3.506A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 206 through 215 removed outlier: 3.690A pdb=" N VAL E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 237 Processing helix chain 'E' and resid 237 through 248 removed outlier: 3.793A pdb=" N VAL E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 263 through 279 Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 291 through 294 Processing helix chain 'E' and resid 295 through 303 Processing helix chain 'E' and resid 305 through 312 removed outlier: 4.626A pdb=" N ALA E 309 " --> pdb=" O PRO E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 329 Processing helix chain 'E' and resid 330 through 336 removed outlier: 3.660A pdb=" N LEU E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 360 Processing helix chain 'E' and resid 363 through 368 removed outlier: 3.984A pdb=" N ASP E 367 " --> pdb=" O LYS E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 380 removed outlier: 3.766A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 424 Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 429 through 436 Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 447 through 454 Processing helix chain 'E' and resid 459 through 477 Processing helix chain 'E' and resid 486 through 495 Processing helix chain 'E' and resid 496 through 500 removed outlier: 4.089A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 508 Processing helix chain 'E' and resid 514 through 518 Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 545 Processing helix chain 'E' and resid 546 through 548 No H-bonds generated for 'chain 'E' and resid 546 through 548' Processing helix chain 'F' and resid 57 through 81 Proline residue: F 70 - end of helix removed outlier: 3.944A pdb=" N GLN F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 105 Processing helix chain 'F' and resid 108 through 123 removed outlier: 3.758A pdb=" N VAL F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 137 through 150 Processing helix chain 'F' and resid 153 through 161 Processing helix chain 'F' and resid 164 through 172 removed outlier: 3.806A pdb=" N ILE F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 193 removed outlier: 3.506A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 Processing helix chain 'F' and resid 206 through 215 removed outlier: 3.690A pdb=" N VAL F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 237 Processing helix chain 'F' and resid 237 through 248 removed outlier: 3.790A pdb=" N VAL F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 254 Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 263 through 279 Processing helix chain 'F' and resid 283 through 290 Processing helix chain 'F' and resid 291 through 294 Processing helix chain 'F' and resid 295 through 303 Processing helix chain 'F' and resid 305 through 312 removed outlier: 4.627A pdb=" N ALA F 309 " --> pdb=" O PRO F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 329 Processing helix chain 'F' and resid 330 through 336 removed outlier: 3.659A pdb=" N LEU F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 360 Processing helix chain 'F' and resid 363 through 368 removed outlier: 3.984A pdb=" N ASP F 367 " --> pdb=" O LYS F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 380 removed outlier: 3.765A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 424 Processing helix chain 'F' and resid 426 through 428 No H-bonds generated for 'chain 'F' and resid 426 through 428' Processing helix chain 'F' and resid 429 through 436 Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 447 through 454 Processing helix chain 'F' and resid 459 through 477 Processing helix chain 'F' and resid 486 through 495 Processing helix chain 'F' and resid 496 through 500 removed outlier: 4.087A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 508 Processing helix chain 'F' and resid 514 through 518 Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 531 through 545 Processing helix chain 'F' and resid 546 through 548 No H-bonds generated for 'chain 'F' and resid 546 through 548' Processing helix chain 'G' and resid 57 through 81 Proline residue: G 70 - end of helix removed outlier: 3.945A pdb=" N GLN G 81 " --> pdb=" O SER G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.757A pdb=" N VAL G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'G' and resid 153 through 161 Processing helix chain 'G' and resid 164 through 172 removed outlier: 3.805A pdb=" N ILE G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 193 removed outlier: 3.506A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 Processing helix chain 'G' and resid 206 through 215 removed outlier: 3.689A pdb=" N VAL G 211 " --> pdb=" O GLY G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 237 Processing helix chain 'G' and resid 237 through 248 removed outlier: 3.790A pdb=" N VAL G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 254 Processing helix chain 'G' and resid 254 through 259 Processing helix chain 'G' and resid 263 through 279 Processing helix chain 'G' and resid 283 through 290 Processing helix chain 'G' and resid 291 through 294 Processing helix chain 'G' and resid 295 through 303 Processing helix chain 'G' and resid 305 through 312 removed outlier: 4.628A pdb=" N ALA G 309 " --> pdb=" O PRO G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 329 Processing helix chain 'G' and resid 330 through 336 removed outlier: 3.661A pdb=" N LEU G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 360 Processing helix chain 'G' and resid 363 through 368 removed outlier: 3.984A pdb=" N ASP G 367 " --> pdb=" O LYS G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.765A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 397 Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 424 Processing helix chain 'G' and resid 426 through 428 No H-bonds generated for 'chain 'G' and resid 426 through 428' Processing helix chain 'G' and resid 429 through 436 Processing helix chain 'G' and resid 439 through 445 Processing helix chain 'G' and resid 447 through 454 Processing helix chain 'G' and resid 459 through 477 Processing helix chain 'G' and resid 486 through 495 Processing helix chain 'G' and resid 496 through 500 removed outlier: 4.087A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 501 through 508 Processing helix chain 'G' and resid 514 through 518 Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 545 Processing helix chain 'G' and resid 546 through 548 No H-bonds generated for 'chain 'G' and resid 546 through 548' Processing helix chain 'H' and resid 57 through 81 Proline residue: H 70 - end of helix removed outlier: 3.944A pdb=" N GLN H 81 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 105 Processing helix chain 'H' and resid 108 through 123 removed outlier: 3.758A pdb=" N VAL H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'H' and resid 137 through 150 Processing helix chain 'H' and resid 153 through 161 Processing helix chain 'H' and resid 164 through 172 removed outlier: 3.806A pdb=" N ILE H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 193 removed outlier: 3.506A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 205 Processing helix chain 'H' and resid 206 through 215 removed outlier: 3.688A pdb=" N VAL H 211 " --> pdb=" O GLY H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 237 Processing helix chain 'H' and resid 237 through 248 removed outlier: 3.791A pdb=" N VAL H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 254 Processing helix chain 'H' and resid 254 through 259 Processing helix chain 'H' and resid 263 through 279 Processing helix chain 'H' and resid 283 through 290 Processing helix chain 'H' and resid 291 through 294 Processing helix chain 'H' and resid 295 through 303 Processing helix chain 'H' and resid 305 through 312 removed outlier: 4.627A pdb=" N ALA H 309 " --> pdb=" O PRO H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 329 Processing helix chain 'H' and resid 330 through 336 removed outlier: 3.661A pdb=" N LEU H 334 " --> pdb=" O LEU H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 360 Processing helix chain 'H' and resid 363 through 368 removed outlier: 3.985A pdb=" N ASP H 367 " --> pdb=" O LYS H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 380 removed outlier: 3.765A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 424 Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 429 through 436 Processing helix chain 'H' and resid 439 through 445 Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 459 through 477 Processing helix chain 'H' and resid 486 through 495 Processing helix chain 'H' and resid 496 through 500 removed outlier: 4.089A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 501 through 508 Processing helix chain 'H' and resid 514 through 518 Processing helix chain 'H' and resid 519 through 526 Processing helix chain 'H' and resid 531 through 545 Processing helix chain 'H' and resid 546 through 548 No H-bonds generated for 'chain 'H' and resid 546 through 548' Processing helix chain 'J' and resid 719 through 733 Processing helix chain 'J' and resid 751 through 760 removed outlier: 3.737A pdb=" N LYS J 755 " --> pdb=" O SER J 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 770 through 776 removed outlier: 3.634A pdb=" N ASP J 773 " --> pdb=" O ASN J 770 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG J 774 " --> pdb=" O SER J 771 " (cutoff:3.500A) Processing helix chain 'J' and resid 783 through 795 Processing helix chain 'J' and resid 812 through 816 Processing helix chain 'J' and resid 820 through 826 Processing helix chain 'J' and resid 835 through 848 Processing helix chain 'I' and resid 719 through 733 Processing helix chain 'I' and resid 751 through 760 removed outlier: 3.737A pdb=" N LYS I 755 " --> pdb=" O SER I 751 " (cutoff:3.500A) Processing helix chain 'I' and resid 770 through 776 removed outlier: 3.635A pdb=" N ASP I 773 " --> pdb=" O ASN I 770 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG I 774 " --> pdb=" O SER I 771 " (cutoff:3.500A) Processing helix chain 'I' and resid 783 through 795 Processing helix chain 'I' and resid 812 through 816 Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 835 through 848 Processing helix chain 'K' and resid 719 through 733 Processing helix chain 'K' and resid 751 through 760 removed outlier: 3.740A pdb=" N LYS K 755 " --> pdb=" O SER K 751 " (cutoff:3.500A) Processing helix chain 'K' and resid 770 through 776 removed outlier: 3.634A pdb=" N ASP K 773 " --> pdb=" O ASN K 770 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG K 774 " --> pdb=" O SER K 771 " (cutoff:3.500A) Processing helix chain 'K' and resid 783 through 795 Processing helix chain 'K' and resid 812 through 816 Processing helix chain 'K' and resid 820 through 826 Processing helix chain 'K' and resid 835 through 848 Processing helix chain 'L' and resid 719 through 733 Processing helix chain 'L' and resid 751 through 760 removed outlier: 3.739A pdb=" N LYS L 755 " --> pdb=" O SER L 751 " (cutoff:3.500A) Processing helix chain 'L' and resid 770 through 776 removed outlier: 3.634A pdb=" N ASP L 773 " --> pdb=" O ASN L 770 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG L 774 " --> pdb=" O SER L 771 " (cutoff:3.500A) Processing helix chain 'L' and resid 783 through 795 Processing helix chain 'L' and resid 812 through 816 Processing helix chain 'L' and resid 820 through 826 Processing helix chain 'L' and resid 835 through 848 Processing helix chain 'M' and resid 719 through 733 Processing helix chain 'M' and resid 751 through 760 removed outlier: 3.739A pdb=" N LYS M 755 " --> pdb=" O SER M 751 " (cutoff:3.500A) Processing helix chain 'M' and resid 770 through 776 removed outlier: 3.634A pdb=" N ASP M 773 " --> pdb=" O ASN M 770 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG M 774 " --> pdb=" O SER M 771 " (cutoff:3.500A) Processing helix chain 'M' and resid 783 through 795 Processing helix chain 'M' and resid 812 through 816 Processing helix chain 'M' and resid 820 through 826 Processing helix chain 'M' and resid 835 through 848 Processing helix chain 'N' and resid 719 through 733 Processing helix chain 'N' and resid 751 through 760 removed outlier: 3.740A pdb=" N LYS N 755 " --> pdb=" O SER N 751 " (cutoff:3.500A) Processing helix chain 'N' and resid 770 through 776 removed outlier: 3.633A pdb=" N ASP N 773 " --> pdb=" O ASN N 770 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG N 774 " --> pdb=" O SER N 771 " (cutoff:3.500A) Processing helix chain 'N' and resid 783 through 795 Processing helix chain 'N' and resid 812 through 816 Processing helix chain 'N' and resid 820 through 826 Processing helix chain 'N' and resid 835 through 848 Processing helix chain 'O' and resid 719 through 733 Processing helix chain 'O' and resid 751 through 760 removed outlier: 3.741A pdb=" N LYS O 755 " --> pdb=" O SER O 751 " (cutoff:3.500A) Processing helix chain 'O' and resid 770 through 776 removed outlier: 3.634A pdb=" N ASP O 773 " --> pdb=" O ASN O 770 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG O 774 " --> pdb=" O SER O 771 " (cutoff:3.500A) Processing helix chain 'O' and resid 783 through 795 Processing helix chain 'O' and resid 812 through 816 Processing helix chain 'O' and resid 820 through 826 Processing helix chain 'O' and resid 835 through 848 Processing helix chain 'P' and resid 719 through 733 Processing helix chain 'P' and resid 751 through 760 removed outlier: 3.738A pdb=" N LYS P 755 " --> pdb=" O SER P 751 " (cutoff:3.500A) Processing helix chain 'P' and resid 770 through 776 removed outlier: 3.634A pdb=" N ASP P 773 " --> pdb=" O ASN P 770 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG P 774 " --> pdb=" O SER P 771 " (cutoff:3.500A) Processing helix chain 'P' and resid 783 through 795 Processing helix chain 'P' and resid 812 through 816 Processing helix chain 'P' and resid 820 through 826 Processing helix chain 'P' and resid 835 through 848 Processing sheet with id=AA1, first strand: chain 'J' and resid 737 through 739 removed outlier: 6.738A pdb=" N VAL J 710 " --> pdb=" O PHE J 738 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 737 through 739 removed outlier: 6.738A pdb=" N VAL I 710 " --> pdb=" O PHE I 738 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 737 through 739 removed outlier: 6.738A pdb=" N VAL K 710 " --> pdb=" O PHE K 738 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 737 through 739 removed outlier: 6.737A pdb=" N VAL L 710 " --> pdb=" O PHE L 738 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 737 through 739 removed outlier: 6.738A pdb=" N VAL M 710 " --> pdb=" O PHE M 738 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 737 through 739 removed outlier: 6.737A pdb=" N VAL N 710 " --> pdb=" O PHE N 738 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 737 through 739 removed outlier: 6.739A pdb=" N VAL O 710 " --> pdb=" O PHE O 738 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 737 through 739 removed outlier: 6.736A pdb=" N VAL P 710 " --> pdb=" O PHE P 738 " (cutoff:3.500A) 2448 hydrogen bonds defined for protein. 6984 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: 8.02 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9819 1.34 - 1.47: 12820 1.47 - 1.60: 18577 1.60 - 1.72: 32 1.72 - 1.85: 224 Bond restraints: 41472 Sorted by residual: bond pdb=" CA ALA A 536 " pdb=" CB ALA A 536 " ideal model delta sigma weight residual 1.528 1.466 0.062 1.56e-02 4.11e+03 1.60e+01 bond pdb=" CA ALA H 536 " pdb=" CB ALA H 536 " ideal model delta sigma weight residual 1.528 1.466 0.062 1.56e-02 4.11e+03 1.59e+01 bond pdb=" CA ALA G 536 " pdb=" CB ALA G 536 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.56e-02 4.11e+03 1.55e+01 bond pdb=" CA ALA C 536 " pdb=" CB ALA C 536 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.56e-02 4.11e+03 1.55e+01 bond pdb=" CA ALA E 536 " pdb=" CB ALA E 536 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.56e-02 4.11e+03 1.55e+01 ... (remaining 41467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 46642 2.07 - 4.14: 8195 4.14 - 6.20: 1132 6.20 - 8.27: 151 8.27 - 10.34: 24 Bond angle restraints: 56144 Sorted by residual: angle pdb=" C ARG F 465 " pdb=" CA ARG F 465 " pdb=" CB ARG F 465 " ideal model delta sigma weight residual 110.85 100.65 10.20 1.70e+00 3.46e-01 3.60e+01 angle pdb=" C ARG D 465 " pdb=" CA ARG D 465 " pdb=" CB ARG D 465 " ideal model delta sigma weight residual 110.85 100.70 10.15 1.70e+00 3.46e-01 3.57e+01 angle pdb=" C ARG H 465 " pdb=" CA ARG H 465 " pdb=" CB ARG H 465 " ideal model delta sigma weight residual 110.85 100.70 10.15 1.70e+00 3.46e-01 3.56e+01 angle pdb=" C ARG A 465 " pdb=" CA ARG A 465 " pdb=" CB ARG A 465 " ideal model delta sigma weight residual 110.85 100.71 10.14 1.70e+00 3.46e-01 3.56e+01 angle pdb=" C ARG E 465 " pdb=" CA ARG E 465 " pdb=" CB ARG E 465 " ideal model delta sigma weight residual 110.85 100.71 10.14 1.70e+00 3.46e-01 3.56e+01 ... (remaining 56139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 22856 16.14 - 32.28: 2082 32.28 - 48.42: 423 48.42 - 64.56: 119 64.56 - 80.71: 40 Dihedral angle restraints: 25520 sinusoidal: 10656 harmonic: 14864 Sorted by residual: dihedral pdb=" CA ASP D 367 " pdb=" C ASP D 367 " pdb=" N ILE D 368 " pdb=" CA ILE D 368 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ASP F 367 " pdb=" C ASP F 367 " pdb=" N ILE F 368 " pdb=" CA ILE F 368 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ASP B 367 " pdb=" C ASP B 367 " pdb=" N ILE B 368 " pdb=" CA ILE B 368 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 25517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3784 0.089 - 0.179: 1895 0.179 - 0.268: 602 0.268 - 0.357: 118 0.357 - 0.447: 17 Chirality restraints: 6416 Sorted by residual: chirality pdb=" CA ARG H 497 " pdb=" N ARG H 497 " pdb=" C ARG H 497 " pdb=" CB ARG H 497 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA ARG D 497 " pdb=" N ARG D 497 " pdb=" C ARG D 497 " pdb=" CB ARG D 497 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA ARG G 497 " pdb=" N ARG G 497 " pdb=" C ARG G 497 " pdb=" CB ARG G 497 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 6413 not shown) Planarity restraints: 7256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD F 901 " -0.058 2.00e-02 2.50e+03 4.90e-02 4.80e+01 pdb=" C2N NAD F 901 " 0.093 2.00e-02 2.50e+03 pdb=" C3N NAD F 901 " -0.003 2.00e-02 2.50e+03 pdb=" C4N NAD F 901 " -0.065 2.00e-02 2.50e+03 pdb=" C5N NAD F 901 " 0.048 2.00e-02 2.50e+03 pdb=" C6N NAD F 901 " -0.006 2.00e-02 2.50e+03 pdb=" C7N NAD F 901 " -0.022 2.00e-02 2.50e+03 pdb=" N1N NAD F 901 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 901 " -0.060 2.00e-02 2.50e+03 4.77e-02 4.55e+01 pdb=" C2N NAD B 901 " 0.089 2.00e-02 2.50e+03 pdb=" C3N NAD B 901 " -0.003 2.00e-02 2.50e+03 pdb=" C4N NAD B 901 " -0.065 2.00e-02 2.50e+03 pdb=" C5N NAD B 901 " 0.043 2.00e-02 2.50e+03 pdb=" C6N NAD B 901 " 0.002 2.00e-02 2.50e+03 pdb=" C7N NAD B 901 " -0.019 2.00e-02 2.50e+03 pdb=" N1N NAD B 901 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 901 " -0.057 2.00e-02 2.50e+03 4.71e-02 4.44e+01 pdb=" C2N NAD D 901 " 0.086 2.00e-02 2.50e+03 pdb=" C3N NAD D 901 " -0.003 2.00e-02 2.50e+03 pdb=" C4N NAD D 901 " -0.066 2.00e-02 2.50e+03 pdb=" C5N NAD D 901 " 0.047 2.00e-02 2.50e+03 pdb=" C6N NAD D 901 " -0.002 2.00e-02 2.50e+03 pdb=" C7N NAD D 901 " -0.018 2.00e-02 2.50e+03 pdb=" N1N NAD D 901 " 0.013 2.00e-02 2.50e+03 ... (remaining 7253 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 18565 2.97 - 3.45: 44291 3.45 - 3.93: 69115 3.93 - 4.42: 81566 4.42 - 4.90: 127351 Nonbonded interactions: 340888 Sorted by model distance: nonbonded pdb=" O GLU E 149 " pdb=" O3D NAD E 901 " model vdw 2.486 3.040 nonbonded pdb=" O GLU C 149 " pdb=" O3D NAD C 901 " model vdw 2.488 3.040 nonbonded pdb=" O GLU G 149 " pdb=" O3D NAD G 901 " model vdw 2.491 3.040 nonbonded pdb=" O GLU D 149 " pdb=" O3D NAD D 901 " model vdw 2.494 3.040 nonbonded pdb=" O GLU H 149 " pdb=" O3D NAD H 901 " model vdw 2.498 3.040 ... (remaining 340883 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 35.460 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.110 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:7.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 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 : 0.010 0.071 41472 Z= 0.623 Angle : 1.603 10.339 56144 Z= 1.055 Chirality : 0.114 0.447 6416 Planarity : 0.009 0.050 7256 Dihedral : 13.677 80.706 15888 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.56 % Allowed : 3.95 % Favored : 95.49 % Cbeta Deviations : 0.98 % 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: -1.64 (0.11), residues: 5120 helix: -1.40 (0.07), residues: 3544 sheet: 0.28 (0.41), residues: 120 loop : 0.26 (0.18), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG D 110 TYR 0.055 0.012 TYR C 429 PHE 0.039 0.009 PHE H 467 TRP 0.058 0.010 TRP D 103 HIS 0.015 0.004 HIS G 534 Details of bonding type rmsd covalent geometry : bond 0.00953 (41472) covalent geometry : angle 1.60252 (56144) hydrogen bonds : bond 0.17468 ( 2448) hydrogen bonds : angle 6.75288 ( 6984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1028 time to evaluate : 1.688 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 0 residues processed: 1036 average time/residue: 0.8472 time to fit residues: 1035.6244 Evaluate side-chains 590 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 590 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 232 ASN J 852 ASN I 731 GLN I 852 ASN K 731 GLN K 852 ASN M 731 GLN M 852 ASN N 852 ASN O 731 GLN O 852 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.136475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.071947 restraints weight = 80990.933| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.10 r_work: 0.2739 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 41472 Z= 0.342 Angle : 0.855 11.776 56144 Z= 0.422 Chirality : 0.048 0.240 6416 Planarity : 0.005 0.034 7256 Dihedral : 6.824 73.585 6080 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.70 % Allowed : 12.15 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.12), residues: 5120 helix: 0.18 (0.08), residues: 3648 sheet: 0.24 (0.42), residues: 136 loop : 0.73 (0.19), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 131 TYR 0.011 0.002 TYR B 429 PHE 0.015 0.002 PHE P 763 TRP 0.012 0.002 TRP H 420 HIS 0.008 0.002 HIS O 795 Details of bonding type rmsd covalent geometry : bond 0.00791 (41472) covalent geometry : angle 0.85471 (56144) hydrogen bonds : bond 0.05499 ( 2448) hydrogen bonds : angle 5.09100 ( 6984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 654 time to evaluate : 1.652 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.9508 (OUTLIER) cc_final: 0.9100 (p0) REVERT: A 131 ARG cc_start: 0.9305 (mtm110) cc_final: 0.8566 (ptp-170) REVERT: A 212 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8959 (mp) REVERT: A 249 ARG cc_start: 0.8208 (mmm-85) cc_final: 0.7982 (mmm-85) REVERT: A 361 LYS cc_start: 0.9142 (mttp) cc_final: 0.8937 (mptt) REVERT: B 110 ARG cc_start: 0.8854 (ttp80) cc_final: 0.8212 (ttp80) REVERT: B 127 ASP cc_start: 0.9514 (OUTLIER) cc_final: 0.9225 (p0) REVERT: B 449 GLU cc_start: 0.9010 (tp30) cc_final: 0.8719 (tp30) REVERT: C 127 ASP cc_start: 0.9511 (OUTLIER) cc_final: 0.9020 (p0) REVERT: C 131 ARG cc_start: 0.9345 (mtm110) cc_final: 0.8684 (ptp-170) REVERT: C 212 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8960 (mp) REVERT: C 249 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7979 (mmm-85) REVERT: C 288 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8608 (mt-10) REVERT: D 127 ASP cc_start: 0.9522 (OUTLIER) cc_final: 0.9019 (p0) REVERT: D 131 ARG cc_start: 0.9385 (mtm110) cc_final: 0.8746 (ptp-170) REVERT: D 449 GLU cc_start: 0.9011 (tp30) cc_final: 0.8720 (tp30) REVERT: E 127 ASP cc_start: 0.9505 (OUTLIER) cc_final: 0.9096 (p0) REVERT: E 131 ARG cc_start: 0.9307 (mtm110) cc_final: 0.8568 (ptp-170) REVERT: E 212 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8958 (mp) REVERT: E 249 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.8009 (mmm-85) REVERT: E 288 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8605 (mt-10) REVERT: F 110 ARG cc_start: 0.8864 (ttp80) cc_final: 0.8238 (ttp80) REVERT: F 127 ASP cc_start: 0.9511 (OUTLIER) cc_final: 0.9222 (p0) REVERT: F 449 GLU cc_start: 0.9015 (tp30) cc_final: 0.8725 (tp30) REVERT: G 127 ASP cc_start: 0.9515 (OUTLIER) cc_final: 0.9025 (p0) REVERT: G 131 ARG cc_start: 0.9344 (mtm110) cc_final: 0.8681 (ptp-170) REVERT: G 212 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8943 (mp) REVERT: G 249 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7977 (mmm-85) REVERT: G 288 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8606 (mt-10) REVERT: H 110 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8325 (ttp80) REVERT: H 114 GLN cc_start: 0.9228 (tt0) cc_final: 0.9024 (tm-30) REVERT: H 127 ASP cc_start: 0.9522 (OUTLIER) cc_final: 0.9016 (p0) REVERT: H 131 ARG cc_start: 0.9382 (mtm110) cc_final: 0.8742 (ptp-170) REVERT: H 449 GLU cc_start: 0.9013 (tp30) cc_final: 0.8722 (tp30) REVERT: J 715 ARG cc_start: 0.8363 (tpm170) cc_final: 0.7881 (tpm170) REVERT: J 716 ARG cc_start: 0.7063 (tpp-160) cc_final: 0.6589 (tpp-160) REVERT: J 827 ASN cc_start: 0.9072 (m-40) cc_final: 0.8760 (OUTLIER) REVERT: I 706 ASP cc_start: 0.9513 (t0) cc_final: 0.9300 (m-30) REVERT: I 715 ARG cc_start: 0.8388 (tpm170) cc_final: 0.7860 (tpm170) REVERT: I 716 ARG cc_start: 0.6894 (tpp-160) cc_final: 0.6365 (tpp-160) REVERT: I 733 ARG cc_start: 0.8926 (ttm170) cc_final: 0.8453 (mtt90) REVERT: I 742 ASP cc_start: 0.8201 (t70) cc_final: 0.7999 (t0) REVERT: I 795 HIS cc_start: 0.8652 (m-70) cc_final: 0.7923 (m-70) REVERT: I 827 ASN cc_start: 0.9179 (m-40) cc_final: 0.8966 (OUTLIER) REVERT: I 836 GLN cc_start: 0.7219 (pm20) cc_final: 0.6760 (mp10) REVERT: K 715 ARG cc_start: 0.8394 (tpm170) cc_final: 0.7884 (tpm170) REVERT: K 716 ARG cc_start: 0.6902 (tpp-160) cc_final: 0.6391 (tpp-160) REVERT: K 742 ASP cc_start: 0.8230 (t70) cc_final: 0.8014 (t0) REVERT: K 827 ASN cc_start: 0.9158 (m-40) cc_final: 0.8913 (p0) REVERT: K 840 MET cc_start: 0.8986 (tpp) cc_final: 0.8679 (mmm) REVERT: L 715 ARG cc_start: 0.8362 (tpm170) cc_final: 0.7885 (tpm170) REVERT: L 716 ARG cc_start: 0.7040 (tpp-160) cc_final: 0.6541 (tpp-160) REVERT: L 727 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8665 (tmmt) REVERT: L 827 ASN cc_start: 0.8996 (m-40) cc_final: 0.8721 (OUTLIER) REVERT: L 846 PHE cc_start: 0.8846 (m-10) cc_final: 0.8539 (m-80) REVERT: M 706 ASP cc_start: 0.9520 (t0) cc_final: 0.9303 (m-30) REVERT: M 715 ARG cc_start: 0.8421 (tpm170) cc_final: 0.7894 (tpm170) REVERT: M 716 ARG cc_start: 0.6915 (tpp-160) cc_final: 0.6411 (tpp-160) REVERT: M 742 ASP cc_start: 0.8214 (t70) cc_final: 0.8010 (t0) REVERT: M 827 ASN cc_start: 0.9171 (m-40) cc_final: 0.8947 (p0) REVERT: M 836 GLN cc_start: 0.7236 (pm20) cc_final: 0.7016 (mp10) REVERT: N 715 ARG cc_start: 0.8343 (tpm170) cc_final: 0.7854 (tpm170) REVERT: N 716 ARG cc_start: 0.7061 (tpp-160) cc_final: 0.6565 (tpp-160) REVERT: N 727 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8669 (tmmt) REVERT: N 827 ASN cc_start: 0.9049 (m-40) cc_final: 0.8742 (OUTLIER) REVERT: N 846 PHE cc_start: 0.8828 (m-10) cc_final: 0.8509 (m-80) REVERT: O 715 ARG cc_start: 0.8401 (tpm170) cc_final: 0.7892 (tpm170) REVERT: O 716 ARG cc_start: 0.6886 (tpp-160) cc_final: 0.6376 (tpp-160) REVERT: O 742 ASP cc_start: 0.8155 (t70) cc_final: 0.7947 (t0) REVERT: O 786 HIS cc_start: 0.8749 (t-170) cc_final: 0.8549 (t-170) REVERT: O 827 ASN cc_start: 0.9157 (m-40) cc_final: 0.8925 (p0) REVERT: O 840 MET cc_start: 0.8981 (tpp) cc_final: 0.8672 (mmm) REVERT: P 715 ARG cc_start: 0.8359 (tpm170) cc_final: 0.7932 (tpm170) REVERT: P 716 ARG cc_start: 0.7044 (tpp-160) cc_final: 0.6550 (tpp-160) REVERT: P 827 ASN cc_start: 0.8989 (m-40) cc_final: 0.8724 (OUTLIER) REVERT: P 829 VAL cc_start: 0.7721 (t) cc_final: 0.7432 (t) outliers start: 73 outliers final: 32 residues processed: 710 average time/residue: 0.7979 time to fit residues: 678.9554 Evaluate side-chains 551 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 510 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain J residue 727 LYS Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 845 ARG Chi-restraints excluded: chain L residue 727 LYS Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 845 ARG Chi-restraints excluded: chain N residue 727 LYS Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 845 ARG Chi-restraints excluded: chain P residue 727 LYS Chi-restraints excluded: chain P residue 768 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 393 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 425 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 385 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 315 optimal weight: 0.9980 chunk 398 optimal weight: 20.0000 chunk 138 optimal weight: 0.9980 chunk 336 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 758 GLN ** L 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 758 GLN ** N 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.139387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.075182 restraints weight = 79913.277| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.14 r_work: 0.2808 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 41472 Z= 0.153 Angle : 0.714 15.089 56144 Z= 0.348 Chirality : 0.041 0.227 6416 Planarity : 0.004 0.047 7256 Dihedral : 6.411 72.551 6080 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.81 % Allowed : 13.48 % Favored : 84.71 % 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 (0.12), residues: 5120 helix: 0.75 (0.09), residues: 3648 sheet: 0.72 (0.47), residues: 136 loop : 0.67 (0.19), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 845 TYR 0.010 0.001 TYR A 503 PHE 0.025 0.002 PHE P 711 TRP 0.016 0.002 TRP I 831 HIS 0.007 0.001 HIS J 786 Details of bonding type rmsd covalent geometry : bond 0.00350 (41472) covalent geometry : angle 0.71372 (56144) hydrogen bonds : bond 0.04514 ( 2448) hydrogen bonds : angle 4.70711 ( 6984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 604 time to evaluate : 1.788 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: A 127 ASP cc_start: 0.9473 (OUTLIER) cc_final: 0.9134 (p0) REVERT: A 131 ARG cc_start: 0.9299 (mtm110) cc_final: 0.8828 (mtm110) REVERT: A 544 GLU cc_start: 0.8394 (pp20) cc_final: 0.8192 (pp20) REVERT: B 127 ASP cc_start: 0.9506 (OUTLIER) cc_final: 0.9164 (p0) REVERT: B 131 ARG cc_start: 0.9374 (mtm110) cc_final: 0.9102 (mtm110) REVERT: B 449 GLU cc_start: 0.9040 (tp30) cc_final: 0.8744 (tp30) REVERT: C 127 ASP cc_start: 0.9484 (OUTLIER) cc_final: 0.9139 (p0) REVERT: C 131 ARG cc_start: 0.9324 (mtm110) cc_final: 0.8933 (mtm110) REVERT: C 288 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8578 (mt-10) REVERT: C 544 GLU cc_start: 0.8404 (pp20) cc_final: 0.8201 (pp20) REVERT: D 127 ASP cc_start: 0.9506 (OUTLIER) cc_final: 0.9211 (p0) REVERT: D 131 ARG cc_start: 0.9366 (mtm110) cc_final: 0.9082 (mtm110) REVERT: D 288 GLU cc_start: 0.8996 (tt0) cc_final: 0.8636 (mt-10) REVERT: D 449 GLU cc_start: 0.9046 (tp30) cc_final: 0.8753 (tp30) REVERT: E 127 ASP cc_start: 0.9472 (OUTLIER) cc_final: 0.9141 (p0) REVERT: E 131 ARG cc_start: 0.9300 (mtm110) cc_final: 0.8823 (mtm110) REVERT: E 288 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8582 (mt-10) REVERT: E 361 LYS cc_start: 0.9127 (mttp) cc_final: 0.8905 (mptt) REVERT: F 127 ASP cc_start: 0.9504 (OUTLIER) cc_final: 0.9164 (p0) REVERT: F 131 ARG cc_start: 0.9375 (mtm110) cc_final: 0.9103 (mtm110) REVERT: F 449 GLU cc_start: 0.9046 (tp30) cc_final: 0.8750 (tp30) REVERT: G 127 ASP cc_start: 0.9487 (OUTLIER) cc_final: 0.9135 (p0) REVERT: G 131 ARG cc_start: 0.9322 (mtm110) cc_final: 0.8943 (mtm110) REVERT: G 232 ASN cc_start: 0.8544 (m-40) cc_final: 0.8184 (m110) REVERT: G 288 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8589 (mt-10) REVERT: G 361 LYS cc_start: 0.9124 (mttp) cc_final: 0.8898 (mptt) REVERT: H 110 ARG cc_start: 0.8877 (ttp80) cc_final: 0.8426 (ttp80) REVERT: H 127 ASP cc_start: 0.9499 (OUTLIER) cc_final: 0.9201 (p0) REVERT: H 131 ARG cc_start: 0.9359 (mtm110) cc_final: 0.9074 (mtm110) REVERT: H 449 GLU cc_start: 0.9040 (tp30) cc_final: 0.8744 (tp30) REVERT: J 715 ARG cc_start: 0.8393 (tpm170) cc_final: 0.7937 (tpm170) REVERT: J 786 HIS cc_start: 0.8796 (t-170) cc_final: 0.8592 (t-170) REVERT: J 827 ASN cc_start: 0.9020 (m-40) cc_final: 0.8716 (OUTLIER) REVERT: J 840 MET cc_start: 0.8902 (tpp) cc_final: 0.8692 (tpt) REVERT: J 845 ARG cc_start: 0.9544 (mtp-110) cc_final: 0.9142 (mtm110) REVERT: I 711 PHE cc_start: 0.9005 (t80) cc_final: 0.8803 (t80) REVERT: I 713 SER cc_start: 0.8788 (t) cc_final: 0.7841 (p) REVERT: I 714 TYR cc_start: 0.6831 (p90) cc_final: 0.6427 (p90) REVERT: I 715 ARG cc_start: 0.8397 (tpm170) cc_final: 0.7848 (tpm170) REVERT: I 716 ARG cc_start: 0.6992 (tpp-160) cc_final: 0.6464 (tpp-160) REVERT: I 733 ARG cc_start: 0.9074 (ttm170) cc_final: 0.8754 (mtt90) REVERT: I 742 ASP cc_start: 0.8208 (t70) cc_final: 0.7980 (t70) REVERT: I 793 PHE cc_start: 0.7052 (m-80) cc_final: 0.6789 (m-10) REVERT: I 827 ASN cc_start: 0.9173 (m-40) cc_final: 0.8867 (OUTLIER) REVERT: K 715 ARG cc_start: 0.8429 (tpm170) cc_final: 0.8032 (tpm170) REVERT: K 716 ARG cc_start: 0.6980 (tpp-160) cc_final: 0.6530 (tpp-160) REVERT: K 733 ARG cc_start: 0.9215 (ttm170) cc_final: 0.8477 (mtt90) REVERT: K 742 ASP cc_start: 0.8182 (t70) cc_final: 0.7980 (t70) REVERT: K 827 ASN cc_start: 0.9134 (m-40) cc_final: 0.8842 (p0) REVERT: K 840 MET cc_start: 0.8988 (tpp) cc_final: 0.8712 (mmm) REVERT: L 715 ARG cc_start: 0.8396 (tpm170) cc_final: 0.7962 (tpm170) REVERT: L 736 ARG cc_start: 0.7779 (mtp-110) cc_final: 0.7569 (mtp-110) REVERT: L 827 ASN cc_start: 0.9023 (m-40) cc_final: 0.8709 (OUTLIER) REVERT: L 840 MET cc_start: 0.8836 (tpp) cc_final: 0.8603 (tpt) REVERT: M 711 PHE cc_start: 0.9035 (t80) cc_final: 0.8812 (t80) REVERT: M 713 SER cc_start: 0.8787 (t) cc_final: 0.7833 (p) REVERT: M 714 TYR cc_start: 0.6888 (p90) cc_final: 0.6452 (p90) REVERT: M 715 ARG cc_start: 0.8406 (tpm170) cc_final: 0.7967 (tpm170) REVERT: M 716 ARG cc_start: 0.6967 (tpp-160) cc_final: 0.6502 (tpp-160) REVERT: M 733 ARG cc_start: 0.9234 (ttm170) cc_final: 0.8718 (mmt90) REVERT: M 742 ASP cc_start: 0.8194 (t70) cc_final: 0.7971 (t70) REVERT: M 763 PHE cc_start: 0.8628 (t80) cc_final: 0.8415 (t80) REVERT: M 827 ASN cc_start: 0.9151 (m-40) cc_final: 0.8845 (p0) REVERT: N 715 ARG cc_start: 0.8383 (tpm170) cc_final: 0.7949 (tpm170) REVERT: N 736 ARG cc_start: 0.7847 (mtp-110) cc_final: 0.7596 (mtp-110) REVERT: N 827 ASN cc_start: 0.8983 (m-40) cc_final: 0.8638 (OUTLIER) REVERT: O 715 ARG cc_start: 0.8422 (tpm170) cc_final: 0.8019 (tpm170) REVERT: O 716 ARG cc_start: 0.6942 (tpp-160) cc_final: 0.6509 (tpp-160) REVERT: O 733 ARG cc_start: 0.9214 (ttm170) cc_final: 0.8476 (mtt90) REVERT: O 786 HIS cc_start: 0.8765 (t-170) cc_final: 0.8540 (t-170) REVERT: O 827 ASN cc_start: 0.9134 (m-40) cc_final: 0.8841 (p0) REVERT: O 840 MET cc_start: 0.8987 (tpp) cc_final: 0.8712 (mmm) REVERT: P 713 SER cc_start: 0.8879 (t) cc_final: 0.7954 (p) REVERT: P 715 ARG cc_start: 0.8372 (tpm170) cc_final: 0.7916 (tpm170) REVERT: P 736 ARG cc_start: 0.7809 (mtp-110) cc_final: 0.7581 (mtp-110) REVERT: P 827 ASN cc_start: 0.9029 (m-40) cc_final: 0.8773 (OUTLIER) outliers start: 78 outliers final: 38 residues processed: 658 average time/residue: 0.8073 time to fit residues: 639.7197 Evaluate side-chains 569 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 528 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 366 SER Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 845 ARG Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 794 GLU Chi-restraints excluded: chain M residue 845 ARG Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 845 ARG Chi-restraints excluded: chain P residue 768 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 203 optimal weight: 0.0670 chunk 24 optimal weight: 6.9990 chunk 449 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 201 optimal weight: 20.0000 chunk 258 optimal weight: 3.9990 chunk 256 optimal weight: 8.9990 chunk 442 optimal weight: 20.0000 chunk 484 optimal weight: 20.0000 chunk 30 optimal weight: 0.2980 chunk 224 optimal weight: 4.9990 overall best weight: 2.6724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 777 ASN ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.138648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.074462 restraints weight = 79890.635| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.11 r_work: 0.2796 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 41472 Z= 0.177 Angle : 0.679 11.871 56144 Z= 0.331 Chirality : 0.041 0.246 6416 Planarity : 0.004 0.050 7256 Dihedral : 6.151 72.980 6080 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.00 % Allowed : 14.85 % Favored : 83.16 % 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: 1.14 (0.12), residues: 5120 helix: 0.92 (0.09), residues: 3664 sheet: 0.69 (0.49), residues: 136 loop : 0.66 (0.19), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 110 TYR 0.020 0.001 TYR B 213 PHE 0.018 0.001 PHE I 711 TRP 0.018 0.001 TRP I 831 HIS 0.008 0.001 HIS I 795 Details of bonding type rmsd covalent geometry : bond 0.00416 (41472) covalent geometry : angle 0.67899 (56144) hydrogen bonds : bond 0.04346 ( 2448) hydrogen bonds : angle 4.54772 ( 6984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 624 time to evaluate : 1.709 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.9081 (tt0) cc_final: 0.8698 (mt-10) REVERT: B 127 ASP cc_start: 0.9514 (OUTLIER) cc_final: 0.9230 (p0) REVERT: B 288 GLU cc_start: 0.8992 (tt0) cc_final: 0.8648 (mt-10) REVERT: B 449 GLU cc_start: 0.9053 (tp30) cc_final: 0.8747 (tp30) REVERT: C 131 ARG cc_start: 0.9302 (mtm110) cc_final: 0.8799 (ptp-170) REVERT: C 288 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8639 (mt-10) REVERT: D 110 ARG cc_start: 0.8967 (ttp80) cc_final: 0.8530 (ttp80) REVERT: D 449 GLU cc_start: 0.9059 (tp30) cc_final: 0.8753 (tp30) REVERT: E 288 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8641 (mt-10) REVERT: E 361 LYS cc_start: 0.9116 (mttp) cc_final: 0.8751 (mptp) REVERT: F 127 ASP cc_start: 0.9507 (OUTLIER) cc_final: 0.9281 (p0) REVERT: F 288 GLU cc_start: 0.8991 (tt0) cc_final: 0.8644 (mt-10) REVERT: F 449 GLU cc_start: 0.9060 (tp30) cc_final: 0.8753 (tp30) REVERT: G 128 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9120 (pt) REVERT: G 131 ARG cc_start: 0.9301 (mtm110) cc_final: 0.8787 (ptp-170) REVERT: G 232 ASN cc_start: 0.8597 (m-40) cc_final: 0.8160 (m110) REVERT: G 288 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8651 (mt-10) REVERT: H 110 ARG cc_start: 0.8926 (ttp80) cc_final: 0.8468 (ttp80) REVERT: H 288 GLU cc_start: 0.8990 (tt0) cc_final: 0.8646 (mt-10) REVERT: H 449 GLU cc_start: 0.9053 (tp30) cc_final: 0.8744 (tp30) REVERT: J 715 ARG cc_start: 0.8305 (tpm170) cc_final: 0.7641 (tpm170) REVERT: J 716 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6557 (ttm110) REVERT: J 736 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7441 (mtp-110) REVERT: J 827 ASN cc_start: 0.9025 (m-40) cc_final: 0.8694 (OUTLIER) REVERT: J 840 MET cc_start: 0.8899 (tpp) cc_final: 0.8690 (tpt) REVERT: J 845 ARG cc_start: 0.9567 (mtp-110) cc_final: 0.9095 (mtm110) REVERT: I 711 PHE cc_start: 0.9083 (t80) cc_final: 0.8865 (t80) REVERT: I 713 SER cc_start: 0.8860 (t) cc_final: 0.7860 (p) REVERT: I 715 ARG cc_start: 0.8455 (tpm170) cc_final: 0.8000 (tpm170) REVERT: I 733 ARG cc_start: 0.9119 (ttm170) cc_final: 0.8847 (mtt90) REVERT: I 736 ARG cc_start: 0.7907 (mtp-110) cc_final: 0.7618 (mtp-110) REVERT: I 763 PHE cc_start: 0.8639 (t80) cc_final: 0.8418 (t80) REVERT: I 786 HIS cc_start: 0.8843 (t-170) cc_final: 0.8635 (t-170) REVERT: I 827 ASN cc_start: 0.9170 (m-40) cc_final: 0.8838 (OUTLIER) REVERT: I 836 GLN cc_start: 0.7819 (pm20) cc_final: 0.7327 (pm20) REVERT: I 845 ARG cc_start: 0.9532 (mtm-85) cc_final: 0.9155 (mtm-85) REVERT: K 711 PHE cc_start: 0.9022 (t80) cc_final: 0.8739 (t80) REVERT: K 713 SER cc_start: 0.8821 (t) cc_final: 0.7915 (p) REVERT: K 715 ARG cc_start: 0.8475 (tpm170) cc_final: 0.8131 (tpm170) REVERT: K 716 ARG cc_start: 0.7119 (tpp-160) cc_final: 0.6685 (tpp-160) REVERT: K 733 ARG cc_start: 0.9268 (ttm170) cc_final: 0.8648 (mmt90) REVERT: K 736 ARG cc_start: 0.7859 (mtp-110) cc_final: 0.7580 (mtp-110) REVERT: K 786 HIS cc_start: 0.8700 (t-170) cc_final: 0.8436 (t-170) REVERT: K 827 ASN cc_start: 0.9116 (m-40) cc_final: 0.8827 (OUTLIER) REVERT: L 715 ARG cc_start: 0.8327 (tpm170) cc_final: 0.7580 (tpm170) REVERT: L 716 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6562 (ttm110) REVERT: L 827 ASN cc_start: 0.9002 (m-40) cc_final: 0.8713 (OUTLIER) REVERT: L 840 MET cc_start: 0.8846 (tpp) cc_final: 0.8553 (tpt) REVERT: L 845 ARG cc_start: 0.9555 (mtp-110) cc_final: 0.9141 (mtm110) REVERT: M 711 PHE cc_start: 0.9092 (t80) cc_final: 0.8829 (t80) REVERT: M 713 SER cc_start: 0.8873 (t) cc_final: 0.7895 (p) REVERT: M 714 TYR cc_start: 0.6789 (p90) cc_final: 0.6490 (p90) REVERT: M 715 ARG cc_start: 0.8463 (tpm170) cc_final: 0.8097 (tpp-160) REVERT: M 716 ARG cc_start: 0.7044 (tpp-160) cc_final: 0.6686 (tpp-160) REVERT: M 733 ARG cc_start: 0.9179 (ttm170) cc_final: 0.8890 (mtt90) REVERT: M 736 ARG cc_start: 0.7937 (mtp-110) cc_final: 0.7015 (ptp-170) REVERT: M 763 PHE cc_start: 0.8726 (t80) cc_final: 0.8520 (t80) REVERT: M 827 ASN cc_start: 0.9127 (m-40) cc_final: 0.8838 (OUTLIER) REVERT: M 836 GLN cc_start: 0.7902 (pm20) cc_final: 0.7319 (pm20) REVERT: N 736 ARG cc_start: 0.7801 (mtp-110) cc_final: 0.7575 (mtp-110) REVERT: N 827 ASN cc_start: 0.9001 (m-40) cc_final: 0.8676 (OUTLIER) REVERT: N 845 ARG cc_start: 0.9517 (mtp-110) cc_final: 0.9255 (ptp-110) REVERT: O 711 PHE cc_start: 0.9030 (t80) cc_final: 0.8757 (t80) REVERT: O 713 SER cc_start: 0.8815 (t) cc_final: 0.7861 (p) REVERT: O 715 ARG cc_start: 0.8482 (tpm170) cc_final: 0.7887 (tpm170) REVERT: O 716 ARG cc_start: 0.7018 (tpp-160) cc_final: 0.6615 (tpp-160) REVERT: O 733 ARG cc_start: 0.9265 (ttm170) cc_final: 0.8644 (mmt90) REVERT: O 736 ARG cc_start: 0.7834 (mtp-110) cc_final: 0.7552 (mtp-110) REVERT: O 786 HIS cc_start: 0.8787 (t-170) cc_final: 0.8568 (t-170) REVERT: O 827 ASN cc_start: 0.9106 (m-40) cc_final: 0.8807 (OUTLIER) REVERT: P 711 PHE cc_start: 0.9049 (t80) cc_final: 0.8841 (t80) REVERT: P 713 SER cc_start: 0.8881 (t) cc_final: 0.8005 (p) REVERT: P 736 ARG cc_start: 0.7754 (mtp-110) cc_final: 0.7546 (mtp-110) REVERT: P 827 ASN cc_start: 0.9004 (m-40) cc_final: 0.8756 (OUTLIER) outliers start: 86 outliers final: 47 residues processed: 688 average time/residue: 0.7762 time to fit residues: 644.4373 Evaluate side-chains 586 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 542 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 368 ILE Chi-restraints excluded: chain J residue 716 ARG Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain I residue 794 GLU Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 845 ARG Chi-restraints excluded: chain L residue 716 ARG Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 794 GLU Chi-restraints excluded: chain M residue 845 ARG Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 845 ARG Chi-restraints excluded: chain P residue 768 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 95 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 327 optimal weight: 9.9990 chunk 390 optimal weight: 0.4980 chunk 459 optimal weight: 8.9990 chunk 280 optimal weight: 2.9990 chunk 496 optimal weight: 30.0000 chunk 479 optimal weight: 30.0000 chunk 450 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 257 optimal weight: 9.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 786 HIS ** K 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.138613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.074224 restraints weight = 79536.411| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.14 r_work: 0.2795 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 41472 Z= 0.174 Angle : 0.677 11.315 56144 Z= 0.329 Chirality : 0.041 0.256 6416 Planarity : 0.004 0.040 7256 Dihedral : 6.017 73.552 6080 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.44 % Allowed : 15.75 % Favored : 81.81 % 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: 1.31 (0.12), residues: 5120 helix: 1.07 (0.09), residues: 3616 sheet: 0.93 (0.50), residues: 136 loop : 0.65 (0.19), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 249 TYR 0.009 0.001 TYR C 503 PHE 0.025 0.002 PHE L 738 TRP 0.022 0.001 TRP I 831 HIS 0.007 0.001 HIS M 795 Details of bonding type rmsd covalent geometry : bond 0.00409 (41472) covalent geometry : angle 0.67746 (56144) hydrogen bonds : bond 0.04214 ( 2448) hydrogen bonds : angle 4.51503 ( 6984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 594 time to evaluate : 1.649 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.9094 (tt0) cc_final: 0.8712 (mt-10) REVERT: A 328 GLN cc_start: 0.8563 (tp40) cc_final: 0.8304 (tp40) REVERT: A 361 LYS cc_start: 0.9103 (mttp) cc_final: 0.8836 (mptt) REVERT: B 174 GLU cc_start: 0.8719 (mp0) cc_final: 0.8462 (pm20) REVERT: B 449 GLU cc_start: 0.9059 (tp30) cc_final: 0.8745 (tp30) REVERT: C 131 ARG cc_start: 0.9281 (mtm110) cc_final: 0.8770 (ptp-170) REVERT: C 174 GLU cc_start: 0.8661 (mp0) cc_final: 0.8375 (pm20) REVERT: C 232 ASN cc_start: 0.8659 (m-40) cc_final: 0.8102 (m110) REVERT: C 328 GLN cc_start: 0.8560 (tp40) cc_final: 0.8298 (tp40) REVERT: D 110 ARG cc_start: 0.8978 (ttp80) cc_final: 0.8554 (ttp80) REVERT: D 174 GLU cc_start: 0.8732 (mp0) cc_final: 0.8472 (pm20) REVERT: D 288 GLU cc_start: 0.9010 (tt0) cc_final: 0.8671 (mt-10) REVERT: D 449 GLU cc_start: 0.9069 (tp30) cc_final: 0.8755 (tp30) REVERT: E 174 GLU cc_start: 0.8683 (mp0) cc_final: 0.8379 (pm20) REVERT: E 328 GLN cc_start: 0.8558 (tp40) cc_final: 0.8298 (tp40) REVERT: F 174 GLU cc_start: 0.8722 (mp0) cc_final: 0.8459 (pm20) REVERT: F 449 GLU cc_start: 0.9064 (tp30) cc_final: 0.8748 (tp30) REVERT: G 174 GLU cc_start: 0.8677 (mp0) cc_final: 0.8366 (pm20) REVERT: G 232 ASN cc_start: 0.8647 (m-40) cc_final: 0.8183 (m110) REVERT: G 328 GLN cc_start: 0.8566 (tp40) cc_final: 0.8310 (tp40) REVERT: H 110 ARG cc_start: 0.8956 (ttp80) cc_final: 0.8501 (ttp80) REVERT: H 174 GLU cc_start: 0.8724 (mp0) cc_final: 0.8467 (pm20) REVERT: H 449 GLU cc_start: 0.9064 (tp30) cc_final: 0.8749 (tp30) REVERT: J 827 ASN cc_start: 0.9010 (m-40) cc_final: 0.8690 (OUTLIER) REVERT: J 845 ARG cc_start: 0.9604 (mtp-110) cc_final: 0.9178 (mtm110) REVERT: I 711 PHE cc_start: 0.9174 (t80) cc_final: 0.8892 (t80) REVERT: I 713 SER cc_start: 0.8895 (t) cc_final: 0.7862 (p) REVERT: I 715 ARG cc_start: 0.8530 (tpm170) cc_final: 0.8260 (tpp-160) REVERT: I 733 ARG cc_start: 0.9168 (ttm170) cc_final: 0.8592 (mtt90) REVERT: I 736 ARG cc_start: 0.7864 (mtp-110) cc_final: 0.7601 (mtp-110) REVERT: I 763 PHE cc_start: 0.8702 (t80) cc_final: 0.8497 (t80) REVERT: I 793 PHE cc_start: 0.6798 (m-10) cc_final: 0.5970 (m-10) REVERT: I 822 MET cc_start: 0.8400 (pmm) cc_final: 0.8155 (pmm) REVERT: I 826 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.5022 (m-80) REVERT: I 827 ASN cc_start: 0.9139 (m-40) cc_final: 0.8857 (p0) REVERT: I 845 ARG cc_start: 0.9558 (mtm-85) cc_final: 0.9270 (ptp-110) REVERT: K 711 PHE cc_start: 0.9106 (t80) cc_final: 0.8866 (t80) REVERT: K 713 SER cc_start: 0.8880 (t) cc_final: 0.7964 (p) REVERT: K 715 ARG cc_start: 0.8492 (tpm170) cc_final: 0.8130 (tpp-160) REVERT: K 716 ARG cc_start: 0.6848 (tpp-160) cc_final: 0.6614 (tpp-160) REVERT: K 733 ARG cc_start: 0.9219 (ttm170) cc_final: 0.8915 (mtt90) REVERT: K 736 ARG cc_start: 0.7856 (mtp-110) cc_final: 0.7586 (mtp-110) REVERT: K 793 PHE cc_start: 0.6841 (m-80) cc_final: 0.5984 (m-10) REVERT: K 826 TYR cc_start: 0.6984 (OUTLIER) cc_final: 0.5068 (m-80) REVERT: K 827 ASN cc_start: 0.9081 (m-40) cc_final: 0.8819 (p0) REVERT: K 836 GLN cc_start: 0.7927 (pm20) cc_final: 0.7360 (pm20) REVERT: K 845 ARG cc_start: 0.9526 (OUTLIER) cc_final: 0.9262 (mtm-85) REVERT: L 713 SER cc_start: 0.8845 (t) cc_final: 0.8001 (p) REVERT: L 715 ARG cc_start: 0.8338 (tpm170) cc_final: 0.7992 (tpm170) REVERT: L 738 PHE cc_start: 0.8940 (t80) cc_final: 0.8718 (t80) REVERT: L 827 ASN cc_start: 0.8976 (m-40) cc_final: 0.8677 (OUTLIER) REVERT: M 711 PHE cc_start: 0.9161 (t80) cc_final: 0.8907 (t80) REVERT: M 713 SER cc_start: 0.8882 (t) cc_final: 0.7887 (p) REVERT: M 714 TYR cc_start: 0.6755 (p90) cc_final: 0.6484 (p90) REVERT: M 715 ARG cc_start: 0.8483 (tpm170) cc_final: 0.8159 (tpp-160) REVERT: M 716 ARG cc_start: 0.6955 (tpp-160) cc_final: 0.6728 (tpp-160) REVERT: M 733 ARG cc_start: 0.9248 (ttm170) cc_final: 0.8917 (mtt90) REVERT: M 736 ARG cc_start: 0.7916 (mtp-110) cc_final: 0.7658 (mtp-110) REVERT: M 793 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6147 (m-10) REVERT: M 826 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.5167 (m-80) REVERT: M 827 ASN cc_start: 0.9084 (m-40) cc_final: 0.8822 (OUTLIER) REVERT: M 845 ARG cc_start: 0.9526 (OUTLIER) cc_final: 0.9246 (mtm-85) REVERT: N 713 SER cc_start: 0.8904 (t) cc_final: 0.7989 (p) REVERT: N 715 ARG cc_start: 0.8488 (tpm170) cc_final: 0.7877 (tpp-160) REVERT: N 738 PHE cc_start: 0.8937 (t80) cc_final: 0.8648 (t80) REVERT: N 827 ASN cc_start: 0.8979 (m-40) cc_final: 0.8659 (OUTLIER) REVERT: N 840 MET cc_start: 0.8944 (tpp) cc_final: 0.8710 (tpt) REVERT: N 845 ARG cc_start: 0.9534 (mtp-110) cc_final: 0.9256 (ptp-110) REVERT: O 711 PHE cc_start: 0.9089 (t80) cc_final: 0.8838 (t80) REVERT: O 713 SER cc_start: 0.8864 (t) cc_final: 0.7946 (p) REVERT: O 715 ARG cc_start: 0.8514 (tpm170) cc_final: 0.8123 (tpp-160) REVERT: O 716 ARG cc_start: 0.7016 (tpp-160) cc_final: 0.6772 (tpp-160) REVERT: O 733 ARG cc_start: 0.9223 (ttm170) cc_final: 0.8921 (mtt90) REVERT: O 736 ARG cc_start: 0.7859 (mtp-110) cc_final: 0.7591 (mtp-110) REVERT: O 793 PHE cc_start: 0.6905 (m-10) cc_final: 0.6305 (m-10) REVERT: O 826 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.5218 (m-80) REVERT: O 827 ASN cc_start: 0.9078 (m-40) cc_final: 0.8810 (OUTLIER) REVERT: O 836 GLN cc_start: 0.7922 (pm20) cc_final: 0.7384 (pm20) REVERT: P 713 SER cc_start: 0.8972 (t) cc_final: 0.7962 (p) REVERT: P 715 ARG cc_start: 0.8487 (tpm170) cc_final: 0.7847 (tpp-160) REVERT: P 736 ARG cc_start: 0.7851 (mtp-110) cc_final: 0.7626 (mtp-110) REVERT: P 827 ASN cc_start: 0.9031 (m-40) cc_final: 0.8777 (p0) REVERT: P 845 ARG cc_start: 0.9379 (ptp-110) cc_final: 0.9130 (ptp-110) outliers start: 105 outliers final: 55 residues processed: 678 average time/residue: 0.7648 time to fit residues: 625.8110 Evaluate side-chains 593 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 536 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 368 ILE Chi-restraints excluded: chain J residue 758 GLN Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain I residue 794 GLU Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 826 TYR Chi-restraints excluded: chain K residue 845 ARG Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 793 PHE Chi-restraints excluded: chain M residue 794 GLU Chi-restraints excluded: chain M residue 826 TYR Chi-restraints excluded: chain M residue 845 ARG Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 826 TYR Chi-restraints excluded: chain P residue 768 THR Chi-restraints excluded: chain P residue 846 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 128 optimal weight: 0.6980 chunk 444 optimal weight: 10.0000 chunk 412 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 403 optimal weight: 10.0000 chunk 445 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 299 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN D 97 GLN F 97 GLN H 97 GLN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 758 GLN K 786 HIS ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 777 ASN ** M 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 777 ASN ** O 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 777 ASN P 777 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.137984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.073896 restraints weight = 79817.136| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.09 r_work: 0.2789 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 41472 Z= 0.192 Angle : 0.687 11.782 56144 Z= 0.334 Chirality : 0.041 0.267 6416 Planarity : 0.004 0.039 7256 Dihedral : 5.960 73.917 6080 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.97 % Allowed : 18.40 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.12), residues: 5120 helix: 1.12 (0.09), residues: 3568 sheet: 0.78 (0.49), residues: 136 loop : 0.55 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 716 TYR 0.008 0.001 TYR A 213 PHE 0.025 0.001 PHE P 711 TRP 0.025 0.002 TRP I 831 HIS 0.006 0.001 HIS I 786 Details of bonding type rmsd covalent geometry : bond 0.00449 (41472) covalent geometry : angle 0.68690 (56144) hydrogen bonds : bond 0.04243 ( 2448) hydrogen bonds : angle 4.51828 ( 6984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 575 time to evaluate : 1.721 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.9429 (m-30) cc_final: 0.9087 (p0) REVERT: A 131 ARG cc_start: 0.9302 (mtm110) cc_final: 0.8989 (mtm110) REVERT: A 288 GLU cc_start: 0.9086 (tt0) cc_final: 0.8729 (mt-10) REVERT: A 328 GLN cc_start: 0.8593 (tp40) cc_final: 0.8331 (tp40) REVERT: B 131 ARG cc_start: 0.9275 (mtm110) cc_final: 0.8793 (mtm110) REVERT: B 288 GLU cc_start: 0.8984 (tt0) cc_final: 0.8630 (mt-10) REVERT: B 328 GLN cc_start: 0.8553 (tp40) cc_final: 0.8278 (tp40) REVERT: B 449 GLU cc_start: 0.9079 (tp30) cc_final: 0.8764 (tp30) REVERT: C 127 ASP cc_start: 0.9455 (m-30) cc_final: 0.9146 (p0) REVERT: C 131 ARG cc_start: 0.9284 (mtm110) cc_final: 0.9051 (mtm110) REVERT: C 328 GLN cc_start: 0.8582 (tp40) cc_final: 0.8319 (tp40) REVERT: D 110 ARG cc_start: 0.8984 (ttp80) cc_final: 0.8567 (ttp80) REVERT: D 288 GLU cc_start: 0.9021 (tt0) cc_final: 0.8684 (mt-10) REVERT: D 328 GLN cc_start: 0.8555 (tp40) cc_final: 0.8279 (tp40) REVERT: D 449 GLU cc_start: 0.9084 (tp30) cc_final: 0.8770 (tp30) REVERT: E 127 ASP cc_start: 0.9451 (m-30) cc_final: 0.9146 (p0) REVERT: E 131 ARG cc_start: 0.9267 (mtm110) cc_final: 0.9025 (mtm110) REVERT: E 328 GLN cc_start: 0.8575 (tp40) cc_final: 0.8313 (tp40) REVERT: E 361 LYS cc_start: 0.9105 (mttp) cc_final: 0.8836 (mptt) REVERT: F 127 ASP cc_start: 0.9500 (m-30) cc_final: 0.9247 (p0) REVERT: F 131 ARG cc_start: 0.9272 (mtm110) cc_final: 0.8750 (mtm110) REVERT: F 288 GLU cc_start: 0.8983 (tt0) cc_final: 0.8628 (mt-10) REVERT: F 328 GLN cc_start: 0.8541 (tp40) cc_final: 0.8267 (tp40) REVERT: F 449 GLU cc_start: 0.9085 (tp30) cc_final: 0.8770 (tp30) REVERT: G 127 ASP cc_start: 0.9453 (m-30) cc_final: 0.8985 (p0) REVERT: G 131 ARG cc_start: 0.9281 (mtm110) cc_final: 0.8507 (ptp-170) REVERT: G 162 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8439 (ptt-90) REVERT: G 328 GLN cc_start: 0.8579 (tp40) cc_final: 0.8319 (tp40) REVERT: G 361 LYS cc_start: 0.9095 (mttp) cc_final: 0.8827 (mptt) REVERT: H 110 ARG cc_start: 0.8954 (ttp80) cc_final: 0.8612 (ttp80) REVERT: H 114 GLN cc_start: 0.9273 (tt0) cc_final: 0.9042 (tm-30) REVERT: H 288 GLU cc_start: 0.8983 (tt0) cc_final: 0.8627 (mt-10) REVERT: H 328 GLN cc_start: 0.8552 (tp40) cc_final: 0.8270 (tp40) REVERT: H 449 GLU cc_start: 0.9086 (tp30) cc_final: 0.8772 (tp30) REVERT: J 713 SER cc_start: 0.8952 (t) cc_final: 0.8023 (p) REVERT: J 733 ARG cc_start: 0.9446 (ttm110) cc_final: 0.8654 (mtt90) REVERT: J 827 ASN cc_start: 0.8983 (m-40) cc_final: 0.8643 (OUTLIER) REVERT: J 845 ARG cc_start: 0.9598 (mtp-110) cc_final: 0.9336 (mtp-110) REVERT: I 711 PHE cc_start: 0.9188 (t80) cc_final: 0.8907 (t80) REVERT: I 713 SER cc_start: 0.8961 (t) cc_final: 0.7940 (p) REVERT: I 715 ARG cc_start: 0.8531 (tpm170) cc_final: 0.8322 (tpp-160) REVERT: I 733 ARG cc_start: 0.9201 (ttm170) cc_final: 0.8617 (mtt90) REVERT: I 736 ARG cc_start: 0.7862 (mtp-110) cc_final: 0.7613 (mtp-110) REVERT: I 763 PHE cc_start: 0.8757 (t80) cc_final: 0.8539 (t80) REVERT: I 793 PHE cc_start: 0.6834 (m-10) cc_final: 0.6022 (m-10) REVERT: I 826 TYR cc_start: 0.6964 (OUTLIER) cc_final: 0.5005 (m-80) REVERT: I 827 ASN cc_start: 0.9094 (m-40) cc_final: 0.8794 (p0) REVERT: I 845 ARG cc_start: 0.9556 (mtm-85) cc_final: 0.9255 (ptp-110) REVERT: K 711 PHE cc_start: 0.9162 (t80) cc_final: 0.8930 (t80) REVERT: K 713 SER cc_start: 0.8988 (t) cc_final: 0.7993 (p) REVERT: K 715 ARG cc_start: 0.8594 (tpm170) cc_final: 0.8181 (tpp-160) REVERT: K 716 ARG cc_start: 0.6965 (tpp-160) cc_final: 0.6648 (ttm110) REVERT: K 733 ARG cc_start: 0.9279 (ttm170) cc_final: 0.8902 (mtt90) REVERT: K 736 ARG cc_start: 0.7856 (mtp-110) cc_final: 0.7597 (mtp-110) REVERT: K 793 PHE cc_start: 0.6885 (m-80) cc_final: 0.6214 (m-10) REVERT: K 826 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.5175 (m-80) REVERT: K 827 ASN cc_start: 0.9072 (m-40) cc_final: 0.8786 (p0) REVERT: K 845 ARG cc_start: 0.9529 (OUTLIER) cc_final: 0.9309 (ptp90) REVERT: L 715 ARG cc_start: 0.8579 (tpm170) cc_final: 0.8108 (tpm170) REVERT: L 733 ARG cc_start: 0.9340 (ttm110) cc_final: 0.9125 (ttm170) REVERT: L 736 ARG cc_start: 0.7527 (mtp-110) cc_final: 0.6843 (ptt180) REVERT: L 827 ASN cc_start: 0.9022 (m-40) cc_final: 0.8724 (p0) REVERT: L 845 ARG cc_start: 0.9525 (mtp-110) cc_final: 0.9257 (ptp-110) REVERT: M 711 PHE cc_start: 0.9199 (t80) cc_final: 0.8960 (t80) REVERT: M 713 SER cc_start: 0.8971 (t) cc_final: 0.7930 (p) REVERT: M 715 ARG cc_start: 0.8562 (tpm170) cc_final: 0.8200 (tpp-160) REVERT: M 716 ARG cc_start: 0.7031 (tpp-160) cc_final: 0.6698 (tpp-160) REVERT: M 733 ARG cc_start: 0.9239 (ttm170) cc_final: 0.8909 (mtt90) REVERT: M 736 ARG cc_start: 0.7925 (mtp-110) cc_final: 0.7696 (mtp-110) REVERT: M 793 PHE cc_start: 0.6889 (m-10) cc_final: 0.6258 (m-10) REVERT: M 826 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.5219 (m-80) REVERT: M 827 ASN cc_start: 0.9065 (m-40) cc_final: 0.8772 (OUTLIER) REVERT: M 831 TRP cc_start: 0.7711 (t60) cc_final: 0.7169 (t60) REVERT: M 845 ARG cc_start: 0.9527 (OUTLIER) cc_final: 0.9297 (ptp90) REVERT: N 713 SER cc_start: 0.8892 (t) cc_final: 0.7943 (p) REVERT: N 715 ARG cc_start: 0.8386 (tpm170) cc_final: 0.8115 (tpp-160) REVERT: N 736 ARG cc_start: 0.7395 (mtp-110) cc_final: 0.7151 (mtp-110) REVERT: N 774 ARG cc_start: 0.7363 (ttt-90) cc_final: 0.7116 (ttt-90) REVERT: N 827 ASN cc_start: 0.8976 (m-40) cc_final: 0.8656 (p0) REVERT: N 845 ARG cc_start: 0.9547 (mtp-110) cc_final: 0.9241 (ptp-110) REVERT: O 711 PHE cc_start: 0.9111 (t80) cc_final: 0.8872 (t80) REVERT: O 713 SER cc_start: 0.8970 (t) cc_final: 0.8016 (p) REVERT: O 715 ARG cc_start: 0.8580 (tpm170) cc_final: 0.8202 (tpp-160) REVERT: O 716 ARG cc_start: 0.7159 (tpp-160) cc_final: 0.6893 (tpp-160) REVERT: O 733 ARG cc_start: 0.9270 (ttm170) cc_final: 0.8888 (mtt90) REVERT: O 736 ARG cc_start: 0.7857 (mtp-110) cc_final: 0.7601 (mtp-110) REVERT: O 793 PHE cc_start: 0.6972 (m-10) cc_final: 0.6500 (m-10) REVERT: O 826 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.5360 (m-80) REVERT: O 827 ASN cc_start: 0.9064 (m-40) cc_final: 0.8781 (p0) REVERT: O 845 ARG cc_start: 0.9550 (ptp90) cc_final: 0.9203 (ptp-110) REVERT: P 713 SER cc_start: 0.8853 (t) cc_final: 0.7938 (p) REVERT: P 774 ARG cc_start: 0.7439 (ttt-90) cc_final: 0.7204 (ttt-90) REVERT: P 827 ASN cc_start: 0.9055 (m-40) cc_final: 0.8819 (p0) outliers start: 85 outliers final: 48 residues processed: 650 average time/residue: 0.7478 time to fit residues: 584.8026 Evaluate side-chains 577 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 524 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 368 ILE Chi-restraints excluded: chain J residue 758 GLN Chi-restraints excluded: chain J residue 764 ILE Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain I residue 768 THR Chi-restraints excluded: chain I residue 794 GLU Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 826 TYR Chi-restraints excluded: chain K residue 845 ARG Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain L residue 785 VAL Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 794 GLU Chi-restraints excluded: chain M residue 826 TYR Chi-restraints excluded: chain M residue 845 ARG Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 826 TYR Chi-restraints excluded: chain P residue 846 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 142 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 chunk 210 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 345 optimal weight: 0.7980 chunk 332 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 476 optimal weight: 40.0000 chunk 426 optimal weight: 20.0000 chunk 492 optimal weight: 7.9990 chunk 429 optimal weight: 30.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 ASN ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 758 GLN K 777 ASN ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 731 GLN ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.138991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.075313 restraints weight = 79315.690| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.15 r_work: 0.2821 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41472 Z= 0.145 Angle : 0.688 12.116 56144 Z= 0.334 Chirality : 0.041 0.275 6416 Planarity : 0.004 0.040 7256 Dihedral : 5.892 74.485 6080 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.86 % Allowed : 19.42 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.12), residues: 5120 helix: 1.13 (0.09), residues: 3608 sheet: 0.57 (0.48), residues: 136 loop : 0.66 (0.18), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 249 TYR 0.011 0.001 TYR A 503 PHE 0.027 0.001 PHE K 738 TRP 0.018 0.001 TRP I 831 HIS 0.006 0.001 HIS I 786 Details of bonding type rmsd covalent geometry : bond 0.00339 (41472) covalent geometry : angle 0.68750 (56144) hydrogen bonds : bond 0.03953 ( 2448) hydrogen bonds : angle 4.45070 ( 6984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 611 time to evaluate : 1.790 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: symmetry clash 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: symmetry clash 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: A 127 ASP cc_start: 0.9391 (m-30) cc_final: 0.9005 (p0) REVERT: A 131 ARG cc_start: 0.9261 (mtm110) cc_final: 0.8902 (mtm110) REVERT: A 288 GLU cc_start: 0.9085 (tt0) cc_final: 0.8722 (mt-10) REVERT: A 328 GLN cc_start: 0.8559 (tp40) cc_final: 0.8278 (tp40) REVERT: A 361 LYS cc_start: 0.9095 (mttp) cc_final: 0.8819 (mptt) REVERT: B 127 ASP cc_start: 0.9476 (m-30) cc_final: 0.9124 (p0) REVERT: B 131 ARG cc_start: 0.9258 (mtm110) cc_final: 0.8960 (mtm110) REVERT: B 288 GLU cc_start: 0.8995 (tt0) cc_final: 0.8647 (mt-10) REVERT: B 303 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7823 (mm) REVERT: B 328 GLN cc_start: 0.8525 (tp40) cc_final: 0.8221 (tp40) REVERT: B 449 GLU cc_start: 0.9074 (tp30) cc_final: 0.8741 (tp30) REVERT: C 127 ASP cc_start: 0.9430 (m-30) cc_final: 0.9215 (p0) REVERT: C 131 ARG cc_start: 0.9266 (mtm110) cc_final: 0.8860 (mtm110) REVERT: C 174 GLU cc_start: 0.8735 (mp0) cc_final: 0.8465 (pm20) REVERT: C 328 GLN cc_start: 0.8573 (tp40) cc_final: 0.8288 (tp40) REVERT: D 110 ARG cc_start: 0.8988 (ttp80) cc_final: 0.8569 (ttp80) REVERT: D 127 ASP cc_start: 0.9492 (m-30) cc_final: 0.9113 (p0) REVERT: D 174 GLU cc_start: 0.8739 (mp0) cc_final: 0.8460 (pm20) REVERT: D 288 GLU cc_start: 0.8997 (tt0) cc_final: 0.8655 (mt-10) REVERT: D 328 GLN cc_start: 0.8538 (tp40) cc_final: 0.8238 (tp40) REVERT: D 352 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8708 (mp0) REVERT: D 403 ARG cc_start: 0.8578 (pmm-80) cc_final: 0.8361 (pmm-80) REVERT: D 449 GLU cc_start: 0.9085 (tp30) cc_final: 0.8752 (tp30) REVERT: E 127 ASP cc_start: 0.9419 (m-30) cc_final: 0.9090 (p0) REVERT: E 131 ARG cc_start: 0.9237 (mtm110) cc_final: 0.8973 (mtm110) REVERT: E 174 GLU cc_start: 0.8731 (mp0) cc_final: 0.8457 (pm20) REVERT: E 328 GLN cc_start: 0.8551 (tp40) cc_final: 0.8271 (tp40) REVERT: E 361 LYS cc_start: 0.9097 (mttp) cc_final: 0.8827 (mptt) REVERT: E 403 ARG cc_start: 0.8506 (pmm-80) cc_final: 0.8294 (pmm-80) REVERT: F 127 ASP cc_start: 0.9481 (m-30) cc_final: 0.9138 (p0) REVERT: F 131 ARG cc_start: 0.9254 (mtm110) cc_final: 0.8960 (mtm110) REVERT: F 174 GLU cc_start: 0.8762 (mp0) cc_final: 0.8423 (pm20) REVERT: F 288 GLU cc_start: 0.8976 (tt0) cc_final: 0.8629 (mt-10) REVERT: F 328 GLN cc_start: 0.8518 (tp40) cc_final: 0.8248 (tp40) REVERT: F 352 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8698 (mp0) REVERT: F 403 ARG cc_start: 0.8584 (pmm-80) cc_final: 0.8372 (pmm-80) REVERT: F 449 GLU cc_start: 0.9080 (tp30) cc_final: 0.8747 (tp30) REVERT: G 127 ASP cc_start: 0.9422 (m-30) cc_final: 0.9093 (p0) REVERT: G 131 ARG cc_start: 0.9239 (mtm110) cc_final: 0.8945 (mtm110) REVERT: G 159 ARG cc_start: 0.8912 (mmm160) cc_final: 0.8702 (tmt-80) REVERT: G 162 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8407 (ptt-90) REVERT: G 174 GLU cc_start: 0.8725 (mp0) cc_final: 0.8452 (pm20) REVERT: G 328 GLN cc_start: 0.8571 (tp40) cc_final: 0.8291 (tp40) REVERT: G 361 LYS cc_start: 0.9097 (mttp) cc_final: 0.8827 (mptt) REVERT: G 403 ARG cc_start: 0.8509 (pmm-80) cc_final: 0.8298 (pmm-80) REVERT: H 110 ARG cc_start: 0.8947 (ttp80) cc_final: 0.8622 (ttp80) REVERT: H 114 GLN cc_start: 0.9270 (tt0) cc_final: 0.9040 (tm-30) REVERT: H 127 ASP cc_start: 0.9488 (m-30) cc_final: 0.9108 (p0) REVERT: H 174 GLU cc_start: 0.8736 (mp0) cc_final: 0.8450 (pm20) REVERT: H 288 GLU cc_start: 0.8991 (tt0) cc_final: 0.8638 (mt-10) REVERT: H 328 GLN cc_start: 0.8540 (tp40) cc_final: 0.8226 (tp40) REVERT: H 352 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8707 (mp0) REVERT: H 403 ARG cc_start: 0.8582 (pmm-80) cc_final: 0.8371 (pmm-80) REVERT: H 449 GLU cc_start: 0.9082 (tp30) cc_final: 0.8750 (tp30) REVERT: J 733 ARG cc_start: 0.9425 (ttm110) cc_final: 0.8998 (mtt90) REVERT: J 736 ARG cc_start: 0.7581 (mtp-110) cc_final: 0.6877 (ptt180) REVERT: J 827 ASN cc_start: 0.8965 (m-40) cc_final: 0.8635 (OUTLIER) REVERT: J 845 ARG cc_start: 0.9595 (mtp-110) cc_final: 0.9271 (ptp-110) REVERT: I 711 PHE cc_start: 0.9147 (t80) cc_final: 0.8868 (t80) REVERT: I 713 SER cc_start: 0.8913 (t) cc_final: 0.7768 (p) REVERT: I 715 ARG cc_start: 0.8531 (tpm170) cc_final: 0.8167 (tpp-160) REVERT: I 716 ARG cc_start: 0.7047 (tpp-160) cc_final: 0.6708 (ttm110) REVERT: I 733 ARG cc_start: 0.9214 (ttm170) cc_final: 0.8655 (mtt90) REVERT: I 736 ARG cc_start: 0.7871 (mtp-110) cc_final: 0.7631 (mtp-110) REVERT: I 793 PHE cc_start: 0.6895 (m-10) cc_final: 0.6081 (m-10) REVERT: I 822 MET cc_start: 0.8468 (pmm) cc_final: 0.8250 (pmm) REVERT: I 826 TYR cc_start: 0.6892 (OUTLIER) cc_final: 0.4961 (m-80) REVERT: I 827 ASN cc_start: 0.9060 (m-40) cc_final: 0.8759 (p0) REVERT: I 845 ARG cc_start: 0.9566 (mtm-85) cc_final: 0.9251 (ptp-110) REVERT: K 711 PHE cc_start: 0.9163 (t80) cc_final: 0.8881 (t80) REVERT: K 713 SER cc_start: 0.8932 (t) cc_final: 0.7919 (p) REVERT: K 715 ARG cc_start: 0.8590 (tpm170) cc_final: 0.8137 (tpp-160) REVERT: K 716 ARG cc_start: 0.7276 (tpp-160) cc_final: 0.6997 (ttm110) REVERT: K 733 ARG cc_start: 0.9292 (ttm170) cc_final: 0.8921 (mtt90) REVERT: K 736 ARG cc_start: 0.7872 (mtp-110) cc_final: 0.7632 (mtp-110) REVERT: K 793 PHE cc_start: 0.6759 (m-80) cc_final: 0.6187 (m-10) REVERT: K 821 ARG cc_start: 0.7552 (ttm110) cc_final: 0.7351 (ptp-110) REVERT: K 826 TYR cc_start: 0.6861 (OUTLIER) cc_final: 0.5215 (m-80) REVERT: K 827 ASN cc_start: 0.9043 (m-40) cc_final: 0.8741 (p0) REVERT: L 713 SER cc_start: 0.8812 (t) cc_final: 0.8088 (p) REVERT: L 715 ARG cc_start: 0.8540 (tpm170) cc_final: 0.8278 (tpp-160) REVERT: L 827 ASN cc_start: 0.9005 (m-40) cc_final: 0.8701 (p0) REVERT: L 845 ARG cc_start: 0.9539 (mtp-110) cc_final: 0.9243 (ptp-110) REVERT: M 711 PHE cc_start: 0.9183 (t80) cc_final: 0.8941 (t80) REVERT: M 713 SER cc_start: 0.8929 (t) cc_final: 0.7887 (p) REVERT: M 715 ARG cc_start: 0.8557 (tpm170) cc_final: 0.8235 (tpp-160) REVERT: M 716 ARG cc_start: 0.7002 (tpp-160) cc_final: 0.6761 (tpp-160) REVERT: M 733 ARG cc_start: 0.9356 (ttm170) cc_final: 0.8934 (mtt90) REVERT: M 736 ARG cc_start: 0.7923 (mtp-110) cc_final: 0.7694 (mtp-110) REVERT: M 793 PHE cc_start: 0.6767 (m-10) cc_final: 0.6170 (m-10) REVERT: M 826 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.5263 (m-80) REVERT: M 827 ASN cc_start: 0.9015 (m-40) cc_final: 0.8713 (p0) REVERT: N 713 SER cc_start: 0.8733 (t) cc_final: 0.7885 (p) REVERT: N 715 ARG cc_start: 0.8339 (tpm170) cc_final: 0.8081 (tpp-160) REVERT: N 774 ARG cc_start: 0.7530 (ttt-90) cc_final: 0.7300 (ttt-90) REVERT: N 827 ASN cc_start: 0.8941 (m-40) cc_final: 0.8622 (p0) REVERT: N 845 ARG cc_start: 0.9540 (mtp-110) cc_final: 0.9218 (ptp-110) REVERT: O 711 PHE cc_start: 0.9116 (t80) cc_final: 0.8857 (t80) REVERT: O 713 SER cc_start: 0.8929 (t) cc_final: 0.7952 (p) REVERT: O 715 ARG cc_start: 0.8583 (tpm170) cc_final: 0.8273 (tpp-160) REVERT: O 733 ARG cc_start: 0.9291 (ttm170) cc_final: 0.8942 (mtt90) REVERT: O 736 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7628 (mtp-110) REVERT: O 793 PHE cc_start: 0.6920 (m-10) cc_final: 0.6473 (m-10) REVERT: O 826 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.5438 (m-80) REVERT: O 827 ASN cc_start: 0.9019 (m-40) cc_final: 0.8714 (p0) REVERT: O 845 ARG cc_start: 0.9541 (ptp90) cc_final: 0.9208 (ptp-110) REVERT: P 713 SER cc_start: 0.8815 (t) cc_final: 0.7954 (p) REVERT: P 715 ARG cc_start: 0.8396 (tpp-160) cc_final: 0.8097 (tpp-160) REVERT: P 774 ARG cc_start: 0.7649 (ttt-90) cc_final: 0.7449 (ttt-90) REVERT: P 827 ASN cc_start: 0.9053 (m-40) cc_final: 0.8793 (p0) outliers start: 80 outliers final: 48 residues processed: 674 average time/residue: 0.8286 time to fit residues: 669.0121 Evaluate side-chains 610 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 554 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 352 GLU Chi-restraints excluded: chain H residue 368 ILE Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain I residue 764 ILE Chi-restraints excluded: chain I residue 794 GLU Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 846 PHE Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 826 TYR Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain L residue 785 VAL Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 794 GLU Chi-restraints excluded: chain M residue 826 TYR Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain O residue 764 ILE Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 826 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 398 optimal weight: 30.0000 chunk 494 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 445 optimal weight: 6.9990 chunk 452 optimal weight: 9.9990 chunk 42 optimal weight: 0.0060 chunk 290 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 731 GLN I 777 ASN K 731 GLN ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 731 GLN ** P 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.139405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.075843 restraints weight = 79303.377| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.10 r_work: 0.2831 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 41472 Z= 0.139 Angle : 0.691 12.870 56144 Z= 0.330 Chirality : 0.040 0.281 6416 Planarity : 0.004 0.041 7256 Dihedral : 5.815 74.965 6080 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.60 % Allowed : 20.12 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.12), residues: 5120 helix: 1.27 (0.09), residues: 3552 sheet: 0.35 (0.47), residues: 136 loop : 0.64 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 845 TYR 0.011 0.001 TYR C 213 PHE 0.029 0.001 PHE J 738 TRP 0.026 0.001 TRP B 214 HIS 0.006 0.001 HIS I 786 Details of bonding type rmsd covalent geometry : bond 0.00327 (41472) covalent geometry : angle 0.69129 (56144) hydrogen bonds : bond 0.03888 ( 2448) hydrogen bonds : angle 4.43809 ( 6984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 595 time to evaluate : 1.683 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: symmetry clash 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: symmetry clash 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: A 127 ASP cc_start: 0.9391 (m-30) cc_final: 0.9020 (p0) REVERT: A 162 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8381 (ptt-90) REVERT: A 288 GLU cc_start: 0.9060 (tt0) cc_final: 0.8696 (mt-10) REVERT: A 328 GLN cc_start: 0.8538 (tp40) cc_final: 0.8274 (tp40) REVERT: A 361 LYS cc_start: 0.9101 (mttp) cc_final: 0.8820 (mptt) REVERT: B 127 ASP cc_start: 0.9443 (m-30) cc_final: 0.9200 (p0) REVERT: B 131 ARG cc_start: 0.9259 (mtm110) cc_final: 0.8763 (mtm110) REVERT: B 174 GLU cc_start: 0.8728 (mp0) cc_final: 0.8449 (pm20) REVERT: B 280 ASN cc_start: 0.8535 (t0) cc_final: 0.8093 (t0) REVERT: B 285 ARG cc_start: 0.9070 (tpp80) cc_final: 0.8846 (tpp-160) REVERT: B 288 GLU cc_start: 0.8961 (tt0) cc_final: 0.8641 (mt-10) REVERT: B 303 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7808 (mm) REVERT: B 328 GLN cc_start: 0.8497 (tp40) cc_final: 0.8217 (tp40) REVERT: B 352 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8634 (mp0) REVERT: B 403 ARG cc_start: 0.8593 (pmm-80) cc_final: 0.8334 (pmm-80) REVERT: B 449 GLU cc_start: 0.9091 (tp30) cc_final: 0.8748 (tp30) REVERT: C 127 ASP cc_start: 0.9393 (m-30) cc_final: 0.9042 (p0) REVERT: C 131 ARG cc_start: 0.9235 (mtm110) cc_final: 0.8980 (mtm110) REVERT: C 162 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8377 (ptt-90) REVERT: C 174 GLU cc_start: 0.8714 (mp0) cc_final: 0.8444 (pm20) REVERT: C 280 ASN cc_start: 0.8594 (t0) cc_final: 0.8264 (t0) REVERT: C 328 GLN cc_start: 0.8531 (tp40) cc_final: 0.8283 (tp40) REVERT: C 403 ARG cc_start: 0.8515 (pmm-80) cc_final: 0.8269 (pmm-80) REVERT: D 110 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8553 (ttp80) REVERT: D 127 ASP cc_start: 0.9452 (m-30) cc_final: 0.9112 (p0) REVERT: D 280 ASN cc_start: 0.8528 (t0) cc_final: 0.8084 (t0) REVERT: D 285 ARG cc_start: 0.9039 (tpp80) cc_final: 0.8824 (tpp-160) REVERT: D 288 GLU cc_start: 0.8954 (tt0) cc_final: 0.8596 (mt-10) REVERT: D 328 GLN cc_start: 0.8506 (tp40) cc_final: 0.8220 (tp40) REVERT: D 403 ARG cc_start: 0.8586 (pmm-80) cc_final: 0.8338 (pmm-80) REVERT: D 449 GLU cc_start: 0.9082 (tp30) cc_final: 0.8735 (tp30) REVERT: E 127 ASP cc_start: 0.9412 (m-30) cc_final: 0.9070 (p0) REVERT: E 131 ARG cc_start: 0.9213 (mtm110) cc_final: 0.8985 (mtm110) REVERT: E 162 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8391 (ptt-90) REVERT: E 174 GLU cc_start: 0.8711 (mp0) cc_final: 0.8437 (pm20) REVERT: E 280 ASN cc_start: 0.8592 (t0) cc_final: 0.8262 (t0) REVERT: E 328 GLN cc_start: 0.8529 (tp40) cc_final: 0.8260 (tp40) REVERT: E 403 ARG cc_start: 0.8506 (pmm-80) cc_final: 0.8261 (pmm-80) REVERT: F 127 ASP cc_start: 0.9440 (m-30) cc_final: 0.9172 (p0) REVERT: F 131 ARG cc_start: 0.9253 (mtm110) cc_final: 0.8752 (mtm110) REVERT: F 174 GLU cc_start: 0.8732 (mp0) cc_final: 0.8449 (pm20) REVERT: F 260 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8327 (p) REVERT: F 280 ASN cc_start: 0.8537 (t0) cc_final: 0.8096 (t0) REVERT: F 285 ARG cc_start: 0.9070 (tpp80) cc_final: 0.8847 (tpp-160) REVERT: F 288 GLU cc_start: 0.8959 (tt0) cc_final: 0.8635 (mt-10) REVERT: F 328 GLN cc_start: 0.8527 (tp40) cc_final: 0.8244 (tp40) REVERT: F 403 ARG cc_start: 0.8607 (pmm-80) cc_final: 0.8351 (pmm-80) REVERT: F 449 GLU cc_start: 0.9085 (tp30) cc_final: 0.8740 (tp30) REVERT: G 127 ASP cc_start: 0.9417 (m-30) cc_final: 0.9058 (p0) REVERT: G 131 ARG cc_start: 0.9210 (mtm110) cc_final: 0.8972 (mtm110) REVERT: G 174 GLU cc_start: 0.8715 (mp0) cc_final: 0.8439 (pm20) REVERT: G 280 ASN cc_start: 0.8592 (t0) cc_final: 0.8263 (t0) REVERT: G 328 GLN cc_start: 0.8548 (tp40) cc_final: 0.8280 (tp40) REVERT: G 403 ARG cc_start: 0.8516 (pmm-80) cc_final: 0.8271 (pmm-80) REVERT: H 110 ARG cc_start: 0.8950 (ttp80) cc_final: 0.8527 (ttp80) REVERT: H 127 ASP cc_start: 0.9444 (m-30) cc_final: 0.9101 (p0) REVERT: H 174 GLU cc_start: 0.8730 (mp0) cc_final: 0.8458 (pm20) REVERT: H 260 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8365 (p) REVERT: H 280 ASN cc_start: 0.8535 (t0) cc_final: 0.8094 (t0) REVERT: H 285 ARG cc_start: 0.9067 (tpp80) cc_final: 0.8846 (tpp-160) REVERT: H 288 GLU cc_start: 0.8956 (tt0) cc_final: 0.8631 (mt-10) REVERT: H 328 GLN cc_start: 0.8497 (tp40) cc_final: 0.8225 (tp40) REVERT: H 449 GLU cc_start: 0.9094 (tp30) cc_final: 0.8746 (tp30) REVERT: J 713 SER cc_start: 0.8839 (t) cc_final: 0.8064 (p) REVERT: J 733 ARG cc_start: 0.9516 (ttm110) cc_final: 0.9090 (mtt90) REVERT: J 736 ARG cc_start: 0.7642 (mtp-110) cc_final: 0.6924 (ptt180) REVERT: J 827 ASN cc_start: 0.8875 (m-40) cc_final: 0.8544 (OUTLIER) REVERT: J 845 ARG cc_start: 0.9609 (mtp-110) cc_final: 0.9212 (mtm110) REVERT: I 715 ARG cc_start: 0.8556 (tpm170) cc_final: 0.8188 (tpp-160) REVERT: I 716 ARG cc_start: 0.7103 (tpp-160) cc_final: 0.6766 (ttm110) REVERT: I 733 ARG cc_start: 0.9237 (ttm170) cc_final: 0.8746 (mtt90) REVERT: I 736 ARG cc_start: 0.7895 (mtp-110) cc_final: 0.7657 (mtp-110) REVERT: I 793 PHE cc_start: 0.6940 (m-10) cc_final: 0.6116 (m-10) REVERT: I 826 TYR cc_start: 0.6809 (OUTLIER) cc_final: 0.4854 (m-80) REVERT: I 827 ASN cc_start: 0.9066 (m-40) cc_final: 0.8770 (p0) REVERT: I 845 ARG cc_start: 0.9576 (mtm-85) cc_final: 0.9256 (ptp-110) REVERT: K 711 PHE cc_start: 0.9169 (t80) cc_final: 0.8876 (t80) REVERT: K 713 SER cc_start: 0.8922 (t) cc_final: 0.7837 (p) REVERT: K 715 ARG cc_start: 0.8594 (tpm170) cc_final: 0.8135 (tpp-160) REVERT: K 716 ARG cc_start: 0.7266 (tpp-160) cc_final: 0.6960 (ttm110) REVERT: K 733 ARG cc_start: 0.9302 (ttm170) cc_final: 0.8716 (mtt90) REVERT: K 736 ARG cc_start: 0.7903 (mtp-110) cc_final: 0.7668 (mtp-110) REVERT: K 793 PHE cc_start: 0.6651 (m-80) cc_final: 0.6108 (m-10) REVERT: K 826 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.5263 (m-80) REVERT: K 827 ASN cc_start: 0.9039 (m-40) cc_final: 0.8741 (p0) REVERT: K 845 ARG cc_start: 0.9486 (ptp-110) cc_final: 0.9105 (ptp-110) REVERT: L 713 SER cc_start: 0.8823 (t) cc_final: 0.7982 (p) REVERT: L 733 ARG cc_start: 0.9293 (ttm170) cc_final: 0.8996 (mmt90) REVERT: L 736 ARG cc_start: 0.7672 (mtp-110) cc_final: 0.6954 (ptt180) REVERT: L 827 ASN cc_start: 0.8998 (m-40) cc_final: 0.8761 (p0) REVERT: L 845 ARG cc_start: 0.9541 (mtp-110) cc_final: 0.9220 (ptp-110) REVERT: M 711 PHE cc_start: 0.9202 (t80) cc_final: 0.8915 (t80) REVERT: M 713 SER cc_start: 0.8906 (t) cc_final: 0.7866 (p) REVERT: M 715 ARG cc_start: 0.8528 (tpm170) cc_final: 0.8235 (tpp-160) REVERT: M 716 ARG cc_start: 0.6989 (tpp-160) cc_final: 0.6785 (tpp-160) REVERT: M 733 ARG cc_start: 0.9347 (ttm170) cc_final: 0.8998 (mtt90) REVERT: M 736 ARG cc_start: 0.7948 (mtp-110) cc_final: 0.7613 (mtp-110) REVERT: M 786 HIS cc_start: 0.8897 (t-170) cc_final: 0.8686 (t-170) REVERT: M 793 PHE cc_start: 0.6748 (m-10) cc_final: 0.6175 (m-10) REVERT: M 826 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.5261 (m-80) REVERT: M 827 ASN cc_start: 0.8977 (m-40) cc_final: 0.8657 (p0) REVERT: N 713 SER cc_start: 0.8767 (t) cc_final: 0.7915 (p) REVERT: N 715 ARG cc_start: 0.8358 (tpm170) cc_final: 0.8041 (tpp-160) REVERT: N 736 ARG cc_start: 0.7595 (mtp-110) cc_final: 0.6963 (ptt180) REVERT: N 774 ARG cc_start: 0.7666 (ttt-90) cc_final: 0.7451 (ttt-90) REVERT: N 827 ASN cc_start: 0.8853 (m-40) cc_final: 0.8536 (p0) REVERT: N 845 ARG cc_start: 0.9568 (mtp-110) cc_final: 0.9236 (ptp-110) REVERT: O 715 ARG cc_start: 0.8617 (tpm170) cc_final: 0.8310 (tpp-160) REVERT: O 733 ARG cc_start: 0.9324 (ttm170) cc_final: 0.8998 (mtt90) REVERT: O 736 ARG cc_start: 0.7914 (mtp-110) cc_final: 0.7678 (mtp-110) REVERT: O 793 PHE cc_start: 0.6901 (m-10) cc_final: 0.6508 (m-10) REVERT: O 826 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.5546 (m-80) REVERT: O 827 ASN cc_start: 0.9019 (m-40) cc_final: 0.8707 (p0) REVERT: O 845 ARG cc_start: 0.9540 (ptp90) cc_final: 0.9293 (ptp-110) REVERT: P 713 SER cc_start: 0.8802 (t) cc_final: 0.7962 (p) REVERT: P 715 ARG cc_start: 0.8181 (tpp-160) cc_final: 0.7971 (tpp-160) REVERT: P 774 ARG cc_start: 0.7702 (ttt-90) cc_final: 0.7489 (ttt-90) REVERT: P 827 ASN cc_start: 0.8998 (m-40) cc_final: 0.8759 (p0) outliers start: 69 outliers final: 37 residues processed: 652 average time/residue: 0.7938 time to fit residues: 620.0048 Evaluate side-chains 598 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 551 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 368 ILE Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain I residue 794 GLU Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain K residue 764 ILE Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 826 TYR Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain L residue 785 VAL Chi-restraints excluded: chain M residue 764 ILE Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 794 GLU Chi-restraints excluded: chain M residue 826 TYR Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 826 TYR Chi-restraints excluded: chain P residue 846 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 192 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 432 optimal weight: 30.0000 chunk 481 optimal weight: 6.9990 chunk 306 optimal weight: 6.9990 chunk 490 optimal weight: 20.0000 chunk 222 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 440 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 74 GLN H 74 GLN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.138616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.074788 restraints weight = 79961.034| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.12 r_work: 0.2812 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 41472 Z= 0.168 Angle : 0.732 15.385 56144 Z= 0.349 Chirality : 0.042 0.284 6416 Planarity : 0.004 0.042 7256 Dihedral : 5.789 75.045 6080 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.32 % Allowed : 20.82 % Favored : 77.86 % 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: 1.52 (0.12), residues: 5120 helix: 1.30 (0.09), residues: 3552 sheet: 0.23 (0.45), residues: 136 loop : 0.59 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG P 845 TYR 0.024 0.001 TYR B 213 PHE 0.030 0.001 PHE L 711 TRP 0.030 0.002 TRP C 214 HIS 0.008 0.001 HIS O 786 Details of bonding type rmsd covalent geometry : bond 0.00402 (41472) covalent geometry : angle 0.73150 (56144) hydrogen bonds : bond 0.03985 ( 2448) hydrogen bonds : angle 4.48132 ( 6984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 562 time to evaluate : 1.562 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.9374 (m-30) cc_final: 0.9102 (p0) REVERT: A 131 ARG cc_start: 0.9194 (mtm110) cc_final: 0.8640 (mtm110) REVERT: A 162 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8406 (ptt-90) REVERT: A 288 GLU cc_start: 0.9066 (tt0) cc_final: 0.8730 (mt-10) REVERT: A 328 GLN cc_start: 0.8580 (tp40) cc_final: 0.8339 (tp40) REVERT: A 403 ARG cc_start: 0.8558 (pmm-80) cc_final: 0.8280 (pmm-80) REVERT: B 127 ASP cc_start: 0.9397 (m-30) cc_final: 0.9080 (p0) REVERT: B 131 ARG cc_start: 0.9239 (mtm110) cc_final: 0.8965 (mtm110) REVERT: B 174 GLU cc_start: 0.8726 (mp0) cc_final: 0.8470 (pm20) REVERT: B 280 ASN cc_start: 0.8587 (t0) cc_final: 0.8131 (t0) REVERT: B 285 ARG cc_start: 0.9030 (tpp80) cc_final: 0.8808 (tpp-160) REVERT: B 288 GLU cc_start: 0.8967 (tt0) cc_final: 0.8642 (mt-10) REVERT: B 303 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7856 (mm) REVERT: B 328 GLN cc_start: 0.8540 (tp40) cc_final: 0.8260 (tp40) REVERT: B 352 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8730 (mp0) REVERT: B 403 ARG cc_start: 0.8591 (pmm-80) cc_final: 0.8353 (pmm-80) REVERT: B 449 GLU cc_start: 0.9098 (tp30) cc_final: 0.8748 (tp30) REVERT: C 127 ASP cc_start: 0.9398 (m-30) cc_final: 0.9063 (p0) REVERT: C 131 ARG cc_start: 0.9230 (mtm110) cc_final: 0.9012 (ttm110) REVERT: C 162 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8407 (ptt-90) REVERT: C 328 GLN cc_start: 0.8564 (tp40) cc_final: 0.8314 (tp40) REVERT: C 403 ARG cc_start: 0.8534 (pmm-80) cc_final: 0.8301 (pmm-80) REVERT: D 127 ASP cc_start: 0.9416 (m-30) cc_final: 0.9022 (p0) REVERT: D 131 ARG cc_start: 0.9235 (mtm110) cc_final: 0.8907 (mtm110) REVERT: D 174 GLU cc_start: 0.8740 (mp0) cc_final: 0.8501 (pm20) REVERT: D 280 ASN cc_start: 0.8586 (t0) cc_final: 0.8130 (t0) REVERT: D 285 ARG cc_start: 0.9039 (tpp80) cc_final: 0.8813 (tpp-160) REVERT: D 328 GLN cc_start: 0.8542 (tp40) cc_final: 0.8258 (tp40) REVERT: D 403 ARG cc_start: 0.8587 (pmm-80) cc_final: 0.8352 (pmm-80) REVERT: D 449 GLU cc_start: 0.9102 (tp30) cc_final: 0.8761 (tp30) REVERT: E 127 ASP cc_start: 0.9397 (m-30) cc_final: 0.9066 (p0) REVERT: E 162 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8398 (ptt-90) REVERT: E 328 GLN cc_start: 0.8558 (tp40) cc_final: 0.8284 (tp40) REVERT: E 403 ARG cc_start: 0.8522 (pmm-80) cc_final: 0.8290 (pmm-80) REVERT: F 127 ASP cc_start: 0.9415 (m-30) cc_final: 0.9095 (p0) REVERT: F 131 ARG cc_start: 0.9240 (mtm110) cc_final: 0.8966 (mtm110) REVERT: F 174 GLU cc_start: 0.8732 (mp0) cc_final: 0.8487 (pm20) REVERT: F 260 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8259 (p) REVERT: F 280 ASN cc_start: 0.8586 (t0) cc_final: 0.8130 (t0) REVERT: F 285 ARG cc_start: 0.9064 (tpp80) cc_final: 0.8841 (tpp-160) REVERT: F 288 GLU cc_start: 0.8973 (tt0) cc_final: 0.8649 (mt-10) REVERT: F 328 GLN cc_start: 0.8539 (tp40) cc_final: 0.8269 (tp40) REVERT: F 403 ARG cc_start: 0.8596 (pmm-80) cc_final: 0.8358 (pmm-80) REVERT: F 449 GLU cc_start: 0.9091 (tp30) cc_final: 0.8749 (tp30) REVERT: G 127 ASP cc_start: 0.9396 (m-30) cc_final: 0.9075 (p0) REVERT: G 328 GLN cc_start: 0.8562 (tp40) cc_final: 0.8287 (tp40) REVERT: G 403 ARG cc_start: 0.8523 (pmm-80) cc_final: 0.8291 (pmm-80) REVERT: H 110 ARG cc_start: 0.8948 (ttp80) cc_final: 0.8517 (ttp80) REVERT: H 127 ASP cc_start: 0.9412 (m-30) cc_final: 0.9023 (p0) REVERT: H 131 ARG cc_start: 0.9234 (mtm110) cc_final: 0.8906 (mtm110) REVERT: H 174 GLU cc_start: 0.8725 (mp0) cc_final: 0.8485 (pm20) REVERT: H 260 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8426 (p) REVERT: H 280 ASN cc_start: 0.8580 (t0) cc_final: 0.8123 (t0) REVERT: H 285 ARG cc_start: 0.9062 (tpp80) cc_final: 0.8840 (tpp-160) REVERT: H 288 GLU cc_start: 0.8966 (tt0) cc_final: 0.8640 (mt-10) REVERT: H 328 GLN cc_start: 0.8525 (tp40) cc_final: 0.8244 (tp40) REVERT: H 449 GLU cc_start: 0.9098 (tp30) cc_final: 0.8756 (tp30) REVERT: J 713 SER cc_start: 0.8836 (t) cc_final: 0.8059 (p) REVERT: J 733 ARG cc_start: 0.9552 (ttm110) cc_final: 0.9119 (mtt90) REVERT: J 736 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.6919 (ptt180) REVERT: J 827 ASN cc_start: 0.8862 (m-40) cc_final: 0.8533 (p0) REVERT: J 845 ARG cc_start: 0.9605 (mtp-110) cc_final: 0.9204 (mtm110) REVERT: I 713 SER cc_start: 0.8795 (t) cc_final: 0.7867 (p) REVERT: I 715 ARG cc_start: 0.8593 (tpm170) cc_final: 0.8182 (tpp-160) REVERT: I 716 ARG cc_start: 0.7201 (tpp-160) cc_final: 0.6806 (ttm110) REVERT: I 733 ARG cc_start: 0.9291 (ttm170) cc_final: 0.8754 (mtt90) REVERT: I 736 ARG cc_start: 0.7926 (mtp-110) cc_final: 0.7687 (mtp-110) REVERT: I 793 PHE cc_start: 0.6924 (m-10) cc_final: 0.6152 (m-10) REVERT: I 826 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.4866 (m-80) REVERT: I 827 ASN cc_start: 0.9059 (m-40) cc_final: 0.8779 (p0) REVERT: I 845 ARG cc_start: 0.9575 (mtm-85) cc_final: 0.9252 (ptp-110) REVERT: K 715 ARG cc_start: 0.8620 (tpm170) cc_final: 0.8178 (tpp-160) REVERT: K 716 ARG cc_start: 0.7260 (tpp-160) cc_final: 0.6948 (ttm110) REVERT: K 733 ARG cc_start: 0.9355 (ttm170) cc_final: 0.8918 (mtt90) REVERT: K 736 ARG cc_start: 0.7897 (mtp-110) cc_final: 0.7658 (mtp-110) REVERT: K 793 PHE cc_start: 0.6696 (m-80) cc_final: 0.6203 (m-10) REVERT: K 826 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.5385 (m-80) REVERT: K 827 ASN cc_start: 0.8984 (m-40) cc_final: 0.8640 (OUTLIER) REVERT: K 845 ARG cc_start: 0.9458 (ptp-110) cc_final: 0.9036 (ptp-110) REVERT: L 713 SER cc_start: 0.8852 (t) cc_final: 0.8136 (p) REVERT: L 733 ARG cc_start: 0.9231 (ttm170) cc_final: 0.8739 (mtt90) REVERT: L 827 ASN cc_start: 0.8957 (m-40) cc_final: 0.8680 (p0) REVERT: L 845 ARG cc_start: 0.9543 (mtp-110) cc_final: 0.9222 (ptp-110) REVERT: M 711 PHE cc_start: 0.9237 (t80) cc_final: 0.8970 (t80) REVERT: M 713 SER cc_start: 0.8988 (t) cc_final: 0.8006 (p) REVERT: M 715 ARG cc_start: 0.8571 (tpm170) cc_final: 0.8287 (tpp-160) REVERT: M 733 ARG cc_start: 0.9344 (ttm170) cc_final: 0.8779 (mtt90) REVERT: M 736 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7698 (mtp-110) REVERT: M 786 HIS cc_start: 0.8898 (t-170) cc_final: 0.8655 (t-170) REVERT: M 793 PHE cc_start: 0.6808 (m-10) cc_final: 0.6312 (m-10) REVERT: M 826 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.5299 (m-80) REVERT: M 827 ASN cc_start: 0.8967 (m-40) cc_final: 0.8624 (p0) REVERT: N 713 SER cc_start: 0.8815 (t) cc_final: 0.8093 (p) REVERT: N 715 ARG cc_start: 0.8418 (tpm170) cc_final: 0.8107 (tpp-160) REVERT: N 738 PHE cc_start: 0.8857 (t80) cc_final: 0.8609 (t80) REVERT: N 827 ASN cc_start: 0.8813 (m-40) cc_final: 0.8484 (p0) REVERT: N 840 MET cc_start: 0.8809 (tpp) cc_final: 0.8529 (tpt) REVERT: N 845 ARG cc_start: 0.9579 (mtp-110) cc_final: 0.9236 (ptp-110) REVERT: O 713 SER cc_start: 0.8887 (t) cc_final: 0.8020 (p) REVERT: O 715 ARG cc_start: 0.8661 (tpm170) cc_final: 0.8289 (tpp-160) REVERT: O 716 ARG cc_start: 0.6830 (tpp-160) cc_final: 0.6545 (tpp-160) REVERT: O 733 ARG cc_start: 0.9396 (ttm170) cc_final: 0.8797 (mtt90) REVERT: O 736 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7693 (mtp-110) REVERT: O 793 PHE cc_start: 0.6948 (m-10) cc_final: 0.6520 (m-10) REVERT: O 826 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.5536 (m-80) REVERT: O 827 ASN cc_start: 0.8979 (m-40) cc_final: 0.8661 (p0) REVERT: O 845 ARG cc_start: 0.9519 (ptp90) cc_final: 0.9251 (ptp-110) REVERT: P 713 SER cc_start: 0.8856 (t) cc_final: 0.8042 (p) REVERT: P 716 ARG cc_start: 0.7217 (tpp-160) cc_final: 0.6839 (mmm160) REVERT: P 774 ARG cc_start: 0.7782 (ttt-90) cc_final: 0.7579 (ttt-90) REVERT: P 827 ASN cc_start: 0.8969 (m-40) cc_final: 0.8725 (p0) outliers start: 57 outliers final: 34 residues processed: 608 average time/residue: 0.7810 time to fit residues: 568.0394 Evaluate side-chains 584 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 540 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 368 ILE Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain I residue 794 GLU Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 826 TYR Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 794 GLU Chi-restraints excluded: chain M residue 826 TYR Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 826 TYR Chi-restraints excluded: chain P residue 846 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 195 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 210 optimal weight: 7.9990 chunk 218 optimal weight: 0.8980 chunk 446 optimal weight: 20.0000 chunk 288 optimal weight: 0.8980 chunk 387 optimal weight: 1.9990 chunk 321 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 356 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.140340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.076965 restraints weight = 79272.841| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.15 r_work: 0.2810 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 41472 Z= 0.135 Angle : 0.750 16.472 56144 Z= 0.354 Chirality : 0.042 0.293 6416 Planarity : 0.004 0.042 7256 Dihedral : 5.746 75.627 6080 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.07 % Allowed : 21.14 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.12), residues: 5120 helix: 1.29 (0.09), residues: 3552 sheet: 0.04 (0.44), residues: 136 loop : 0.59 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 131 TYR 0.016 0.001 TYR C 213 PHE 0.030 0.001 PHE I 711 TRP 0.028 0.001 TRP C 214 HIS 0.008 0.001 HIS O 786 Details of bonding type rmsd covalent geometry : bond 0.00316 (41472) covalent geometry : angle 0.74997 (56144) hydrogen bonds : bond 0.03748 ( 2448) hydrogen bonds : angle 4.44972 ( 6984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10240 Ramachandran restraints generated. 5120 Oldfield, 0 Emsley, 5120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 572 time to evaluate : 1.308 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.9376 (m-30) cc_final: 0.9016 (p0) REVERT: A 162 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8341 (ptt-90) REVERT: A 280 ASN cc_start: 0.8472 (t0) cc_final: 0.8163 (t0) REVERT: A 288 GLU cc_start: 0.9028 (tt0) cc_final: 0.8677 (mt-10) REVERT: A 328 GLN cc_start: 0.8508 (tp40) cc_final: 0.8267 (tp40) REVERT: A 363 LYS cc_start: 0.9311 (tppp) cc_final: 0.9024 (mppt) REVERT: B 127 ASP cc_start: 0.9422 (m-30) cc_final: 0.9081 (p0) REVERT: B 131 ARG cc_start: 0.9223 (mtm110) cc_final: 0.8947 (mtm110) REVERT: B 280 ASN cc_start: 0.8436 (t0) cc_final: 0.8058 (t0) REVERT: B 285 ARG cc_start: 0.9054 (tpp80) cc_final: 0.8823 (tpp-160) REVERT: B 288 GLU cc_start: 0.8950 (tt0) cc_final: 0.8623 (mt-10) REVERT: B 303 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7674 (mm) REVERT: B 328 GLN cc_start: 0.8459 (tp40) cc_final: 0.8179 (tp40) REVERT: B 403 ARG cc_start: 0.8572 (pmm-80) cc_final: 0.8314 (pmm-80) REVERT: B 449 GLU cc_start: 0.9091 (tp30) cc_final: 0.8737 (tp30) REVERT: C 127 ASP cc_start: 0.9390 (m-30) cc_final: 0.9104 (p0) REVERT: C 131 ARG cc_start: 0.9227 (mtm110) cc_final: 0.8660 (mtm110) REVERT: C 162 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8342 (ptt-90) REVERT: C 174 GLU cc_start: 0.8656 (pm20) cc_final: 0.8338 (pm20) REVERT: C 280 ASN cc_start: 0.8459 (t0) cc_final: 0.8159 (t0) REVERT: C 328 GLN cc_start: 0.8451 (tp40) cc_final: 0.8216 (tp40) REVERT: C 361 LYS cc_start: 0.9068 (mttp) cc_final: 0.8809 (mptt) REVERT: C 403 ARG cc_start: 0.8577 (pmm-80) cc_final: 0.8334 (pmm-80) REVERT: D 127 ASP cc_start: 0.9415 (m-30) cc_final: 0.9013 (p0) REVERT: D 131 ARG cc_start: 0.9199 (mtm110) cc_final: 0.8839 (mtm110) REVERT: D 280 ASN cc_start: 0.8422 (t0) cc_final: 0.8044 (t0) REVERT: D 285 ARG cc_start: 0.9049 (tpp80) cc_final: 0.8806 (tpp-160) REVERT: D 328 GLN cc_start: 0.8447 (tp40) cc_final: 0.8167 (tp40) REVERT: D 403 ARG cc_start: 0.8571 (pmm-80) cc_final: 0.8321 (pmm-80) REVERT: D 449 GLU cc_start: 0.9087 (tp30) cc_final: 0.8738 (tp30) REVERT: D 545 MET cc_start: 0.7916 (ttm) cc_final: 0.7668 (ttm) REVERT: E 127 ASP cc_start: 0.9385 (m-30) cc_final: 0.9098 (p0) REVERT: E 131 ARG cc_start: 0.9222 (mtm110) cc_final: 0.8612 (mtm110) REVERT: E 162 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8346 (ptt-90) REVERT: E 174 GLU cc_start: 0.8651 (pm20) cc_final: 0.8343 (pm20) REVERT: E 280 ASN cc_start: 0.8457 (t0) cc_final: 0.8157 (t0) REVERT: E 328 GLN cc_start: 0.8482 (tp40) cc_final: 0.8243 (tp40) REVERT: E 403 ARG cc_start: 0.8572 (pmm-80) cc_final: 0.8332 (pmm-80) REVERT: F 127 ASP cc_start: 0.9427 (m-30) cc_final: 0.9098 (p0) REVERT: F 131 ARG cc_start: 0.9227 (mtm110) cc_final: 0.8949 (mtm110) REVERT: F 260 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8317 (p) REVERT: F 280 ASN cc_start: 0.8430 (t0) cc_final: 0.8053 (t0) REVERT: F 285 ARG cc_start: 0.9057 (tpp80) cc_final: 0.8825 (tpp-160) REVERT: F 288 GLU cc_start: 0.8944 (tt0) cc_final: 0.8616 (mt-10) REVERT: F 328 GLN cc_start: 0.8462 (tp40) cc_final: 0.8182 (tp40) REVERT: F 403 ARG cc_start: 0.8580 (pmm-80) cc_final: 0.8322 (pmm-80) REVERT: F 449 GLU cc_start: 0.9090 (tp30) cc_final: 0.8742 (tp30) REVERT: G 127 ASP cc_start: 0.9388 (m-30) cc_final: 0.9089 (p0) REVERT: G 131 ARG cc_start: 0.9221 (mtm110) cc_final: 0.8635 (mtm110) REVERT: G 174 GLU cc_start: 0.8602 (pm20) cc_final: 0.8319 (pm20) REVERT: G 280 ASN cc_start: 0.8463 (t0) cc_final: 0.8163 (t0) REVERT: G 328 GLN cc_start: 0.8456 (tp40) cc_final: 0.8221 (tp40) REVERT: G 403 ARG cc_start: 0.8567 (pmm-80) cc_final: 0.8331 (pmm-80) REVERT: H 110 ARG cc_start: 0.8950 (ttp80) cc_final: 0.8539 (ttp80) REVERT: H 127 ASP cc_start: 0.9412 (m-30) cc_final: 0.9011 (p0) REVERT: H 131 ARG cc_start: 0.9202 (mtm110) cc_final: 0.8843 (mtm110) REVERT: H 174 GLU cc_start: 0.8703 (mp0) cc_final: 0.8459 (pm20) REVERT: H 260 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8399 (p) REVERT: H 280 ASN cc_start: 0.8419 (t0) cc_final: 0.8038 (t0) REVERT: H 285 ARG cc_start: 0.9045 (tpp80) cc_final: 0.8814 (tpp-160) REVERT: H 288 GLU cc_start: 0.8939 (tt0) cc_final: 0.8611 (mt-10) REVERT: H 328 GLN cc_start: 0.8454 (tp40) cc_final: 0.8166 (tp40) REVERT: H 449 GLU cc_start: 0.9088 (tp30) cc_final: 0.8739 (tp30) REVERT: J 711 PHE cc_start: 0.8997 (t80) cc_final: 0.8796 (t80) REVERT: J 713 SER cc_start: 0.8829 (t) cc_final: 0.8042 (p) REVERT: J 733 ARG cc_start: 0.9509 (ttm110) cc_final: 0.9144 (mtt90) REVERT: J 774 ARG cc_start: 0.7715 (ttt180) cc_final: 0.7501 (ttt90) REVERT: J 827 ASN cc_start: 0.8854 (m-40) cc_final: 0.8513 (p0) REVERT: J 845 ARG cc_start: 0.9625 (mtp-110) cc_final: 0.9237 (mtm110) REVERT: I 713 SER cc_start: 0.8669 (t) cc_final: 0.7770 (p) REVERT: I 715 ARG cc_start: 0.8548 (tpm170) cc_final: 0.8135 (tpp-160) REVERT: I 716 ARG cc_start: 0.7092 (tpp-160) cc_final: 0.6746 (ttm110) REVERT: I 733 ARG cc_start: 0.9247 (ttm170) cc_final: 0.8769 (mtt90) REVERT: I 736 ARG cc_start: 0.7902 (mtp-110) cc_final: 0.7675 (mtp-110) REVERT: I 793 PHE cc_start: 0.6904 (m-10) cc_final: 0.6163 (m-10) REVERT: I 826 TYR cc_start: 0.6747 (OUTLIER) cc_final: 0.4836 (m-80) REVERT: I 827 ASN cc_start: 0.9035 (m-40) cc_final: 0.8713 (p0) REVERT: I 845 ARG cc_start: 0.9592 (mtm-85) cc_final: 0.9255 (ptp-110) REVERT: K 715 ARG cc_start: 0.8577 (tpm170) cc_final: 0.8124 (tpp-160) REVERT: K 716 ARG cc_start: 0.7107 (tpp-160) cc_final: 0.6849 (ttm110) REVERT: K 733 ARG cc_start: 0.9387 (ttm170) cc_final: 0.8962 (mtt90) REVERT: K 736 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.7583 (mtp-110) REVERT: K 793 PHE cc_start: 0.6698 (m-80) cc_final: 0.6189 (m-80) REVERT: K 826 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.5459 (m-80) REVERT: K 827 ASN cc_start: 0.8976 (m-40) cc_final: 0.8625 (p0) REVERT: L 711 PHE cc_start: 0.9063 (t80) cc_final: 0.8788 (t80) REVERT: L 713 SER cc_start: 0.8920 (t) cc_final: 0.7996 (p) REVERT: L 714 TYR cc_start: 0.6932 (p90) cc_final: 0.6634 (p90) REVERT: L 733 ARG cc_start: 0.9243 (ttm170) cc_final: 0.8923 (mtt90) REVERT: L 736 ARG cc_start: 0.7658 (mtp-110) cc_final: 0.6935 (ptt180) REVERT: L 827 ASN cc_start: 0.8978 (m-40) cc_final: 0.8701 (p0) REVERT: L 845 ARG cc_start: 0.9557 (mtp-110) cc_final: 0.9238 (ptp-110) REVERT: M 715 ARG cc_start: 0.8494 (tpm170) cc_final: 0.8247 (tpp-160) REVERT: M 733 ARG cc_start: 0.9340 (ttm170) cc_final: 0.9010 (mtt90) REVERT: M 736 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7643 (mtp-110) REVERT: M 786 HIS cc_start: 0.8917 (t-170) cc_final: 0.8691 (t-170) REVERT: M 793 PHE cc_start: 0.6773 (m-10) cc_final: 0.6281 (m-10) REVERT: M 826 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.5314 (m-80) REVERT: M 827 ASN cc_start: 0.8966 (m-40) cc_final: 0.8617 (p0) REVERT: N 711 PHE cc_start: 0.9001 (t80) cc_final: 0.8792 (t80) REVERT: N 713 SER cc_start: 0.8756 (t) cc_final: 0.7900 (p) REVERT: N 716 ARG cc_start: 0.7028 (tpp-160) cc_final: 0.6686 (mmm-85) REVERT: N 736 ARG cc_start: 0.7632 (mtp-110) cc_final: 0.6985 (ptt180) REVERT: N 774 ARG cc_start: 0.7625 (ttt-90) cc_final: 0.7304 (ttt90) REVERT: N 827 ASN cc_start: 0.8780 (m-40) cc_final: 0.8466 (p0) REVERT: N 840 MET cc_start: 0.8762 (tpp) cc_final: 0.8489 (tpt) REVERT: N 845 ARG cc_start: 0.9590 (mtp-110) cc_final: 0.9258 (ptp-110) REVERT: O 713 SER cc_start: 0.8760 (t) cc_final: 0.7856 (p) REVERT: O 715 ARG cc_start: 0.8607 (tpm170) cc_final: 0.8278 (tpp-160) REVERT: O 716 ARG cc_start: 0.6776 (tpp-160) cc_final: 0.6519 (tpp-160) REVERT: O 733 ARG cc_start: 0.9382 (ttm170) cc_final: 0.9030 (mtt90) REVERT: O 736 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.7569 (mtp-110) REVERT: O 793 PHE cc_start: 0.6943 (m-10) cc_final: 0.6375 (m-10) REVERT: O 826 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.5578 (m-80) REVERT: O 827 ASN cc_start: 0.8966 (m-40) cc_final: 0.8614 (p0) REVERT: O 845 ARG cc_start: 0.9527 (ptp90) cc_final: 0.9243 (ptp-110) REVERT: P 713 SER cc_start: 0.8761 (t) cc_final: 0.7955 (p) REVERT: P 738 PHE cc_start: 0.8922 (t80) cc_final: 0.8686 (t80) REVERT: P 774 ARG cc_start: 0.7791 (ttt-90) cc_final: 0.7565 (ttt-90) REVERT: P 827 ASN cc_start: 0.8917 (m-40) cc_final: 0.8666 (p0) outliers start: 46 outliers final: 34 residues processed: 613 average time/residue: 0.7772 time to fit residues: 573.2488 Evaluate side-chains 581 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 537 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 368 ILE Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 368 ILE Chi-restraints excluded: chain J residue 742 ASP Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain I residue 794 GLU Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 846 PHE Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 826 TYR Chi-restraints excluded: chain L residue 768 THR Chi-restraints excluded: chain M residue 768 THR Chi-restraints excluded: chain M residue 794 GLU Chi-restraints excluded: chain M residue 826 TYR Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain O residue 768 THR Chi-restraints excluded: chain O residue 826 TYR Chi-restraints excluded: chain O residue 846 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 191 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 491 optimal weight: 6.9990 chunk 376 optimal weight: 5.9990 chunk 402 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 300 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN C 383 ASN D 383 ASN E 383 ASN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN G 383 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 383 ASN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 758 GLN ** M 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.137803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.073785 restraints weight = 79621.577| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.11 r_work: 0.2782 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 41472 Z= 0.223 Angle : 0.779 16.659 56144 Z= 0.372 Chirality : 0.044 0.316 6416 Planarity : 0.004 0.046 7256 Dihedral : 5.757 75.553 6080 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.14 % Allowed : 21.56 % Favored : 77.30 % 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: 1.46 (0.12), residues: 5120 helix: 1.28 (0.09), residues: 3552 sheet: -0.08 (0.42), residues: 136 loop : 0.54 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 249 TYR 0.026 0.001 TYR H 213 PHE 0.027 0.001 PHE I 738 TRP 0.022 0.002 TRP E 214 HIS 0.008 0.001 HIS O 786 Details of bonding type rmsd covalent geometry : bond 0.00529 (41472) covalent geometry : angle 0.77898 (56144) hydrogen bonds : bond 0.04175 ( 2448) hydrogen bonds : angle 4.55617 ( 6984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22066.85 seconds wall clock time: 374 minutes 47.88 seconds (22487.88 seconds total)