Starting phenix.real_space_refine on Sat Mar 7 04:46:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cm5_30401/03_2026/7cm5_30401.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cm5_30401/03_2026/7cm5_30401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cm5_30401/03_2026/7cm5_30401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cm5_30401/03_2026/7cm5_30401.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cm5_30401/03_2026/7cm5_30401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cm5_30401/03_2026/7cm5_30401.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 184 5.16 5 C 24200 2.51 5 N 6896 2.21 5 O 7024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38304 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4788 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 5.42, per 1000 atoms: 0.14 Number of scatterers: 38304 At special positions: 0 Unit cell: (214.165, 213.11, 83.345, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 184 16.00 O 7024 8.00 N 6896 7.00 C 24200 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: 2.76 Conformation dependent library (CDL) restraints added in 1.5 seconds 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9120 Finding SS restraints... Secondary structure from input PDB file: 320 helices and 8 sheets defined 71.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 62 through 82 removed outlier: 3.581A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 85 through 104 removed outlier: 3.711A pdb=" N LEU A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.502A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 138 through 152 removed outlier: 3.675A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 removed outlier: 4.463A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.529A pdb=" N ALA A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.566A pdb=" N ALA A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.690A pdb=" N GLN A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 283 through 291 Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.897A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.605A pdb=" N PHE A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 338 through 359 removed outlier: 3.516A pdb=" N GLN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.083A pdb=" N SER A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 4.134A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 removed outlier: 3.513A pdb=" N SER A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 425 removed outlier: 3.636A pdb=" N VAL A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) 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 435 removed outlier: 3.799A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.545A pdb=" N PHE A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.874A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.668A pdb=" N VAL A 518 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 Processing helix chain 'A' and resid 531 through 545 Processing helix chain 'A' and resid 573 through 586 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 669 through 678 removed outlier: 4.681A pdb=" N ALA A 674 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 675 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 678 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'B' and resid 62 through 82 removed outlier: 3.582A pdb=" N GLU B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 85 through 104 removed outlier: 3.711A pdb=" N LEU B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 123 removed outlier: 3.501A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 138 through 152 removed outlier: 3.674A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 removed outlier: 4.462A pdb=" N ARG B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.528A pdb=" N ALA B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.566A pdb=" N ALA B 205 " --> pdb=" O ARG B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.691A pdb=" N GLN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 260 Processing helix chain 'B' and resid 264 through 279 Processing helix chain 'B' and resid 283 through 291 Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.897A pdb=" N LEU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.604A pdb=" N PHE B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 338 through 359 removed outlier: 3.516A pdb=" N GLN B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.082A pdb=" N SER B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 4.134A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 removed outlier: 3.513A pdb=" N SER B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 425 removed outlier: 3.636A pdb=" N VAL B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) 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 435 removed outlier: 3.799A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 459 through 476 removed outlier: 3.545A pdb=" N PHE B 476 " --> pdb=" O GLU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.873A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 501 through 507 Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.669A pdb=" N VAL B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 Processing helix chain 'B' and resid 531 through 545 Processing helix chain 'B' and resid 573 through 586 Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 637 through 650 Processing helix chain 'B' and resid 669 through 678 removed outlier: 4.680A pdb=" N ALA B 674 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 675 " --> pdb=" O MET B 672 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 678 " --> pdb=" O VAL B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'C' and resid 62 through 82 removed outlier: 3.582A pdb=" N GLU C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Proline residue: C 70 - end of helix Processing helix chain 'C' and resid 85 through 104 removed outlier: 3.710A pdb=" N LEU C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 123 removed outlier: 3.501A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 133 Processing helix chain 'C' and resid 138 through 152 removed outlier: 3.675A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 removed outlier: 4.462A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.529A pdb=" N ALA C 181 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.566A pdb=" N ALA C 205 " --> pdb=" O ARG C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 236 Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.690A pdb=" N GLN C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 260 Processing helix chain 'C' and resid 264 through 279 Processing helix chain 'C' and resid 283 through 291 Processing helix chain 'C' and resid 295 through 303 removed outlier: 3.897A pdb=" N LEU C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.605A pdb=" N PHE C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 338 through 359 removed outlier: 3.516A pdb=" N GLN C 359 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 removed outlier: 4.083A pdb=" N SER C 366 " --> pdb=" O THR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 4.133A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 removed outlier: 3.513A pdb=" N SER C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 425 removed outlier: 3.635A pdb=" N VAL C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) 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 435 removed outlier: 3.798A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 447 through 453 Processing helix chain 'C' and resid 459 through 476 removed outlier: 3.545A pdb=" N PHE C 476 " --> pdb=" O GLU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.874A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 500 No H-bonds generated for 'chain 'C' and resid 498 through 500' Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.668A pdb=" N VAL C 518 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 Processing helix chain 'C' and resid 531 through 545 Processing helix chain 'C' and resid 573 through 586 Processing helix chain 'C' and resid 606 through 614 Processing helix chain 'C' and resid 637 through 650 Processing helix chain 'C' and resid 669 through 678 removed outlier: 4.680A pdb=" N ALA C 674 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 675 " --> pdb=" O MET C 672 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C 678 " --> pdb=" O VAL C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 697 Processing helix chain 'D' and resid 62 through 82 removed outlier: 3.582A pdb=" N GLU D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 85 through 104 removed outlier: 3.711A pdb=" N LEU D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 123 removed outlier: 3.502A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.675A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 removed outlier: 4.462A pdb=" N ARG D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'D' and resid 177 through 192 removed outlier: 3.528A pdb=" N ALA D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.566A pdb=" N ALA D 205 " --> pdb=" O ARG D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 236 Processing helix chain 'D' and resid 238 through 248 removed outlier: 3.690A pdb=" N GLN D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 260 Processing helix chain 'D' and resid 264 through 279 Processing helix chain 'D' and resid 283 through 291 Processing helix chain 'D' and resid 295 through 303 removed outlier: 3.896A pdb=" N LEU D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.604A pdb=" N PHE D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 338 through 359 removed outlier: 3.515A pdb=" N GLN D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 369 removed outlier: 4.082A pdb=" N SER D 366 " --> pdb=" O THR D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 380 removed outlier: 4.133A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 removed outlier: 3.512A pdb=" N SER D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 425 removed outlier: 3.636A pdb=" N VAL D 417 " --> pdb=" O LYS D 413 " (cutoff:3.500A) 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 435 removed outlier: 3.799A pdb=" N GLU D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 447 through 453 Processing helix chain 'D' and resid 459 through 476 removed outlier: 3.545A pdb=" N PHE D 476 " --> pdb=" O GLU D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.874A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 500 No H-bonds generated for 'chain 'D' and resid 498 through 500' Processing helix chain 'D' and resid 501 through 507 Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.668A pdb=" N VAL D 518 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 525 Processing helix chain 'D' and resid 531 through 545 Processing helix chain 'D' and resid 573 through 586 Processing helix chain 'D' and resid 606 through 614 Processing helix chain 'D' and resid 637 through 650 Processing helix chain 'D' and resid 669 through 678 removed outlier: 4.681A pdb=" N ALA D 674 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 675 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE D 678 " --> pdb=" O VAL D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 697 Processing helix chain 'E' and resid 62 through 82 removed outlier: 3.583A pdb=" N GLU E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 85 through 104 removed outlier: 3.711A pdb=" N LEU E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 123 removed outlier: 3.501A pdb=" N VAL E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 133 Processing helix chain 'E' and resid 138 through 152 removed outlier: 3.674A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 163 removed outlier: 4.462A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 172 Processing helix chain 'E' and resid 177 through 192 removed outlier: 3.529A pdb=" N ALA E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.567A pdb=" N ALA E 205 " --> pdb=" O ARG E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 236 Processing helix chain 'E' and resid 238 through 248 removed outlier: 3.690A pdb=" N GLN E 242 " --> pdb=" O GLY E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 260 Processing helix chain 'E' and resid 264 through 279 Processing helix chain 'E' and resid 283 through 291 Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.897A pdb=" N LEU E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 309 removed outlier: 3.605A pdb=" N PHE E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 338 through 359 removed outlier: 3.516A pdb=" N GLN E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 369 removed outlier: 4.082A pdb=" N SER E 366 " --> pdb=" O THR E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 380 removed outlier: 4.133A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 removed outlier: 3.512A pdb=" N SER E 387 " --> pdb=" O ASN E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 425 removed outlier: 3.635A pdb=" N VAL E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) 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 435 removed outlier: 3.797A pdb=" N GLU E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 447 through 453 Processing helix chain 'E' and resid 459 through 476 removed outlier: 3.544A pdb=" N PHE E 476 " --> pdb=" O GLU E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.874A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 500 No H-bonds generated for 'chain 'E' and resid 498 through 500' Processing helix chain 'E' and resid 501 through 507 Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.668A pdb=" N VAL E 518 " --> pdb=" O LEU E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 525 Processing helix chain 'E' and resid 531 through 545 Processing helix chain 'E' and resid 573 through 586 Processing helix chain 'E' and resid 606 through 614 Processing helix chain 'E' and resid 637 through 650 Processing helix chain 'E' and resid 669 through 678 removed outlier: 4.680A pdb=" N ALA E 674 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL E 675 " --> pdb=" O MET E 672 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE E 678 " --> pdb=" O VAL E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 697 Processing helix chain 'F' and resid 62 through 82 removed outlier: 3.582A pdb=" N GLU F 66 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 85 through 104 removed outlier: 3.711A pdb=" N LEU F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 123 removed outlier: 3.501A pdb=" N VAL F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 138 through 152 removed outlier: 3.674A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 163 removed outlier: 4.463A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 172 Processing helix chain 'F' and resid 177 through 192 removed outlier: 3.528A pdb=" N ALA F 181 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.565A pdb=" N ALA F 205 " --> pdb=" O ARG F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 236 Processing helix chain 'F' and resid 238 through 248 removed outlier: 3.690A pdb=" N GLN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 260 Processing helix chain 'F' and resid 264 through 279 Processing helix chain 'F' and resid 283 through 291 Processing helix chain 'F' and resid 295 through 303 removed outlier: 3.896A pdb=" N LEU F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 309 removed outlier: 3.604A pdb=" N PHE F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 338 through 359 removed outlier: 3.515A pdb=" N GLN F 359 " --> pdb=" O ILE F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 369 removed outlier: 4.082A pdb=" N SER F 366 " --> pdb=" O THR F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 380 removed outlier: 4.133A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 removed outlier: 3.513A pdb=" N SER F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 425 removed outlier: 3.636A pdb=" N VAL F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) 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 435 removed outlier: 3.798A pdb=" N GLU F 435 " --> pdb=" O GLU F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 447 through 453 Processing helix chain 'F' and resid 459 through 476 removed outlier: 3.545A pdb=" N PHE F 476 " --> pdb=" O GLU F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.873A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 500 No H-bonds generated for 'chain 'F' and resid 498 through 500' Processing helix chain 'F' and resid 501 through 507 Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.669A pdb=" N VAL F 518 " --> pdb=" O LEU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 525 Processing helix chain 'F' and resid 531 through 545 Processing helix chain 'F' and resid 573 through 586 Processing helix chain 'F' and resid 606 through 614 Processing helix chain 'F' and resid 637 through 650 Processing helix chain 'F' and resid 669 through 678 removed outlier: 4.681A pdb=" N ALA F 674 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL F 675 " --> pdb=" O MET F 672 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE F 678 " --> pdb=" O VAL F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 697 Processing helix chain 'G' and resid 62 through 82 removed outlier: 3.582A pdb=" N GLU G 66 " --> pdb=" O GLN G 62 " (cutoff:3.500A) Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 85 through 104 removed outlier: 3.710A pdb=" N LEU G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.502A pdb=" N VAL G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 138 through 152 removed outlier: 3.674A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 163 removed outlier: 4.462A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 172 Processing helix chain 'G' and resid 177 through 192 removed outlier: 3.529A pdb=" N ALA G 181 " --> pdb=" O PRO G 177 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.565A pdb=" N ALA G 205 " --> pdb=" O ARG G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL G 211 " --> pdb=" O GLY G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 236 Processing helix chain 'G' and resid 238 through 248 removed outlier: 3.691A pdb=" N GLN G 242 " --> pdb=" O GLY G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 260 Processing helix chain 'G' and resid 264 through 279 Processing helix chain 'G' and resid 283 through 291 Processing helix chain 'G' and resid 295 through 303 removed outlier: 3.897A pdb=" N LEU G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 309 removed outlier: 3.604A pdb=" N PHE G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 328 Processing helix chain 'G' and resid 338 through 359 removed outlier: 3.515A pdb=" N GLN G 359 " --> pdb=" O ILE G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 369 removed outlier: 4.083A pdb=" N SER G 366 " --> pdb=" O THR G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 380 removed outlier: 4.133A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 397 removed outlier: 3.512A pdb=" N SER G 387 " --> pdb=" O ASN G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 425 removed outlier: 3.636A pdb=" N VAL G 417 " --> pdb=" O LYS G 413 " (cutoff:3.500A) 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 435 removed outlier: 3.799A pdb=" N GLU G 435 " --> pdb=" O GLU G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 444 Processing helix chain 'G' and resid 447 through 453 Processing helix chain 'G' and resid 459 through 476 removed outlier: 3.545A pdb=" N PHE G 476 " --> pdb=" O GLU G 472 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.874A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 500 No H-bonds generated for 'chain 'G' and resid 498 through 500' Processing helix chain 'G' and resid 501 through 507 Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.668A pdb=" N VAL G 518 " --> pdb=" O LEU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 525 Processing helix chain 'G' and resid 531 through 545 Processing helix chain 'G' and resid 573 through 586 Processing helix chain 'G' and resid 606 through 614 Processing helix chain 'G' and resid 637 through 650 Processing helix chain 'G' and resid 669 through 678 removed outlier: 4.680A pdb=" N ALA G 674 " --> pdb=" O ASP G 671 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL G 675 " --> pdb=" O MET G 672 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE G 678 " --> pdb=" O VAL G 675 " (cutoff:3.500A) Processing helix chain 'G' and resid 687 through 697 Processing helix chain 'H' and resid 62 through 82 removed outlier: 3.582A pdb=" N GLU H 66 " --> pdb=" O GLN H 62 " (cutoff:3.500A) Proline residue: H 70 - end of helix Processing helix chain 'H' and resid 85 through 104 removed outlier: 3.711A pdb=" N LEU H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 123 removed outlier: 3.501A pdb=" N VAL H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 138 through 152 removed outlier: 3.675A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 163 removed outlier: 4.463A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 172 Processing helix chain 'H' and resid 177 through 192 removed outlier: 3.529A pdb=" N ALA H 181 " --> pdb=" O PRO H 177 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 205 removed outlier: 3.565A pdb=" N ALA H 205 " --> pdb=" O ARG H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL H 211 " --> pdb=" O GLY H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 236 Processing helix chain 'H' and resid 238 through 248 removed outlier: 3.690A pdb=" N GLN H 242 " --> pdb=" O GLY H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 260 Processing helix chain 'H' and resid 264 through 279 Processing helix chain 'H' and resid 283 through 291 Processing helix chain 'H' and resid 295 through 303 removed outlier: 3.897A pdb=" N LEU H 299 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 309 removed outlier: 3.605A pdb=" N PHE H 308 " --> pdb=" O ASP H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 328 Processing helix chain 'H' and resid 338 through 359 removed outlier: 3.516A pdb=" N GLN H 359 " --> pdb=" O ILE H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 369 removed outlier: 4.083A pdb=" N SER H 366 " --> pdb=" O THR H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 380 removed outlier: 4.134A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 removed outlier: 3.511A pdb=" N SER H 387 " --> pdb=" O ASN H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 425 removed outlier: 3.636A pdb=" N VAL H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) 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 435 removed outlier: 3.799A pdb=" N GLU H 435 " --> pdb=" O GLU H 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 444 Processing helix chain 'H' and resid 447 through 453 Processing helix chain 'H' and resid 459 through 476 removed outlier: 3.544A pdb=" N PHE H 476 " --> pdb=" O GLU H 472 " (cutoff:3.500A) Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.873A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 500 No H-bonds generated for 'chain 'H' and resid 498 through 500' Processing helix chain 'H' and resid 501 through 507 Processing helix chain 'H' and resid 514 through 518 removed outlier: 3.669A pdb=" N VAL H 518 " --> pdb=" O LEU H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 525 Processing helix chain 'H' and resid 531 through 545 Processing helix chain 'H' and resid 573 through 586 Processing helix chain 'H' and resid 606 through 614 Processing helix chain 'H' and resid 637 through 650 Processing helix chain 'H' and resid 669 through 678 removed outlier: 4.681A pdb=" N ALA H 674 " --> pdb=" O ASP H 671 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL H 675 " --> pdb=" O MET H 672 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE H 678 " --> pdb=" O VAL H 675 " (cutoff:3.500A) Processing helix chain 'H' and resid 687 through 697 Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.696A pdb=" N VAL A 564 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE A 565 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL A 620 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE A 681 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 591 through 592 removed outlier: 6.695A pdb=" N VAL B 564 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE B 565 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL B 620 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE B 681 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 591 through 592 removed outlier: 6.696A pdb=" N VAL C 564 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE C 565 " --> pdb=" O VAL C 618 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL C 620 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE C 681 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 591 through 592 removed outlier: 6.696A pdb=" N VAL D 564 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE D 565 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL D 620 " --> pdb=" O PHE D 565 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE D 681 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 591 through 592 removed outlier: 6.695A pdb=" N VAL E 564 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE E 565 " --> pdb=" O VAL E 618 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL E 620 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE E 681 " --> pdb=" O ILE E 653 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 591 through 592 removed outlier: 6.695A pdb=" N VAL F 564 " --> pdb=" O PHE F 592 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE F 565 " --> pdb=" O VAL F 618 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL F 620 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE F 681 " --> pdb=" O ILE F 653 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 591 through 592 removed outlier: 6.696A pdb=" N VAL G 564 " --> pdb=" O PHE G 592 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE G 565 " --> pdb=" O VAL G 618 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL G 620 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE G 681 " --> pdb=" O ILE G 653 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 591 through 592 removed outlier: 6.695A pdb=" N VAL H 564 " --> pdb=" O PHE H 592 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE H 565 " --> pdb=" O VAL H 618 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL H 620 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE H 681 " --> pdb=" O ILE H 653 " (cutoff:3.500A) 2048 hydrogen bonds defined for protein. 5976 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: 7.64 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12970 1.34 - 1.46: 5381 1.46 - 1.58: 20337 1.58 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 38928 Sorted by residual: bond pdb=" N ASN C 337 " pdb=" CA ASN C 337 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.04e+00 bond pdb=" N ASN F 337 " pdb=" CA ASN F 337 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.00e+00 bond pdb=" N ASN B 337 " pdb=" CA ASN B 337 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.98e+00 bond pdb=" N ASN D 337 " pdb=" CA ASN D 337 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.89e+00 bond pdb=" N ASN H 337 " pdb=" CA ASN H 337 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.86e+00 ... (remaining 38923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 51231 1.97 - 3.94: 1124 3.94 - 5.91: 181 5.91 - 7.89: 48 7.89 - 9.86: 24 Bond angle restraints: 52608 Sorted by residual: angle pdb=" C SER H 336 " pdb=" N ASN H 337 " pdb=" CA ASN H 337 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C SER B 336 " pdb=" N ASN B 337 " pdb=" CA ASN B 337 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C SER A 336 " pdb=" N ASN A 337 " pdb=" CA ASN A 337 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C SER G 336 " pdb=" N ASN G 337 " pdb=" CA ASN G 337 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C SER D 336 " pdb=" N ASN D 337 " pdb=" CA ASN D 337 " ideal model delta sigma weight residual 121.54 130.18 -8.64 1.91e+00 2.74e-01 2.05e+01 ... (remaining 52603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.08: 22969 15.08 - 30.16: 615 30.16 - 45.24: 120 45.24 - 60.32: 8 60.32 - 75.40: 16 Dihedral angle restraints: 23728 sinusoidal: 9680 harmonic: 14048 Sorted by residual: dihedral pdb=" CA GLU G 174 " pdb=" C GLU G 174 " pdb=" N ARG G 175 " pdb=" CA ARG G 175 " ideal model delta harmonic sigma weight residual -180.00 -162.51 -17.49 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA GLU B 174 " pdb=" C GLU B 174 " pdb=" N ARG B 175 " pdb=" CA ARG B 175 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA GLU E 174 " pdb=" C GLU E 174 " pdb=" N ARG E 175 " pdb=" CA ARG E 175 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 23725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4321 0.042 - 0.085: 1357 0.085 - 0.127: 298 0.127 - 0.170: 25 0.170 - 0.212: 23 Chirality restraints: 6024 Sorted by residual: chirality pdb=" CA ASN G 337 " pdb=" N ASN G 337 " pdb=" C ASN G 337 " pdb=" CB ASN G 337 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ASN A 337 " pdb=" N ASN A 337 " pdb=" C ASN A 337 " pdb=" CB ASN A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ASN E 337 " pdb=" N ASN E 337 " pdb=" C ASN E 337 " pdb=" CB ASN E 337 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 6021 not shown) Planarity restraints: 6816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 283 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C VAL G 283 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL G 283 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU G 284 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 283 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C VAL H 283 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL H 283 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU H 284 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 283 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C VAL D 283 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL D 283 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU D 284 " 0.014 2.00e-02 2.50e+03 ... (remaining 6813 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 11276 2.83 - 3.35: 33651 3.35 - 3.86: 60935 3.86 - 4.38: 71804 4.38 - 4.90: 123065 Nonbonded interactions: 300731 Sorted by model distance: nonbonded pdb=" OE1 GLN D 436 " pdb=" OG SER E 459 " model vdw 2.309 3.040 nonbonded pdb=" OE1 GLN C 436 " pdb=" OG SER D 459 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR A 568 " pdb=" OD1 ASP A 594 " model vdw 2.331 3.040 nonbonded pdb=" OH TYR C 568 " pdb=" OD1 ASP C 594 " model vdw 2.331 3.040 nonbonded pdb=" OH TYR G 568 " pdb=" OD1 ASP G 594 " model vdw 2.331 3.040 ... (remaining 300726 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: 0.11 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' } 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 28.640 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 0.003 0.048 38928 Z= 0.187 Angle : 0.766 9.858 52608 Z= 0.440 Chirality : 0.044 0.212 6024 Planarity : 0.006 0.055 6816 Dihedral : 8.238 75.399 14608 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -3.70 (0.09), residues: 4824 helix: -2.56 (0.06), residues: 3160 sheet: -1.27 (0.43), residues: 152 loop : -1.85 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 121 TYR 0.009 0.001 TYR H 568 PHE 0.032 0.002 PHE C 192 TRP 0.015 0.002 TRP F 214 HIS 0.010 0.002 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00336 (38928) covalent geometry : angle 0.76602 (52608) hydrogen bonds : bond 0.15684 ( 2048) hydrogen bonds : angle 6.49489 ( 5976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1013 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8558 (tp) cc_final: 0.8348 (tm) REVERT: A 174 GLU cc_start: 0.7180 (tt0) cc_final: 0.6915 (tp30) REVERT: A 580 LEU cc_start: 0.8642 (mt) cc_final: 0.7824 (tm) REVERT: A 589 PHE cc_start: 0.7563 (m-10) cc_final: 0.7098 (m-80) REVERT: A 608 ILE cc_start: 0.6242 (mt) cc_final: 0.6030 (pp) REVERT: A 686 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7242 (tm-30) REVERT: A 694 LYS cc_start: 0.7984 (tttt) cc_final: 0.7668 (tptp) REVERT: B 114 GLN cc_start: 0.7543 (mt0) cc_final: 0.7110 (mm-40) REVERT: B 171 LEU cc_start: 0.7283 (mt) cc_final: 0.6964 (mt) REVERT: B 686 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6823 (tm-30) REVERT: B 694 LYS cc_start: 0.7846 (tttt) cc_final: 0.7601 (ttpt) REVERT: C 114 GLN cc_start: 0.7708 (mt0) cc_final: 0.7362 (tm-30) REVERT: C 117 CYS cc_start: 0.7607 (m) cc_final: 0.7235 (m) REVERT: C 580 LEU cc_start: 0.8542 (mt) cc_final: 0.7834 (tm) REVERT: C 608 ILE cc_start: 0.6300 (mt) cc_final: 0.6029 (pp) REVERT: C 643 ILE cc_start: 0.8160 (mt) cc_final: 0.7887 (tp) REVERT: C 686 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7240 (tt0) REVERT: C 694 LYS cc_start: 0.7929 (tttt) cc_final: 0.7588 (tptp) REVERT: C 696 ILE cc_start: 0.7931 (mt) cc_final: 0.7693 (pt) REVERT: D 98 LEU cc_start: 0.7914 (tt) cc_final: 0.7691 (tp) REVERT: D 694 LYS cc_start: 0.7868 (tttt) cc_final: 0.7607 (ttmt) REVERT: E 571 ASN cc_start: 0.7757 (m-40) cc_final: 0.7244 (t0) REVERT: E 580 LEU cc_start: 0.8404 (mt) cc_final: 0.7741 (tm) REVERT: E 696 ILE cc_start: 0.7893 (mt) cc_final: 0.7687 (pt) REVERT: F 580 LEU cc_start: 0.8850 (mt) cc_final: 0.8118 (tm) REVERT: F 686 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6756 (tm-30) REVERT: F 694 LYS cc_start: 0.7989 (tttt) cc_final: 0.7579 (ttmt) REVERT: G 114 GLN cc_start: 0.7783 (mt0) cc_final: 0.7578 (tm-30) REVERT: G 580 LEU cc_start: 0.8537 (mt) cc_final: 0.7808 (tm) REVERT: G 608 ILE cc_start: 0.6337 (mt) cc_final: 0.6069 (pp) REVERT: G 672 MET cc_start: 0.5110 (ptm) cc_final: 0.4833 (ppp) REVERT: G 694 LYS cc_start: 0.7941 (tttt) cc_final: 0.7654 (tptp) REVERT: G 696 ILE cc_start: 0.7934 (mt) cc_final: 0.7704 (pt) REVERT: H 114 GLN cc_start: 0.7504 (mt0) cc_final: 0.7147 (mm-40) REVERT: H 694 LYS cc_start: 0.7768 (tttt) cc_final: 0.7543 (ttpt) outliers start: 0 outliers final: 0 residues processed: 1013 average time/residue: 0.8409 time to fit residues: 995.7102 Evaluate side-chains 372 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.6980 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 1.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN A 609 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN B 143 GLN B 150 GLN B 534 HIS ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN C 534 HIS ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN C 616 ASN D 143 GLN D 150 GLN D 280 ASN D 534 HIS ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN F 170 ASN F 280 ASN F 337 ASN F 534 HIS ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 GLN ** G 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 609 GLN G 616 ASN H 97 GLN H 150 GLN H 170 ASN H 534 HIS ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.168409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109381 restraints weight = 52238.838| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.96 r_work: 0.3244 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 38928 Z= 0.117 Angle : 0.559 10.470 52608 Z= 0.280 Chirality : 0.039 0.160 6024 Planarity : 0.005 0.063 6816 Dihedral : 4.009 14.736 5312 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.26 % Allowed : 11.18 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.11), residues: 4824 helix: -0.64 (0.08), residues: 3280 sheet: -0.95 (0.41), residues: 152 loop : -1.04 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 403 TYR 0.010 0.002 TYR B 503 PHE 0.023 0.002 PHE C 433 TRP 0.018 0.001 TRP F 412 HIS 0.005 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00272 (38928) covalent geometry : angle 0.55870 (52608) hydrogen bonds : bond 0.03482 ( 2048) hydrogen bonds : angle 3.76790 ( 5976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 482 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.7243 (mp10) cc_final: 0.7004 (pp30) REVERT: A 131 ARG cc_start: 0.7755 (mtm110) cc_final: 0.7440 (mtm-85) REVERT: A 174 GLU cc_start: 0.7966 (tt0) cc_final: 0.7614 (mt-10) REVERT: A 252 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: A 285 ARG cc_start: 0.7842 (mmt-90) cc_final: 0.7625 (mmt-90) REVERT: A 355 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7227 (mt) REVERT: A 367 ASP cc_start: 0.7376 (t0) cc_final: 0.6981 (m-30) REVERT: A 434 ARG cc_start: 0.8399 (ttp80) cc_final: 0.8005 (ttp-110) REVERT: A 521 GLN cc_start: 0.8746 (tt0) cc_final: 0.8466 (tp40) REVERT: A 580 LEU cc_start: 0.8342 (mt) cc_final: 0.7716 (tm) REVERT: A 615 ARG cc_start: 0.6437 (ttt180) cc_final: 0.5929 (ttt-90) REVERT: A 630 MET cc_start: 0.4127 (mmp) cc_final: 0.3792 (ppp) REVERT: A 686 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7320 (tm-30) REVERT: A 694 LYS cc_start: 0.7985 (tttt) cc_final: 0.7478 (tptp) REVERT: B 98 LEU cc_start: 0.7809 (pp) cc_final: 0.7565 (pt) REVERT: B 521 GLN cc_start: 0.8908 (tt0) cc_final: 0.8529 (tp-100) REVERT: B 580 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8294 (mm) REVERT: B 615 ARG cc_start: 0.7415 (ttt180) cc_final: 0.6971 (ttt-90) REVERT: B 655 PRO cc_start: 0.7823 (Cg_exo) cc_final: 0.7457 (Cg_endo) REVERT: B 686 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6871 (tm-30) REVERT: B 694 LYS cc_start: 0.7942 (tttt) cc_final: 0.7587 (tmmt) REVERT: C 150 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7695 (tp40) REVERT: C 252 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: C 285 ARG cc_start: 0.7802 (mmt-90) cc_final: 0.7572 (mmt-90) REVERT: C 355 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7122 (mt) REVERT: C 367 ASP cc_start: 0.7238 (m-30) cc_final: 0.6948 (m-30) REVERT: C 449 GLU cc_start: 0.8476 (tp30) cc_final: 0.8063 (mp0) REVERT: C 521 GLN cc_start: 0.8682 (tt0) cc_final: 0.8443 (tp40) REVERT: C 655 PRO cc_start: 0.7314 (Cg_exo) cc_final: 0.6921 (Cg_endo) REVERT: C 686 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7447 (tm-30) REVERT: C 694 LYS cc_start: 0.7998 (tttt) cc_final: 0.7485 (tptp) REVERT: D 521 GLN cc_start: 0.8867 (tt0) cc_final: 0.8520 (tp40) REVERT: D 580 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8227 (mm) REVERT: D 615 ARG cc_start: 0.7328 (ttt180) cc_final: 0.7024 (mmm-85) REVERT: D 655 PRO cc_start: 0.7797 (Cg_exo) cc_final: 0.7418 (Cg_endo) REVERT: E 114 GLN cc_start: 0.7367 (tm-30) cc_final: 0.6819 (tm-30) REVERT: E 118 ASP cc_start: 0.8235 (m-30) cc_final: 0.8004 (m-30) REVERT: E 288 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7834 (mt-10) REVERT: E 403 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.7080 (mtp180) REVERT: E 580 LEU cc_start: 0.8303 (mt) cc_final: 0.7689 (tm) REVERT: E 615 ARG cc_start: 0.6504 (ttt180) cc_final: 0.6303 (mtp180) REVERT: E 630 MET cc_start: 0.3630 (mmp) cc_final: 0.3250 (ppp) REVERT: E 655 PRO cc_start: 0.7290 (Cg_exo) cc_final: 0.6945 (Cg_endo) REVERT: E 672 MET cc_start: 0.5384 (ptm) cc_final: 0.5002 (ppp) REVERT: F 98 LEU cc_start: 0.7562 (pp) cc_final: 0.7185 (pp) REVERT: F 174 GLU cc_start: 0.7950 (tt0) cc_final: 0.7618 (mt-10) REVERT: F 363 LYS cc_start: 0.8020 (tppt) cc_final: 0.7779 (tppt) REVERT: F 521 GLN cc_start: 0.8856 (tt0) cc_final: 0.8497 (tp-100) REVERT: F 655 PRO cc_start: 0.7784 (Cg_exo) cc_final: 0.7406 (Cg_endo) REVERT: F 686 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6818 (tm-30) REVERT: G 252 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: G 285 ARG cc_start: 0.7817 (mmt-90) cc_final: 0.7588 (mmt-90) REVERT: G 367 ASP cc_start: 0.7316 (m-30) cc_final: 0.7106 (m-30) REVERT: G 434 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7987 (ttp-110) REVERT: G 449 GLU cc_start: 0.8533 (tp30) cc_final: 0.8234 (mp0) REVERT: G 521 GLN cc_start: 0.8712 (tt0) cc_final: 0.8468 (tp40) REVERT: G 615 ARG cc_start: 0.6301 (ttt-90) cc_final: 0.6031 (ttt-90) REVERT: G 655 PRO cc_start: 0.7288 (Cg_exo) cc_final: 0.6883 (Cg_endo) REVERT: G 672 MET cc_start: 0.5552 (ptm) cc_final: 0.5193 (ppp) REVERT: G 694 LYS cc_start: 0.8051 (tttt) cc_final: 0.7530 (tptp) REVERT: H 98 LEU cc_start: 0.7675 (pp) cc_final: 0.7296 (pp) REVERT: H 138 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6727 (tm) REVERT: H 363 LYS cc_start: 0.7997 (tppt) cc_final: 0.7759 (tppt) REVERT: H 521 GLN cc_start: 0.8878 (tt0) cc_final: 0.8560 (tp-100) REVERT: H 580 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8250 (mm) REVERT: H 615 ARG cc_start: 0.7461 (ttt180) cc_final: 0.7035 (ttt-90) REVERT: H 655 PRO cc_start: 0.7821 (Cg_exo) cc_final: 0.7451 (Cg_endo) REVERT: H 694 LYS cc_start: 0.7645 (tttt) cc_final: 0.7404 (ttpt) outliers start: 133 outliers final: 20 residues processed: 590 average time/residue: 0.8064 time to fit residues: 561.7742 Evaluate side-chains 354 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 324 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 360 optimal weight: 5.9990 chunk 439 optimal weight: 0.5980 chunk 402 optimal weight: 0.0770 chunk 114 optimal weight: 7.9990 chunk 270 optimal weight: 1.9990 chunk 454 optimal weight: 0.7980 chunk 225 optimal weight: 0.1980 chunk 470 optimal weight: 0.8980 chunk 482 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 365 optimal weight: 5.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 585 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS C 383 ASN C 423 GLN C 575 GLN C 700 GLN D 269 HIS ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 HIS ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 GLN G 575 GLN H 452 GLN H 534 HIS ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.166646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.107199 restraints weight = 51613.045| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.06 r_work: 0.3192 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 38928 Z= 0.101 Angle : 0.511 10.595 52608 Z= 0.254 Chirality : 0.038 0.147 6024 Planarity : 0.004 0.046 6816 Dihedral : 3.730 14.622 5312 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.45 % Allowed : 12.82 % Favored : 84.73 % 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: -0.10 (0.12), residues: 4824 helix: 0.24 (0.09), residues: 3256 sheet: -0.74 (0.39), residues: 152 loop : -0.39 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 131 TYR 0.009 0.001 TYR B 503 PHE 0.013 0.001 PHE F 433 TRP 0.011 0.001 TRP F 103 HIS 0.003 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00230 (38928) covalent geometry : angle 0.51080 (52608) hydrogen bonds : bond 0.03236 ( 2048) hydrogen bonds : angle 3.43788 ( 5976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 389 time to evaluate : 1.277 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: A 97 GLN cc_start: 0.7326 (mp10) cc_final: 0.7019 (pp30) REVERT: A 174 GLU cc_start: 0.7998 (tt0) cc_final: 0.7569 (mt-10) REVERT: A 252 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: A 355 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7219 (mt) REVERT: A 367 ASP cc_start: 0.7371 (t0) cc_final: 0.7039 (m-30) REVERT: A 449 GLU cc_start: 0.8547 (tp30) cc_final: 0.8321 (mp0) REVERT: A 521 GLN cc_start: 0.8778 (tt0) cc_final: 0.8460 (tp40) REVERT: A 580 LEU cc_start: 0.8351 (mt) cc_final: 0.7764 (tm) REVERT: A 686 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7425 (tm-30) REVERT: A 694 LYS cc_start: 0.8045 (tttt) cc_final: 0.7527 (tptp) REVERT: B 130 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8059 (mm) REVERT: B 521 GLN cc_start: 0.8849 (tt0) cc_final: 0.8541 (tp40) REVERT: B 569 ARG cc_start: 0.7300 (tpp80) cc_final: 0.7050 (tpp-160) REVERT: B 580 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8338 (mm) REVERT: B 615 ARG cc_start: 0.7440 (ttt180) cc_final: 0.7028 (ttt-90) REVERT: B 655 PRO cc_start: 0.7764 (Cg_exo) cc_final: 0.7407 (Cg_endo) REVERT: B 686 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6822 (tm-30) REVERT: C 149 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7504 (tm-30) REVERT: C 150 GLN cc_start: 0.7990 (tp40) cc_final: 0.7574 (tp40) REVERT: C 252 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: C 285 ARG cc_start: 0.7819 (mmt-90) cc_final: 0.7608 (mmt-90) REVERT: C 355 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7195 (mt) REVERT: C 449 GLU cc_start: 0.8584 (tp30) cc_final: 0.8235 (mp0) REVERT: C 521 GLN cc_start: 0.8720 (tt0) cc_final: 0.8448 (tp40) REVERT: C 615 ARG cc_start: 0.6600 (mtp180) cc_final: 0.6389 (ttt-90) REVERT: C 686 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7455 (tm-30) REVERT: C 694 LYS cc_start: 0.8036 (tttt) cc_final: 0.7506 (tptp) REVERT: D 97 GLN cc_start: 0.7378 (tm130) cc_final: 0.7055 (tm130) REVERT: D 146 ARG cc_start: 0.7731 (mtm110) cc_final: 0.7444 (ptm-80) REVERT: D 363 LYS cc_start: 0.7933 (tppt) cc_final: 0.7598 (tppp) REVERT: D 521 GLN cc_start: 0.8911 (tt0) cc_final: 0.8571 (tp40) REVERT: D 580 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8261 (mm) REVERT: D 615 ARG cc_start: 0.7501 (ttt180) cc_final: 0.7137 (ttt-90) REVERT: D 655 PRO cc_start: 0.7738 (Cg_exo) cc_final: 0.7371 (Cg_endo) REVERT: E 114 GLN cc_start: 0.7495 (tm-30) cc_final: 0.7001 (tm-30) REVERT: E 118 ASP cc_start: 0.8233 (m-30) cc_final: 0.7984 (m-30) REVERT: E 151 ILE cc_start: 0.8079 (tp) cc_final: 0.7857 (tp) REVERT: E 288 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7772 (mt-10) REVERT: E 355 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7429 (mt) REVERT: E 521 GLN cc_start: 0.8770 (tt0) cc_final: 0.8435 (tp40) REVERT: E 580 LEU cc_start: 0.8324 (mt) cc_final: 0.7734 (tm) REVERT: E 655 PRO cc_start: 0.7526 (Cg_exo) cc_final: 0.7184 (Cg_endo) REVERT: F 174 GLU cc_start: 0.7928 (tt0) cc_final: 0.7662 (mt-10) REVERT: F 363 LYS cc_start: 0.8120 (tppt) cc_final: 0.7641 (tptm) REVERT: F 521 GLN cc_start: 0.8801 (tt0) cc_final: 0.8382 (tp40) REVERT: F 580 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8270 (mm) REVERT: F 640 HIS cc_start: 0.7464 (t-90) cc_final: 0.7237 (t-90) REVERT: F 669 PRO cc_start: 0.5459 (Cg_exo) cc_final: 0.4901 (Cg_endo) REVERT: F 686 GLU cc_start: 0.7541 (mt-10) cc_final: 0.6879 (tm-30) REVERT: G 252 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: G 355 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7364 (mt) REVERT: G 449 GLU cc_start: 0.8592 (tp30) cc_final: 0.8272 (mp0) REVERT: G 521 GLN cc_start: 0.8746 (tt0) cc_final: 0.8449 (tp40) REVERT: G 580 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7990 (mm) REVERT: G 589 PHE cc_start: 0.7642 (m-10) cc_final: 0.7150 (m-80) REVERT: G 615 ARG cc_start: 0.6369 (ttt-90) cc_final: 0.6165 (ttt-90) REVERT: G 694 LYS cc_start: 0.8060 (tttt) cc_final: 0.7535 (tptp) REVERT: H 138 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6749 (tm) REVERT: H 249 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.7803 (mmm160) REVERT: H 361 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.8004 (mtmm) REVERT: H 363 LYS cc_start: 0.8019 (tppt) cc_final: 0.7419 (tppp) REVERT: H 434 ARG cc_start: 0.8487 (ttm170) cc_final: 0.8250 (ttp80) REVERT: H 521 GLN cc_start: 0.8884 (tt0) cc_final: 0.8566 (tp40) REVERT: H 580 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8289 (mm) REVERT: H 615 ARG cc_start: 0.7560 (ttt180) cc_final: 0.7157 (ttt-90) REVERT: H 655 PRO cc_start: 0.7771 (Cg_exo) cc_final: 0.7410 (Cg_endo) REVERT: H 694 LYS cc_start: 0.7675 (tttt) cc_final: 0.7434 (ttpt) outliers start: 100 outliers final: 25 residues processed: 469 average time/residue: 0.8329 time to fit residues: 458.3861 Evaluate side-chains 358 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 318 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 580 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 355 ILE Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 334 optimal weight: 0.0980 chunk 336 optimal weight: 0.8980 chunk 217 optimal weight: 0.7980 chunk 234 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 465 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 254 optimal weight: 0.7980 chunk 415 optimal weight: 3.9990 chunk 169 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 143 GLN B 534 HIS ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS D 534 HIS ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN F 534 HIS F 575 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.165147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.104767 restraints weight = 51657.970| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.94 r_work: 0.3171 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 38928 Z= 0.101 Angle : 0.509 11.158 52608 Z= 0.251 Chirality : 0.038 0.184 6024 Planarity : 0.004 0.072 6816 Dihedral : 3.604 13.901 5312 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.79 % Allowed : 13.41 % Favored : 83.80 % 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: 0.54 (0.12), residues: 4824 helix: 0.69 (0.09), residues: 3280 sheet: -0.54 (0.41), residues: 152 loop : -0.05 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 131 TYR 0.009 0.001 TYR B 503 PHE 0.014 0.001 PHE D 96 TRP 0.011 0.001 TRP B 103 HIS 0.003 0.001 HIS F 269 Details of bonding type rmsd covalent geometry : bond 0.00234 (38928) covalent geometry : angle 0.50859 (52608) hydrogen bonds : bond 0.03083 ( 2048) hydrogen bonds : angle 3.24928 ( 5976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 382 time to evaluate : 1.479 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: A 174 GLU cc_start: 0.8014 (tt0) cc_final: 0.7666 (mt-10) REVERT: A 252 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: A 355 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7330 (mt) REVERT: A 367 ASP cc_start: 0.7432 (t0) cc_final: 0.7084 (m-30) REVERT: A 521 GLN cc_start: 0.8772 (tt0) cc_final: 0.8457 (tp40) REVERT: A 580 LEU cc_start: 0.8358 (mt) cc_final: 0.7789 (tm) REVERT: A 686 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7442 (tm-30) REVERT: A 694 LYS cc_start: 0.8064 (tttt) cc_final: 0.7565 (tptp) REVERT: B 130 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8070 (mm) REVERT: B 521 GLN cc_start: 0.8819 (tt0) cc_final: 0.8480 (tp-100) REVERT: B 580 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8291 (mm) REVERT: B 615 ARG cc_start: 0.7493 (ttt180) cc_final: 0.7081 (ttt-90) REVERT: B 655 PRO cc_start: 0.7678 (Cg_exo) cc_final: 0.7339 (Cg_endo) REVERT: B 686 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6836 (tm-30) REVERT: C 97 GLN cc_start: 0.7248 (mp10) cc_final: 0.6992 (pp30) REVERT: C 98 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6834 (pt) REVERT: C 149 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7461 (tm-30) REVERT: C 252 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: C 521 GLN cc_start: 0.8770 (tt0) cc_final: 0.8474 (tp40) REVERT: C 580 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8025 (mm) REVERT: C 686 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7469 (tm-30) REVERT: C 694 LYS cc_start: 0.8035 (tttt) cc_final: 0.7516 (tptp) REVERT: D 97 GLN cc_start: 0.7274 (tm130) cc_final: 0.7017 (tm130) REVERT: D 521 GLN cc_start: 0.8901 (tt0) cc_final: 0.8548 (tp-100) REVERT: D 580 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8261 (mm) REVERT: D 586 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8152 (mm) REVERT: D 615 ARG cc_start: 0.7562 (ttt180) cc_final: 0.7218 (ttt-90) REVERT: D 630 MET cc_start: 0.4625 (mmm) cc_final: 0.3889 (ppp) REVERT: D 655 PRO cc_start: 0.7709 (Cg_exo) cc_final: 0.7379 (Cg_endo) REVERT: E 114 GLN cc_start: 0.7500 (tm-30) cc_final: 0.7245 (tm-30) REVERT: E 118 ASP cc_start: 0.8256 (m-30) cc_final: 0.8012 (m-30) REVERT: E 224 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8137 (mtt180) REVERT: E 288 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7884 (mt-10) REVERT: E 521 GLN cc_start: 0.8772 (tt0) cc_final: 0.8466 (tp40) REVERT: E 580 LEU cc_start: 0.8366 (mt) cc_final: 0.7824 (tm) REVERT: E 694 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7799 (tmmt) REVERT: F 97 GLN cc_start: 0.7266 (pp30) cc_final: 0.7039 (tm130) REVERT: F 146 ARG cc_start: 0.7646 (mtm110) cc_final: 0.7307 (ptm-80) REVERT: F 174 GLU cc_start: 0.7958 (tt0) cc_final: 0.7701 (mt-10) REVERT: F 521 GLN cc_start: 0.8840 (tt0) cc_final: 0.8494 (tp-100) REVERT: F 580 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8247 (mm) REVERT: F 630 MET cc_start: 0.4789 (mmm) cc_final: 0.4127 (ppp) REVERT: F 640 HIS cc_start: 0.7493 (t-90) cc_final: 0.7276 (t-90) REVERT: F 669 PRO cc_start: 0.5337 (Cg_exo) cc_final: 0.4963 (Cg_endo) REVERT: F 686 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6907 (tm-30) REVERT: G 224 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8106 (mtt180) REVERT: G 252 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: G 288 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8119 (mt-10) REVERT: G 449 GLU cc_start: 0.8558 (tp30) cc_final: 0.8355 (mp0) REVERT: G 521 GLN cc_start: 0.8779 (tt0) cc_final: 0.8466 (tp40) REVERT: G 580 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8022 (mm) REVERT: G 615 ARG cc_start: 0.6490 (ttt-90) cc_final: 0.6244 (ttt-90) REVERT: G 630 MET cc_start: 0.3786 (mmm) cc_final: 0.3586 (ppp) REVERT: G 672 MET cc_start: 0.5696 (ptm) cc_final: 0.5393 (pp-130) REVERT: G 694 LYS cc_start: 0.8047 (tttt) cc_final: 0.7530 (tptp) REVERT: H 363 LYS cc_start: 0.8182 (tppt) cc_final: 0.7910 (tptm) REVERT: H 521 GLN cc_start: 0.8846 (tt0) cc_final: 0.8541 (tp40) REVERT: H 569 ARG cc_start: 0.7240 (tpp80) cc_final: 0.7036 (tpp-160) REVERT: H 580 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8281 (mm) REVERT: H 586 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8109 (mm) REVERT: H 615 ARG cc_start: 0.7583 (ttt180) cc_final: 0.7224 (ttt-90) REVERT: H 655 PRO cc_start: 0.7694 (Cg_exo) cc_final: 0.7354 (Cg_endo) REVERT: H 669 PRO cc_start: 0.5607 (Cg_exo) cc_final: 0.5258 (Cg_endo) REVERT: H 694 LYS cc_start: 0.7684 (tttt) cc_final: 0.7459 (ttpt) outliers start: 114 outliers final: 29 residues processed: 472 average time/residue: 0.7807 time to fit residues: 435.6527 Evaluate side-chains 367 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 322 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 612 MET Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 580 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 608 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 41 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 308 optimal weight: 0.7980 chunk 333 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 30 optimal weight: 0.0570 chunk 257 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 321 optimal weight: 0.9980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.163869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103069 restraints weight = 51403.421| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.92 r_work: 0.3139 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 38928 Z= 0.108 Angle : 0.516 10.853 52608 Z= 0.255 Chirality : 0.038 0.195 6024 Planarity : 0.004 0.050 6816 Dihedral : 3.583 12.912 5312 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.77 % Allowed : 14.34 % Favored : 82.89 % 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: 0.79 (0.12), residues: 4824 helix: 0.87 (0.09), residues: 3344 sheet: -0.20 (0.42), residues: 152 loop : 0.01 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 131 TYR 0.009 0.001 TYR E 687 PHE 0.010 0.001 PHE F 617 TRP 0.014 0.001 TRP H 103 HIS 0.003 0.001 HIS F 269 Details of bonding type rmsd covalent geometry : bond 0.00256 (38928) covalent geometry : angle 0.51644 (52608) hydrogen bonds : bond 0.03158 ( 2048) hydrogen bonds : angle 3.21701 ( 5976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 346 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.8010 (tt0) cc_final: 0.7695 (mt-10) REVERT: A 252 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: A 367 ASP cc_start: 0.7355 (t0) cc_final: 0.7030 (m-30) REVERT: A 399 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.6061 (mp0) REVERT: A 521 GLN cc_start: 0.8788 (tt0) cc_final: 0.8472 (tp40) REVERT: A 580 LEU cc_start: 0.8383 (mt) cc_final: 0.7796 (tm) REVERT: A 686 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7470 (tm-30) REVERT: A 694 LYS cc_start: 0.8041 (tttt) cc_final: 0.7553 (tptp) REVERT: B 97 GLN cc_start: 0.7229 (pp30) cc_final: 0.6985 (tm130) REVERT: B 130 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8150 (mm) REVERT: B 363 LYS cc_start: 0.8148 (tppp) cc_final: 0.7908 (tptp) REVERT: B 395 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7548 (mtp180) REVERT: B 521 GLN cc_start: 0.8853 (tt0) cc_final: 0.8410 (tp-100) REVERT: B 580 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8308 (mm) REVERT: B 615 ARG cc_start: 0.7444 (ttt180) cc_final: 0.7126 (ttt-90) REVERT: B 686 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7014 (tm-30) REVERT: B 696 ILE cc_start: 0.8006 (tt) cc_final: 0.7591 (pt) REVERT: C 139 GLU cc_start: 0.7576 (mp0) cc_final: 0.7353 (tm-30) REVERT: C 149 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7499 (tm-30) REVERT: C 252 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: C 399 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5924 (mp0) REVERT: C 521 GLN cc_start: 0.8776 (tt0) cc_final: 0.8475 (tp40) REVERT: C 580 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8018 (mm) REVERT: C 686 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7474 (tm-30) REVERT: C 694 LYS cc_start: 0.8047 (tttt) cc_final: 0.7533 (tptp) REVERT: D 97 GLN cc_start: 0.7272 (tm130) cc_final: 0.7041 (tm130) REVERT: D 521 GLN cc_start: 0.8858 (tt0) cc_final: 0.8530 (tp-100) REVERT: D 580 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8269 (mm) REVERT: D 615 ARG cc_start: 0.7571 (ttt180) cc_final: 0.7237 (ttt-90) REVERT: D 630 MET cc_start: 0.4517 (mmm) cc_final: 0.3848 (ppp) REVERT: D 655 PRO cc_start: 0.7625 (Cg_exo) cc_final: 0.7278 (Cg_endo) REVERT: E 114 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7241 (tm-30) REVERT: E 118 ASP cc_start: 0.8217 (m-30) cc_final: 0.8006 (m-30) REVERT: E 139 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6996 (tm-30) REVERT: E 224 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8160 (mtt180) REVERT: E 288 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7824 (mt-10) REVERT: E 521 GLN cc_start: 0.8768 (tt0) cc_final: 0.8451 (tp40) REVERT: E 580 LEU cc_start: 0.8395 (mt) cc_final: 0.7787 (tm) REVERT: E 694 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7679 (tmmt) REVERT: F 97 GLN cc_start: 0.7301 (pp30) cc_final: 0.7091 (tm130) REVERT: F 174 GLU cc_start: 0.7972 (tt0) cc_final: 0.7694 (mt-10) REVERT: F 395 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7545 (mtp180) REVERT: F 521 GLN cc_start: 0.8785 (tt0) cc_final: 0.8376 (tp-100) REVERT: F 580 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8272 (mm) REVERT: F 630 MET cc_start: 0.4675 (mmm) cc_final: 0.3921 (ppp) REVERT: F 669 PRO cc_start: 0.5358 (Cg_exo) cc_final: 0.5136 (Cg_endo) REVERT: F 686 GLU cc_start: 0.7669 (mt-10) cc_final: 0.6944 (tm-30) REVERT: G 224 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8086 (mtt180) REVERT: G 252 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: G 288 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8129 (mt-10) REVERT: G 521 GLN cc_start: 0.8783 (tt0) cc_final: 0.8469 (tp40) REVERT: G 580 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8021 (mm) REVERT: G 615 ARG cc_start: 0.6482 (ttt-90) cc_final: 0.5760 (ttt-90) REVERT: G 672 MET cc_start: 0.5720 (ptm) cc_final: 0.5357 (pp-130) REVERT: G 694 LYS cc_start: 0.8064 (tttt) cc_final: 0.7554 (tptp) REVERT: H 395 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7610 (mtp180) REVERT: H 434 ARG cc_start: 0.8505 (ttm170) cc_final: 0.8210 (ttp80) REVERT: H 521 GLN cc_start: 0.8842 (tt0) cc_final: 0.8517 (tp-100) REVERT: H 580 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8276 (mm) REVERT: H 615 ARG cc_start: 0.7529 (ttt180) cc_final: 0.7180 (ttt-90) REVERT: H 655 PRO cc_start: 0.7633 (Cg_exo) cc_final: 0.7309 (Cg_endo) REVERT: H 694 LYS cc_start: 0.7725 (tttt) cc_final: 0.7391 (tmmt) outliers start: 113 outliers final: 32 residues processed: 433 average time/residue: 0.8412 time to fit residues: 429.2700 Evaluate side-chains 364 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 315 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 612 MET Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 580 LEU Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 150 optimal weight: 7.9990 chunk 222 optimal weight: 0.6980 chunk 327 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 461 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 307 optimal weight: 0.9980 chunk 311 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 423 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.162927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.101867 restraints weight = 51471.579| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.91 r_work: 0.3120 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 38928 Z= 0.115 Angle : 0.530 13.646 52608 Z= 0.260 Chirality : 0.038 0.190 6024 Planarity : 0.004 0.057 6816 Dihedral : 3.604 12.882 5312 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.52 % Allowed : 15.17 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.12), residues: 4824 helix: 1.03 (0.09), residues: 3344 sheet: 0.05 (0.43), residues: 152 loop : 0.09 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 131 TYR 0.011 0.001 TYR G 687 PHE 0.015 0.001 PHE D 96 TRP 0.011 0.001 TRP B 103 HIS 0.004 0.001 HIS F 269 Details of bonding type rmsd covalent geometry : bond 0.00275 (38928) covalent geometry : angle 0.53042 (52608) hydrogen bonds : bond 0.03228 ( 2048) hydrogen bonds : angle 3.20795 ( 5976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 337 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.7567 (mp0) cc_final: 0.7324 (tm-30) REVERT: A 174 GLU cc_start: 0.7992 (tt0) cc_final: 0.7683 (mt-10) REVERT: A 395 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7313 (mtp180) REVERT: A 399 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6046 (mp0) REVERT: A 521 GLN cc_start: 0.8808 (tt0) cc_final: 0.8478 (tp40) REVERT: A 576 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8328 (tp) REVERT: A 580 LEU cc_start: 0.8338 (mt) cc_final: 0.7713 (tm) REVERT: A 686 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7472 (tm-30) REVERT: A 694 LYS cc_start: 0.8040 (tttt) cc_final: 0.7547 (tptp) REVERT: B 97 GLN cc_start: 0.7232 (pp30) cc_final: 0.6982 (tm130) REVERT: B 130 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8089 (mm) REVERT: B 395 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7590 (mtp180) REVERT: B 521 GLN cc_start: 0.8829 (tt0) cc_final: 0.8398 (tp-100) REVERT: B 580 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8370 (mm) REVERT: B 686 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7180 (tm-30) REVERT: B 696 ILE cc_start: 0.7896 (tt) cc_final: 0.7543 (pt) REVERT: C 149 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7555 (tm-30) REVERT: C 252 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: C 399 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.6049 (mp0) REVERT: C 403 ARG cc_start: 0.7152 (tmm160) cc_final: 0.6752 (ptm-80) REVERT: C 521 GLN cc_start: 0.8771 (tt0) cc_final: 0.8467 (tp40) REVERT: C 580 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7978 (mm) REVERT: C 669 PRO cc_start: 0.6213 (Cg_exo) cc_final: 0.5964 (Cg_endo) REVERT: C 686 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7501 (tm-30) REVERT: C 694 LYS cc_start: 0.8060 (tttt) cc_final: 0.7549 (tptp) REVERT: D 97 GLN cc_start: 0.7271 (tm130) cc_final: 0.7051 (tm130) REVERT: D 395 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7581 (mtp180) REVERT: D 454 ASP cc_start: 0.8841 (m-30) cc_final: 0.8574 (m-30) REVERT: D 521 GLN cc_start: 0.8875 (tt0) cc_final: 0.8422 (tp-100) REVERT: D 580 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8311 (mm) REVERT: D 615 ARG cc_start: 0.7475 (ttt180) cc_final: 0.7181 (ttt-90) REVERT: D 630 MET cc_start: 0.4454 (mmm) cc_final: 0.3811 (ppp) REVERT: D 696 ILE cc_start: 0.7965 (tt) cc_final: 0.7578 (pt) REVERT: E 114 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7250 (tm-30) REVERT: E 118 ASP cc_start: 0.8174 (m-30) cc_final: 0.7950 (m-30) REVERT: E 224 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8151 (mtt180) REVERT: E 288 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7922 (mt-10) REVERT: E 399 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6068 (mp0) REVERT: E 403 ARG cc_start: 0.7141 (tmm160) cc_final: 0.6851 (tmm-80) REVERT: E 521 GLN cc_start: 0.8803 (tt0) cc_final: 0.8481 (tp40) REVERT: E 580 LEU cc_start: 0.8412 (mt) cc_final: 0.7818 (tm) REVERT: E 589 PHE cc_start: 0.7228 (m-10) cc_final: 0.6988 (m-10) REVERT: E 694 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7661 (tmmt) REVERT: F 97 GLN cc_start: 0.7405 (pp30) cc_final: 0.7167 (tm130) REVERT: F 361 LYS cc_start: 0.8287 (mtmt) cc_final: 0.8080 (pttp) REVERT: F 395 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7584 (mtp180) REVERT: F 454 ASP cc_start: 0.8829 (m-30) cc_final: 0.8494 (m-30) REVERT: F 521 GLN cc_start: 0.8815 (tt0) cc_final: 0.8381 (tp-100) REVERT: F 580 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8211 (mm) REVERT: F 630 MET cc_start: 0.4347 (mmm) cc_final: 0.3788 (ppp) REVERT: F 669 PRO cc_start: 0.5445 (Cg_exo) cc_final: 0.5209 (Cg_endo) REVERT: F 686 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7026 (tm-30) REVERT: G 224 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8122 (mtt180) REVERT: G 252 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: G 288 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8154 (mt-10) REVERT: G 395 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7324 (mtp180) REVERT: G 399 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6178 (mp0) REVERT: G 521 GLN cc_start: 0.8791 (tt0) cc_final: 0.8480 (tp40) REVERT: G 580 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7988 (mm) REVERT: G 615 ARG cc_start: 0.6520 (ttt-90) cc_final: 0.5858 (ttt-90) REVERT: G 672 MET cc_start: 0.5786 (ptm) cc_final: 0.5472 (pp-130) REVERT: G 694 LYS cc_start: 0.8076 (tttt) cc_final: 0.7570 (tptp) REVERT: H 97 GLN cc_start: 0.7146 (pp30) cc_final: 0.6888 (tm130) REVERT: H 245 MET cc_start: 0.8528 (mtp) cc_final: 0.8233 (mtp) REVERT: H 395 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7572 (mtp180) REVERT: H 434 ARG cc_start: 0.8597 (ttm170) cc_final: 0.8201 (ttm-80) REVERT: H 454 ASP cc_start: 0.8924 (m-30) cc_final: 0.8568 (m-30) REVERT: H 521 GLN cc_start: 0.8842 (tt0) cc_final: 0.8505 (tp-100) REVERT: H 580 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8329 (mm) REVERT: H 615 ARG cc_start: 0.7495 (ttt180) cc_final: 0.7107 (ttt-90) REVERT: H 655 PRO cc_start: 0.7584 (Cg_exo) cc_final: 0.7270 (Cg_endo) REVERT: H 694 LYS cc_start: 0.7735 (tttt) cc_final: 0.7519 (ttpt) REVERT: H 696 ILE cc_start: 0.8145 (tp) cc_final: 0.7759 (pt) outliers start: 103 outliers final: 32 residues processed: 422 average time/residue: 0.7849 time to fit residues: 394.3288 Evaluate side-chains 361 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 307 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 580 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 355 ILE Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 244 optimal weight: 20.0000 chunk 352 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 292 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 480 optimal weight: 0.0050 chunk 385 optimal weight: 0.9990 chunk 277 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.163585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.102678 restraints weight = 51521.323| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.92 r_work: 0.3128 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 38928 Z= 0.104 Angle : 0.521 13.238 52608 Z= 0.256 Chirality : 0.038 0.205 6024 Planarity : 0.004 0.060 6816 Dihedral : 3.539 12.761 5312 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.45 % Allowed : 15.10 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.12), residues: 4824 helix: 1.23 (0.09), residues: 3336 sheet: 0.33 (0.44), residues: 152 loop : 0.22 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 131 TYR 0.011 0.001 TYR G 687 PHE 0.014 0.001 PHE D 96 TRP 0.010 0.001 TRP H 103 HIS 0.004 0.001 HIS H 269 Details of bonding type rmsd covalent geometry : bond 0.00244 (38928) covalent geometry : angle 0.52060 (52608) hydrogen bonds : bond 0.03058 ( 2048) hydrogen bonds : angle 3.14737 ( 5976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 337 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.7600 (mp0) cc_final: 0.7355 (tm-30) REVERT: A 174 GLU cc_start: 0.7964 (tt0) cc_final: 0.7692 (mt-10) REVERT: A 259 PHE cc_start: 0.8495 (t80) cc_final: 0.8108 (t80) REVERT: A 363 LYS cc_start: 0.7995 (tmtt) cc_final: 0.7757 (tppp) REVERT: A 395 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7358 (mtp180) REVERT: A 399 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5988 (mp0) REVERT: A 521 GLN cc_start: 0.8802 (tt0) cc_final: 0.8481 (tp40) REVERT: A 576 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8340 (tp) REVERT: A 580 LEU cc_start: 0.8388 (mt) cc_final: 0.7763 (tm) REVERT: A 686 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7479 (tm-30) REVERT: A 694 LYS cc_start: 0.8037 (tttt) cc_final: 0.7544 (tptp) REVERT: B 97 GLN cc_start: 0.7278 (pp30) cc_final: 0.7034 (tm130) REVERT: B 130 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7930 (mm) REVERT: B 361 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8002 (mtmm) REVERT: B 395 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7563 (mtp180) REVERT: B 454 ASP cc_start: 0.8823 (m-30) cc_final: 0.8548 (m-30) REVERT: B 521 GLN cc_start: 0.8836 (tt0) cc_final: 0.8407 (tp-100) REVERT: B 580 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8398 (mm) REVERT: B 630 MET cc_start: 0.3681 (mmt) cc_final: 0.3281 (ppp) REVERT: B 686 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7142 (tm-30) REVERT: B 696 ILE cc_start: 0.7872 (tt) cc_final: 0.7517 (pt) REVERT: C 97 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6892 (pp30) REVERT: C 98 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7093 (pt) REVERT: C 149 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7516 (tm-30) REVERT: C 395 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7249 (mtp180) REVERT: C 399 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6062 (mp0) REVERT: C 403 ARG cc_start: 0.7077 (tmm160) cc_final: 0.6653 (ptm-80) REVERT: C 521 GLN cc_start: 0.8767 (tt0) cc_final: 0.8473 (tp40) REVERT: C 580 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8028 (mm) REVERT: C 669 PRO cc_start: 0.6144 (Cg_exo) cc_final: 0.5910 (Cg_endo) REVERT: C 686 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7563 (tm-30) REVERT: C 694 LYS cc_start: 0.8077 (tttt) cc_final: 0.7572 (tptp) REVERT: D 286 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7331 (mp0) REVERT: D 395 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7569 (mtp180) REVERT: D 454 ASP cc_start: 0.8826 (m-30) cc_final: 0.8572 (m-30) REVERT: D 521 GLN cc_start: 0.8877 (tt0) cc_final: 0.8412 (tp-100) REVERT: D 580 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8352 (mm) REVERT: D 615 ARG cc_start: 0.7485 (ttt180) cc_final: 0.7201 (ttt-90) REVERT: D 630 MET cc_start: 0.4541 (mmm) cc_final: 0.3807 (ppp) REVERT: D 696 ILE cc_start: 0.7895 (tt) cc_final: 0.7495 (pt) REVERT: E 114 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7277 (tm-30) REVERT: E 118 ASP cc_start: 0.8201 (m-30) cc_final: 0.7991 (m-30) REVERT: E 224 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8147 (mtt180) REVERT: E 286 GLU cc_start: 0.7920 (mp0) cc_final: 0.7589 (tp30) REVERT: E 288 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7899 (mt-10) REVERT: E 304 ASP cc_start: 0.8416 (t0) cc_final: 0.7998 (t0) REVERT: E 395 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7367 (mtp180) REVERT: E 399 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: E 403 ARG cc_start: 0.7106 (tmm160) cc_final: 0.6659 (ptm-80) REVERT: E 521 GLN cc_start: 0.8807 (tt0) cc_final: 0.8484 (tp40) REVERT: E 580 LEU cc_start: 0.8417 (mt) cc_final: 0.7819 (tm) REVERT: E 586 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7931 (mm) REVERT: E 694 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7699 (tmmt) REVERT: F 97 GLN cc_start: 0.7370 (pp30) cc_final: 0.7159 (tm130) REVERT: F 395 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7599 (mtp180) REVERT: F 454 ASP cc_start: 0.8833 (m-30) cc_final: 0.8498 (m-30) REVERT: F 521 GLN cc_start: 0.8810 (tt0) cc_final: 0.8381 (tp-100) REVERT: F 580 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8239 (mm) REVERT: F 630 MET cc_start: 0.4462 (mmm) cc_final: 0.3896 (ppp) REVERT: F 669 PRO cc_start: 0.5408 (Cg_exo) cc_final: 0.5042 (Cg_endo) REVERT: F 686 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7109 (tm-30) REVERT: G 224 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8106 (mtt180) REVERT: G 252 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: G 286 GLU cc_start: 0.7547 (mp0) cc_final: 0.7288 (tp30) REVERT: G 395 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7365 (mtp180) REVERT: G 399 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6167 (mp0) REVERT: G 521 GLN cc_start: 0.8779 (tt0) cc_final: 0.8476 (tp40) REVERT: G 571 ASN cc_start: 0.8232 (m-40) cc_final: 0.7381 (t0) REVERT: G 580 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7627 (tm) REVERT: G 672 MET cc_start: 0.5826 (ptm) cc_final: 0.5542 (pp-130) REVERT: G 694 LYS cc_start: 0.8074 (tttt) cc_final: 0.7568 (tptp) REVERT: H 97 GLN cc_start: 0.7286 (pp30) cc_final: 0.7040 (tm130) REVERT: H 363 LYS cc_start: 0.8119 (tptp) cc_final: 0.7768 (tptp) REVERT: H 367 ASP cc_start: 0.7803 (m-30) cc_final: 0.7245 (m-30) REVERT: H 395 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7565 (mtp180) REVERT: H 434 ARG cc_start: 0.8635 (ttm170) cc_final: 0.8198 (ttm-80) REVERT: H 454 ASP cc_start: 0.8816 (m-30) cc_final: 0.8566 (m-30) REVERT: H 521 GLN cc_start: 0.8847 (tt0) cc_final: 0.8508 (tp-100) REVERT: H 580 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8369 (mm) REVERT: H 615 ARG cc_start: 0.7502 (ttt180) cc_final: 0.7127 (ttt-90) REVERT: H 694 LYS cc_start: 0.7736 (tttt) cc_final: 0.7516 (ttpt) REVERT: H 696 ILE cc_start: 0.8174 (tp) cc_final: 0.7809 (pt) outliers start: 100 outliers final: 33 residues processed: 420 average time/residue: 0.7943 time to fit residues: 394.6408 Evaluate side-chains 375 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 315 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 580 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 355 ILE Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 187 optimal weight: 0.1980 chunk 335 optimal weight: 0.8980 chunk 169 optimal weight: 0.0270 chunk 369 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 277 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 193 optimal weight: 0.3980 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.165846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.104860 restraints weight = 50811.065| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.97 r_work: 0.3134 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 38928 Z= 0.100 Angle : 0.519 12.839 52608 Z= 0.255 Chirality : 0.038 0.186 6024 Planarity : 0.004 0.063 6816 Dihedral : 3.482 12.794 5312 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.91 % Allowed : 15.47 % Favored : 82.62 % 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: 1.49 (0.12), residues: 4824 helix: 1.36 (0.09), residues: 3336 sheet: 0.62 (0.45), residues: 152 loop : 0.28 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 131 TYR 0.011 0.001 TYR G 687 PHE 0.018 0.001 PHE D 259 TRP 0.010 0.001 TRP A 103 HIS 0.003 0.001 HIS F 269 Details of bonding type rmsd covalent geometry : bond 0.00229 (38928) covalent geometry : angle 0.51857 (52608) hydrogen bonds : bond 0.02964 ( 2048) hydrogen bonds : angle 3.12769 ( 5976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 334 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.7615 (mp0) cc_final: 0.7365 (tm-30) REVERT: A 174 GLU cc_start: 0.7939 (tt0) cc_final: 0.7661 (mt-10) REVERT: A 259 PHE cc_start: 0.8426 (t80) cc_final: 0.8064 (t80) REVERT: A 395 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7400 (mtp180) REVERT: A 399 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5941 (mp0) REVERT: A 521 GLN cc_start: 0.8798 (tt0) cc_final: 0.8447 (tp40) REVERT: A 576 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8262 (tp) REVERT: A 580 LEU cc_start: 0.8393 (mt) cc_final: 0.7770 (tm) REVERT: A 686 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7470 (tm-30) REVERT: A 694 LYS cc_start: 0.8019 (tttt) cc_final: 0.7529 (tptp) REVERT: B 97 GLN cc_start: 0.7265 (pp30) cc_final: 0.7026 (tm130) REVERT: B 130 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7792 (mm) REVERT: B 363 LYS cc_start: 0.8302 (tppt) cc_final: 0.7856 (tppp) REVERT: B 395 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7627 (mtp180) REVERT: B 454 ASP cc_start: 0.8804 (m-30) cc_final: 0.8506 (m-30) REVERT: B 521 GLN cc_start: 0.8845 (tt0) cc_final: 0.8384 (tp-100) REVERT: B 580 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8353 (mm) REVERT: B 630 MET cc_start: 0.3631 (mmt) cc_final: 0.3138 (ppp) REVERT: B 686 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7139 (tm-30) REVERT: B 696 ILE cc_start: 0.8119 (tt) cc_final: 0.7712 (pt) REVERT: C 149 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7467 (tm-30) REVERT: C 395 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7310 (mtp180) REVERT: C 399 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.6017 (mp0) REVERT: C 403 ARG cc_start: 0.7092 (tmm160) cc_final: 0.6647 (ptm-80) REVERT: C 521 GLN cc_start: 0.8726 (tt0) cc_final: 0.8412 (tp40) REVERT: C 580 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7976 (mm) REVERT: C 669 PRO cc_start: 0.6181 (Cg_exo) cc_final: 0.5935 (Cg_endo) REVERT: C 686 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7594 (tm-30) REVERT: C 694 LYS cc_start: 0.8092 (tttt) cc_final: 0.7588 (tptp) REVERT: D 97 GLN cc_start: 0.7201 (tm130) cc_final: 0.6994 (tm130) REVERT: D 286 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7215 (mp0) REVERT: D 361 LYS cc_start: 0.8329 (mtmt) cc_final: 0.8042 (mtmm) REVERT: D 395 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7558 (mtp180) REVERT: D 454 ASP cc_start: 0.8792 (m-30) cc_final: 0.8530 (m-30) REVERT: D 521 GLN cc_start: 0.8882 (tt0) cc_final: 0.8379 (tp-100) REVERT: D 580 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8309 (mm) REVERT: D 615 ARG cc_start: 0.7459 (ttt180) cc_final: 0.7166 (ttt-90) REVERT: D 630 MET cc_start: 0.4534 (mmm) cc_final: 0.3800 (ppp) REVERT: D 669 PRO cc_start: 0.5774 (Cg_exo) cc_final: 0.5502 (Cg_endo) REVERT: D 696 ILE cc_start: 0.7958 (tt) cc_final: 0.7542 (pt) REVERT: E 97 GLN cc_start: 0.7179 (pp30) cc_final: 0.6970 (tm130) REVERT: E 114 GLN cc_start: 0.7608 (tm-30) cc_final: 0.7267 (tm-30) REVERT: E 118 ASP cc_start: 0.8242 (m-30) cc_final: 0.8024 (m-30) REVERT: E 224 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8092 (mtt180) REVERT: E 286 GLU cc_start: 0.7875 (mp0) cc_final: 0.7542 (tp30) REVERT: E 288 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7825 (mt-10) REVERT: E 304 ASP cc_start: 0.8384 (t0) cc_final: 0.7859 (t0) REVERT: E 395 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7386 (mtp180) REVERT: E 399 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5998 (mp0) REVERT: E 403 ARG cc_start: 0.7084 (tmm160) cc_final: 0.6527 (tmm160) REVERT: E 521 GLN cc_start: 0.8808 (tt0) cc_final: 0.8458 (tp40) REVERT: E 580 LEU cc_start: 0.8384 (mt) cc_final: 0.7788 (tm) REVERT: E 586 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7914 (mm) REVERT: E 694 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7695 (tmmt) REVERT: F 97 GLN cc_start: 0.7311 (pp30) cc_final: 0.7093 (tm130) REVERT: F 361 LYS cc_start: 0.8174 (pttp) cc_final: 0.7940 (pttp) REVERT: F 395 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7636 (mtp180) REVERT: F 454 ASP cc_start: 0.8793 (m-30) cc_final: 0.8484 (m-30) REVERT: F 521 GLN cc_start: 0.8821 (tt0) cc_final: 0.8345 (tp-100) REVERT: F 580 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8194 (mm) REVERT: F 630 MET cc_start: 0.4356 (mmm) cc_final: 0.3830 (ppp) REVERT: F 669 PRO cc_start: 0.5458 (Cg_exo) cc_final: 0.5246 (Cg_endo) REVERT: F 686 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7111 (tm-30) REVERT: G 151 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.8002 (tp) REVERT: G 224 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8079 (mtt180) REVERT: G 252 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: G 286 GLU cc_start: 0.7478 (mp0) cc_final: 0.7269 (tp30) REVERT: G 395 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7362 (mtp180) REVERT: G 399 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6177 (mp0) REVERT: G 521 GLN cc_start: 0.8780 (tt0) cc_final: 0.8433 (tp40) REVERT: G 580 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7587 (tm) REVERT: G 655 PRO cc_start: 0.7264 (Cg_exo) cc_final: 0.6833 (Cg_endo) REVERT: G 672 MET cc_start: 0.5845 (ptm) cc_final: 0.5550 (pp-130) REVERT: G 694 LYS cc_start: 0.8068 (tttt) cc_final: 0.7568 (tptp) REVERT: H 97 GLN cc_start: 0.7359 (pp30) cc_final: 0.7110 (tm130) REVERT: H 130 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7887 (mm) REVERT: H 363 LYS cc_start: 0.8054 (tptp) cc_final: 0.7680 (tptp) REVERT: H 367 ASP cc_start: 0.7733 (m-30) cc_final: 0.7220 (m-30) REVERT: H 395 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7612 (mtp180) REVERT: H 434 ARG cc_start: 0.8589 (ttm170) cc_final: 0.8151 (ttm-80) REVERT: H 454 ASP cc_start: 0.8807 (m-30) cc_final: 0.8493 (m-30) REVERT: H 521 GLN cc_start: 0.8847 (tt0) cc_final: 0.8485 (tp-100) REVERT: H 576 LEU cc_start: 0.8737 (tp) cc_final: 0.8468 (tm) REVERT: H 580 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8348 (mm) REVERT: H 615 ARG cc_start: 0.7493 (ttt180) cc_final: 0.7114 (ttt-90) REVERT: H 696 ILE cc_start: 0.8132 (tp) cc_final: 0.7776 (pt) outliers start: 78 outliers final: 23 residues processed: 398 average time/residue: 0.7886 time to fit residues: 372.0993 Evaluate side-chains 369 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 320 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 580 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 399 optimal weight: 6.9990 chunk 335 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 411 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 433 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 213 optimal weight: 3.9990 chunk 389 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 GLN C 114 GLN D 143 GLN D 150 GLN E 269 HIS ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 700 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 700 GLN G 97 GLN G 700 GLN ** H 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.160154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096852 restraints weight = 50943.741| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.94 r_work: 0.3020 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.142 38928 Z= 0.283 Angle : 0.715 13.801 52608 Z= 0.353 Chirality : 0.046 0.187 6024 Planarity : 0.006 0.067 6816 Dihedral : 4.109 15.417 5312 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.35 % Allowed : 15.27 % Favored : 82.38 % 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: 0.79 (0.12), residues: 4824 helix: 0.80 (0.09), residues: 3336 sheet: 0.25 (0.44), residues: 152 loop : 0.15 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 131 TYR 0.017 0.003 TYR F 429 PHE 0.026 0.003 PHE B 259 TRP 0.015 0.002 TRP E 214 HIS 0.010 0.002 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00703 (38928) covalent geometry : angle 0.71515 (52608) hydrogen bonds : bond 0.04652 ( 2048) hydrogen bonds : angle 3.67265 ( 5976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 307 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.8002 (tt0) cc_final: 0.7691 (mt-10) REVERT: A 395 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7168 (mtp180) REVERT: A 414 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8357 (mt-10) REVERT: A 521 GLN cc_start: 0.8793 (tt0) cc_final: 0.8475 (tp40) REVERT: A 686 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7675 (tm-30) REVERT: A 694 LYS cc_start: 0.8155 (tttt) cc_final: 0.7669 (tptp) REVERT: B 165 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7982 (mp) REVERT: B 286 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7471 (mp0) REVERT: B 361 LYS cc_start: 0.8299 (mtmm) cc_final: 0.8049 (mtmm) REVERT: B 363 LYS cc_start: 0.8113 (tppt) cc_final: 0.7647 (tppp) REVERT: B 395 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7753 (mtp180) REVERT: B 521 GLN cc_start: 0.8891 (tt0) cc_final: 0.8536 (tp-100) REVERT: B 576 LEU cc_start: 0.8774 (tp) cc_final: 0.8482 (tm) REVERT: B 580 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8359 (mm) REVERT: B 686 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7309 (tm-30) REVERT: B 696 ILE cc_start: 0.7912 (tt) cc_final: 0.7519 (pt) REVERT: C 395 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7160 (mtp180) REVERT: C 403 ARG cc_start: 0.7394 (tmm160) cc_final: 0.6906 (ptm-80) REVERT: C 414 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: C 521 GLN cc_start: 0.8734 (tt0) cc_final: 0.8463 (tp40) REVERT: C 589 PHE cc_start: 0.7777 (m-10) cc_final: 0.7409 (m-80) REVERT: C 686 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7635 (tm-30) REVERT: C 694 LYS cc_start: 0.8146 (tttt) cc_final: 0.7687 (tptp) REVERT: D 165 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8098 (mp) REVERT: D 367 ASP cc_start: 0.7878 (m-30) cc_final: 0.7631 (m-30) REVERT: D 395 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7775 (mtp180) REVERT: D 521 GLN cc_start: 0.8914 (tt0) cc_final: 0.8542 (tp-100) REVERT: D 576 LEU cc_start: 0.8801 (tp) cc_final: 0.8511 (tm) REVERT: D 580 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8357 (mm) REVERT: D 615 ARG cc_start: 0.7428 (ttt180) cc_final: 0.7139 (ttt-90) REVERT: D 630 MET cc_start: 0.3970 (mmm) cc_final: 0.3603 (ppp) REVERT: D 696 ILE cc_start: 0.7927 (tt) cc_final: 0.7504 (pt) REVERT: E 114 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7386 (tm-30) REVERT: E 118 ASP cc_start: 0.8202 (m-30) cc_final: 0.8001 (m-30) REVERT: E 288 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7960 (mt-10) REVERT: E 304 ASP cc_start: 0.8438 (t0) cc_final: 0.8137 (t0) REVERT: E 395 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7126 (mtp180) REVERT: E 521 GLN cc_start: 0.8784 (tt0) cc_final: 0.8480 (tp40) REVERT: E 586 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7903 (mm) REVERT: E 694 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7880 (tmmt) REVERT: F 97 GLN cc_start: 0.7438 (pp30) cc_final: 0.7180 (tm130) REVERT: F 165 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8049 (mp) REVERT: F 286 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7441 (mp0) REVERT: F 361 LYS cc_start: 0.8305 (pttp) cc_final: 0.8032 (pttp) REVERT: F 395 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7765 (mtp180) REVERT: F 521 GLN cc_start: 0.8884 (tt0) cc_final: 0.8528 (tp-100) REVERT: F 580 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8378 (mm) REVERT: F 686 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7352 (tm-30) REVERT: G 252 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: G 395 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7108 (mtp180) REVERT: G 414 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8433 (mp0) REVERT: G 521 GLN cc_start: 0.8749 (tt0) cc_final: 0.8459 (tp40) REVERT: G 580 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8040 (mm) REVERT: G 589 PHE cc_start: 0.7500 (m-10) cc_final: 0.7189 (m-10) REVERT: G 672 MET cc_start: 0.5548 (ptm) cc_final: 0.5259 (pp-130) REVERT: G 694 LYS cc_start: 0.8093 (tttt) cc_final: 0.7631 (tptp) REVERT: H 130 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7990 (mm) REVERT: H 286 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7443 (mp0) REVERT: H 363 LYS cc_start: 0.8087 (tptp) cc_final: 0.7877 (tptp) REVERT: H 395 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7790 (mtp180) REVERT: H 434 ARG cc_start: 0.8671 (ttm170) cc_final: 0.8281 (ttm-80) REVERT: H 521 GLN cc_start: 0.8897 (tt0) cc_final: 0.8534 (tp-100) REVERT: H 576 LEU cc_start: 0.8855 (tp) cc_final: 0.8565 (tm) REVERT: H 580 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8370 (mm) REVERT: H 615 ARG cc_start: 0.7413 (ttt180) cc_final: 0.7096 (ttt-90) REVERT: H 696 ILE cc_start: 0.8139 (tp) cc_final: 0.7728 (pt) outliers start: 96 outliers final: 44 residues processed: 396 average time/residue: 0.8526 time to fit residues: 396.2136 Evaluate side-chains 346 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 280 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 580 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain G residue 414 GLU Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 72 optimal weight: 0.0060 chunk 356 optimal weight: 10.0000 chunk 390 optimal weight: 3.9990 chunk 349 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 392 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 378 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 142 optimal weight: 0.0570 overall best weight: 0.5114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** H 575 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 = 0.4112 r_free = 0.4112 target = 0.162006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100952 restraints weight = 51172.041| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.90 r_work: 0.3109 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 38928 Z= 0.107 Angle : 0.558 13.165 52608 Z= 0.275 Chirality : 0.038 0.207 6024 Planarity : 0.004 0.059 6816 Dihedral : 3.716 15.431 5312 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.35 % Allowed : 16.67 % Favored : 81.99 % 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: 1.29 (0.12), residues: 4824 helix: 1.22 (0.09), residues: 3336 sheet: 0.62 (0.45), residues: 152 loop : 0.18 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 131 TYR 0.011 0.001 TYR G 687 PHE 0.029 0.001 PHE A 96 TRP 0.011 0.001 TRP H 103 HIS 0.003 0.001 HIS F 269 Details of bonding type rmsd covalent geometry : bond 0.00246 (38928) covalent geometry : angle 0.55767 (52608) hydrogen bonds : bond 0.03125 ( 2048) hydrogen bonds : angle 3.31018 ( 5976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 325 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.8026 (tt0) cc_final: 0.7716 (mt-10) REVERT: A 286 GLU cc_start: 0.7870 (mp0) cc_final: 0.7545 (tp30) REVERT: A 395 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7413 (mtp180) REVERT: A 399 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.6105 (mp0) REVERT: A 521 GLN cc_start: 0.8796 (tt0) cc_final: 0.8479 (tp40) REVERT: A 686 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7638 (tm-30) REVERT: A 694 LYS cc_start: 0.8099 (tttt) cc_final: 0.7593 (tptp) REVERT: B 97 GLN cc_start: 0.7294 (pp30) cc_final: 0.7090 (tm130) REVERT: B 286 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7275 (mp0) REVERT: B 338 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8124 (ttm-80) REVERT: B 361 LYS cc_start: 0.8258 (mtmm) cc_final: 0.8012 (mtmm) REVERT: B 363 LYS cc_start: 0.7961 (tppt) cc_final: 0.7573 (tppp) REVERT: B 395 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7650 (mtp180) REVERT: B 399 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: B 454 ASP cc_start: 0.8791 (m-30) cc_final: 0.8434 (m-30) REVERT: B 521 GLN cc_start: 0.8859 (tt0) cc_final: 0.8408 (tp-100) REVERT: B 576 LEU cc_start: 0.8695 (tp) cc_final: 0.8422 (tm) REVERT: B 580 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8336 (mm) REVERT: B 630 MET cc_start: 0.3813 (mmt) cc_final: 0.3243 (ppp) REVERT: B 686 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7344 (tm-30) REVERT: B 696 ILE cc_start: 0.7897 (tt) cc_final: 0.7518 (pt) REVERT: C 137 GLU cc_start: 0.6165 (mp0) cc_final: 0.5886 (mp0) REVERT: C 149 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7479 (tm-30) REVERT: C 259 PHE cc_start: 0.8686 (t80) cc_final: 0.8425 (t80) REVERT: C 521 GLN cc_start: 0.8684 (tt0) cc_final: 0.8410 (tp40) REVERT: C 686 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7569 (tm-30) REVERT: C 694 LYS cc_start: 0.8062 (tttt) cc_final: 0.7562 (tptp) REVERT: D 286 GLU cc_start: 0.7593 (mp0) cc_final: 0.7309 (tp30) REVERT: D 395 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7651 (mtp180) REVERT: D 399 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: D 454 ASP cc_start: 0.8835 (m-30) cc_final: 0.8539 (m-30) REVERT: D 521 GLN cc_start: 0.8827 (tt0) cc_final: 0.8383 (tp-100) REVERT: D 576 LEU cc_start: 0.8672 (tp) cc_final: 0.8413 (tm) REVERT: D 580 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8299 (mm) REVERT: D 615 ARG cc_start: 0.7456 (ttt180) cc_final: 0.7175 (ttt-90) REVERT: D 630 MET cc_start: 0.4320 (mmm) cc_final: 0.3723 (ppp) REVERT: D 696 ILE cc_start: 0.7870 (tt) cc_final: 0.7471 (pt) REVERT: E 97 GLN cc_start: 0.7159 (mm-40) cc_final: 0.6903 (mm110) REVERT: E 114 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7385 (tm-30) REVERT: E 118 ASP cc_start: 0.8139 (m-30) cc_final: 0.7933 (m-30) REVERT: E 131 ARG cc_start: 0.7949 (mtm110) cc_final: 0.7588 (mtm-85) REVERT: E 137 GLU cc_start: 0.6424 (mp0) cc_final: 0.6216 (mp0) REVERT: E 259 PHE cc_start: 0.8719 (t80) cc_final: 0.8417 (t80) REVERT: E 286 GLU cc_start: 0.7857 (mp0) cc_final: 0.7530 (tp30) REVERT: E 304 ASP cc_start: 0.8476 (t0) cc_final: 0.7986 (t0) REVERT: E 403 ARG cc_start: 0.7132 (tmm160) cc_final: 0.6730 (ptm-80) REVERT: E 521 GLN cc_start: 0.8794 (tt0) cc_final: 0.8475 (tp40) REVERT: E 571 ASN cc_start: 0.8240 (m-40) cc_final: 0.7375 (t0) REVERT: E 580 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7661 (tm) REVERT: E 586 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7914 (mm) REVERT: E 694 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7751 (tmmt) REVERT: F 97 GLN cc_start: 0.7506 (pp30) cc_final: 0.7267 (tm130) REVERT: F 286 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7303 (mp0) REVERT: F 338 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8041 (ttm-80) REVERT: F 395 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7574 (mtp180) REVERT: F 399 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6305 (mp0) REVERT: F 454 ASP cc_start: 0.8820 (m-30) cc_final: 0.8460 (m-30) REVERT: F 521 GLN cc_start: 0.8866 (tt0) cc_final: 0.8385 (tp-100) REVERT: F 580 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8353 (mm) REVERT: F 630 MET cc_start: 0.3618 (mmm) cc_final: 0.3101 (pp-130) REVERT: F 686 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7309 (tm-30) REVERT: G 252 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: G 259 PHE cc_start: 0.8651 (t80) cc_final: 0.8412 (t80) REVERT: G 399 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6252 (mp0) REVERT: G 521 GLN cc_start: 0.8750 (tt0) cc_final: 0.8451 (tp40) REVERT: G 571 ASN cc_start: 0.8222 (m-40) cc_final: 0.7342 (t0) REVERT: G 580 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7993 (mm) REVERT: G 630 MET cc_start: 0.4104 (mmp) cc_final: 0.3822 (ppp) REVERT: G 694 LYS cc_start: 0.8059 (tttt) cc_final: 0.7577 (tptp) REVERT: H 130 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7994 (mm) REVERT: H 286 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7279 (mp0) REVERT: H 338 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8109 (ttm-80) REVERT: H 363 LYS cc_start: 0.8003 (tptp) cc_final: 0.7749 (tptp) REVERT: H 395 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7642 (mtp180) REVERT: H 399 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6345 (mp0) REVERT: H 434 ARG cc_start: 0.8664 (ttm170) cc_final: 0.8313 (ttm-80) REVERT: H 454 ASP cc_start: 0.8857 (m-30) cc_final: 0.8515 (m-30) REVERT: H 521 GLN cc_start: 0.8799 (tt0) cc_final: 0.8490 (tp-100) REVERT: H 576 LEU cc_start: 0.8680 (tp) cc_final: 0.8442 (tm) REVERT: H 580 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8318 (mm) REVERT: H 615 ARG cc_start: 0.7448 (ttt180) cc_final: 0.7029 (ttt-90) REVERT: H 696 ILE cc_start: 0.8126 (tp) cc_final: 0.7762 (pt) outliers start: 55 outliers final: 13 residues processed: 378 average time/residue: 0.8176 time to fit residues: 364.3878 Evaluate side-chains 340 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 304 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 580 LEU Chi-restraints excluded: chain F residue 608 ILE Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 361 LYS Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 580 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 73 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 430 optimal weight: 0.9980 chunk 411 optimal weight: 0.7980 chunk 416 optimal weight: 8.9990 chunk 339 optimal weight: 1.9990 chunk 112 optimal weight: 0.0010 chunk 7 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 343 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 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 = 0.4108 r_free = 0.4108 target = 0.161573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.100379 restraints weight = 51474.257| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.92 r_work: 0.3097 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38928 Z= 0.117 Angle : 0.571 14.928 52608 Z= 0.281 Chirality : 0.039 0.212 6024 Planarity : 0.004 0.059 6816 Dihedral : 3.676 15.148 5312 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.13 % Allowed : 17.30 % Favored : 81.57 % 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: 1.43 (0.12), residues: 4824 helix: 1.29 (0.09), residues: 3352 sheet: 0.79 (0.47), residues: 152 loop : 0.30 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 131 TYR 0.015 0.001 TYR G 687 PHE 0.024 0.001 PHE F 259 TRP 0.009 0.001 TRP H 253 HIS 0.004 0.001 HIS F 269 Details of bonding type rmsd covalent geometry : bond 0.00279 (38928) covalent geometry : angle 0.57071 (52608) hydrogen bonds : bond 0.03264 ( 2048) hydrogen bonds : angle 3.30335 ( 5976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19077.47 seconds wall clock time: 323 minutes 13.24 seconds (19393.24 seconds total)