Starting phenix.real_space_refine on Mon Jul 6 23:26:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8p2l_17369/07_2026/8p2l_17369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2l_17369/07_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_17369/07_2026/8p2l_17369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2l_17369/07_2026/8p2l_17369.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8p2l_17369/07_2026/8p2l_17369.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8p2l_17369/07_2026/8p2l_17369.cif" model { file = "/net/cci-nas-00/data/ceres_data/8p2l_17369/07_2026/8p2l_17369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2l_17369/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 8.05, per 1000 atoms: 0.20 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: 3.42 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: 1.18 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: 8.56 Time building geometry restraints manager: 4.26 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: 22595 16.14 - 32.28: 2001 32.28 - 48.42: 381 48.42 - 64.56: 111 64.56 - 80.71: 32 Dihedral angle restraints: 25120 sinusoidal: 10256 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 25117 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: 0.15 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: 2.020 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: 0.040 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.140 Process input model: 35.060 Find NCS groups from input model: 0.400 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:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 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 : 13.431 80.706 15488 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/Z covalent geometry : bond 0.00953 / 0.62 (41472) covalent geometry : angle 1.60252 / 1.05 (56144) hydrogen bonds : bond 0.17468 / 11.76 ( 2448) hydrogen bonds : angle 6.75288 / 4.90 ( 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 : 1.200 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: 0.7994 time to fit residues: 984.8778 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 : 1.645 ------------------------------------------------------------------------------- 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... 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 = 51)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.072000 restraints weight = 80905.917| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.09 r_work: 0.2739 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2924 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= 0.339 Angle : 0.858 11.537 56144 Z= 0.425 Chirality : 0.048 0.232 6416 Planarity : 0.005 0.033 7256 Dihedral : 5.451 26.602 5680 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.70 % Allowed : 11.92 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.26 (0.12), residues: 5120 helix: 0.15 (0.08), residues: 3648 sheet: 0.23 (0.42), residues: 136 loop : 0.74 (0.19), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 131 TYR 0.011 0.002 TYR H 429 PHE 0.015 0.002 PHE P 763 TRP 0.012 0.002 TRP H 420 HIS 0.007 0.002 HIS O 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00792 / 0.34 (41472) covalent geometry : angle 0.85798 / 0.42 (56144) hydrogen bonds : bond 0.05667 / 3.87 ( 2448) hydrogen bonds : angle 5.11955 / 3.72 ( 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 725 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 652 time to evaluate : 1.467 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: 0.9508 (OUTLIER) cc_final: 0.9148 (p0) REVERT: A 131 ARG cc_start: 0.9294 (mtm110) cc_final: 0.8967 (mtm110) REVERT: A 212 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8970 (mp) REVERT: B 110 ARG cc_start: 0.8826 (ttp80) cc_final: 0.8183 (ttp80) REVERT: B 127 ASP cc_start: 0.9512 (OUTLIER) cc_final: 0.9223 (p0) REVERT: B 449 GLU cc_start: 0.8995 (tp30) cc_final: 0.8746 (tp30) REVERT: C 127 ASP cc_start: 0.9511 (OUTLIER) cc_final: 0.8964 (p0) REVERT: C 131 ARG cc_start: 0.9329 (mtm110) cc_final: 0.8650 (ptp90) REVERT: C 212 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8971 (mp) REVERT: C 361 LYS cc_start: 0.9150 (mttp) cc_final: 0.8944 (mptt) REVERT: D 127 ASP cc_start: 0.9518 (OUTLIER) cc_final: 0.9020 (p0) REVERT: D 131 ARG cc_start: 0.9376 (mtm110) cc_final: 0.8743 (ptp-170) REVERT: D 449 GLU cc_start: 0.8992 (tp30) cc_final: 0.8744 (tp30) REVERT: E 127 ASP cc_start: 0.9503 (OUTLIER) cc_final: 0.9143 (p0) REVERT: E 131 ARG cc_start: 0.9296 (mtm110) cc_final: 0.8972 (mtm110) REVERT: E 212 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8971 (mp) REVERT: E 361 LYS cc_start: 0.9135 (mttp) cc_final: 0.8935 (mptt) REVERT: F 110 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8171 (ttp80) REVERT: F 127 ASP cc_start: 0.9508 (OUTLIER) cc_final: 0.9218 (p0) REVERT: F 449 GLU cc_start: 0.9002 (tp30) cc_final: 0.8756 (tp30) REVERT: G 127 ASP cc_start: 0.9513 (OUTLIER) cc_final: 0.9024 (p0) REVERT: G 131 ARG cc_start: 0.9321 (mtm110) cc_final: 0.8677 (ptp-170) REVERT: G 212 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8970 (mp) REVERT: G 361 LYS cc_start: 0.9137 (mttp) cc_final: 0.8936 (mptt) REVERT: H 110 ARG cc_start: 0.8825 (ttp80) cc_final: 0.8188 (ttp80) REVERT: H 127 ASP cc_start: 0.9518 (OUTLIER) cc_final: 0.9017 (p0) REVERT: H 131 ARG cc_start: 0.9365 (mtm110) cc_final: 0.8724 (ptp-170) REVERT: H 449 GLU cc_start: 0.8999 (tp30) cc_final: 0.8752 (tp30) REVERT: J 715 ARG cc_start: 0.8364 (tpm170) cc_final: 0.7866 (tpm170) REVERT: J 716 ARG cc_start: 0.7039 (tpp-160) cc_final: 0.6539 (tpp-160) REVERT: J 827 ASN cc_start: 0.9067 (m-40) cc_final: 0.8760 (OUTLIER) REVERT: I 706 ASP cc_start: 0.9523 (t0) cc_final: 0.9304 (m-30) REVERT: I 715 ARG cc_start: 0.8365 (tpm170) cc_final: 0.7844 (tpm170) REVERT: I 716 ARG cc_start: 0.6863 (tpp-160) cc_final: 0.6360 (tpp-160) REVERT: I 733 ARG cc_start: 0.8961 (ttm170) cc_final: 0.8437 (mtt90) REVERT: I 742 ASP cc_start: 0.8211 (t70) cc_final: 0.8003 (t0) REVERT: I 827 ASN cc_start: 0.9183 (m-40) cc_final: 0.8976 (OUTLIER) REVERT: I 831 TRP cc_start: 0.7556 (t60) cc_final: 0.7354 (t60) REVERT: I 836 GLN cc_start: 0.7295 (pm20) cc_final: 0.6884 (mp10) REVERT: I 845 ARG cc_start: 0.9525 (mtm-85) cc_final: 0.9210 (mtm-85) REVERT: K 706 ASP cc_start: 0.9526 (t0) cc_final: 0.9304 (m-30) REVERT: K 715 ARG cc_start: 0.8387 (tpm170) cc_final: 0.7884 (tpm170) REVERT: K 716 ARG cc_start: 0.6825 (tpp-160) cc_final: 0.6314 (tpp-160) REVERT: K 742 ASP cc_start: 0.8197 (t70) cc_final: 0.7968 (t0) REVERT: K 786 HIS cc_start: 0.8735 (t-170) cc_final: 0.8529 (t-170) REVERT: K 827 ASN cc_start: 0.9153 (m-40) cc_final: 0.8915 (p0) REVERT: K 836 GLN cc_start: 0.7249 (pm20) cc_final: 0.6969 (mp10) REVERT: L 715 ARG cc_start: 0.8346 (tpm170) cc_final: 0.7857 (tpm170) REVERT: L 716 ARG cc_start: 0.7035 (tpp-160) cc_final: 0.6514 (tpp-160) REVERT: L 827 ASN cc_start: 0.9010 (m-40) cc_final: 0.8741 (OUTLIER) REVERT: L 846 PHE cc_start: 0.8847 (m-10) cc_final: 0.8532 (m-80) REVERT: M 706 ASP cc_start: 0.9528 (t0) cc_final: 0.9304 (m-30) REVERT: M 715 ARG cc_start: 0.8388 (tpm170) cc_final: 0.7857 (tpm170) REVERT: M 716 ARG cc_start: 0.6826 (tpp-160) cc_final: 0.6323 (tpp-160) REVERT: M 742 ASP cc_start: 0.8194 (t70) cc_final: 0.7974 (t0) REVERT: M 827 ASN cc_start: 0.9166 (m-40) cc_final: 0.8948 (p0) REVERT: M 836 GLN cc_start: 0.7262 (pm20) cc_final: 0.6945 (mp10) REVERT: N 715 ARG cc_start: 0.8350 (tpm170) cc_final: 0.7876 (tpm170) REVERT: N 716 ARG cc_start: 0.7055 (tpp-160) cc_final: 0.6535 (tpp-160) REVERT: N 827 ASN cc_start: 0.9062 (m-40) cc_final: 0.8779 (OUTLIER) REVERT: N 846 PHE cc_start: 0.8832 (m-10) cc_final: 0.8508 (m-10) REVERT: O 706 ASP cc_start: 0.9539 (t0) cc_final: 0.9315 (m-30) REVERT: O 715 ARG cc_start: 0.8387 (tpm170) cc_final: 0.7880 (tpm170) REVERT: O 716 ARG cc_start: 0.6839 (tpp-160) cc_final: 0.6335 (tpp-160) REVERT: O 742 ASP cc_start: 0.8137 (t70) cc_final: 0.7918 (t0) REVERT: O 827 ASN cc_start: 0.9147 (m-40) cc_final: 0.8922 (p0) REVERT: O 836 GLN cc_start: 0.7247 (pm20) cc_final: 0.6947 (mp10) REVERT: P 715 ARG cc_start: 0.8325 (tpm170) cc_final: 0.7850 (tpm170) REVERT: P 716 ARG cc_start: 0.7031 (tpp-160) cc_final: 0.6509 (tpp-160) REVERT: P 827 ASN cc_start: 0.9000 (m-40) cc_final: 0.8742 (OUTLIER) REVERT: P 829 VAL cc_start: 0.7758 (t) cc_final: 0.7471 (t) outliers start: 73 outliers final: 30 residues processed: 708 average time/residue: 0.7453 time to fit residues: 637.8133 Evaluate side-chains 551 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 514 time to evaluate : 1.616 ------------------------------------------------------------------------------- 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 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 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 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 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: 9.9990 chunk 425 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 385 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 315 optimal weight: 0.9980 chunk 398 optimal weight: 20.0000 chunk 138 optimal weight: 0.9980 chunk 336 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 758 GLN ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 758 GLN ** N 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 721 GLN ** 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 = 0.4141 r_free = 0.4141 target = 0.139246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.075014 restraints weight = 80025.903| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.13 r_work: 0.2804 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 41472 Z= 0.161 Angle : 0.712 14.158 56144 Z= 0.346 Chirality : 0.041 0.223 6416 Planarity : 0.004 0.045 7256 Dihedral : 4.905 20.151 5680 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.79 % Allowed : 13.66 % Favored : 84.55 % 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: 0.92 (0.12), residues: 5120 helix: 0.71 (0.09), residues: 3648 sheet: 0.74 (0.47), residues: 136 loop : 0.70 (0.19), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 249 TYR 0.010 0.001 TYR A 503 PHE 0.025 0.002 PHE P 711 TRP 0.012 0.002 TRP A 214 HIS 0.007 0.001 HIS J 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (41472) covalent geometry : angle 0.71164 / 0.35 (56144) hydrogen bonds : bond 0.04537 / 3.10 ( 2448) hydrogen bonds : angle 4.69601 / 3.41 ( 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 685 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 608 time to evaluate : 1.697 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: 0.9476 (OUTLIER) cc_final: 0.9138 (p0) REVERT: A 131 ARG cc_start: 0.9296 (mtm110) cc_final: 0.8824 (mtm110) REVERT: A 245 MET cc_start: 0.8936 (mtm) cc_final: 0.8664 (mtp) REVERT: A 544 GLU cc_start: 0.8403 (pp20) cc_final: 0.8197 (pp20) REVERT: A 545 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8224 (ttm) REVERT: B 127 ASP cc_start: 0.9503 (OUTLIER) cc_final: 0.9157 (p0) REVERT: B 131 ARG cc_start: 0.9369 (mtm110) cc_final: 0.9096 (mtm110) REVERT: B 339 LEU cc_start: 0.8270 (tp) cc_final: 0.8059 (tm) REVERT: B 449 GLU cc_start: 0.9031 (tp30) cc_final: 0.8737 (tp30) REVERT: C 127 ASP cc_start: 0.9486 (OUTLIER) cc_final: 0.9141 (p0) REVERT: C 131 ARG cc_start: 0.9312 (mtm110) cc_final: 0.8939 (mtm110) REVERT: C 545 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8232 (ttm) REVERT: D 127 ASP cc_start: 0.9503 (OUTLIER) cc_final: 0.9204 (p0) REVERT: D 131 ARG cc_start: 0.9346 (mtm110) cc_final: 0.9047 (mtm110) REVERT: D 449 GLU cc_start: 0.9042 (tp30) cc_final: 0.8749 (tp30) REVERT: E 127 ASP cc_start: 0.9474 (OUTLIER) cc_final: 0.9189 (p0) REVERT: E 131 ARG cc_start: 0.9287 (mtm110) cc_final: 0.8970 (mtm110) REVERT: E 361 LYS cc_start: 0.9117 (mttp) cc_final: 0.8771 (mptp) REVERT: F 127 ASP cc_start: 0.9483 (OUTLIER) cc_final: 0.9151 (p0) REVERT: F 131 ARG cc_start: 0.9369 (mtm110) cc_final: 0.9097 (mtm110) REVERT: F 449 GLU cc_start: 0.9037 (tp30) cc_final: 0.8741 (tp30) REVERT: G 127 ASP cc_start: 0.9490 (OUTLIER) cc_final: 0.9138 (p0) REVERT: G 131 ARG cc_start: 0.9319 (mtm110) cc_final: 0.8948 (mtm110) REVERT: G 232 ASN cc_start: 0.8536 (m-40) cc_final: 0.8171 (m110) REVERT: G 361 LYS cc_start: 0.9122 (mttp) cc_final: 0.8768 (mptp) REVERT: H 127 ASP cc_start: 0.9500 (OUTLIER) cc_final: 0.9179 (p0) REVERT: H 131 ARG cc_start: 0.9342 (mtm110) cc_final: 0.9046 (mtm110) REVERT: H 339 LEU cc_start: 0.8265 (tp) cc_final: 0.8056 (tm) REVERT: H 449 GLU cc_start: 0.9027 (tp30) cc_final: 0.8732 (tp30) REVERT: J 715 ARG cc_start: 0.8394 (tpm170) cc_final: 0.7935 (tpm170) REVERT: J 736 ARG cc_start: 0.7840 (mtp-110) cc_final: 0.7616 (mtp-110) REVERT: J 786 HIS cc_start: 0.8772 (t-170) cc_final: 0.8536 (t-170) REVERT: J 827 ASN cc_start: 0.9004 (m-40) cc_final: 0.8708 (OUTLIER) REVERT: I 713 SER cc_start: 0.8797 (t) cc_final: 0.7864 (p) REVERT: I 715 ARG cc_start: 0.8388 (tpm170) cc_final: 0.7850 (tpm170) REVERT: I 716 ARG cc_start: 0.6983 (tpp-160) cc_final: 0.6430 (tpp-160) REVERT: I 733 ARG cc_start: 0.9032 (ttm170) cc_final: 0.8467 (mtt90) REVERT: I 742 ASP cc_start: 0.8197 (t70) cc_final: 0.7968 (t70) REVERT: I 793 PHE cc_start: 0.7047 (m-80) cc_final: 0.6787 (m-10) REVERT: I 827 ASN cc_start: 0.9162 (m-40) cc_final: 0.8874 (OUTLIER) REVERT: K 715 ARG cc_start: 0.8425 (tpm170) cc_final: 0.8030 (tpm170) REVERT: K 716 ARG cc_start: 0.6992 (tpp-160) cc_final: 0.6519 (tpp-160) REVERT: K 733 ARG cc_start: 0.9278 (ttm170) cc_final: 0.8641 (mtt90) REVERT: K 742 ASP cc_start: 0.8204 (t70) cc_final: 0.7980 (t70) REVERT: K 786 HIS cc_start: 0.8740 (t-170) cc_final: 0.8498 (t-170) REVERT: K 827 ASN cc_start: 0.9128 (m-40) cc_final: 0.8847 (p0) REVERT: K 840 MET cc_start: 0.8921 (tpp) cc_final: 0.8605 (mmm) REVERT: L 715 ARG cc_start: 0.8384 (tpm170) cc_final: 0.7946 (tpm170) REVERT: L 827 ASN cc_start: 0.9021 (m-40) cc_final: 0.8718 (OUTLIER) REVERT: L 840 MET cc_start: 0.8808 (tpp) cc_final: 0.8564 (tpt) REVERT: M 715 ARG cc_start: 0.8402 (tpm170) cc_final: 0.8004 (tpm170) REVERT: M 716 ARG cc_start: 0.6985 (tpp-160) cc_final: 0.6520 (tpp-160) REVERT: M 733 ARG cc_start: 0.9252 (ttm170) cc_final: 0.8690 (mmt90) REVERT: M 742 ASP cc_start: 0.8216 (t70) cc_final: 0.8016 (t70) REVERT: M 827 ASN cc_start: 0.9136 (m-40) cc_final: 0.8847 (p0) REVERT: N 715 ARG cc_start: 0.8388 (tpm170) cc_final: 0.7966 (tpm170) REVERT: N 827 ASN cc_start: 0.8988 (m-40) cc_final: 0.8646 (OUTLIER) REVERT: O 715 ARG cc_start: 0.8421 (tpm170) cc_final: 0.8021 (tpm170) REVERT: O 716 ARG cc_start: 0.6947 (tpp-160) cc_final: 0.6502 (tpp-160) REVERT: O 733 ARG cc_start: 0.9010 (ttm170) cc_final: 0.8800 (mtt90) REVERT: O 827 ASN cc_start: 0.9128 (m-40) cc_final: 0.8841 (p0) REVERT: P 713 SER cc_start: 0.8897 (t) cc_final: 0.7949 (p) REVERT: P 715 ARG cc_start: 0.8402 (tpm170) cc_final: 0.7721 (tpm170) REVERT: P 827 ASN cc_start: 0.9027 (m-40) cc_final: 0.8778 (OUTLIER) outliers start: 77 outliers final: 32 residues processed: 664 average time/residue: 0.7003 time to fit residues: 567.4353 Evaluate side-chains 557 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 520 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 366 SER 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 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 366 SER 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 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 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 H residue 127 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: 0.8980 chunk 24 optimal weight: 5.9990 chunk 449 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 258 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 442 optimal weight: 8.9990 chunk 484 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 GLN ** 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** ** 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.139139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.075061 restraints weight = 80049.089| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.14 r_work: 0.2805 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 41472 Z= 0.160 Angle : 0.670 11.861 56144 Z= 0.326 Chirality : 0.041 0.245 6416 Planarity : 0.004 0.046 7256 Dihedral : 4.578 19.351 5680 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.91 % Allowed : 15.01 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.12), residues: 5120 helix: 0.92 (0.09), residues: 3664 sheet: 0.77 (0.50), residues: 136 loop : 0.63 (0.19), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 110 TYR 0.019 0.001 TYR H 213 PHE 0.015 0.001 PHE P 763 TRP 0.010 0.001 TRP F 214 HIS 0.007 0.001 HIS I 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (41472) covalent geometry : angle 0.66984 / 0.33 (56144) hydrogen bonds : bond 0.04268 / 2.91 ( 2448) hydrogen bonds : angle 4.51488 / 3.28 ( 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 700 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 618 time to evaluate : 1.482 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: symmetry clash REVERT: A 245 MET cc_start: 0.8987 (mtm) cc_final: 0.8707 (mtp) REVERT: A 288 GLU cc_start: 0.9063 (tt0) cc_final: 0.8711 (mt-10) REVERT: A 363 LYS cc_start: 0.9368 (tppp) cc_final: 0.9048 (mppt) REVERT: B 449 GLU cc_start: 0.9061 (tp30) cc_final: 0.8750 (tp30) REVERT: C 128 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9110 (pt) REVERT: C 131 ARG cc_start: 0.9297 (mtm110) cc_final: 0.8779 (ptp-170) REVERT: C 232 ASN cc_start: 0.8572 (m-40) cc_final: 0.8061 (m110) REVERT: C 288 GLU cc_start: 0.9063 (tt0) cc_final: 0.8712 (mt-10) REVERT: D 110 ARG cc_start: 0.8814 (ttp80) cc_final: 0.8184 (ttp80) REVERT: D 174 GLU cc_start: 0.8704 (mp0) cc_final: 0.8366 (pm20) REVERT: D 288 GLU cc_start: 0.8998 (tt0) cc_final: 0.8663 (mt-10) REVERT: D 449 GLU cc_start: 0.9067 (tp30) cc_final: 0.8760 (tp30) REVERT: E 288 GLU cc_start: 0.9059 (tt0) cc_final: 0.8700 (mt-10) REVERT: E 361 LYS cc_start: 0.9095 (mttp) cc_final: 0.8854 (mptt) REVERT: F 127 ASP cc_start: 0.9480 (OUTLIER) cc_final: 0.9207 (p0) REVERT: F 449 GLU cc_start: 0.9070 (tp30) cc_final: 0.8763 (tp30) REVERT: G 128 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9123 (pt) REVERT: G 131 ARG cc_start: 0.9297 (mtm110) cc_final: 0.8781 (ptp-170) REVERT: G 232 ASN cc_start: 0.8560 (m-40) cc_final: 0.8146 (m110) REVERT: G 288 GLU cc_start: 0.9059 (tt0) cc_final: 0.8705 (mt-10) REVERT: G 361 LYS cc_start: 0.9114 (mttp) cc_final: 0.8880 (mptt) REVERT: H 128 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9109 (pt) REVERT: H 131 ARG cc_start: 0.9352 (mtm110) cc_final: 0.8842 (mtm110) REVERT: H 449 GLU cc_start: 0.9058 (tp30) cc_final: 0.8748 (tp30) REVERT: J 715 ARG cc_start: 0.8278 (tpm170) cc_final: 0.7974 (tpm170) REVERT: J 716 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6670 (ttm110) REVERT: J 736 ARG cc_start: 0.7835 (mtp-110) cc_final: 0.7614 (mtp-110) REVERT: J 786 HIS cc_start: 0.8812 (t-170) cc_final: 0.8543 (t-170) REVERT: J 827 ASN cc_start: 0.9039 (m-40) cc_final: 0.8719 (OUTLIER) REVERT: I 711 PHE cc_start: 0.9019 (t80) cc_final: 0.8753 (t80) REVERT: I 713 SER cc_start: 0.8769 (t) cc_final: 0.7861 (p) REVERT: I 714 TYR cc_start: 0.6932 (p90) cc_final: 0.6165 (p90) REVERT: I 733 ARG cc_start: 0.9056 (ttm170) cc_final: 0.8455 (mtt90) REVERT: I 736 ARG cc_start: 0.7924 (mtp-110) cc_final: 0.7626 (mtp-110) REVERT: I 763 PHE cc_start: 0.8582 (t80) cc_final: 0.8357 (t80) REVERT: I 827 ASN cc_start: 0.9156 (m-40) cc_final: 0.8830 (OUTLIER) REVERT: I 831 TRP cc_start: 0.7645 (t60) cc_final: 0.7387 (t60) REVERT: I 836 GLN cc_start: 0.7730 (pm20) cc_final: 0.7223 (pm20) REVERT: I 845 ARG cc_start: 0.9549 (mtm-85) cc_final: 0.9191 (mtm-85) REVERT: K 711 PHE cc_start: 0.9033 (t80) cc_final: 0.8696 (t80) REVERT: K 713 SER cc_start: 0.8784 (t) cc_final: 0.7845 (p) REVERT: K 715 ARG cc_start: 0.8449 (tpm170) cc_final: 0.8114 (tpm170) REVERT: K 733 ARG cc_start: 0.9276 (ttm170) cc_final: 0.8676 (mtt90) REVERT: K 736 ARG cc_start: 0.7993 (mtp-110) cc_final: 0.7122 (ptp-170) REVERT: K 786 HIS cc_start: 0.8762 (t-170) cc_final: 0.8558 (t-170) REVERT: K 827 ASN cc_start: 0.9108 (m-40) cc_final: 0.8812 (OUTLIER) REVERT: K 836 GLN cc_start: 0.7840 (pm20) cc_final: 0.7259 (pm20) REVERT: K 840 MET cc_start: 0.8951 (tpp) cc_final: 0.8694 (mmm) REVERT: K 845 ARG cc_start: 0.9537 (OUTLIER) cc_final: 0.9272 (mtm-85) REVERT: L 715 ARG cc_start: 0.8300 (tpm170) cc_final: 0.7832 (tpm170) REVERT: L 716 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6749 (ttm110) REVERT: L 736 ARG cc_start: 0.7753 (mtp-110) cc_final: 0.7509 (mtp-110) REVERT: L 827 ASN cc_start: 0.9000 (m-40) cc_final: 0.8701 (OUTLIER) REVERT: L 840 MET cc_start: 0.8812 (tpp) cc_final: 0.8532 (tpt) REVERT: L 845 ARG cc_start: 0.9562 (mtp-110) cc_final: 0.9165 (mtm110) REVERT: M 711 PHE cc_start: 0.8984 (t80) cc_final: 0.8711 (t80) REVERT: M 713 SER cc_start: 0.8771 (t) cc_final: 0.7842 (p) REVERT: M 714 TYR cc_start: 0.7037 (p90) cc_final: 0.6515 (p90) REVERT: M 715 ARG cc_start: 0.8447 (tpm170) cc_final: 0.8185 (tpm170) REVERT: M 733 ARG cc_start: 0.9157 (ttm170) cc_final: 0.8888 (mtt90) REVERT: M 786 HIS cc_start: 0.8800 (t-170) cc_final: 0.8586 (t-170) REVERT: M 827 ASN cc_start: 0.9122 (m-40) cc_final: 0.8825 (OUTLIER) REVERT: M 836 GLN cc_start: 0.7866 (pm20) cc_final: 0.7298 (pm20) REVERT: M 845 ARG cc_start: 0.9534 (OUTLIER) cc_final: 0.9267 (mtm-85) REVERT: N 711 PHE cc_start: 0.9022 (t80) cc_final: 0.8743 (t80) REVERT: N 713 SER cc_start: 0.8794 (t) cc_final: 0.7848 (p) REVERT: N 715 ARG cc_start: 0.8251 (tpm170) cc_final: 0.7586 (tpm170) REVERT: N 716 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6706 (ttm110) REVERT: N 827 ASN cc_start: 0.9000 (m-40) cc_final: 0.8672 (OUTLIER) REVERT: N 845 ARG cc_start: 0.9530 (mtp-110) cc_final: 0.9265 (ptp-110) REVERT: O 711 PHE cc_start: 0.9018 (t80) cc_final: 0.8702 (t80) REVERT: O 713 SER cc_start: 0.8771 (t) cc_final: 0.7812 (p) REVERT: O 714 TYR cc_start: 0.6921 (p90) cc_final: 0.6499 (p90) REVERT: O 715 ARG cc_start: 0.8447 (tpm170) cc_final: 0.8007 (tpm170) REVERT: O 733 ARG cc_start: 0.9030 (ttm170) cc_final: 0.8759 (mtt90) REVERT: O 753 LEU cc_start: 0.8997 (mm) cc_final: 0.8789 (pt) REVERT: O 786 HIS cc_start: 0.8774 (t-170) cc_final: 0.8533 (t-170) REVERT: O 827 ASN cc_start: 0.9106 (m-40) cc_final: 0.8802 (OUTLIER) REVERT: O 836 GLN cc_start: 0.7816 (pm20) cc_final: 0.7267 (pm20) REVERT: P 711 PHE cc_start: 0.9025 (t80) cc_final: 0.8786 (t80) REVERT: P 713 SER cc_start: 0.8814 (t) cc_final: 0.7842 (p) REVERT: P 715 ARG cc_start: 0.8275 (tpm170) cc_final: 0.7772 (tpm170) REVERT: P 716 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6684 (ttm110) REVERT: P 827 ASN cc_start: 0.9009 (m-40) cc_final: 0.8734 (OUTLIER) outliers start: 82 outliers final: 46 residues processed: 682 average time/residue: 0.7104 time to fit residues: 591.5787 Evaluate side-chains 598 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 550 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 368 ILE 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 128 LEU 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 260 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 368 ILE 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 167 VAL 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 368 ILE Chi-restraints excluded: chain H residue 128 LEU 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 716 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 716 ARG Chi-restraints excluded: chain P residue 768 THR Chi-restraints excluded: chain P residue 846 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 95 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 327 optimal weight: 0.9990 chunk 390 optimal weight: 0.2980 chunk 459 optimal weight: 30.0000 chunk 280 optimal weight: 4.9990 chunk 496 optimal weight: 40.0000 chunk 479 optimal weight: 4.9990 chunk 450 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 257 optimal weight: 7.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 777 ASN ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 777 ASN ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 777 ASN ** P 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 777 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.140606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.076856 restraints weight = 79549.317| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.17 r_work: 0.2861 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3915 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= 0.131 Angle : 0.661 11.487 56144 Z= 0.320 Chirality : 0.039 0.242 6416 Planarity : 0.004 0.040 7256 Dihedral : 4.389 19.343 5680 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.11 % Allowed : 15.61 % Favored : 82.27 % 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: 1.42 (0.12), residues: 5120 helix: 1.15 (0.09), residues: 3520 sheet: 0.95 (0.51), residues: 136 loop : 0.74 (0.18), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 249 TYR 0.012 0.001 TYR C 503 PHE 0.025 0.001 PHE L 738 TRP 0.019 0.001 TRP E 214 HIS 0.006 0.001 HIS I 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (41472) covalent geometry : angle 0.66110 / 0.32 (56144) hydrogen bonds : bond 0.03880 / 2.64 ( 2448) hydrogen bonds : angle 4.41316 / 3.21 ( 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 731 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 640 time to evaluate : 1.585 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: 0.9439 (m-30) cc_final: 0.9118 (p0) REVERT: A 131 ARG cc_start: 0.9238 (mtm110) cc_final: 0.8957 (mtm110) REVERT: A 174 GLU cc_start: 0.8713 (mp0) cc_final: 0.8475 (pm20) REVERT: A 245 MET cc_start: 0.8886 (mtm) cc_final: 0.8587 (mtp) REVERT: A 288 GLU cc_start: 0.9086 (tt0) cc_final: 0.8725 (mt-10) REVERT: B 127 ASP cc_start: 0.9484 (m-30) cc_final: 0.9171 (p0) REVERT: B 174 GLU cc_start: 0.8730 (mp0) cc_final: 0.8463 (pm20) REVERT: B 339 LEU cc_start: 0.8250 (tp) cc_final: 0.8041 (tm) REVERT: B 449 GLU cc_start: 0.9060 (tp30) cc_final: 0.8741 (tp30) REVERT: B 525 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9258 (mt-10) REVERT: C 127 ASP cc_start: 0.9448 (m-30) cc_final: 0.9149 (p0) REVERT: C 131 ARG cc_start: 0.9261 (mtm110) cc_final: 0.9018 (mtm110) REVERT: C 174 GLU cc_start: 0.8690 (mp0) cc_final: 0.8404 (pm20) REVERT: C 232 ASN cc_start: 0.8553 (m-40) cc_final: 0.8068 (m110) REVERT: C 288 GLU cc_start: 0.9084 (tt0) cc_final: 0.8725 (mt-10) REVERT: C 361 LYS cc_start: 0.9104 (mttp) cc_final: 0.8836 (mptt) REVERT: D 110 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8384 (ttp80) REVERT: D 127 ASP cc_start: 0.9488 (m-30) cc_final: 0.9140 (p0) REVERT: D 131 ARG cc_start: 0.9321 (mtm110) cc_final: 0.9062 (mtm110) REVERT: D 288 GLU cc_start: 0.9006 (tt0) cc_final: 0.8654 (mt-10) REVERT: D 339 LEU cc_start: 0.8240 (tp) cc_final: 0.8026 (tm) REVERT: D 449 GLU cc_start: 0.9070 (tp30) cc_final: 0.8751 (tp30) REVERT: D 525 GLU cc_start: 0.9474 (mt-10) cc_final: 0.9255 (mt-10) REVERT: E 127 ASP cc_start: 0.9426 (m-30) cc_final: 0.9077 (p0) REVERT: E 131 ARG cc_start: 0.9245 (mtm110) cc_final: 0.8949 (mtm110) REVERT: E 174 GLU cc_start: 0.8673 (mp0) cc_final: 0.8384 (pm20) REVERT: E 232 ASN cc_start: 0.8571 (m-40) cc_final: 0.8058 (m110) REVERT: E 288 GLU cc_start: 0.9082 (tt0) cc_final: 0.8722 (mt-10) REVERT: E 361 LYS cc_start: 0.9132 (mttp) cc_final: 0.8876 (mptt) REVERT: F 127 ASP cc_start: 0.9499 (m-30) cc_final: 0.9145 (p0) REVERT: F 131 ARG cc_start: 0.9336 (mtm110) cc_final: 0.9123 (mtm110) REVERT: F 174 GLU cc_start: 0.8730 (mp0) cc_final: 0.8461 (pm20) REVERT: F 288 GLU cc_start: 0.8952 (tt0) cc_final: 0.8610 (mt-10) REVERT: F 339 LEU cc_start: 0.8221 (tp) cc_final: 0.8011 (tm) REVERT: F 449 GLU cc_start: 0.9069 (tp30) cc_final: 0.8752 (tp30) REVERT: F 525 GLU cc_start: 0.9471 (mt-10) cc_final: 0.9252 (mt-10) REVERT: G 127 ASP cc_start: 0.9449 (m-30) cc_final: 0.9136 (p0) REVERT: G 131 ARG cc_start: 0.9268 (mtm110) cc_final: 0.9025 (mtm110) REVERT: G 174 GLU cc_start: 0.8650 (mp0) cc_final: 0.8313 (pm20) REVERT: G 232 ASN cc_start: 0.8589 (m-40) cc_final: 0.8175 (m110) REVERT: G 288 GLU cc_start: 0.9081 (tt0) cc_final: 0.8722 (mt-10) REVERT: G 361 LYS cc_start: 0.9136 (mttp) cc_final: 0.8881 (mptt) REVERT: H 127 ASP cc_start: 0.9473 (m-30) cc_final: 0.9270 (p0) REVERT: H 128 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9036 (pt) REVERT: H 131 ARG cc_start: 0.9291 (mtm110) cc_final: 0.8756 (mtm110) REVERT: H 174 GLU cc_start: 0.8732 (mp0) cc_final: 0.8462 (pm20) REVERT: H 339 LEU cc_start: 0.8251 (tp) cc_final: 0.8042 (tm) REVERT: H 449 GLU cc_start: 0.9055 (tp30) cc_final: 0.8735 (tp30) REVERT: H 525 GLU cc_start: 0.9474 (mt-10) cc_final: 0.9254 (mt-10) REVERT: J 736 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7729 (mtp-110) REVERT: J 786 HIS cc_start: 0.8871 (t-170) cc_final: 0.8577 (t-170) REVERT: J 827 ASN cc_start: 0.9039 (m-40) cc_final: 0.8722 (p0) REVERT: J 840 MET cc_start: 0.8921 (tpp) cc_final: 0.8671 (tpt) REVERT: J 845 ARG cc_start: 0.9346 (ptp-110) cc_final: 0.8979 (ptp-110) REVERT: I 711 PHE cc_start: 0.9111 (t80) cc_final: 0.8850 (t80) REVERT: I 713 SER cc_start: 0.8911 (t) cc_final: 0.7821 (p) REVERT: I 733 ARG cc_start: 0.9178 (ttm170) cc_final: 0.8605 (mtt90) REVERT: I 736 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7729 (mtp-110) REVERT: I 763 PHE cc_start: 0.8657 (t80) cc_final: 0.8441 (t80) REVERT: I 793 PHE cc_start: 0.6788 (m-10) cc_final: 0.5912 (m-10) REVERT: I 822 MET cc_start: 0.8417 (pmm) cc_final: 0.8172 (pmm) REVERT: I 826 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.5006 (m-80) REVERT: I 827 ASN cc_start: 0.9128 (m-40) cc_final: 0.8833 (p0) REVERT: K 711 PHE cc_start: 0.9103 (t80) cc_final: 0.8872 (t80) REVERT: K 713 SER cc_start: 0.8908 (t) cc_final: 0.7957 (p) REVERT: K 715 ARG cc_start: 0.8556 (tpm170) cc_final: 0.8147 (tpp-160) REVERT: K 733 ARG cc_start: 0.9339 (ttm170) cc_final: 0.8732 (mtt90) REVERT: K 736 ARG cc_start: 0.8022 (mtp-110) cc_final: 0.7757 (mtp-110) REVERT: K 786 HIS cc_start: 0.8758 (t-170) cc_final: 0.8545 (t-170) REVERT: K 793 PHE cc_start: 0.6878 (m-80) cc_final: 0.6134 (m-10) REVERT: K 826 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.5248 (m-80) REVERT: K 827 ASN cc_start: 0.9078 (m-40) cc_final: 0.8819 (p0) REVERT: K 840 MET cc_start: 0.8993 (tpp) cc_final: 0.8739 (mmm) REVERT: K 845 ARG cc_start: 0.9526 (OUTLIER) cc_final: 0.9246 (mtm-85) REVERT: L 713 SER cc_start: 0.8836 (t) cc_final: 0.7948 (p) REVERT: L 715 ARG cc_start: 0.8385 (tpm170) cc_final: 0.7849 (tpm170) REVERT: L 716 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6907 (ttm110) REVERT: L 827 ASN cc_start: 0.8969 (m-40) cc_final: 0.8673 (OUTLIER) REVERT: L 840 MET cc_start: 0.8857 (tpp) cc_final: 0.8567 (tpt) REVERT: L 845 ARG cc_start: 0.9576 (mtp-110) cc_final: 0.9150 (mtm110) REVERT: M 711 PHE cc_start: 0.9076 (t80) cc_final: 0.8817 (t80) REVERT: M 713 SER cc_start: 0.8861 (t) cc_final: 0.7898 (p) REVERT: M 715 ARG cc_start: 0.8570 (tpm170) cc_final: 0.8285 (tpp-160) REVERT: M 733 ARG cc_start: 0.9277 (ttm170) cc_final: 0.8907 (mtt90) REVERT: M 736 ARG cc_start: 0.8025 (mtp-110) cc_final: 0.7760 (mtp-110) REVERT: M 786 HIS cc_start: 0.8856 (t-170) cc_final: 0.8646 (t-170) REVERT: M 793 PHE cc_start: 0.6939 (m-10) cc_final: 0.6216 (m-10) REVERT: M 826 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.5136 (m-80) REVERT: M 827 ASN cc_start: 0.9080 (m-40) cc_final: 0.8817 (OUTLIER) REVERT: N 711 PHE cc_start: 0.9106 (t80) cc_final: 0.8830 (t80) REVERT: N 713 SER cc_start: 0.8892 (t) cc_final: 0.8009 (p) REVERT: N 715 ARG cc_start: 0.8376 (tpm170) cc_final: 0.7843 (tpm170) REVERT: N 716 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6998 (ttm110) REVERT: N 827 ASN cc_start: 0.8977 (m-40) cc_final: 0.8664 (OUTLIER) REVERT: N 845 ARG cc_start: 0.9529 (mtp-110) cc_final: 0.9250 (ptp-110) REVERT: O 713 SER cc_start: 0.8865 (t) cc_final: 0.7934 (p) REVERT: O 715 ARG cc_start: 0.8536 (tpm170) cc_final: 0.8176 (tpp-160) REVERT: O 716 ARG cc_start: 0.7121 (tpp-160) cc_final: 0.6751 (ttm110) REVERT: O 733 ARG cc_start: 0.9194 (ttm170) cc_final: 0.8832 (mtt90) REVERT: O 736 ARG cc_start: 0.8052 (mtp-110) cc_final: 0.7750 (mtp-110) REVERT: O 786 HIS cc_start: 0.8832 (t-170) cc_final: 0.8589 (t-170) REVERT: O 793 PHE cc_start: 0.6903 (m-10) cc_final: 0.6357 (m-10) REVERT: O 826 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.5352 (m-80) REVERT: O 827 ASN cc_start: 0.9074 (m-40) cc_final: 0.8822 (OUTLIER) REVERT: P 713 SER cc_start: 0.8906 (t) cc_final: 0.7922 (p) REVERT: P 715 ARG cc_start: 0.8376 (tpm170) cc_final: 0.7712 (tpm170) REVERT: P 716 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6996 (ttm110) REVERT: P 827 ASN cc_start: 0.9078 (m-40) cc_final: 0.8868 (p0) outliers start: 91 outliers final: 44 residues processed: 700 average time/residue: 0.6867 time to fit residues: 587.4653 Evaluate side-chains 627 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 578 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 368 ILE 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 260 SER Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 368 ILE 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 260 SER Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 368 ILE 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 128 LEU Chi-restraints excluded: chain H residue 260 SER Chi-restraints excluded: chain H residue 303 LEU Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 368 ILE Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain J residue 846 PHE 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 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 826 TYR Chi-restraints excluded: chain N residue 716 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 716 ARG 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: 4.9990 chunk 444 optimal weight: 0.9980 chunk 412 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 403 optimal weight: 30.0000 chunk 445 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 299 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 O 777 ASN ** 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 = 0.4137 r_free = 0.4137 target = 0.138797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.074867 restraints weight = 79927.537| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.13 r_work: 0.2809 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41472 Z= 0.171 Angle : 0.671 10.864 56144 Z= 0.325 Chirality : 0.041 0.268 6416 Planarity : 0.004 0.044 7256 Dihedral : 4.302 17.639 5680 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.95 % Allowed : 17.43 % Favored : 80.62 % 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: 1.48 (0.12), residues: 5120 helix: 1.20 (0.09), residues: 3616 sheet: 0.70 (0.49), residues: 136 loop : 0.71 (0.19), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 249 TYR 0.008 0.001 TYR A 213 PHE 0.024 0.001 PHE P 711 TRP 0.019 0.001 TRP F 214 HIS 0.008 0.001 HIS M 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (41472) covalent geometry : angle 0.67117 / 0.32 (56144) hydrogen bonds : bond 0.04070 / 2.77 ( 2448) hydrogen bonds : angle 4.42652 / 3.22 ( 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 667 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 583 time to evaluate : 1.438 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: 0.9421 (m-30) cc_final: 0.9101 (p0) REVERT: A 131 ARG cc_start: 0.9256 (mtm110) cc_final: 0.8994 (mtm110) REVERT: A 245 MET cc_start: 0.8985 (mtm) cc_final: 0.8736 (mtp) REVERT: A 288 GLU cc_start: 0.9108 (tt0) cc_final: 0.8767 (mt-10) REVERT: A 328 GLN cc_start: 0.8500 (tp40) cc_final: 0.8211 (tp40) REVERT: A 363 LYS cc_start: 0.9320 (tppp) cc_final: 0.9046 (mppt) REVERT: A 403 ARG cc_start: 0.8497 (pmm-80) cc_final: 0.8283 (pmm-80) REVERT: B 127 ASP cc_start: 0.9489 (m-30) cc_final: 0.9147 (p0) REVERT: B 303 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7813 (mm) REVERT: B 328 GLN cc_start: 0.8551 (tp40) cc_final: 0.8261 (tp40) REVERT: B 449 GLU cc_start: 0.9082 (tp30) cc_final: 0.8747 (tp30) REVERT: C 127 ASP cc_start: 0.9444 (m-30) cc_final: 0.9088 (p0) REVERT: C 131 ARG cc_start: 0.9269 (mtm110) cc_final: 0.8975 (mtm110) REVERT: C 288 GLU cc_start: 0.9103 (tt0) cc_final: 0.8765 (mt-10) REVERT: C 328 GLN cc_start: 0.8521 (tp40) cc_final: 0.8230 (tp40) REVERT: D 110 ARG cc_start: 0.8891 (ttp80) cc_final: 0.8447 (ttp80) REVERT: D 127 ASP cc_start: 0.9499 (m-30) cc_final: 0.9161 (p0) REVERT: D 174 GLU cc_start: 0.8749 (mp0) cc_final: 0.8463 (pm20) REVERT: D 288 GLU cc_start: 0.8982 (tt0) cc_final: 0.8638 (mt-10) REVERT: D 328 GLN cc_start: 0.8552 (tp40) cc_final: 0.8262 (tp40) REVERT: D 449 GLU cc_start: 0.9093 (tp30) cc_final: 0.8771 (tp30) REVERT: E 127 ASP cc_start: 0.9422 (m-30) cc_final: 0.9091 (p0) REVERT: E 131 ARG cc_start: 0.9247 (mtm110) cc_final: 0.8980 (mtm110) REVERT: E 288 GLU cc_start: 0.9104 (tt0) cc_final: 0.8765 (mt-10) REVERT: E 328 GLN cc_start: 0.8540 (tp40) cc_final: 0.8259 (tp40) REVERT: E 361 LYS cc_start: 0.9114 (mttp) cc_final: 0.8862 (mptt) REVERT: F 127 ASP cc_start: 0.9495 (m-30) cc_final: 0.9080 (p0) REVERT: F 131 ARG cc_start: 0.9353 (mtm110) cc_final: 0.9099 (mtm110) REVERT: F 288 GLU cc_start: 0.8990 (tt0) cc_final: 0.8663 (mt-10) REVERT: F 328 GLN cc_start: 0.8556 (tp40) cc_final: 0.8267 (tp40) REVERT: F 449 GLU cc_start: 0.9087 (tp30) cc_final: 0.8761 (tp30) REVERT: G 127 ASP cc_start: 0.9445 (m-30) cc_final: 0.9087 (p0) REVERT: G 131 ARG cc_start: 0.9277 (mtm110) cc_final: 0.8984 (mtm110) REVERT: G 288 GLU cc_start: 0.9100 (tt0) cc_final: 0.8757 (mt-10) REVERT: G 328 GLN cc_start: 0.8534 (tp40) cc_final: 0.8247 (tp40) REVERT: H 127 ASP cc_start: 0.9482 (m-30) cc_final: 0.9210 (p0) REVERT: H 128 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8907 (pt) REVERT: H 131 ARG cc_start: 0.9308 (mtm110) cc_final: 0.8738 (mtm110) REVERT: H 328 GLN cc_start: 0.8556 (tp40) cc_final: 0.8266 (tp40) REVERT: H 449 GLU cc_start: 0.9080 (tp30) cc_final: 0.8745 (tp30) REVERT: J 716 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7047 (ttm110) REVERT: J 827 ASN cc_start: 0.8967 (m-40) cc_final: 0.8643 (OUTLIER) REVERT: J 840 MET cc_start: 0.8910 (tpp) cc_final: 0.8646 (tpt) REVERT: I 711 PHE cc_start: 0.9051 (t80) cc_final: 0.8827 (t80) REVERT: I 713 SER cc_start: 0.8798 (t) cc_final: 0.7936 (p) REVERT: I 733 ARG cc_start: 0.9205 (ttm170) cc_final: 0.8672 (mtt90) REVERT: I 736 ARG cc_start: 0.7929 (mtp-110) cc_final: 0.7683 (mtp-110) REVERT: I 793 PHE cc_start: 0.6858 (m-10) cc_final: 0.6060 (m-10) REVERT: I 826 TYR cc_start: 0.6939 (OUTLIER) cc_final: 0.5025 (m-80) REVERT: I 827 ASN cc_start: 0.9101 (m-40) cc_final: 0.8800 (p0) REVERT: K 711 PHE cc_start: 0.9100 (t80) cc_final: 0.8891 (t80) REVERT: K 713 SER cc_start: 0.8809 (t) cc_final: 0.7800 (p) REVERT: K 715 ARG cc_start: 0.8410 (tpm170) cc_final: 0.8135 (tpp-160) REVERT: K 716 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6511 (ttm110) REVERT: K 736 ARG cc_start: 0.8012 (mtp-110) cc_final: 0.7770 (mtp-110) REVERT: K 786 HIS cc_start: 0.8716 (t-170) cc_final: 0.8485 (t-170) REVERT: K 793 PHE cc_start: 0.6860 (m-80) cc_final: 0.6234 (m-10) REVERT: K 826 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.5265 (m-80) REVERT: K 827 ASN cc_start: 0.9055 (m-40) cc_final: 0.8767 (p0) REVERT: K 845 ARG cc_start: 0.9540 (OUTLIER) cc_final: 0.9317 (ptp90) REVERT: L 715 ARG cc_start: 0.8350 (tpm170) cc_final: 0.8112 (tpm170) REVERT: L 827 ASN cc_start: 0.9025 (m-40) cc_final: 0.8728 (p0) REVERT: L 845 ARG cc_start: 0.9582 (mtp-110) cc_final: 0.9234 (ptp-110) REVERT: M 711 PHE cc_start: 0.9087 (t80) cc_final: 0.8829 (t80) REVERT: M 713 SER cc_start: 0.8844 (t) cc_final: 0.7787 (p) REVERT: M 715 ARG cc_start: 0.8508 (tpm170) cc_final: 0.8143 (tpp-160) REVERT: M 716 ARG cc_start: 0.6914 (tpp-160) cc_final: 0.6542 (ttm110) REVERT: M 733 ARG cc_start: 0.9326 (ttm170) cc_final: 0.8982 (mtt90) REVERT: M 736 ARG cc_start: 0.7937 (mtp-110) cc_final: 0.7699 (mtp-110) REVERT: M 793 PHE cc_start: 0.6919 (m-10) cc_final: 0.6227 (m-10) REVERT: M 826 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.5148 (m-80) REVERT: M 827 ASN cc_start: 0.9062 (m-40) cc_final: 0.8755 (p0) REVERT: N 711 PHE cc_start: 0.9101 (t80) cc_final: 0.8887 (t80) REVERT: N 713 SER cc_start: 0.8849 (t) cc_final: 0.7908 (p) REVERT: N 715 ARG cc_start: 0.8369 (tpm170) cc_final: 0.7786 (tpm170) REVERT: N 716 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6953 (ttm110) REVERT: N 827 ASN cc_start: 0.8973 (m-40) cc_final: 0.8673 (p0) REVERT: N 845 ARG cc_start: 0.9535 (mtp-110) cc_final: 0.9217 (ptp-110) REVERT: O 713 SER cc_start: 0.8793 (t) cc_final: 0.7818 (p) REVERT: O 715 ARG cc_start: 0.8517 (tpm170) cc_final: 0.8146 (tpp-160) REVERT: O 716 ARG cc_start: 0.7179 (tpp-160) cc_final: 0.6820 (ttm110) REVERT: O 733 ARG cc_start: 0.9234 (ttm170) cc_final: 0.8984 (mtt90) REVERT: O 736 ARG cc_start: 0.8024 (mtp-110) cc_final: 0.7654 (mtp-110) REVERT: O 786 HIS cc_start: 0.8810 (t-170) cc_final: 0.8598 (t-170) REVERT: O 793 PHE cc_start: 0.6906 (m-10) cc_final: 0.6419 (m-10) REVERT: O 826 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.5370 (m-80) REVERT: O 827 ASN cc_start: 0.9056 (m-40) cc_final: 0.8773 (p0) REVERT: P 713 SER cc_start: 0.8713 (t) cc_final: 0.7876 (p) REVERT: P 715 ARG cc_start: 0.8356 (tpm170) cc_final: 0.7749 (tpm170) REVERT: P 716 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6950 (ttm110) REVERT: P 827 ASN cc_start: 0.9049 (m-40) cc_final: 0.8801 (p0) REVERT: P 845 ARG cc_start: 0.9263 (ptp-110) cc_final: 0.8926 (ptp-110) outliers start: 84 outliers final: 46 residues processed: 648 average time/residue: 0.7094 time to fit residues: 560.3171 Evaluate side-chains 593 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 537 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 368 ILE 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 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 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 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 128 LEU 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 716 ARG Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain J residue 846 PHE 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 I residue 832 VAL Chi-restraints excluded: chain K residue 716 ARG 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 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 716 ARG 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 Chi-restraints excluded: chain P residue 716 ARG Chi-restraints excluded: chain P residue 768 THR Chi-restraints excluded: chain P residue 785 VAL 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: 0.9980 chunk 286 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 345 optimal weight: 0.9980 chunk 332 optimal weight: 0.1980 chunk 137 optimal weight: 1.9990 chunk 476 optimal weight: 20.0000 chunk 426 optimal weight: 20.0000 chunk 492 optimal weight: 10.0000 chunk 429 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 ASN ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 731 GLN ** I 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 731 GLN ** M 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 786 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.140094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.076525 restraints weight = 79409.938| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.17 r_work: 0.2848 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 41472 Z= 0.131 Angle : 0.667 10.697 56144 Z= 0.323 Chirality : 0.040 0.258 6416 Planarity : 0.004 0.048 7256 Dihedral : 4.232 19.125 5680 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.07 % Allowed : 18.66 % Favored : 79.28 % 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: 1.54 (0.12), residues: 5120 helix: 1.29 (0.09), residues: 3568 sheet: 0.40 (0.46), residues: 136 loop : 0.69 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 249 TYR 0.011 0.001 TYR E 503 PHE 0.027 0.001 PHE O 738 TRP 0.016 0.001 TRP F 214 HIS 0.007 0.001 HIS J 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (41472) covalent geometry : angle 0.66724 / 0.32 (56144) hydrogen bonds : bond 0.03748 / 2.55 ( 2448) hydrogen bonds : angle 4.34090 / 3.16 ( 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 693 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 604 time to evaluate : 1.642 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: A 127 ASP cc_start: 0.9401 (m-30) cc_final: 0.9065 (p0) REVERT: A 131 ARG cc_start: 0.9221 (mtm110) cc_final: 0.8945 (mtm110) REVERT: A 174 GLU cc_start: 0.8694 (mp0) cc_final: 0.8451 (pm20) REVERT: A 245 MET cc_start: 0.8904 (mtm) cc_final: 0.8640 (mtp) REVERT: A 280 ASN cc_start: 0.8610 (t0) cc_final: 0.8310 (t0) REVERT: A 288 GLU cc_start: 0.9058 (tt0) cc_final: 0.8710 (mt-10) REVERT: A 328 GLN cc_start: 0.8467 (tp40) cc_final: 0.8212 (tp40) REVERT: A 363 LYS cc_start: 0.9305 (tppp) cc_final: 0.9045 (mppt) REVERT: A 403 ARG cc_start: 0.8508 (pmm-80) cc_final: 0.8212 (pmm-80) REVERT: B 127 ASP cc_start: 0.9464 (m-30) cc_final: 0.9075 (p0) REVERT: B 260 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8315 (p) REVERT: B 280 ASN cc_start: 0.8546 (t0) cc_final: 0.8144 (t0) REVERT: B 285 ARG cc_start: 0.9047 (tpp80) cc_final: 0.8813 (tpp-160) REVERT: B 303 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7727 (mm) REVERT: B 328 GLN cc_start: 0.8531 (tp40) cc_final: 0.8223 (tp40) REVERT: B 339 LEU cc_start: 0.8253 (tp) cc_final: 0.8038 (tm) REVERT: B 352 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8685 (mp0) REVERT: B 449 GLU cc_start: 0.9082 (tp30) cc_final: 0.8724 (tp30) REVERT: C 127 ASP cc_start: 0.9420 (m-30) cc_final: 0.9016 (p0) REVERT: C 131 ARG cc_start: 0.9238 (mtm110) cc_final: 0.8967 (mtm110) REVERT: C 174 GLU cc_start: 0.8716 (mp0) cc_final: 0.8384 (pm20) REVERT: C 280 ASN cc_start: 0.8598 (t0) cc_final: 0.8275 (t0) REVERT: C 288 GLU cc_start: 0.9055 (tt0) cc_final: 0.8709 (mt-10) REVERT: C 328 GLN cc_start: 0.8454 (tp40) cc_final: 0.8199 (tp40) REVERT: C 403 ARG cc_start: 0.8512 (pmm-80) cc_final: 0.8187 (pmm-80) REVERT: D 110 ARG cc_start: 0.8866 (ttp80) cc_final: 0.8421 (ttp80) REVERT: D 127 ASP cc_start: 0.9471 (m-30) cc_final: 0.9153 (p0) REVERT: D 131 ARG cc_start: 0.9293 (mtm110) cc_final: 0.8827 (mtm110) REVERT: D 174 GLU cc_start: 0.8756 (mp0) cc_final: 0.8499 (pm20) REVERT: D 280 ASN cc_start: 0.8539 (t0) cc_final: 0.8128 (t0) REVERT: D 285 ARG cc_start: 0.9044 (tpp80) cc_final: 0.8834 (tpp-160) REVERT: D 288 GLU cc_start: 0.8968 (tt0) cc_final: 0.8612 (mt-10) REVERT: D 328 GLN cc_start: 0.8542 (tp40) cc_final: 0.8235 (tp40) REVERT: D 352 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8687 (mp0) REVERT: D 403 ARG cc_start: 0.8532 (pmm-80) cc_final: 0.8308 (pmm-80) REVERT: D 449 GLU cc_start: 0.9084 (tp30) cc_final: 0.8744 (tp30) REVERT: E 127 ASP cc_start: 0.9390 (m-30) cc_final: 0.9054 (p0) REVERT: E 131 ARG cc_start: 0.9202 (mtm110) cc_final: 0.8927 (mtm110) REVERT: E 174 GLU cc_start: 0.8727 (mp0) cc_final: 0.8395 (pm20) REVERT: E 280 ASN cc_start: 0.8607 (t0) cc_final: 0.8297 (t0) REVERT: E 288 GLU cc_start: 0.9056 (tt0) cc_final: 0.8709 (mt-10) REVERT: E 328 GLN cc_start: 0.8472 (tp40) cc_final: 0.8217 (tp40) REVERT: E 361 LYS cc_start: 0.9110 (mttp) cc_final: 0.8854 (mptt) REVERT: E 403 ARG cc_start: 0.8503 (pmm-80) cc_final: 0.8191 (pmm-80) REVERT: F 127 ASP cc_start: 0.9456 (m-30) cc_final: 0.9124 (p0) REVERT: F 280 ASN cc_start: 0.8545 (t0) cc_final: 0.8140 (t0) REVERT: F 285 ARG cc_start: 0.9054 (tpp80) cc_final: 0.8834 (tpp-160) REVERT: F 288 GLU cc_start: 0.8963 (tt0) cc_final: 0.8635 (mt-10) REVERT: F 328 GLN cc_start: 0.8539 (tp40) cc_final: 0.8234 (tp40) REVERT: F 352 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8680 (mp0) REVERT: F 403 ARG cc_start: 0.8532 (pmm-80) cc_final: 0.8303 (pmm-80) REVERT: F 449 GLU cc_start: 0.9080 (tp30) cc_final: 0.8736 (tp30) REVERT: G 127 ASP cc_start: 0.9421 (m-30) cc_final: 0.9017 (p0) REVERT: G 131 ARG cc_start: 0.9225 (mtm110) cc_final: 0.8955 (mtm110) REVERT: G 174 GLU cc_start: 0.8704 (mp0) cc_final: 0.8425 (pm20) REVERT: G 280 ASN cc_start: 0.8596 (t0) cc_final: 0.8285 (t0) REVERT: G 288 GLU cc_start: 0.9050 (tt0) cc_final: 0.8703 (mt-10) REVERT: G 328 GLN cc_start: 0.8479 (tp40) cc_final: 0.8222 (tp40) REVERT: G 403 ARG cc_start: 0.8506 (pmm-80) cc_final: 0.8194 (pmm-80) REVERT: H 127 ASP cc_start: 0.9465 (m-30) cc_final: 0.9204 (p0) REVERT: H 128 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8995 (pt) REVERT: H 131 ARG cc_start: 0.9285 (mtm110) cc_final: 0.8821 (mtm110) REVERT: H 260 SER cc_start: 0.8574 (OUTLIER) cc_final: 0.8324 (p) REVERT: H 280 ASN cc_start: 0.8544 (t0) cc_final: 0.8140 (t0) REVERT: H 285 ARG cc_start: 0.9041 (tpp80) cc_final: 0.8806 (tpp-160) REVERT: H 328 GLN cc_start: 0.8535 (tp40) cc_final: 0.8227 (tp40) REVERT: H 339 LEU cc_start: 0.8257 (tp) cc_final: 0.8042 (tm) REVERT: H 352 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8691 (mp0) REVERT: H 403 ARG cc_start: 0.8527 (pmm-80) cc_final: 0.8301 (pmm-80) REVERT: H 449 GLU cc_start: 0.9085 (tp30) cc_final: 0.8726 (tp30) REVERT: J 713 SER cc_start: 0.8706 (t) cc_final: 0.7967 (p) REVERT: J 716 ARG cc_start: 0.7349 (ttm110) cc_final: 0.7003 (ttm110) REVERT: J 736 ARG cc_start: 0.7521 (mtp-110) cc_final: 0.6939 (ptt180) REVERT: J 827 ASN cc_start: 0.8988 (m-40) cc_final: 0.8647 (OUTLIER) REVERT: J 840 MET cc_start: 0.8875 (tpp) cc_final: 0.8550 (tpt) REVERT: J 845 ARG cc_start: 0.9319 (ptp-110) cc_final: 0.8975 (ptp-110) REVERT: I 711 PHE cc_start: 0.9082 (t80) cc_final: 0.8848 (t80) REVERT: I 713 SER cc_start: 0.8885 (t) cc_final: 0.7934 (p) REVERT: I 715 ARG cc_start: 0.8306 (tpp-160) cc_final: 0.8090 (tpp-160) REVERT: I 716 ARG cc_start: 0.6856 (tpp-160) cc_final: 0.6644 (ttm110) REVERT: I 736 ARG cc_start: 0.7963 (mtp-110) cc_final: 0.7723 (mtp-110) REVERT: I 793 PHE cc_start: 0.6866 (m-10) cc_final: 0.6028 (m-10) REVERT: I 826 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.4939 (m-80) REVERT: I 827 ASN cc_start: 0.9062 (m-40) cc_final: 0.8764 (p0) REVERT: K 711 PHE cc_start: 0.9059 (t80) cc_final: 0.8851 (t80) REVERT: K 713 SER cc_start: 0.8747 (t) cc_final: 0.7886 (p) REVERT: K 715 ARG cc_start: 0.8438 (tpm170) cc_final: 0.8177 (tpp-160) REVERT: K 716 ARG cc_start: 0.6972 (ttm110) cc_final: 0.6708 (ttm110) REVERT: K 733 ARG cc_start: 0.9262 (ttm170) cc_final: 0.8490 (mtt90) REVERT: K 736 ARG cc_start: 0.8062 (mtp-110) cc_final: 0.7819 (mtp-110) REVERT: K 793 PHE cc_start: 0.6858 (m-80) cc_final: 0.6366 (m-10) REVERT: K 826 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.5341 (m-80) REVERT: K 827 ASN cc_start: 0.9026 (m-40) cc_final: 0.8730 (p0) REVERT: L 713 SER cc_start: 0.8800 (t) cc_final: 0.8029 (p) REVERT: L 715 ARG cc_start: 0.8530 (tpm170) cc_final: 0.8210 (tpp-160) REVERT: L 733 ARG cc_start: 0.9308 (ttm170) cc_final: 0.8901 (mtt90) REVERT: L 774 ARG cc_start: 0.7621 (ttt-90) cc_final: 0.7300 (ttt90) REVERT: L 827 ASN cc_start: 0.8991 (m-40) cc_final: 0.8731 (p0) REVERT: L 845 ARG cc_start: 0.9578 (mtp-110) cc_final: 0.9217 (ptp-110) REVERT: M 715 ARG cc_start: 0.8522 (tpm170) cc_final: 0.8167 (tpp-160) REVERT: M 716 ARG cc_start: 0.6992 (tpp-160) cc_final: 0.6623 (ttm110) REVERT: M 733 ARG cc_start: 0.9354 (ttm170) cc_final: 0.9011 (mtt90) REVERT: M 736 ARG cc_start: 0.7963 (mtp-110) cc_final: 0.7722 (mtp-110) REVERT: M 793 PHE cc_start: 0.6837 (m-10) cc_final: 0.6204 (m-10) REVERT: M 826 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.5107 (m-80) REVERT: M 827 ASN cc_start: 0.9018 (m-40) cc_final: 0.8712 (p0) REVERT: M 845 ARG cc_start: 0.9331 (ptp-110) cc_final: 0.8970 (ptp-110) REVERT: N 711 PHE cc_start: 0.9097 (t80) cc_final: 0.8893 (t80) REVERT: N 713 SER cc_start: 0.8834 (t) cc_final: 0.7935 (p) REVERT: N 715 ARG cc_start: 0.8354 (tpm170) cc_final: 0.7986 (tpp-160) REVERT: N 716 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.7106 (ttm110) REVERT: N 774 ARG cc_start: 0.7638 (ttt-90) cc_final: 0.7312 (ttt90) REVERT: N 827 ASN cc_start: 0.8876 (m-40) cc_final: 0.8537 (p0) REVERT: N 840 MET cc_start: 0.8950 (tpp) cc_final: 0.8691 (tpt) REVERT: N 845 ARG cc_start: 0.9541 (mtp-110) cc_final: 0.9222 (ptp-110) REVERT: O 715 ARG cc_start: 0.8552 (tpm170) cc_final: 0.8184 (tpp-160) REVERT: O 716 ARG cc_start: 0.7152 (tpp-160) cc_final: 0.6806 (ttm110) REVERT: O 733 ARG cc_start: 0.9291 (ttm170) cc_final: 0.8903 (mtt90) REVERT: O 736 ARG cc_start: 0.8061 (mtp-110) cc_final: 0.7691 (mtp-110) REVERT: O 786 HIS cc_start: 0.8791 (t-170) cc_final: 0.8556 (t-170) REVERT: O 793 PHE cc_start: 0.6844 (m-10) cc_final: 0.6431 (m-10) REVERT: O 826 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.5439 (m-80) REVERT: O 827 ASN cc_start: 0.9010 (m-40) cc_final: 0.8707 (p0) REVERT: O 845 ARG cc_start: 0.9331 (ptp-110) cc_final: 0.8980 (ptp-110) REVERT: P 713 SER cc_start: 0.8721 (t) cc_final: 0.7925 (p) REVERT: P 715 ARG cc_start: 0.8368 (tpm170) cc_final: 0.7988 (tpp-160) REVERT: P 716 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7047 (ttm110) REVERT: P 827 ASN cc_start: 0.9029 (m-40) cc_final: 0.8766 (p0) REVERT: P 845 ARG cc_start: 0.9260 (ptp-110) cc_final: 0.8910 (ptp-110) outliers start: 89 outliers final: 42 residues processed: 669 average time/residue: 0.7582 time to fit residues: 613.6752 Evaluate side-chains 629 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 574 time to evaluate : 1.576 ------------------------------------------------------------------------------- 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 368 ILE Chi-restraints excluded: chain B residue 260 SER 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 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 260 SER 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 368 ILE 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 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 128 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 768 THR Chi-restraints excluded: chain I residue 794 GLU Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 832 VAL 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 794 GLU Chi-restraints excluded: chain M residue 826 TYR Chi-restraints excluded: chain M residue 846 PHE Chi-restraints excluded: chain N residue 716 ARG Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain N residue 785 VAL Chi-restraints excluded: chain O residue 826 TYR Chi-restraints excluded: chain O residue 846 PHE Chi-restraints excluded: chain P residue 716 ARG Chi-restraints excluded: chain P residue 768 THR Chi-restraints excluded: chain P residue 785 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 398 optimal weight: 0.0020 chunk 494 optimal weight: 8.9990 chunk 219 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 445 optimal weight: 30.0000 chunk 452 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 290 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN F 74 GLN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 777 ASN K 786 HIS ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 756 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.140067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.076801 restraints weight = 79100.100| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.11 r_work: 0.2853 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 41472 Z= 0.133 Angle : 0.677 10.359 56144 Z= 0.326 Chirality : 0.040 0.286 6416 Planarity : 0.004 0.043 7256 Dihedral : 4.161 19.379 5680 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.70 % Allowed : 19.54 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.12), residues: 5120 helix: 1.36 (0.09), residues: 3552 sheet: 0.34 (0.45), residues: 136 loop : 0.68 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 733 TYR 0.022 0.001 TYR F 213 PHE 0.030 0.001 PHE P 711 TRP 0.030 0.001 TRP C 214 HIS 0.005 0.001 HIS M 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (41472) covalent geometry : angle 0.67701 / 0.33 (56144) hydrogen bonds : bond 0.03737 / 2.55 ( 2448) hydrogen bonds : angle 4.33143 / 3.15 ( 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 659 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 586 time to evaluate : 1.615 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: A 127 ASP cc_start: 0.9396 (m-30) cc_final: 0.9054 (p0) REVERT: A 131 ARG cc_start: 0.9203 (mtm110) cc_final: 0.8974 (mtm110) REVERT: A 174 GLU cc_start: 0.8691 (mp0) cc_final: 0.8386 (mp0) REVERT: A 245 MET cc_start: 0.8864 (mtm) cc_final: 0.8614 (mtp) REVERT: A 280 ASN cc_start: 0.8530 (t0) cc_final: 0.8245 (t0) REVERT: A 328 GLN cc_start: 0.8438 (tp40) cc_final: 0.8183 (tp40) REVERT: A 403 ARG cc_start: 0.8498 (pmm-80) cc_final: 0.8219 (pmm-80) REVERT: B 127 ASP cc_start: 0.9440 (m-30) cc_final: 0.9116 (p0) REVERT: B 131 ARG cc_start: 0.9324 (mtm110) cc_final: 0.8913 (mtm110) REVERT: B 260 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8314 (p) REVERT: B 280 ASN cc_start: 0.8501 (t0) cc_final: 0.8115 (t0) REVERT: B 285 ARG cc_start: 0.9030 (tpp80) cc_final: 0.8788 (tpp-160) REVERT: B 303 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7664 (mm) REVERT: B 328 GLN cc_start: 0.8513 (tp40) cc_final: 0.8238 (tp40) REVERT: B 339 LEU cc_start: 0.8231 (tp) cc_final: 0.8011 (tm) REVERT: B 352 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8699 (mp0) REVERT: B 449 GLU cc_start: 0.9098 (tp30) cc_final: 0.8737 (tp30) REVERT: C 127 ASP cc_start: 0.9411 (m-30) cc_final: 0.9053 (p0) REVERT: C 131 ARG cc_start: 0.9224 (mtm110) cc_final: 0.9023 (mtm110) REVERT: C 162 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8381 (ptt-90) REVERT: C 174 GLU cc_start: 0.8721 (mp0) cc_final: 0.8509 (mp0) REVERT: C 280 ASN cc_start: 0.8518 (t0) cc_final: 0.8214 (t0) REVERT: C 328 GLN cc_start: 0.8469 (tp40) cc_final: 0.8225 (tp40) REVERT: C 403 ARG cc_start: 0.8499 (pmm-80) cc_final: 0.8269 (pmm-80) REVERT: D 127 ASP cc_start: 0.9443 (m-30) cc_final: 0.9125 (p0) REVERT: D 131 ARG cc_start: 0.9309 (mtm110) cc_final: 0.8783 (mtm110) REVERT: D 174 GLU cc_start: 0.8753 (mp0) cc_final: 0.8497 (pm20) REVERT: D 260 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8339 (p) REVERT: D 280 ASN cc_start: 0.8492 (t0) cc_final: 0.8097 (t0) REVERT: D 285 ARG cc_start: 0.9061 (tpp80) cc_final: 0.8847 (tpp-160) REVERT: D 288 GLU cc_start: 0.8966 (tt0) cc_final: 0.8612 (mt-10) REVERT: D 328 GLN cc_start: 0.8518 (tp40) cc_final: 0.8244 (tp40) REVERT: D 352 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8705 (mp0) REVERT: D 403 ARG cc_start: 0.8535 (pmm-80) cc_final: 0.8316 (pmm-80) REVERT: D 449 GLU cc_start: 0.9099 (tp30) cc_final: 0.8757 (tp30) REVERT: E 127 ASP cc_start: 0.9396 (m-30) cc_final: 0.9023 (p0) REVERT: E 131 ARG cc_start: 0.9196 (mtm110) cc_final: 0.8879 (mtm110) REVERT: E 162 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8382 (ptt-90) REVERT: E 174 GLU cc_start: 0.8718 (mp0) cc_final: 0.8503 (mp0) REVERT: E 280 ASN cc_start: 0.8522 (t0) cc_final: 0.8219 (t0) REVERT: E 328 GLN cc_start: 0.8442 (tp40) cc_final: 0.8187 (tp40) REVERT: E 403 ARG cc_start: 0.8499 (pmm-80) cc_final: 0.8271 (pmm-80) REVERT: F 127 ASP cc_start: 0.9442 (m-30) cc_final: 0.9006 (p0) REVERT: F 131 ARG cc_start: 0.9333 (mtm110) cc_final: 0.9068 (ttm110) REVERT: F 174 GLU cc_start: 0.8725 (mp0) cc_final: 0.8472 (pm20) REVERT: F 260 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8365 (p) REVERT: F 280 ASN cc_start: 0.8498 (t0) cc_final: 0.8108 (t0) REVERT: F 285 ARG cc_start: 0.9055 (tpp80) cc_final: 0.8826 (tpp-160) REVERT: F 288 GLU cc_start: 0.8956 (tt0) cc_final: 0.8617 (mt-10) REVERT: F 328 GLN cc_start: 0.8519 (tp40) cc_final: 0.8245 (tp40) REVERT: F 352 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8704 (mp0) REVERT: F 403 ARG cc_start: 0.8544 (pmm-80) cc_final: 0.8334 (pmm-80) REVERT: F 449 GLU cc_start: 0.9095 (tp30) cc_final: 0.8753 (tp30) REVERT: G 127 ASP cc_start: 0.9424 (m-30) cc_final: 0.9059 (p0) REVERT: G 131 ARG cc_start: 0.9220 (mtm110) cc_final: 0.9019 (mtm110) REVERT: G 174 GLU cc_start: 0.8658 (mp0) cc_final: 0.8452 (mp0) REVERT: G 280 ASN cc_start: 0.8518 (t0) cc_final: 0.8216 (t0) REVERT: G 328 GLN cc_start: 0.8435 (tp40) cc_final: 0.8181 (tp40) REVERT: G 403 ARG cc_start: 0.8500 (pmm-80) cc_final: 0.8273 (pmm-80) REVERT: H 127 ASP cc_start: 0.9433 (m-30) cc_final: 0.9163 (p0) REVERT: H 128 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8959 (pt) REVERT: H 131 ARG cc_start: 0.9298 (mtm110) cc_final: 0.8787 (mtm110) REVERT: H 260 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8351 (p) REVERT: H 280 ASN cc_start: 0.8487 (t0) cc_final: 0.8098 (t0) REVERT: H 285 ARG cc_start: 0.9023 (tpp80) cc_final: 0.8782 (tpp-160) REVERT: H 328 GLN cc_start: 0.8522 (tp40) cc_final: 0.8244 (tp40) REVERT: H 339 LEU cc_start: 0.8238 (tp) cc_final: 0.8017 (tm) REVERT: H 352 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8697 (mp0) REVERT: H 403 ARG cc_start: 0.8526 (pmm-80) cc_final: 0.8317 (pmm-80) REVERT: H 449 GLU cc_start: 0.9096 (tp30) cc_final: 0.8739 (tp30) REVERT: J 711 PHE cc_start: 0.8968 (t80) cc_final: 0.8764 (t80) REVERT: J 713 SER cc_start: 0.8812 (t) cc_final: 0.8015 (p) REVERT: J 736 ARG cc_start: 0.7586 (mtp-110) cc_final: 0.6939 (ptt180) REVERT: J 827 ASN cc_start: 0.8923 (m-40) cc_final: 0.8596 (OUTLIER) REVERT: J 840 MET cc_start: 0.8887 (tpp) cc_final: 0.8663 (tpt) REVERT: I 711 PHE cc_start: 0.9096 (t80) cc_final: 0.8834 (t80) REVERT: I 713 SER cc_start: 0.8904 (t) cc_final: 0.7982 (p) REVERT: I 715 ARG cc_start: 0.8339 (tpp-160) cc_final: 0.8100 (tpp-160) REVERT: I 716 ARG cc_start: 0.6955 (tpp-160) cc_final: 0.6671 (ttm110) REVERT: I 736 ARG cc_start: 0.7991 (mtp-110) cc_final: 0.7753 (mtp-110) REVERT: I 793 PHE cc_start: 0.7038 (m-10) cc_final: 0.6272 (m-10) REVERT: I 826 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.4825 (m-80) REVERT: I 827 ASN cc_start: 0.9031 (m-40) cc_final: 0.8740 (p0) REVERT: I 845 ARG cc_start: 0.9525 (mtp-110) cc_final: 0.9176 (mtm110) REVERT: K 713 SER cc_start: 0.8795 (t) cc_final: 0.7921 (p) REVERT: K 715 ARG cc_start: 0.8442 (tpm170) cc_final: 0.8180 (tpp-160) REVERT: K 716 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6835 (ttm110) REVERT: K 733 ARG cc_start: 0.9317 (ttm170) cc_final: 0.8588 (mtt90) REVERT: K 736 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7707 (mtp-110) REVERT: K 793 PHE cc_start: 0.6944 (m-80) cc_final: 0.6433 (m-10) REVERT: K 826 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.5269 (m-80) REVERT: K 827 ASN cc_start: 0.9042 (m-40) cc_final: 0.8747 (p0) REVERT: L 713 SER cc_start: 0.8806 (t) cc_final: 0.7971 (p) REVERT: L 715 ARG cc_start: 0.8524 (tpm170) cc_final: 0.8320 (tpp-160) REVERT: L 733 ARG cc_start: 0.9216 (ttm170) cc_final: 0.8609 (mtt180) REVERT: L 827 ASN cc_start: 0.8996 (m-40) cc_final: 0.8755 (p0) REVERT: L 845 ARG cc_start: 0.9585 (mtp-110) cc_final: 0.9239 (ptp-110) REVERT: M 713 SER cc_start: 0.8780 (t) cc_final: 0.7828 (p) REVERT: M 715 ARG cc_start: 0.8577 (tpm170) cc_final: 0.8167 (tpp-160) REVERT: M 716 ARG cc_start: 0.7083 (tpp-160) cc_final: 0.6705 (ttm110) REVERT: M 733 ARG cc_start: 0.9370 (ttm170) cc_final: 0.9025 (mtt90) REVERT: M 736 ARG cc_start: 0.8025 (mtp-110) cc_final: 0.7791 (mtp-110) REVERT: M 793 PHE cc_start: 0.6868 (m-10) cc_final: 0.6163 (m-10) REVERT: M 826 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.5105 (m-80) REVERT: M 827 ASN cc_start: 0.8989 (m-40) cc_final: 0.8666 (p0) REVERT: N 713 SER cc_start: 0.8804 (t) cc_final: 0.8048 (p) REVERT: N 715 ARG cc_start: 0.8361 (tpm170) cc_final: 0.8113 (tpp-160) REVERT: N 716 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7031 (ttm110) REVERT: N 736 ARG cc_start: 0.7641 (mtp-110) cc_final: 0.6910 (ptt180) REVERT: N 827 ASN cc_start: 0.8878 (m-40) cc_final: 0.8568 (p0) REVERT: N 840 MET cc_start: 0.8889 (tpp) cc_final: 0.8586 (tpt) REVERT: N 845 ARG cc_start: 0.9569 (mtp-110) cc_final: 0.9233 (ptp-110) REVERT: O 715 ARG cc_start: 0.8613 (tpm170) cc_final: 0.8223 (tpp-160) REVERT: O 716 ARG cc_start: 0.7172 (tpp-160) cc_final: 0.6809 (ttm110) REVERT: O 733 ARG cc_start: 0.9317 (ttm170) cc_final: 0.8919 (mtt90) REVERT: O 736 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7702 (mtp-110) REVERT: O 793 PHE cc_start: 0.6940 (m-10) cc_final: 0.6493 (m-10) REVERT: O 826 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.5447 (m-80) REVERT: O 827 ASN cc_start: 0.9049 (m-40) cc_final: 0.8749 (p0) REVERT: P 713 SER cc_start: 0.8740 (t) cc_final: 0.7894 (p) REVERT: P 716 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7023 (ttm110) REVERT: P 736 ARG cc_start: 0.7864 (mtp-110) cc_final: 0.7174 (ptt180) REVERT: P 827 ASN cc_start: 0.8994 (m-40) cc_final: 0.8748 (p0) outliers start: 73 outliers final: 37 residues processed: 645 average time/residue: 0.7415 time to fit residues: 579.9147 Evaluate side-chains 598 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 543 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 368 ILE 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 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 260 SER Chi-restraints excluded: chain D residue 352 GLU 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 352 GLU 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 128 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 753 LEU Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain I residue 794 GLU Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 832 VAL Chi-restraints excluded: chain K residue 716 ARG 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 794 GLU Chi-restraints excluded: chain M residue 826 TYR Chi-restraints excluded: chain N residue 716 ARG Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain O residue 826 TYR Chi-restraints excluded: chain P residue 716 ARG Chi-restraints excluded: chain P residue 768 THR Chi-restraints excluded: chain P residue 785 VAL 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: 0.7980 chunk 42 optimal weight: 0.9990 chunk 432 optimal weight: 0.9990 chunk 481 optimal weight: 40.0000 chunk 306 optimal weight: 9.9990 chunk 490 optimal weight: 6.9990 chunk 222 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 chunk 324 optimal weight: 0.9990 chunk 135 optimal weight: 0.3980 chunk 440 optimal weight: 5.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 758 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.140555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.077432 restraints weight = 79646.631| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.17 r_work: 0.2868 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41472 Z= 0.133 Angle : 0.712 14.646 56144 Z= 0.342 Chirality : 0.041 0.266 6416 Planarity : 0.004 0.050 7256 Dihedral : 4.115 21.284 5680 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.53 % Allowed : 20.12 % Favored : 78.35 % 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: 1.59 (0.12), residues: 5120 helix: 1.32 (0.09), residues: 3600 sheet: 0.13 (0.44), residues: 136 loop : 0.71 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 249 TYR 0.011 0.001 TYR E 503 PHE 0.028 0.001 PHE M 738 TRP 0.019 0.001 TRP G 214 HIS 0.005 0.001 HIS O 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (41472) covalent geometry : angle 0.71190 / 0.34 (56144) hydrogen bonds : bond 0.03657 / 2.50 ( 2448) hydrogen bonds : angle 4.32168 / 3.14 ( 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 660 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 594 time to evaluate : 1.690 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: 0.9354 (m-30) cc_final: 0.8976 (p0) REVERT: A 131 ARG cc_start: 0.9216 (mtm110) cc_final: 0.8830 (mtm110) REVERT: A 162 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8387 (ptt-90) REVERT: A 260 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8293 (p) REVERT: A 280 ASN cc_start: 0.8497 (t0) cc_final: 0.8223 (t0) REVERT: A 328 GLN cc_start: 0.8430 (tp40) cc_final: 0.8196 (tp40) REVERT: A 363 LYS cc_start: 0.9239 (tppp) cc_final: 0.8960 (mppt) REVERT: A 403 ARG cc_start: 0.8523 (pmm-80) cc_final: 0.8262 (pmm-80) REVERT: B 127 ASP cc_start: 0.9392 (m-30) cc_final: 0.8969 (p0) REVERT: B 131 ARG cc_start: 0.9284 (mtm110) cc_final: 0.9033 (ttm110) REVERT: B 260 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.8309 (p) REVERT: B 280 ASN cc_start: 0.8463 (t0) cc_final: 0.8117 (t0) REVERT: B 285 ARG cc_start: 0.9022 (tpp80) cc_final: 0.8785 (tpp-160) REVERT: B 303 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7619 (mm) REVERT: B 328 GLN cc_start: 0.8506 (tp40) cc_final: 0.8243 (tp40) REVERT: B 339 LEU cc_start: 0.8245 (tp) cc_final: 0.8022 (tm) REVERT: B 352 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8703 (mp0) REVERT: B 449 GLU cc_start: 0.9091 (tp30) cc_final: 0.8709 (tp30) REVERT: C 127 ASP cc_start: 0.9380 (m-30) cc_final: 0.8977 (p0) REVERT: C 131 ARG cc_start: 0.9237 (mtm110) cc_final: 0.8913 (mtm110) REVERT: C 162 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8394 (ptt-90) REVERT: C 174 GLU cc_start: 0.8587 (mp0) cc_final: 0.8351 (pm20) REVERT: C 260 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8301 (p) REVERT: C 280 ASN cc_start: 0.8472 (t0) cc_final: 0.8175 (t0) REVERT: C 328 GLN cc_start: 0.8430 (tp40) cc_final: 0.8195 (tp40) REVERT: C 403 ARG cc_start: 0.8504 (pmm-80) cc_final: 0.8284 (pmm-80) REVERT: D 127 ASP cc_start: 0.9405 (m-30) cc_final: 0.8984 (p0) REVERT: D 131 ARG cc_start: 0.9290 (mtm110) cc_final: 0.9017 (mtm110) REVERT: D 174 GLU cc_start: 0.8718 (mp0) cc_final: 0.8478 (pm20) REVERT: D 260 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8288 (p) REVERT: D 280 ASN cc_start: 0.8469 (t0) cc_final: 0.8115 (t0) REVERT: D 285 ARG cc_start: 0.9063 (tpp80) cc_final: 0.8837 (tpp-160) REVERT: D 288 GLU cc_start: 0.8968 (tt0) cc_final: 0.8615 (mt-10) REVERT: D 328 GLN cc_start: 0.8498 (tp40) cc_final: 0.8256 (tp40) REVERT: D 352 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8709 (mp0) REVERT: D 449 GLU cc_start: 0.9097 (tp30) cc_final: 0.8757 (tp30) REVERT: E 127 ASP cc_start: 0.9356 (m-30) cc_final: 0.8979 (p0) REVERT: E 131 ARG cc_start: 0.9201 (mtm110) cc_final: 0.8812 (mtm110) REVERT: E 162 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8374 (ptt-90) REVERT: E 280 ASN cc_start: 0.8465 (t0) cc_final: 0.8169 (t0) REVERT: E 328 GLN cc_start: 0.8423 (tp40) cc_final: 0.8186 (tp40) REVERT: E 361 LYS cc_start: 0.9095 (mttp) cc_final: 0.8836 (mptt) REVERT: E 403 ARG cc_start: 0.8505 (pmm-80) cc_final: 0.8285 (pmm-80) REVERT: F 127 ASP cc_start: 0.9397 (m-30) cc_final: 0.8979 (p0) REVERT: F 131 ARG cc_start: 0.9285 (mtm110) cc_final: 0.9030 (ttm110) REVERT: F 174 GLU cc_start: 0.8698 (mp0) cc_final: 0.8469 (pm20) REVERT: F 260 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8360 (p) REVERT: F 280 ASN cc_start: 0.8467 (t0) cc_final: 0.8115 (t0) REVERT: F 285 ARG cc_start: 0.9055 (tpp80) cc_final: 0.8825 (tpp-160) REVERT: F 288 GLU cc_start: 0.8963 (tt0) cc_final: 0.8621 (mt-10) REVERT: F 328 GLN cc_start: 0.8505 (tp40) cc_final: 0.8241 (tp40) REVERT: F 449 GLU cc_start: 0.9090 (tp30) cc_final: 0.8749 (tp30) REVERT: G 127 ASP cc_start: 0.9384 (m-30) cc_final: 0.8979 (p0) REVERT: G 131 ARG cc_start: 0.9241 (mtm110) cc_final: 0.8918 (mtm110) REVERT: G 162 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8380 (ptt-90) REVERT: G 174 GLU cc_start: 0.8543 (mp0) cc_final: 0.8306 (pm20) REVERT: G 260 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8352 (p) REVERT: G 280 ASN cc_start: 0.8468 (t0) cc_final: 0.8174 (t0) REVERT: G 328 GLN cc_start: 0.8419 (tp40) cc_final: 0.8181 (tp40) REVERT: G 403 ARG cc_start: 0.8502 (pmm-80) cc_final: 0.8282 (pmm-80) REVERT: H 127 ASP cc_start: 0.9395 (m-30) cc_final: 0.8968 (p0) REVERT: H 128 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8915 (pt) REVERT: H 131 ARG cc_start: 0.9255 (mtm110) cc_final: 0.8884 (mtm110) REVERT: H 260 SER cc_start: 0.8587 (OUTLIER) cc_final: 0.8354 (p) REVERT: H 280 ASN cc_start: 0.8459 (t0) cc_final: 0.8110 (t0) REVERT: H 285 ARG cc_start: 0.9026 (tpp80) cc_final: 0.8791 (tpp-160) REVERT: H 328 GLN cc_start: 0.8500 (tp40) cc_final: 0.8256 (tp40) REVERT: H 339 LEU cc_start: 0.8250 (tp) cc_final: 0.8030 (tm) REVERT: H 352 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8707 (mp0) REVERT: H 449 GLU cc_start: 0.9100 (tp30) cc_final: 0.8717 (tp30) REVERT: J 713 SER cc_start: 0.8859 (t) cc_final: 0.8092 (p) REVERT: J 716 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7234 (tpp-160) REVERT: J 736 ARG cc_start: 0.7590 (mtp-110) cc_final: 0.6956 (ptt180) REVERT: J 827 ASN cc_start: 0.8819 (m-40) cc_final: 0.8497 (p0) REVERT: J 840 MET cc_start: 0.8832 (tpp) cc_final: 0.8608 (tpt) REVERT: I 711 PHE cc_start: 0.8999 (t80) cc_final: 0.8770 (t80) REVERT: I 713 SER cc_start: 0.8829 (t) cc_final: 0.7855 (p) REVERT: I 715 ARG cc_start: 0.8373 (tpp-160) cc_final: 0.8122 (tpp-160) REVERT: I 716 ARG cc_start: 0.7031 (tpp-160) cc_final: 0.6715 (ttm110) REVERT: I 733 ARG cc_start: 0.9621 (tpp-160) cc_final: 0.9243 (mtt90) REVERT: I 736 ARG cc_start: 0.7983 (mtp-110) cc_final: 0.7746 (mtp-110) REVERT: I 793 PHE cc_start: 0.7059 (m-10) cc_final: 0.6330 (m-10) REVERT: I 826 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.4835 (m-80) REVERT: I 827 ASN cc_start: 0.9036 (m-40) cc_final: 0.8728 (p0) REVERT: I 845 ARG cc_start: 0.9529 (mtp-110) cc_final: 0.9172 (mtm110) REVERT: K 713 SER cc_start: 0.8738 (t) cc_final: 0.7848 (p) REVERT: K 715 ARG cc_start: 0.8435 (tpm170) cc_final: 0.8165 (tpp-160) REVERT: K 716 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6895 (ttm110) REVERT: K 733 ARG cc_start: 0.9210 (ttm170) cc_final: 0.8528 (mtt90) REVERT: K 736 ARG cc_start: 0.8052 (mtp-110) cc_final: 0.7706 (mtp-110) REVERT: K 826 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.5360 (m-80) REVERT: K 827 ASN cc_start: 0.9004 (m-40) cc_final: 0.8670 (p0) REVERT: L 713 SER cc_start: 0.8779 (t) cc_final: 0.8008 (p) REVERT: L 733 ARG cc_start: 0.9147 (ttm170) cc_final: 0.8875 (mtt90) REVERT: L 774 ARG cc_start: 0.7807 (ttt-90) cc_final: 0.7493 (ttt90) REVERT: L 827 ASN cc_start: 0.8978 (m-40) cc_final: 0.8718 (p0) REVERT: L 845 ARG cc_start: 0.9574 (mtp-110) cc_final: 0.9266 (ptp-110) REVERT: M 713 SER cc_start: 0.8735 (t) cc_final: 0.7795 (p) REVERT: M 715 ARG cc_start: 0.8590 (tpm170) cc_final: 0.8172 (tpp-160) REVERT: M 716 ARG cc_start: 0.7065 (tpp-160) cc_final: 0.6702 (ttm110) REVERT: M 733 ARG cc_start: 0.9329 (ttm170) cc_final: 0.9058 (mmt90) REVERT: M 736 ARG cc_start: 0.7992 (mtp-110) cc_final: 0.7768 (mtp-110) REVERT: M 793 PHE cc_start: 0.6831 (m-10) cc_final: 0.6216 (m-10) REVERT: M 826 TYR cc_start: 0.6783 (OUTLIER) cc_final: 0.5186 (m-80) REVERT: M 827 ASN cc_start: 0.8978 (m-40) cc_final: 0.8625 (p0) REVERT: N 713 SER cc_start: 0.8901 (t) cc_final: 0.8106 (p) REVERT: N 774 ARG cc_start: 0.7843 (ttt-90) cc_final: 0.7532 (ttt90) REVERT: N 827 ASN cc_start: 0.8814 (m-40) cc_final: 0.8513 (p0) REVERT: N 840 MET cc_start: 0.8865 (tpp) cc_final: 0.8568 (tpt) REVERT: N 845 ARG cc_start: 0.9567 (mtp-110) cc_final: 0.9229 (ptp-110) REVERT: O 713 SER cc_start: 0.8758 (t) cc_final: 0.7840 (p) REVERT: O 715 ARG cc_start: 0.8631 (tpm170) cc_final: 0.8232 (tpp-160) REVERT: O 716 ARG cc_start: 0.7179 (tpp-160) cc_final: 0.6793 (ttm110) REVERT: O 733 ARG cc_start: 0.9281 (ttm170) cc_final: 0.8953 (mtt90) REVERT: O 736 ARG cc_start: 0.8029 (mtp-110) cc_final: 0.7668 (mtp-110) REVERT: O 793 PHE cc_start: 0.6910 (m-10) cc_final: 0.6331 (m-10) REVERT: O 826 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.5394 (m-80) REVERT: O 827 ASN cc_start: 0.8972 (m-40) cc_final: 0.8633 (OUTLIER) REVERT: P 713 SER cc_start: 0.8791 (t) cc_final: 0.8090 (p) REVERT: P 736 ARG cc_start: 0.7831 (mtp-110) cc_final: 0.7137 (ptt180) REVERT: P 738 PHE cc_start: 0.8954 (t80) cc_final: 0.8629 (t80) REVERT: P 827 ASN cc_start: 0.8909 (m-40) cc_final: 0.8557 (p0) REVERT: P 846 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.8701 (t80) outliers start: 66 outliers final: 34 residues processed: 645 average time/residue: 0.7414 time to fit residues: 577.6594 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 : 1.534 ------------------------------------------------------------------------------- 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 260 SER 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 260 SER Chi-restraints excluded: chain D residue 352 GLU 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 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 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 368 ILE Chi-restraints excluded: chain H residue 128 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 716 ARG Chi-restraints excluded: chain J residue 753 LEU Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain I residue 794 GLU Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 832 VAL Chi-restraints excluded: chain I residue 846 PHE Chi-restraints excluded: chain K residue 716 ARG 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 794 GLU Chi-restraints excluded: chain M residue 826 TYR Chi-restraints excluded: chain M residue 846 PHE Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain O residue 826 TYR Chi-restraints excluded: chain O residue 846 PHE Chi-restraints excluded: chain P residue 768 THR 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: 0.6980 chunk 210 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 chunk 446 optimal weight: 30.0000 chunk 288 optimal weight: 0.9980 chunk 387 optimal weight: 2.9990 chunk 321 optimal weight: 0.0030 chunk 25 optimal weight: 0.0770 chunk 356 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.4948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 GLN B 383 ASN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 786 HIS K 731 GLN ** L 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.141745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.080112 restraints weight = 78376.747| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.08 r_work: 0.2858 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4633 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= 0.135 Angle : 0.741 16.831 56144 Z= 0.354 Chirality : 0.041 0.279 6416 Planarity : 0.004 0.046 7256 Dihedral : 4.077 23.321 5680 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.56 % Allowed : 20.63 % Favored : 77.81 % 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: 1.56 (0.12), residues: 5120 helix: 1.34 (0.09), residues: 3528 sheet: -0.10 (0.42), residues: 136 loop : 0.66 (0.18), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 845 TYR 0.024 0.001 TYR F 213 PHE 0.039 0.001 PHE N 711 TRP 0.029 0.001 TRP H 214 HIS 0.006 0.001 HIS O 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (41472) covalent geometry : angle 0.74131 / 0.35 (56144) hydrogen bonds : bond 0.03618 / 2.48 ( 2448) hydrogen bonds : angle 4.36906 / 3.17 ( 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 642 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 575 time to evaluate : 1.682 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 162 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8330 (ptt-90) REVERT: A 260 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8334 (p) REVERT: A 280 ASN cc_start: 0.8419 (t0) cc_final: 0.8161 (t0) REVERT: A 328 GLN cc_start: 0.8409 (tp40) cc_final: 0.8179 (tp40) REVERT: A 363 LYS cc_start: 0.9239 (tppp) cc_final: 0.8979 (mppt) REVERT: A 403 ARG cc_start: 0.8586 (pmm-80) cc_final: 0.8324 (pmm-80) REVERT: B 131 ARG cc_start: 0.9231 (mtm110) cc_final: 0.9016 (ttm110) REVERT: B 260 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8265 (p) REVERT: B 280 ASN cc_start: 0.8411 (t0) cc_final: 0.8130 (t0) REVERT: B 285 ARG cc_start: 0.9049 (tpp80) cc_final: 0.8796 (tpp-160) REVERT: B 303 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7568 (mm) REVERT: B 328 GLN cc_start: 0.8473 (tp40) cc_final: 0.8210 (tp40) REVERT: B 339 LEU cc_start: 0.8237 (tp) cc_final: 0.8018 (tm) REVERT: B 352 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8689 (mp0) REVERT: B 361 LYS cc_start: 0.9155 (mttp) cc_final: 0.8740 (mptt) REVERT: B 449 GLU cc_start: 0.9102 (tp30) cc_final: 0.8704 (tp30) REVERT: B 525 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9233 (mt-10) REVERT: C 162 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8353 (ptt-90) REVERT: C 260 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8399 (p) REVERT: C 280 ASN cc_start: 0.8386 (t0) cc_final: 0.8130 (t0) REVERT: C 328 GLN cc_start: 0.8417 (tp40) cc_final: 0.8176 (tp40) REVERT: C 363 LYS cc_start: 0.9296 (tppp) cc_final: 0.8990 (mppt) REVERT: C 403 ARG cc_start: 0.8577 (pmm-80) cc_final: 0.8314 (pmm-80) REVERT: D 127 ASP cc_start: 0.9413 (m-30) cc_final: 0.8983 (p0) REVERT: D 131 ARG cc_start: 0.9263 (mtm110) cc_final: 0.8991 (mtm110) REVERT: D 174 GLU cc_start: 0.8703 (mp0) cc_final: 0.8474 (pm20) REVERT: D 260 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8388 (p) REVERT: D 280 ASN cc_start: 0.8415 (t0) cc_final: 0.8126 (t0) REVERT: D 285 ARG cc_start: 0.9073 (tpp80) cc_final: 0.8837 (tpp-160) REVERT: D 288 GLU cc_start: 0.8983 (tt0) cc_final: 0.8635 (mt-10) REVERT: D 328 GLN cc_start: 0.8454 (tp40) cc_final: 0.8193 (tp40) REVERT: D 352 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8699 (mp0) REVERT: D 449 GLU cc_start: 0.9106 (tp30) cc_final: 0.8735 (tp30) REVERT: D 525 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9226 (mt-10) REVERT: E 162 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8340 (ptt-90) REVERT: E 171 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8723 (mt) REVERT: E 174 GLU cc_start: 0.8668 (mp0) cc_final: 0.8466 (pm20) REVERT: E 280 ASN cc_start: 0.8390 (t0) cc_final: 0.8138 (t0) REVERT: E 328 GLN cc_start: 0.8416 (tp40) cc_final: 0.8171 (tp40) REVERT: E 361 LYS cc_start: 0.9090 (mttp) cc_final: 0.8826 (mptt) REVERT: E 403 ARG cc_start: 0.8569 (pmm-80) cc_final: 0.8309 (pmm-80) REVERT: F 131 ARG cc_start: 0.9239 (mtm110) cc_final: 0.9021 (ttm110) REVERT: F 174 GLU cc_start: 0.8709 (mp0) cc_final: 0.8498 (pm20) REVERT: F 260 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8436 (p) REVERT: F 280 ASN cc_start: 0.8410 (t0) cc_final: 0.8122 (t0) REVERT: F 285 ARG cc_start: 0.9064 (tpp80) cc_final: 0.8821 (tpp-160) REVERT: F 288 GLU cc_start: 0.8981 (tt0) cc_final: 0.8654 (mt-10) REVERT: F 328 GLN cc_start: 0.8444 (tp40) cc_final: 0.8195 (tp40) REVERT: F 361 LYS cc_start: 0.9164 (mttp) cc_final: 0.8753 (mptt) REVERT: F 449 GLU cc_start: 0.9103 (tp30) cc_final: 0.8731 (tp30) REVERT: F 525 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9241 (mt-10) REVERT: G 127 ASP cc_start: 0.9365 (m-30) cc_final: 0.8989 (p0) REVERT: G 162 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8348 (ptt-90) REVERT: G 260 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8404 (p) REVERT: G 280 ASN cc_start: 0.8386 (t0) cc_final: 0.8129 (t0) REVERT: G 328 GLN cc_start: 0.8418 (tp40) cc_final: 0.8184 (tp40) REVERT: G 361 LYS cc_start: 0.9094 (mttp) cc_final: 0.8830 (mptt) REVERT: G 403 ARG cc_start: 0.8574 (pmm-80) cc_final: 0.8315 (pmm-80) REVERT: H 127 ASP cc_start: 0.9385 (m-30) cc_final: 0.8987 (p0) REVERT: H 128 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8889 (pt) REVERT: H 131 ARG cc_start: 0.9261 (mtm110) cc_final: 0.8970 (mtm110) REVERT: H 260 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8328 (p) REVERT: H 280 ASN cc_start: 0.8403 (t0) cc_final: 0.8118 (t0) REVERT: H 285 ARG cc_start: 0.9048 (tpp80) cc_final: 0.8797 (tpp-160) REVERT: H 328 GLN cc_start: 0.8477 (tp40) cc_final: 0.8214 (tp40) REVERT: H 339 LEU cc_start: 0.8253 (tp) cc_final: 0.8032 (tm) REVERT: H 352 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8693 (mp0) REVERT: H 361 LYS cc_start: 0.9152 (mttp) cc_final: 0.8740 (mptt) REVERT: H 383 ASN cc_start: 0.7963 (t0) cc_final: 0.7750 (t0) REVERT: H 449 GLU cc_start: 0.9114 (tp30) cc_final: 0.8717 (tp30) REVERT: H 525 GLU cc_start: 0.9437 (mt-10) cc_final: 0.9231 (mt-10) REVERT: J 713 SER cc_start: 0.8832 (t) cc_final: 0.7960 (p) REVERT: J 716 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7283 (tpp-160) REVERT: J 736 ARG cc_start: 0.7678 (mtp-110) cc_final: 0.6995 (ptt180) REVERT: J 827 ASN cc_start: 0.8819 (m-40) cc_final: 0.8497 (p0) REVERT: J 840 MET cc_start: 0.8805 (tpp) cc_final: 0.8563 (tpt) REVERT: J 845 ARG cc_start: 0.9668 (ttp80) cc_final: 0.9334 (ptp-110) REVERT: I 711 PHE cc_start: 0.9012 (t80) cc_final: 0.8794 (t80) REVERT: I 713 SER cc_start: 0.8871 (t) cc_final: 0.7947 (p) REVERT: I 715 ARG cc_start: 0.8423 (tpp-160) cc_final: 0.8178 (tpp-160) REVERT: I 716 ARG cc_start: 0.7049 (tpp-160) cc_final: 0.6726 (ttm110) REVERT: I 733 ARG cc_start: 0.9611 (tpp-160) cc_final: 0.9160 (mtt90) REVERT: I 736 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7854 (mtp-110) REVERT: I 826 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.6321 (t80) REVERT: I 827 ASN cc_start: 0.9023 (m-40) cc_final: 0.8603 (p0) REVERT: I 845 ARG cc_start: 0.9532 (mtp-110) cc_final: 0.9214 (ptp-110) REVERT: K 713 SER cc_start: 0.8777 (t) cc_final: 0.7824 (p) REVERT: K 715 ARG cc_start: 0.8452 (tpm170) cc_final: 0.8198 (tpp-160) REVERT: K 716 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.7030 (ttm110) REVERT: K 733 ARG cc_start: 0.9310 (ttm170) cc_final: 0.8619 (mtt90) REVERT: K 736 ARG cc_start: 0.8126 (mtp-110) cc_final: 0.7777 (mtp-110) REVERT: K 793 PHE cc_start: 0.6994 (m-10) cc_final: 0.6449 (m-10) REVERT: K 826 TYR cc_start: 0.6785 (OUTLIER) cc_final: 0.5359 (m-80) REVERT: K 827 ASN cc_start: 0.8991 (m-40) cc_final: 0.8668 (p0) REVERT: L 713 SER cc_start: 0.8881 (t) cc_final: 0.8072 (p) REVERT: L 714 TYR cc_start: 0.6980 (p90) cc_final: 0.6716 (p90) REVERT: L 733 ARG cc_start: 0.9379 (ttm170) cc_final: 0.8975 (mtt90) REVERT: L 827 ASN cc_start: 0.8989 (m-40) cc_final: 0.8769 (p0) REVERT: L 845 ARG cc_start: 0.9558 (mtp-110) cc_final: 0.9221 (ptp-110) REVERT: M 713 SER cc_start: 0.8724 (t) cc_final: 0.7816 (p) REVERT: M 715 ARG cc_start: 0.8622 (tpm170) cc_final: 0.8192 (tpp-160) REVERT: M 716 ARG cc_start: 0.7126 (tpp-160) cc_final: 0.6745 (ttm110) REVERT: M 733 ARG cc_start: 0.9515 (ttm170) cc_final: 0.9117 (mtt90) REVERT: M 736 ARG cc_start: 0.8042 (mtp-110) cc_final: 0.7741 (mtp-110) REVERT: M 826 TYR cc_start: 0.6763 (OUTLIER) cc_final: 0.6338 (t80) REVERT: M 827 ASN cc_start: 0.8978 (m-40) cc_final: 0.8552 (p0) REVERT: N 736 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.6870 (ptt180) REVERT: N 826 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.6482 (t80) REVERT: N 827 ASN cc_start: 0.8795 (m-40) cc_final: 0.8414 (p0) REVERT: N 845 ARG cc_start: 0.9577 (mtp-110) cc_final: 0.9279 (ptp-110) REVERT: N 846 PHE cc_start: 0.9258 (m-80) cc_final: 0.9028 (m-80) REVERT: O 713 SER cc_start: 0.8726 (t) cc_final: 0.7852 (p) REVERT: O 715 ARG cc_start: 0.8623 (tpm170) cc_final: 0.8213 (tpp-160) REVERT: O 716 ARG cc_start: 0.7251 (tpp-160) cc_final: 0.6850 (ttm110) REVERT: O 733 ARG cc_start: 0.9470 (ttm170) cc_final: 0.8995 (mtt90) REVERT: O 736 ARG cc_start: 0.8105 (mtp-110) cc_final: 0.7746 (mtp-110) REVERT: O 793 PHE cc_start: 0.6883 (m-10) cc_final: 0.6508 (m-10) REVERT: O 826 TYR cc_start: 0.6820 (OUTLIER) cc_final: 0.5457 (m-80) REVERT: O 827 ASN cc_start: 0.8979 (m-40) cc_final: 0.8658 (p0) REVERT: P 711 PHE cc_start: 0.9091 (t80) cc_final: 0.8821 (t80) REVERT: P 713 SER cc_start: 0.8977 (t) cc_final: 0.8070 (p) REVERT: P 736 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7148 (ptt180) REVERT: P 827 ASN cc_start: 0.8936 (m-40) cc_final: 0.8623 (p0) REVERT: P 840 MET cc_start: 0.9113 (tpp) cc_final: 0.8909 (tpt) REVERT: P 845 ARG cc_start: 0.9216 (ptp-110) cc_final: 0.8704 (ptp-170) REVERT: P 846 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.8701 (t80) outliers start: 67 outliers final: 33 residues processed: 633 average time/residue: 0.7677 time to fit residues: 587.7779 Evaluate side-chains 589 residues out of total 4304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 531 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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 260 SER 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 158 ASP 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 260 SER Chi-restraints excluded: chain D residue 352 GLU 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 171 LEU Chi-restraints excluded: chain E residue 241 VAL 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 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 368 ILE Chi-restraints excluded: chain H residue 128 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 716 ARG Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain I residue 794 GLU Chi-restraints excluded: chain I residue 826 TYR Chi-restraints excluded: chain I residue 832 VAL Chi-restraints excluded: chain I residue 846 PHE Chi-restraints excluded: chain K residue 716 ARG Chi-restraints excluded: chain K residue 826 TYR Chi-restraints excluded: chain L 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 846 PHE Chi-restraints excluded: chain N residue 768 THR Chi-restraints excluded: chain N residue 826 TYR Chi-restraints excluded: chain O residue 826 TYR Chi-restraints excluded: chain O residue 846 PHE Chi-restraints excluded: chain P residue 768 THR 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 191 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 491 optimal weight: 0.6980 chunk 376 optimal weight: 9.9990 chunk 402 optimal weight: 8.9990 chunk 241 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 300 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 ASN C 383 ASN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN E 383 ASN G 383 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** P 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.140778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.077660 restraints weight = 79349.265| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.19 r_work: 0.2884 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 41472 Z= 0.140 Angle : 0.753 16.870 56144 Z= 0.360 Chirality : 0.042 0.278 6416 Planarity : 0.004 0.045 7256 Dihedral : 4.066 24.459 5680 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.28 % Allowed : 21.00 % Favored : 77.72 % 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: 1.53 (0.12), residues: 5120 helix: 1.35 (0.09), residues: 3576 sheet: -0.09 (0.41), residues: 136 loop : 0.52 (0.18), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 249 TYR 0.010 0.001 TYR E 503 PHE 0.029 0.001 PHE L 711 TRP 0.022 0.001 TRP H 214 HIS 0.006 0.001 HIS O 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (41472) covalent geometry : angle 0.75311 / 0.36 (56144) hydrogen bonds : bond 0.03663 / 2.51 ( 2448) hydrogen bonds : angle 4.37133 / 3.18 ( 6984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19795.85 seconds wall clock time: 336 minutes 34.31 seconds (20194.31 seconds total)