Starting phenix.real_space_refine on Sat Mar 7 05:20:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cm6_30402/03_2026/7cm6_30402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cm6_30402/03_2026/7cm6_30402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cm6_30402/03_2026/7cm6_30402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cm6_30402/03_2026/7cm6_30402.map" model { file = "/net/cci-nas-00/data/ceres_data/7cm6_30402/03_2026/7cm6_30402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cm6_30402/03_2026/7cm6_30402.cif" } resolution = 3.0 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 184 5.16 5 C 24384 2.51 5 N 6960 2.21 5 O 7136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.04s 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: 38680 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 5.91, per 1000 atoms: 0.15 Number of scatterers: 38680 At special positions: 0 Unit cell: (214.165, 214.165, 82.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 16 15.00 O 7136 8.00 N 6960 7.00 C 24384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.3 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: 312 helices and 8 sheets defined 70.0% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 62 through 82 removed outlier: 3.520A 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 86 through 104 removed outlier: 3.550A pdb=" N LEU A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.559A pdb=" N LEU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.941A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.794A pdb=" N VAL A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.543A pdb=" N HIS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.924A pdb=" N GLN A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 removed outlier: 3.570A pdb=" N SER A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.553A pdb=" N LEU A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 Processing helix chain 'A' and resid 295 through 302 removed outlier: 3.861A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.661A 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: 3.541A pdb=" N GLN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.823A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 removed outlier: 3.576A 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: 3.639A pdb=" N VAL A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 424 " --> pdb=" O TRP A 420 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 removed outlier: 3.647A 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 Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.675A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (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 removed outlier: 3.523A pdb=" N SER A 507 " --> pdb=" O TYR A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.723A pdb=" N VAL A 518 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 586 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL A 675 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 676 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 677 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A 678 " --> pdb=" O VAL A 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 672 through 678' Processing helix chain 'A' and resid 687 through 698 removed outlier: 3.549A pdb=" N THR A 691 " --> pdb=" O TYR A 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 82 removed outlier: 3.520A 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 86 through 104 removed outlier: 3.550A pdb=" N LEU B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.559A pdb=" N LEU B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.941A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 removed outlier: 4.196A pdb=" N ARG B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 removed outlier: 3.543A pdb=" N HIS B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.923A pdb=" N GLN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 248 " --> pdb=" O ARG B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 260 removed outlier: 3.571A pdb=" N SER B 260 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 removed outlier: 3.552A pdb=" N LEU B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 Processing helix chain 'B' and resid 295 through 302 removed outlier: 3.861A pdb=" N LEU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 removed outlier: 3.660A 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: 3.542A pdb=" N GLN B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 369 Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.823A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 removed outlier: 3.576A 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: 3.640A pdb=" N VAL B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 424 " --> pdb=" O TRP B 420 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 435 removed outlier: 3.647A 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 Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.675A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 494 " --> pdb=" O TRP B 490 " (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 removed outlier: 3.524A pdb=" N SER B 507 " --> pdb=" O TYR B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.722A pdb=" N VAL B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 586 Processing helix chain 'B' and resid 607 through 614 Processing helix chain 'B' and resid 637 through 650 Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL B 675 " --> pdb=" O MET B 672 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 676 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 677 " --> pdb=" O ALA B 674 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 678 " --> pdb=" O VAL B 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 672 through 678' Processing helix chain 'B' and resid 687 through 698 removed outlier: 3.549A pdb=" N THR B 691 " --> pdb=" O TYR B 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 82 removed outlier: 3.519A 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 86 through 104 removed outlier: 3.550A pdb=" N LEU C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 133 removed outlier: 3.559A pdb=" N LEU C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 150 removed outlier: 3.942A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA C 181 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 236 removed outlier: 3.544A pdb=" N HIS C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.924A pdb=" N GLN C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 248 " --> pdb=" O ARG C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 260 removed outlier: 3.571A pdb=" N SER C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 removed outlier: 3.552A pdb=" N LEU C 268 " --> pdb=" O GLU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 Processing helix chain 'C' and resid 295 through 302 removed outlier: 3.861A pdb=" N LEU C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 312 removed outlier: 3.660A 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: 3.541A pdb=" N GLN C 359 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.822A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 removed outlier: 3.576A 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: 3.639A pdb=" N VAL C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 424 " --> pdb=" O TRP C 420 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 removed outlier: 3.648A 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 Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.675A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (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 removed outlier: 3.524A pdb=" N SER C 507 " --> pdb=" O TYR C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.722A pdb=" N VAL C 518 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 through 545 removed outlier: 3.936A pdb=" N MET C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 586 Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 637 through 650 Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL C 675 " --> pdb=" O MET C 672 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 676 " --> pdb=" O GLN C 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 677 " --> pdb=" O ALA C 674 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 678 " --> pdb=" O VAL C 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 672 through 678' Processing helix chain 'C' and resid 687 through 698 removed outlier: 3.548A pdb=" N THR C 691 " --> pdb=" O TYR C 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 82 removed outlier: 3.520A 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 86 through 104 removed outlier: 3.550A pdb=" N LEU D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 removed outlier: 3.558A pdb=" N LEU D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 150 removed outlier: 3.941A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 236 removed outlier: 3.544A pdb=" N HIS D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 248 removed outlier: 3.924A pdb=" N GLN D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 260 removed outlier: 3.570A pdb=" N SER D 260 " --> pdb=" O PRO D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 removed outlier: 3.552A pdb=" N LEU D 268 " --> pdb=" O GLU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 291 Processing helix chain 'D' and resid 295 through 302 removed outlier: 3.860A pdb=" N LEU D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 312 removed outlier: 3.660A 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: 3.541A pdb=" N GLN D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 369 Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.822A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 removed outlier: 3.576A 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: 3.640A pdb=" N VAL D 417 " --> pdb=" O LYS D 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 424 " --> pdb=" O TRP D 420 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 425 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 435 removed outlier: 3.648A 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 Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.675A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU D 494 " --> pdb=" O TRP D 490 " (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 removed outlier: 3.523A pdb=" N SER D 507 " --> pdb=" O TYR D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.723A pdb=" N VAL D 518 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 586 Processing helix chain 'D' and resid 607 through 614 Processing helix chain 'D' and resid 637 through 650 Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL D 675 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU D 676 " --> pdb=" O GLN D 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 677 " --> pdb=" O ALA D 674 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE D 678 " --> pdb=" O VAL D 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 672 through 678' Processing helix chain 'D' and resid 687 through 698 removed outlier: 3.549A pdb=" N THR D 691 " --> pdb=" O TYR D 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 82 removed outlier: 3.520A 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 86 through 104 removed outlier: 3.550A pdb=" N LEU E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 124 removed outlier: 3.554A pdb=" N VAL E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 133 removed outlier: 3.559A pdb=" N LEU E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 150 removed outlier: 3.942A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 236 removed outlier: 3.544A pdb=" N HIS E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 248 removed outlier: 3.924A pdb=" N GLN E 242 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS E 248 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 260 removed outlier: 3.570A pdb=" N SER E 260 " --> pdb=" O PRO E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 278 removed outlier: 3.553A pdb=" N LEU E 268 " --> pdb=" O GLU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 291 Processing helix chain 'E' and resid 295 through 302 removed outlier: 3.860A pdb=" N LEU E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 312 removed outlier: 3.660A 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: 3.541A pdb=" N GLN E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 369 Processing helix chain 'E' and resid 369 through 380 removed outlier: 3.822A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 removed outlier: 3.576A 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: 3.640A pdb=" N VAL E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 424 " --> pdb=" O TRP E 420 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY E 425 " --> pdb=" O LEU E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 435 removed outlier: 3.647A 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 Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.675A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (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 removed outlier: 3.523A pdb=" N SER E 507 " --> pdb=" O TYR E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.722A pdb=" N VAL E 518 " --> pdb=" O LEU E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 586 Processing helix chain 'E' and resid 607 through 614 Processing helix chain 'E' and resid 637 through 650 Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.715A pdb=" N VAL E 675 " --> pdb=" O MET E 672 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU E 676 " --> pdb=" O GLN E 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR E 677 " --> pdb=" O ALA E 674 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE E 678 " --> pdb=" O VAL E 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 672 through 678' Processing helix chain 'E' and resid 687 through 698 removed outlier: 3.550A pdb=" N THR E 691 " --> pdb=" O TYR E 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 82 removed outlier: 3.520A 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 86 through 104 removed outlier: 3.551A pdb=" N LEU F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 133 removed outlier: 3.558A pdb=" N LEU F 128 " --> pdb=" O GLY F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 150 removed outlier: 3.942A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA F 181 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 Processing helix chain 'F' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 236 removed outlier: 3.545A pdb=" N HIS F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 248 removed outlier: 3.924A pdb=" N GLN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 248 " --> pdb=" O ARG F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 260 removed outlier: 3.571A pdb=" N SER F 260 " --> pdb=" O PRO F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 278 removed outlier: 3.552A pdb=" N LEU F 268 " --> pdb=" O GLU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 291 Processing helix chain 'F' and resid 295 through 302 removed outlier: 3.861A pdb=" N LEU F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 312 removed outlier: 3.660A 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: 3.541A pdb=" N GLN F 359 " --> pdb=" O ILE F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 369 Processing helix chain 'F' and resid 369 through 380 removed outlier: 3.823A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 removed outlier: 3.576A 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: 3.640A pdb=" N VAL F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE F 424 " --> pdb=" O TRP F 420 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY F 425 " --> pdb=" O LEU F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 435 removed outlier: 3.647A 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 Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.676A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU F 494 " --> pdb=" O TRP F 490 " (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 removed outlier: 3.524A pdb=" N SER F 507 " --> pdb=" O TYR F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.722A pdb=" N VAL F 518 " --> pdb=" O LEU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 586 Processing helix chain 'F' and resid 607 through 614 Processing helix chain 'F' and resid 637 through 650 Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL F 675 " --> pdb=" O MET F 672 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU F 676 " --> pdb=" O GLN F 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR F 677 " --> pdb=" O ALA F 674 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE F 678 " --> pdb=" O VAL F 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 672 through 678' Processing helix chain 'F' and resid 687 through 698 removed outlier: 3.549A pdb=" N THR F 691 " --> pdb=" O TYR F 687 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 82 removed outlier: 3.520A 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 86 through 104 removed outlier: 3.550A pdb=" N LEU G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 133 removed outlier: 3.559A pdb=" N LEU G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.943A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 172 Processing helix chain 'G' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA G 181 " --> pdb=" O PRO G 177 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 Processing helix chain 'G' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL G 211 " --> pdb=" O GLY G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 236 removed outlier: 3.544A pdb=" N HIS G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 248 removed outlier: 3.925A pdb=" N GLN G 242 " --> pdb=" O GLY G 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 260 removed outlier: 3.571A pdb=" N SER G 260 " --> pdb=" O PRO G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 278 removed outlier: 3.552A pdb=" N LEU G 268 " --> pdb=" O GLU G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 291 Processing helix chain 'G' and resid 295 through 302 removed outlier: 3.860A pdb=" N LEU G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 312 removed outlier: 3.660A 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: 3.542A pdb=" N GLN G 359 " --> pdb=" O ILE G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 369 Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.823A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 397 removed outlier: 3.576A 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: 3.640A pdb=" N VAL G 417 " --> pdb=" O LYS G 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE G 424 " --> pdb=" O TRP G 420 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY G 425 " --> pdb=" O LEU G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 435 removed outlier: 3.647A 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 Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.675A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU G 494 " --> pdb=" O TRP G 490 " (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 removed outlier: 3.523A pdb=" N SER G 507 " --> pdb=" O TYR G 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.722A pdb=" N VAL G 518 " --> pdb=" O LEU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET G 545 " --> pdb=" O ALA G 541 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 586 Processing helix chain 'G' and resid 607 through 614 Processing helix chain 'G' and resid 637 through 650 Processing helix chain 'G' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL G 675 " --> pdb=" O MET G 672 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 676 " --> pdb=" O GLN G 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR G 677 " --> pdb=" O ALA G 674 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE G 678 " --> pdb=" O VAL G 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 672 through 678' Processing helix chain 'G' and resid 687 through 698 removed outlier: 3.550A pdb=" N THR G 691 " --> pdb=" O TYR G 687 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 82 removed outlier: 3.520A 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 86 through 104 removed outlier: 3.551A pdb=" N LEU H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 124 removed outlier: 3.553A pdb=" N VAL H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 133 removed outlier: 3.559A pdb=" N LEU H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 150 removed outlier: 3.942A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 163 removed outlier: 4.195A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 172 Processing helix chain 'H' and resid 177 through 192 removed outlier: 3.549A pdb=" N ALA H 181 " --> pdb=" O PRO H 177 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 205 Processing helix chain 'H' and resid 207 through 215 removed outlier: 3.793A pdb=" N VAL H 211 " --> pdb=" O GLY H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 236 removed outlier: 3.544A pdb=" N HIS H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 248 removed outlier: 3.924A pdb=" N GLN H 242 " --> pdb=" O GLY H 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS H 248 " --> pdb=" O ARG H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 260 removed outlier: 3.570A pdb=" N SER H 260 " --> pdb=" O PRO H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 278 removed outlier: 3.553A pdb=" N LEU H 268 " --> pdb=" O GLU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 291 Processing helix chain 'H' and resid 295 through 302 removed outlier: 3.861A pdb=" N LEU H 299 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 312 removed outlier: 3.661A 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: 3.540A pdb=" N GLN H 359 " --> pdb=" O ILE H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 369 Processing helix chain 'H' and resid 369 through 380 removed outlier: 3.822A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 removed outlier: 3.577A 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: 3.640A pdb=" N VAL H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE H 424 " --> pdb=" O TRP H 420 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY H 425 " --> pdb=" O LEU H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 435 removed outlier: 3.647A 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 Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.676A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU H 494 " --> pdb=" O TRP H 490 " (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 removed outlier: 3.523A pdb=" N SER H 507 " --> pdb=" O TYR H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 518 removed outlier: 3.723A pdb=" N VAL H 518 " --> pdb=" O LEU H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 526 Processing helix chain 'H' and resid 531 through 545 removed outlier: 3.937A pdb=" N MET H 545 " --> pdb=" O ALA H 541 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 586 Processing helix chain 'H' and resid 607 through 614 Processing helix chain 'H' and resid 637 through 650 Processing helix chain 'H' and resid 672 through 678 removed outlier: 3.714A pdb=" N VAL H 675 " --> pdb=" O MET H 672 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU H 676 " --> pdb=" O GLN H 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR H 677 " --> pdb=" O ALA H 674 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE H 678 " --> pdb=" O VAL H 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 672 through 678' Processing helix chain 'H' and resid 687 through 698 removed outlier: 3.549A pdb=" N THR H 691 " --> pdb=" O TYR H 687 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.725A pdb=" N VAL A 564 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 565 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL A 620 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 591 through 592 removed outlier: 6.725A pdb=" N VAL B 564 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE B 565 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL B 620 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 591 through 592 removed outlier: 6.725A pdb=" N VAL C 564 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE C 565 " --> pdb=" O VAL C 618 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL C 620 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 591 through 592 removed outlier: 6.725A pdb=" N VAL D 564 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE D 565 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL D 620 " --> pdb=" O PHE D 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 591 through 592 removed outlier: 6.724A pdb=" N VAL E 564 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE E 565 " --> pdb=" O VAL E 618 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL E 620 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 591 through 592 removed outlier: 6.725A pdb=" N VAL F 564 " --> pdb=" O PHE F 592 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE F 565 " --> pdb=" O VAL F 618 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL F 620 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 591 through 592 removed outlier: 6.724A pdb=" N VAL G 564 " --> pdb=" O PHE G 592 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE G 565 " --> pdb=" O VAL G 618 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL G 620 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 591 through 592 removed outlier: 6.725A pdb=" N VAL H 564 " --> pdb=" O PHE H 592 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE H 565 " --> pdb=" O VAL H 618 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL H 620 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) 1960 hydrogen bonds defined for protein. 5784 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: 7.27 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8549 1.33 - 1.45: 7943 1.45 - 1.57: 22572 1.57 - 1.69: 24 1.69 - 1.81: 248 Bond restraints: 39336 Sorted by residual: bond pdb=" C2D NAD A1000 " pdb=" O2D NAD A1000 " ideal model delta sigma weight residual 1.393 1.478 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C2D NAD D1000 " pdb=" O2D NAD D1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C2D NAD B1000 " pdb=" O2D NAD B1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C2D NAD H1000 " pdb=" O2D NAD H1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C2D NAD G1000 " pdb=" O2D NAD G1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 39331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 52380 2.63 - 5.25: 675 5.25 - 7.88: 121 7.88 - 10.50: 32 10.50 - 13.13: 16 Bond angle restraints: 53224 Sorted by residual: angle pdb=" C SER F 336 " pdb=" N ASN F 337 " pdb=" CA ASN F 337 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" N VAL H 108 " pdb=" CA VAL H 108 " pdb=" C VAL H 108 " ideal model delta sigma weight residual 112.12 108.41 3.71 8.40e-01 1.42e+00 1.95e+01 angle pdb=" C SER B 336 " pdb=" N ASN B 337 " pdb=" CA ASN B 337 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 angle pdb=" N VAL B 108 " pdb=" CA VAL B 108 " pdb=" C VAL B 108 " ideal model delta sigma weight residual 112.12 108.42 3.70 8.40e-01 1.42e+00 1.94e+01 angle pdb=" C SER D 336 " pdb=" N ASN D 337 " pdb=" CA ASN D 337 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.93e+01 ... (remaining 53219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 23256 15.00 - 30.00: 704 30.00 - 45.01: 160 45.01 - 60.01: 48 60.01 - 75.01: 16 Dihedral angle restraints: 24184 sinusoidal: 10136 harmonic: 14048 Sorted by residual: dihedral pdb=" CA TRP B 412 " pdb=" C TRP B 412 " pdb=" N LYS B 413 " pdb=" CA LYS B 413 " ideal model delta harmonic sigma weight residual 180.00 164.22 15.78 0 5.00e+00 4.00e-02 9.96e+00 dihedral pdb=" CA TRP H 412 " pdb=" C TRP H 412 " pdb=" N LYS H 413 " pdb=" CA LYS H 413 " ideal model delta harmonic sigma weight residual 180.00 164.24 15.76 0 5.00e+00 4.00e-02 9.94e+00 dihedral pdb=" CA TRP G 412 " pdb=" C TRP G 412 " pdb=" N LYS G 413 " pdb=" CA LYS G 413 " ideal model delta harmonic sigma weight residual 180.00 164.24 15.76 0 5.00e+00 4.00e-02 9.93e+00 ... (remaining 24181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5433 0.069 - 0.138: 592 0.138 - 0.207: 36 0.207 - 0.276: 19 0.276 - 0.345: 8 Chirality restraints: 6088 Sorted by residual: chirality pdb=" C2D NAD D1000 " pdb=" C1D NAD D1000 " pdb=" C3D NAD D1000 " pdb=" O2D NAD D1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.91 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C2D NAD F1000 " pdb=" C1D NAD F1000 " pdb=" C3D NAD F1000 " pdb=" O2D NAD F1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.90 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C2D NAD H1000 " pdb=" C1D NAD H1000 " pdb=" C3D NAD H1000 " pdb=" O2D NAD H1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.90 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 6085 not shown) Planarity restraints: 6848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 283 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C VAL G 283 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL G 283 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU G 284 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 283 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C VAL F 283 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL F 283 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU F 284 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 283 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C VAL B 283 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL B 283 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU B 284 " 0.013 2.00e-02 2.50e+03 ... (remaining 6845 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 10051 2.80 - 3.33: 33292 3.33 - 3.85: 61305 3.85 - 4.38: 72344 4.38 - 4.90: 124832 Nonbonded interactions: 301824 Sorted by model distance: nonbonded pdb=" OE1 GLN D 436 " pdb=" OG SER E 459 " model vdw 2.281 3.040 nonbonded pdb=" OE1 GLN A 436 " pdb=" OG SER B 459 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR B 568 " pdb=" OD1 ASP B 594 " model vdw 2.359 3.040 nonbonded pdb=" OH TYR F 568 " pdb=" OD1 ASP F 594 " model vdw 2.359 3.040 nonbonded pdb=" OH TYR A 568 " pdb=" OD1 ASP A 594 " model vdw 2.359 3.040 ... (remaining 301819 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: 0.12 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 29.740 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 : 0.004 0.085 39336 Z= 0.217 Angle : 0.822 13.125 53224 Z= 0.435 Chirality : 0.047 0.345 6088 Planarity : 0.006 0.053 6848 Dihedral : 8.990 75.011 15064 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: -4.13 (0.09), residues: 4824 helix: -2.88 (0.06), residues: 3184 sheet: -1.48 (0.42), residues: 136 loop : -2.00 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 121 TYR 0.010 0.001 TYR E 568 PHE 0.036 0.002 PHE D 192 TRP 0.016 0.002 TRP C 490 HIS 0.010 0.002 HIS G 269 Details of bonding type rmsd covalent geometry : bond 0.00403 (39336) covalent geometry : angle 0.82208 (53224) hydrogen bonds : bond 0.15012 ( 1960) hydrogen bonds : angle 6.38050 ( 5784) *********************** 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 1045 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1045 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.6678 (tt) cc_final: 0.6456 (mp) REVERT: A 307 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6814 (ttp80) REVERT: A 638 TRP cc_start: 0.4921 (m100) cc_final: 0.4622 (m100) REVERT: A 672 MET cc_start: 0.3714 (ptm) cc_final: 0.3416 (ppp) REVERT: B 118 ASP cc_start: 0.6643 (m-30) cc_final: 0.6424 (m-30) REVERT: B 191 MET cc_start: 0.8527 (mmm) cc_final: 0.8215 (mmp) REVERT: B 638 TRP cc_start: 0.5266 (m100) cc_final: 0.4932 (m100) REVERT: C 307 ARG cc_start: 0.7078 (ttp-110) cc_final: 0.6667 (ttp80) REVERT: C 638 TRP cc_start: 0.4918 (m100) cc_final: 0.4501 (m100) REVERT: D 191 MET cc_start: 0.8640 (mmm) cc_final: 0.8428 (mmp) REVERT: D 638 TRP cc_start: 0.5379 (m100) cc_final: 0.5049 (m100) REVERT: E 191 MET cc_start: 0.8423 (mmm) cc_final: 0.8174 (mmp) REVERT: E 672 MET cc_start: 0.3662 (ptm) cc_final: 0.3401 (ppp) REVERT: F 638 TRP cc_start: 0.5395 (m100) cc_final: 0.5093 (m100) REVERT: G 638 TRP cc_start: 0.4926 (m100) cc_final: 0.4503 (m100) REVERT: G 672 MET cc_start: 0.3436 (ptm) cc_final: 0.3132 (ptm) REVERT: H 118 ASP cc_start: 0.6612 (m-30) cc_final: 0.6310 (m-30) REVERT: H 191 MET cc_start: 0.8516 (mmm) cc_final: 0.8210 (mmp) REVERT: H 638 TRP cc_start: 0.5274 (m100) cc_final: 0.4820 (m100) outliers start: 0 outliers final: 8 residues processed: 1045 average time/residue: 0.9084 time to fit residues: 1101.4815 Evaluate side-chains 410 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 402 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain G residue 472 GLU Chi-restraints excluded: chain H residue 406 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 134 GLN A 236 HIS A 239 GLN A 280 ASN A 575 GLN A 652 ASN B 114 GLN B 134 GLN B 170 ASN B 236 HIS B 280 ASN B 585 GLN B 652 ASN C 236 HIS C 652 ASN D 134 GLN D 236 HIS D 652 ASN E 134 GLN E 236 HIS E 616 ASN E 652 ASN F 134 GLN F 236 HIS F 616 ASN F 652 ASN G 134 GLN G 236 HIS G 280 ASN G 575 GLN G 616 ASN G 652 ASN G 700 GLN H 114 GLN H 134 GLN H 236 HIS H 280 ASN H 585 GLN H 616 ASN H 652 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122291 restraints weight = 54506.227| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.52 r_work: 0.3045 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 39336 Z= 0.190 Angle : 0.606 8.593 53224 Z= 0.310 Chirality : 0.041 0.145 6088 Planarity : 0.005 0.066 6848 Dihedral : 7.579 167.337 5771 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.06 % Allowed : 10.81 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.11), residues: 4824 helix: -0.85 (0.08), residues: 3328 sheet: -1.63 (0.42), residues: 144 loop : -1.06 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 338 TYR 0.017 0.003 TYR C 380 PHE 0.030 0.003 PHE B 433 TRP 0.016 0.002 TRP E 412 HIS 0.006 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00459 (39336) covalent geometry : angle 0.60648 (53224) hydrogen bonds : bond 0.04113 ( 1960) hydrogen bonds : angle 3.79908 ( 5784) *********************** 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 544 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 419 time to evaluate : 1.467 Fit side-chains REVERT: A 259 PHE cc_start: 0.8518 (t80) cc_final: 0.8161 (t80) REVERT: A 326 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: A 570 ARG cc_start: 0.6086 (OUTLIER) cc_final: 0.5320 (mmt90) REVERT: A 672 MET cc_start: 0.4087 (ptm) cc_final: 0.3774 (ppp) REVERT: B 98 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7195 (mp) REVERT: B 545 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.5705 (ppp) REVERT: B 638 TRP cc_start: 0.5729 (m100) cc_final: 0.5254 (m100) REVERT: C 326 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: C 363 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7498 (tppp) REVERT: C 672 MET cc_start: 0.4096 (ptm) cc_final: 0.3893 (ppp) REVERT: D 146 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7706 (ttt-90) REVERT: D 363 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7357 (tppp) REVERT: D 545 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5818 (ppp) REVERT: D 638 TRP cc_start: 0.5692 (m100) cc_final: 0.5187 (m100) REVERT: D 693 GLU cc_start: 0.7461 (tp30) cc_final: 0.6914 (tp30) REVERT: E 147 LEU cc_start: 0.8374 (tp) cc_final: 0.8044 (tt) REVERT: E 159 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7826 (tpp-160) REVERT: E 472 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8450 (tm-30) REVERT: E 638 TRP cc_start: 0.5199 (m100) cc_final: 0.4997 (m100) REVERT: E 641 LYS cc_start: 0.6515 (mttm) cc_final: 0.6248 (tmtt) REVERT: E 672 MET cc_start: 0.4085 (ptm) cc_final: 0.3550 (ppp) REVERT: F 363 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7405 (tppp) REVERT: F 545 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5780 (ppp) REVERT: F 638 TRP cc_start: 0.5701 (m100) cc_final: 0.5251 (m100) REVERT: G 147 LEU cc_start: 0.8407 (tp) cc_final: 0.8080 (tt) REVERT: G 259 PHE cc_start: 0.8224 (t80) cc_final: 0.7954 (t80) REVERT: G 327 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8461 (mp) REVERT: G 638 TRP cc_start: 0.4785 (m100) cc_final: 0.4541 (m100) REVERT: G 672 MET cc_start: 0.4105 (ptm) cc_final: 0.3840 (ppp) REVERT: H 170 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8299 (t0) REVERT: H 245 MET cc_start: 0.8179 (mtp) cc_final: 0.7975 (mtp) REVERT: H 259 PHE cc_start: 0.7806 (t80) cc_final: 0.7602 (t80) REVERT: H 638 TRP cc_start: 0.5648 (m100) cc_final: 0.5176 (m100) outliers start: 125 outliers final: 43 residues processed: 514 average time/residue: 0.8901 time to fit residues: 533.2033 Evaluate side-chains 339 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 282 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain E residue 159 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 LYS Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 545 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 468 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 462 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 182 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 470 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 432 optimal weight: 20.0000 chunk 257 optimal weight: 0.0770 chunk 153 optimal weight: 0.6980 chunk 338 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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** C 62 GLN C 280 ASN C 575 GLN C 609 GLN D 62 GLN D 97 GLN D 269 HIS ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 HIS F 62 GLN F 170 ASN G 700 GLN H 97 GLN H 269 HIS ** H 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 700 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.157036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.124077 restraints weight = 54352.416| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.57 r_work: 0.3066 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 39336 Z= 0.099 Angle : 0.478 9.377 53224 Z= 0.241 Chirality : 0.037 0.137 6088 Planarity : 0.003 0.037 6848 Dihedral : 5.719 41.904 5754 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.65 % Allowed : 12.55 % Favored : 84.80 % 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: -0.29 (0.12), residues: 4824 helix: 0.12 (0.09), residues: 3336 sheet: -1.30 (0.45), residues: 144 loop : -0.51 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 249 TYR 0.015 0.001 TYR E 687 PHE 0.017 0.001 PHE A 476 TRP 0.008 0.001 TRP E 638 HIS 0.003 0.001 HIS E 269 Details of bonding type rmsd covalent geometry : bond 0.00227 (39336) covalent geometry : angle 0.47760 (53224) hydrogen bonds : bond 0.03061 ( 1960) hydrogen bonds : angle 3.37235 ( 5784) *********************** 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 463 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 355 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8461 (tm) cc_final: 0.8111 (tp) REVERT: A 363 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7516 (tppp) REVERT: A 570 ARG cc_start: 0.6112 (OUTLIER) cc_final: 0.5357 (mmt90) REVERT: A 672 MET cc_start: 0.4083 (ptm) cc_final: 0.3757 (ppp) REVERT: B 363 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7296 (tppp) REVERT: B 586 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8055 (mm) REVERT: B 638 TRP cc_start: 0.5660 (m100) cc_final: 0.5216 (m100) REVERT: B 693 GLU cc_start: 0.7300 (tp30) cc_final: 0.6853 (tp30) REVERT: C 150 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: C 259 PHE cc_start: 0.8677 (t80) cc_final: 0.8215 (t80) REVERT: C 628 LYS cc_start: 0.4284 (mttt) cc_final: 0.3646 (mmtp) REVERT: C 672 MET cc_start: 0.4093 (ptm) cc_final: 0.3878 (ppp) REVERT: C 700 GLN cc_start: 0.5293 (mt0) cc_final: 0.4918 (mm-40) REVERT: D 146 ARG cc_start: 0.7755 (ttp-170) cc_final: 0.7503 (ttt-90) REVERT: D 363 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7258 (tppp) REVERT: D 434 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8306 (ttt-90) REVERT: D 638 TRP cc_start: 0.5620 (m100) cc_final: 0.5200 (m100) REVERT: D 693 GLU cc_start: 0.7393 (tp30) cc_final: 0.6924 (tp30) REVERT: E 147 LEU cc_start: 0.8382 (tp) cc_final: 0.8113 (tt) REVERT: E 176 GLU cc_start: 0.7687 (mp0) cc_final: 0.7112 (tp30) REVERT: E 352 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: E 630 MET cc_start: 0.3905 (ttt) cc_final: 0.3359 (mtt) REVERT: E 641 LYS cc_start: 0.6544 (mttm) cc_final: 0.6281 (tmtt) REVERT: E 672 MET cc_start: 0.4069 (ptm) cc_final: 0.3551 (ppp) REVERT: E 699 LEU cc_start: 0.6289 (mt) cc_final: 0.5923 (tp) REVERT: F 149 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7330 (tm-30) REVERT: F 245 MET cc_start: 0.8199 (mtp) cc_final: 0.7971 (mtp) REVERT: F 363 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7345 (tppp) REVERT: F 575 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6652 (pt0) REVERT: F 638 TRP cc_start: 0.5739 (m100) cc_final: 0.5338 (m100) REVERT: G 147 LEU cc_start: 0.8428 (tp) cc_final: 0.8138 (tt) REVERT: G 176 GLU cc_start: 0.7711 (mp0) cc_final: 0.7102 (tp30) REVERT: G 259 PHE cc_start: 0.8316 (t80) cc_final: 0.8012 (t80) REVERT: G 352 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7648 (mm-30) REVERT: G 609 GLN cc_start: 0.5843 (mp10) cc_final: 0.5014 (tp-100) REVERT: G 630 MET cc_start: 0.3854 (OUTLIER) cc_final: 0.3505 (mtt) REVERT: G 672 MET cc_start: 0.3999 (ptm) cc_final: 0.3770 (ppp) REVERT: H 170 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.7990 (t160) REVERT: H 586 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8065 (mm) REVERT: H 638 TRP cc_start: 0.5544 (m100) cc_final: 0.5087 (m100) outliers start: 108 outliers final: 43 residues processed: 440 average time/residue: 0.7489 time to fit residues: 392.8437 Evaluate side-chains 329 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 272 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 LYS Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 586 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 450 optimal weight: 2.9990 chunk 366 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 240 optimal weight: 8.9990 chunk 421 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 242 optimal weight: 3.9990 chunk 161 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN C 280 ASN D 575 GLN D 700 GLN E 383 ASN H 62 GLN ** H 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 700 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.153973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120089 restraints weight = 54013.195| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.58 r_work: 0.3010 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 39336 Z= 0.144 Angle : 0.526 7.238 53224 Z= 0.265 Chirality : 0.039 0.143 6088 Planarity : 0.004 0.039 6848 Dihedral : 5.593 39.497 5754 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.01 % Allowed : 13.53 % Favored : 83.46 % 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: 0.17 (0.12), residues: 4824 helix: 0.49 (0.09), residues: 3368 sheet: -1.35 (0.44), residues: 144 loop : -0.38 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 249 TYR 0.012 0.002 TYR F 380 PHE 0.014 0.002 PHE H 476 TRP 0.008 0.001 TRP E 214 HIS 0.005 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00352 (39336) covalent geometry : angle 0.52613 (53224) hydrogen bonds : bond 0.03556 ( 1960) hydrogen bonds : angle 3.39035 ( 5784) *********************** 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 422 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 299 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: A 363 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7528 (tppp) REVERT: A 570 ARG cc_start: 0.6258 (OUTLIER) cc_final: 0.5304 (mmt90) REVERT: A 672 MET cc_start: 0.4055 (ptm) cc_final: 0.3730 (ppp) REVERT: B 179 GLU cc_start: 0.7487 (mp0) cc_final: 0.7231 (mm-30) REVERT: B 434 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8432 (ttt-90) REVERT: B 586 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8169 (mm) REVERT: B 638 TRP cc_start: 0.5635 (m100) cc_final: 0.5188 (m100) REVERT: B 693 GLU cc_start: 0.7323 (tp30) cc_final: 0.6900 (tp30) REVERT: C 147 LEU cc_start: 0.8465 (tm) cc_final: 0.8249 (tp) REVERT: C 149 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7278 (tm-30) REVERT: C 150 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: C 363 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7571 (tppp) REVERT: C 628 LYS cc_start: 0.4360 (mttt) cc_final: 0.3675 (mmtp) REVERT: C 630 MET cc_start: 0.3835 (mtp) cc_final: 0.2857 (mtt) REVERT: C 700 GLN cc_start: 0.5494 (mt0) cc_final: 0.5138 (mm-40) REVERT: D 434 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8463 (ttt-90) REVERT: D 545 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5933 (ppp) REVERT: D 609 GLN cc_start: 0.6525 (mp10) cc_final: 0.5550 (tp-100) REVERT: D 638 TRP cc_start: 0.5555 (m100) cc_final: 0.5116 (m100) REVERT: D 693 GLU cc_start: 0.7376 (tp30) cc_final: 0.6914 (tp30) REVERT: E 147 LEU cc_start: 0.8458 (tp) cc_final: 0.8148 (tt) REVERT: E 149 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7419 (tm-30) REVERT: E 159 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7956 (tpp-160) REVERT: E 176 GLU cc_start: 0.7722 (mp0) cc_final: 0.7126 (tp30) REVERT: E 352 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7775 (mm-30) REVERT: E 630 MET cc_start: 0.3868 (OUTLIER) cc_final: 0.3229 (mtt) REVERT: E 641 LYS cc_start: 0.6531 (mttm) cc_final: 0.6291 (tmtt) REVERT: E 672 MET cc_start: 0.3814 (ptm) cc_final: 0.3380 (ppp) REVERT: F 149 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7671 (tm-30) REVERT: F 179 GLU cc_start: 0.7453 (mp0) cc_final: 0.7129 (mm-30) REVERT: F 264 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7110 (pt0) REVERT: F 434 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8412 (ttt-90) REVERT: F 575 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6714 (pt0) REVERT: F 638 TRP cc_start: 0.5894 (m100) cc_final: 0.5571 (m100) REVERT: G 147 LEU cc_start: 0.8480 (tp) cc_final: 0.8155 (tt) REVERT: G 149 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7472 (tm-30) REVERT: G 176 GLU cc_start: 0.7820 (mp0) cc_final: 0.7190 (tp30) REVERT: G 259 PHE cc_start: 0.8480 (t80) cc_final: 0.8213 (t80) REVERT: G 630 MET cc_start: 0.3748 (ttt) cc_final: 0.3127 (mtt) REVERT: G 672 MET cc_start: 0.4222 (ptm) cc_final: 0.4018 (ptp) REVERT: H 101 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6526 (mp0) REVERT: H 170 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8268 (t0) REVERT: H 245 MET cc_start: 0.8261 (mtp) cc_final: 0.8053 (mtp) REVERT: H 434 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8396 (ttt-90) REVERT: H 545 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5893 (ppp) REVERT: H 586 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8104 (mm) REVERT: H 609 GLN cc_start: 0.6529 (mp10) cc_final: 0.5510 (tp-100) REVERT: H 638 TRP cc_start: 0.5593 (m100) cc_final: 0.5126 (m100) REVERT: H 657 ILE cc_start: 0.7073 (mp) cc_final: 0.6477 (tp) REVERT: H 700 GLN cc_start: 0.5957 (mt0) cc_final: 0.5494 (mm-40) outliers start: 123 outliers final: 62 residues processed: 396 average time/residue: 0.7348 time to fit residues: 348.6758 Evaluate side-chains 351 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 270 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 159 ARG Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 630 MET Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 672 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 317 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 616 ASN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 575 GLN B 616 ASN B 700 GLN C 328 GLN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 134 GLN F 700 GLN H 134 GLN H 575 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.152580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119274 restraints weight = 53799.909| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.50 r_work: 0.2984 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 39336 Z= 0.170 Angle : 0.549 7.834 53224 Z= 0.276 Chirality : 0.040 0.141 6088 Planarity : 0.004 0.040 6848 Dihedral : 5.664 40.368 5754 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.48 % Allowed : 13.55 % Favored : 82.97 % 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: 0.36 (0.12), residues: 4824 helix: 0.61 (0.09), residues: 3368 sheet: -1.39 (0.43), residues: 144 loop : -0.23 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 499 TYR 0.015 0.002 TYR A 687 PHE 0.013 0.002 PHE B 466 TRP 0.007 0.001 TRP E 638 HIS 0.006 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00421 (39336) covalent geometry : angle 0.54901 (53224) hydrogen bonds : bond 0.03756 ( 1960) hydrogen bonds : angle 3.45188 ( 5784) *********************** 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 443 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 301 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7858 (tp) REVERT: A 147 LEU cc_start: 0.8482 (tm) cc_final: 0.8185 (tp) REVERT: A 326 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: A 363 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7558 (tppp) REVERT: A 570 ARG cc_start: 0.6270 (OUTLIER) cc_final: 0.5321 (mmt90) REVERT: A 672 MET cc_start: 0.3875 (ptm) cc_final: 0.3630 (ppp) REVERT: A 700 GLN cc_start: 0.5333 (mt0) cc_final: 0.5027 (mm-40) REVERT: B 322 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7414 (ptp-170) REVERT: B 363 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7316 (tppp) REVERT: B 434 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8358 (ttt-90) REVERT: B 586 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8057 (mm) REVERT: B 638 TRP cc_start: 0.5751 (m100) cc_final: 0.5336 (m100) REVERT: C 149 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7256 (tm-30) REVERT: C 150 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: C 325 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7316 (p0) REVERT: C 363 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7601 (tppp) REVERT: C 699 LEU cc_start: 0.6068 (mt) cc_final: 0.5814 (tp) REVERT: D 146 ARG cc_start: 0.7810 (ttp-170) cc_final: 0.7499 (ttt-90) REVERT: D 363 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7350 (tppp) REVERT: D 434 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8364 (ttt-90) REVERT: D 545 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5839 (ppp) REVERT: D 638 TRP cc_start: 0.5731 (m100) cc_final: 0.5198 (m100) REVERT: D 693 GLU cc_start: 0.7328 (tp30) cc_final: 0.6831 (tp30) REVERT: D 700 GLN cc_start: 0.6015 (mt0) cc_final: 0.5791 (mm-40) REVERT: E 98 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7407 (tt) REVERT: E 147 LEU cc_start: 0.8488 (tp) cc_final: 0.8175 (tt) REVERT: E 149 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7325 (tm-30) REVERT: E 672 MET cc_start: 0.3777 (ptm) cc_final: 0.3340 (ppp) REVERT: F 179 GLU cc_start: 0.7451 (mp0) cc_final: 0.7162 (mm-30) REVERT: F 264 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7066 (pt0) REVERT: F 363 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7362 (tppp) REVERT: F 434 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8354 (ttt-90) REVERT: F 575 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6755 (pt0) REVERT: F 612 MET cc_start: 0.6848 (mmt) cc_final: 0.6499 (mmm) REVERT: F 638 TRP cc_start: 0.5994 (m100) cc_final: 0.5699 (m100) REVERT: G 101 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6762 (mp0) REVERT: G 147 LEU cc_start: 0.8464 (tp) cc_final: 0.8154 (tt) REVERT: G 149 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7312 (tm-30) REVERT: G 259 PHE cc_start: 0.8542 (t80) cc_final: 0.8246 (t80) REVERT: G 630 MET cc_start: 0.3663 (OUTLIER) cc_final: 0.3410 (mtp) REVERT: H 101 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6582 (mp0) REVERT: H 245 MET cc_start: 0.8420 (mtp) cc_final: 0.8142 (mtp) REVERT: H 264 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7077 (pt0) REVERT: H 322 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7343 (ptp-170) REVERT: H 434 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8387 (ttt-90) REVERT: H 545 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5884 (ppp) REVERT: H 586 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8078 (mm) REVERT: H 609 GLN cc_start: 0.6426 (mp10) cc_final: 0.5455 (tp-100) REVERT: H 638 TRP cc_start: 0.5645 (m100) cc_final: 0.5054 (m100) outliers start: 142 outliers final: 69 residues processed: 408 average time/residue: 0.7399 time to fit residues: 361.2083 Evaluate side-chains 356 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 262 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 LYS Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 672 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 468 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 456 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 219 optimal weight: 0.1980 chunk 201 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 435 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 328 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN C 383 ASN D 585 GLN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 ASN E 700 GLN G 62 GLN G 328 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.153075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119716 restraints weight = 53901.822| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.51 r_work: 0.2991 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39336 Z= 0.145 Angle : 0.529 12.058 53224 Z= 0.264 Chirality : 0.039 0.142 6088 Planarity : 0.004 0.040 6848 Dihedral : 5.505 41.078 5754 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.24 % Allowed : 14.46 % 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: 0.55 (0.13), residues: 4824 helix: 0.74 (0.09), residues: 3392 sheet: -1.60 (0.42), residues: 152 loop : -0.07 (0.19), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 162 TYR 0.011 0.002 TYR C 687 PHE 0.011 0.001 PHE H 476 TRP 0.007 0.001 TRP C 253 HIS 0.005 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00357 (39336) covalent geometry : angle 0.52850 (53224) hydrogen bonds : bond 0.03487 ( 1960) hydrogen bonds : angle 3.37231 ( 5784) *********************** 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 425 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 293 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7795 (tp) REVERT: A 147 LEU cc_start: 0.8480 (tm) cc_final: 0.8210 (tp) REVERT: A 326 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: A 363 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7510 (tppp) REVERT: A 570 ARG cc_start: 0.6349 (OUTLIER) cc_final: 0.5369 (mmt90) REVERT: A 672 MET cc_start: 0.4004 (ptm) cc_final: 0.3561 (ppp) REVERT: A 699 LEU cc_start: 0.6028 (mt) cc_final: 0.5799 (tp) REVERT: B 264 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7071 (pt0) REVERT: B 322 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7319 (ptp-170) REVERT: B 434 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8365 (ttt-90) REVERT: B 586 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8092 (mm) REVERT: B 638 TRP cc_start: 0.5689 (m100) cc_final: 0.5273 (m100) REVERT: C 147 LEU cc_start: 0.8395 (tm) cc_final: 0.8145 (tp) REVERT: C 150 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: C 213 TYR cc_start: 0.8368 (t80) cc_final: 0.8160 (t80) REVERT: C 325 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7314 (p0) REVERT: C 363 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7623 (tppp) REVERT: C 383 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8454 (t0) REVERT: C 607 LEU cc_start: 0.6309 (mt) cc_final: 0.5835 (pp) REVERT: C 699 LEU cc_start: 0.6065 (mt) cc_final: 0.5830 (tp) REVERT: D 146 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7537 (ttt-90) REVERT: D 434 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8391 (ttt-90) REVERT: D 545 MET cc_start: 0.6186 (OUTLIER) cc_final: 0.5879 (ppp) REVERT: D 586 LEU cc_start: 0.8389 (mm) cc_final: 0.8114 (mm) REVERT: D 638 TRP cc_start: 0.5728 (m100) cc_final: 0.5188 (m100) REVERT: D 700 GLN cc_start: 0.5975 (mt0) cc_final: 0.5718 (mm-40) REVERT: E 98 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7388 (tt) REVERT: E 147 LEU cc_start: 0.8447 (tp) cc_final: 0.8123 (tt) REVERT: E 149 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7318 (tm-30) REVERT: E 170 ASN cc_start: 0.8497 (t0) cc_final: 0.7958 (t160) REVERT: E 176 GLU cc_start: 0.7505 (mp0) cc_final: 0.7063 (tp30) REVERT: E 609 GLN cc_start: 0.5789 (mp10) cc_final: 0.5111 (tp-100) REVERT: E 672 MET cc_start: 0.3781 (ptm) cc_final: 0.3297 (ppp) REVERT: E 699 LEU cc_start: 0.6321 (mt) cc_final: 0.5978 (tp) REVERT: F 179 GLU cc_start: 0.7444 (mp0) cc_final: 0.7155 (mm-30) REVERT: F 264 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7070 (pt0) REVERT: F 322 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7431 (ptp-170) REVERT: F 434 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8321 (ttt-90) REVERT: F 575 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6709 (pt0) REVERT: F 612 MET cc_start: 0.6981 (mmt) cc_final: 0.6690 (tpp) REVERT: F 638 TRP cc_start: 0.6064 (m100) cc_final: 0.5776 (m100) REVERT: G 101 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6714 (mp0) REVERT: G 147 LEU cc_start: 0.8488 (tp) cc_final: 0.8169 (tt) REVERT: G 149 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7366 (tm-30) REVERT: G 176 GLU cc_start: 0.7547 (mp0) cc_final: 0.7084 (tp30) REVERT: G 259 PHE cc_start: 0.8525 (t80) cc_final: 0.8285 (t80) REVERT: G 363 LYS cc_start: 0.7807 (tppp) cc_final: 0.7592 (tttp) REVERT: G 545 MET cc_start: 0.5432 (OUTLIER) cc_final: 0.4764 (pmm) REVERT: G 630 MET cc_start: 0.3672 (OUTLIER) cc_final: 0.3468 (mtp) REVERT: G 699 LEU cc_start: 0.6009 (mt) cc_final: 0.5773 (tp) REVERT: H 101 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6551 (mp0) REVERT: H 170 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8344 (t0) REVERT: H 245 MET cc_start: 0.8430 (mtp) cc_final: 0.8138 (mtp) REVERT: H 264 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7044 (pt0) REVERT: H 434 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8381 (ttt-90) REVERT: H 545 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5821 (ppp) REVERT: H 586 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8088 (mm) REVERT: H 638 TRP cc_start: 0.5579 (m100) cc_final: 0.5075 (m100) REVERT: H 657 ILE cc_start: 0.7184 (mp) cc_final: 0.6579 (tp) outliers start: 132 outliers final: 71 residues processed: 394 average time/residue: 0.7400 time to fit residues: 350.9986 Evaluate side-chains 369 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 272 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 545 MET Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 468 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 459 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 311 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 328 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN C 383 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN F 700 GLN G 328 GLN H 652 ASN H 700 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123204 restraints weight = 53969.976| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 3.41 r_work: 0.3017 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 39336 Z= 0.105 Angle : 0.491 12.132 53224 Z= 0.246 Chirality : 0.037 0.142 6088 Planarity : 0.003 0.039 6848 Dihedral : 5.178 44.276 5754 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.60 % Allowed : 15.07 % Favored : 82.33 % 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: 0.96 (0.13), residues: 4824 helix: 1.04 (0.09), residues: 3392 sheet: -1.42 (0.42), residues: 152 loop : 0.08 (0.19), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 162 TYR 0.018 0.001 TYR C 687 PHE 0.010 0.001 PHE H 476 TRP 0.006 0.001 TRP E 638 HIS 0.003 0.001 HIS F 269 Details of bonding type rmsd covalent geometry : bond 0.00247 (39336) covalent geometry : angle 0.49096 (53224) hydrogen bonds : bond 0.03012 ( 1960) hydrogen bonds : angle 3.21770 ( 5784) *********************** 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 406 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 300 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.6893 (mtm110) cc_final: 0.6517 (tmm-80) REVERT: A 147 LEU cc_start: 0.8468 (tm) cc_final: 0.8194 (tp) REVERT: A 326 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: A 363 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7540 (tppp) REVERT: A 545 MET cc_start: 0.5527 (OUTLIER) cc_final: 0.4833 (pmm) REVERT: A 672 MET cc_start: 0.3991 (ptm) cc_final: 0.3553 (ppp) REVERT: A 699 LEU cc_start: 0.6191 (mt) cc_final: 0.5926 (tp) REVERT: B 94 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6633 (pp20) REVERT: B 434 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8372 (ttt-90) REVERT: B 638 TRP cc_start: 0.5727 (m100) cc_final: 0.5333 (m100) REVERT: B 700 GLN cc_start: 0.6120 (mt0) cc_final: 0.5594 (mm-40) REVERT: C 147 LEU cc_start: 0.8391 (tm) cc_final: 0.8156 (tp) REVERT: C 150 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: C 170 ASN cc_start: 0.8357 (t0) cc_final: 0.7850 (t160) REVERT: C 307 ARG cc_start: 0.6835 (ttp80) cc_final: 0.6575 (ttp80) REVERT: C 325 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7330 (p0) REVERT: C 545 MET cc_start: 0.5521 (OUTLIER) cc_final: 0.4797 (pmm) REVERT: C 607 LEU cc_start: 0.6400 (mt) cc_final: 0.5940 (pp) REVERT: C 699 LEU cc_start: 0.6192 (mt) cc_final: 0.5913 (tp) REVERT: D 146 ARG cc_start: 0.7868 (ttp-170) cc_final: 0.7581 (ttt-90) REVERT: D 545 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5752 (ppp) REVERT: D 568 TYR cc_start: 0.7118 (p90) cc_final: 0.6693 (p90) REVERT: D 586 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7990 (mm) REVERT: D 638 TRP cc_start: 0.5711 (m100) cc_final: 0.5181 (m100) REVERT: D 700 GLN cc_start: 0.6128 (mt0) cc_final: 0.5783 (mm-40) REVERT: E 98 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7337 (tt) REVERT: E 147 LEU cc_start: 0.8482 (tp) cc_final: 0.8179 (tt) REVERT: E 170 ASN cc_start: 0.8397 (t0) cc_final: 0.7891 (t160) REVERT: E 176 GLU cc_start: 0.7514 (mp0) cc_final: 0.7055 (tp30) REVERT: E 609 GLN cc_start: 0.5800 (mp10) cc_final: 0.5123 (tp-100) REVERT: E 672 MET cc_start: 0.3751 (ptm) cc_final: 0.3370 (ppp) REVERT: E 699 LEU cc_start: 0.6288 (mt) cc_final: 0.5946 (tp) REVERT: F 179 GLU cc_start: 0.7388 (mp0) cc_final: 0.7090 (mm-30) REVERT: F 264 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7053 (pt0) REVERT: F 322 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7176 (ptp-170) REVERT: F 575 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6654 (pt0) REVERT: F 612 MET cc_start: 0.7049 (mmt) cc_final: 0.6800 (tpp) REVERT: F 638 TRP cc_start: 0.6332 (m100) cc_final: 0.6060 (m100) REVERT: G 101 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6728 (mp0) REVERT: G 147 LEU cc_start: 0.8482 (tp) cc_final: 0.8155 (tt) REVERT: G 149 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7421 (tm-30) REVERT: G 176 GLU cc_start: 0.7567 (mp0) cc_final: 0.7114 (tp30) REVERT: G 609 GLN cc_start: 0.5979 (mp10) cc_final: 0.5289 (tp-100) REVERT: G 630 MET cc_start: 0.3668 (OUTLIER) cc_final: 0.3438 (mtp) REVERT: G 699 LEU cc_start: 0.6062 (mt) cc_final: 0.5826 (tp) REVERT: H 101 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6476 (mp0) REVERT: H 170 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8039 (t160) REVERT: H 245 MET cc_start: 0.8430 (mtp) cc_final: 0.8179 (mtp) REVERT: H 264 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7043 (pt0) REVERT: H 434 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8427 (ttt-90) REVERT: H 545 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.5869 (ppp) REVERT: H 568 TYR cc_start: 0.7159 (p90) cc_final: 0.6948 (p90) REVERT: H 586 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8049 (mm) REVERT: H 638 TRP cc_start: 0.5577 (m100) cc_final: 0.5152 (m100) REVERT: H 657 ILE cc_start: 0.7172 (mp) cc_final: 0.6581 (tp) outliers start: 106 outliers final: 53 residues processed: 381 average time/residue: 0.6823 time to fit residues: 316.5210 Evaluate side-chains 341 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 269 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 238 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 237 optimal weight: 30.0000 chunk 183 optimal weight: 10.9990 chunk 320 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 328 optimal weight: 0.8980 chunk 426 optimal weight: 0.9980 chunk 476 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 280 ASN A 328 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 616 ASN C 616 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 700 GLN ** F 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN H 280 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.152452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119828 restraints weight = 53734.483| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.53 r_work: 0.2979 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 39336 Z= 0.156 Angle : 0.553 13.094 53224 Z= 0.276 Chirality : 0.040 0.163 6088 Planarity : 0.004 0.038 6848 Dihedral : 5.330 42.057 5754 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.06 % Allowed : 14.95 % 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: 0.84 (0.13), residues: 4824 helix: 0.91 (0.09), residues: 3424 sheet: -1.40 (0.42), residues: 152 loop : 0.12 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 249 TYR 0.013 0.002 TYR F 380 PHE 0.045 0.002 PHE G 259 TRP 0.009 0.001 TRP E 638 HIS 0.005 0.001 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00386 (39336) covalent geometry : angle 0.55291 (53224) hydrogen bonds : bond 0.03575 ( 1960) hydrogen bonds : angle 3.38500 ( 5784) *********************** 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 407 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 282 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.6905 (mtm110) cc_final: 0.6469 (tmm-80) REVERT: A 147 LEU cc_start: 0.8496 (tm) cc_final: 0.8257 (tp) REVERT: A 326 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7898 (m-30) REVERT: A 363 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7586 (tppp) REVERT: A 672 MET cc_start: 0.4013 (ptm) cc_final: 0.3587 (ppp) REVERT: A 699 LEU cc_start: 0.6280 (mt) cc_final: 0.6002 (tp) REVERT: B 322 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7334 (ptp-170) REVERT: B 434 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8381 (ttt-90) REVERT: B 545 MET cc_start: 0.6166 (OUTLIER) cc_final: 0.5823 (ppp) REVERT: B 638 TRP cc_start: 0.5772 (m100) cc_final: 0.5387 (m100) REVERT: B 700 GLN cc_start: 0.6157 (mt0) cc_final: 0.5952 (mm-40) REVERT: C 147 LEU cc_start: 0.8392 (tm) cc_final: 0.8140 (tp) REVERT: C 150 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7794 (mp10) REVERT: C 325 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7329 (p0) REVERT: C 363 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7638 (tppp) REVERT: C 607 LEU cc_start: 0.6498 (mt) cc_final: 0.5995 (pp) REVERT: C 699 LEU cc_start: 0.6410 (mt) cc_final: 0.6088 (tp) REVERT: D 146 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7499 (ttt-90) REVERT: D 545 MET cc_start: 0.6205 (OUTLIER) cc_final: 0.5854 (ppp) REVERT: D 586 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7925 (mm) REVERT: D 638 TRP cc_start: 0.5790 (m100) cc_final: 0.5402 (m100) REVERT: E 98 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7356 (tt) REVERT: E 147 LEU cc_start: 0.8487 (tp) cc_final: 0.8165 (tt) REVERT: E 170 ASN cc_start: 0.8494 (t0) cc_final: 0.7959 (t160) REVERT: E 176 GLU cc_start: 0.7483 (mp0) cc_final: 0.7071 (tp30) REVERT: E 672 MET cc_start: 0.3788 (ptm) cc_final: 0.3370 (ppp) REVERT: E 699 LEU cc_start: 0.6208 (mt) cc_final: 0.5914 (tp) REVERT: F 179 GLU cc_start: 0.7396 (mp0) cc_final: 0.7188 (mm-30) REVERT: F 264 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7081 (pt0) REVERT: F 322 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7344 (ptp-170) REVERT: F 545 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.5847 (ppp) REVERT: F 575 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6816 (pt0) REVERT: F 612 MET cc_start: 0.6945 (mmt) cc_final: 0.6658 (mmm) REVERT: F 638 TRP cc_start: 0.6311 (m100) cc_final: 0.6050 (m100) REVERT: G 101 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6672 (mp0) REVERT: G 147 LEU cc_start: 0.8527 (tp) cc_final: 0.8201 (tt) REVERT: G 149 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7647 (tp30) REVERT: G 176 GLU cc_start: 0.7527 (mp0) cc_final: 0.7097 (tp30) REVERT: G 545 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.4951 (pmm) REVERT: G 630 MET cc_start: 0.3835 (OUTLIER) cc_final: 0.3437 (mtp) REVERT: G 699 LEU cc_start: 0.6151 (mt) cc_final: 0.5917 (tp) REVERT: H 170 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8317 (t0) REVERT: H 245 MET cc_start: 0.8463 (mtp) cc_final: 0.8200 (mtp) REVERT: H 264 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7065 (pt0) REVERT: H 322 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7535 (ptp-170) REVERT: H 434 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8362 (ttt-90) REVERT: H 545 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5743 (ppp) REVERT: H 586 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8055 (mm) REVERT: H 638 TRP cc_start: 0.5646 (m100) cc_final: 0.5248 (m100) REVERT: H 657 ILE cc_start: 0.7196 (mp) cc_final: 0.6597 (tp) outliers start: 125 outliers final: 69 residues processed: 378 average time/residue: 0.7094 time to fit residues: 323.6903 Evaluate side-chains 357 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 265 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 545 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 545 MET Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 468 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 338 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 308 optimal weight: 4.9990 chunk 351 optimal weight: 1.9990 chunk 310 optimal weight: 20.0000 chunk 306 optimal weight: 9.9990 chunk 23 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 256 optimal weight: 0.9980 chunk 205 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 700 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 = 0.3992 r_free = 0.3992 target = 0.154348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120931 restraints weight = 53907.866| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.61 r_work: 0.3016 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 39336 Z= 0.106 Angle : 0.508 13.261 53224 Z= 0.254 Chirality : 0.037 0.144 6088 Planarity : 0.003 0.038 6848 Dihedral : 5.040 43.385 5754 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.43 % Allowed : 15.69 % Favored : 81.89 % 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: 1.17 (0.13), residues: 4824 helix: 1.17 (0.09), residues: 3424 sheet: -1.26 (0.43), residues: 152 loop : 0.19 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 249 TYR 0.008 0.001 TYR F 503 PHE 0.010 0.001 PHE C 476 TRP 0.008 0.001 TRP E 638 HIS 0.003 0.001 HIS F 269 Details of bonding type rmsd covalent geometry : bond 0.00250 (39336) covalent geometry : angle 0.50777 (53224) hydrogen bonds : bond 0.02984 ( 1960) hydrogen bonds : angle 3.20572 ( 5784) *********************** 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 393 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 294 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.6797 (mtm110) cc_final: 0.6509 (tmm-80) REVERT: A 326 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7889 (m-30) REVERT: A 363 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7562 (tppp) REVERT: A 672 MET cc_start: 0.3951 (ptm) cc_final: 0.3510 (ppp) REVERT: A 699 LEU cc_start: 0.6457 (mt) cc_final: 0.6207 (tp) REVERT: B 586 LEU cc_start: 0.8406 (mm) cc_final: 0.8107 (mm) REVERT: B 638 TRP cc_start: 0.5761 (m100) cc_final: 0.5385 (m100) REVERT: B 700 GLN cc_start: 0.6038 (mt0) cc_final: 0.5763 (mm-40) REVERT: C 147 LEU cc_start: 0.8384 (tm) cc_final: 0.8096 (tp) REVERT: C 150 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7844 (mp10) REVERT: C 170 ASN cc_start: 0.8356 (t0) cc_final: 0.7839 (t160) REVERT: C 325 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7480 (p0) REVERT: C 545 MET cc_start: 0.5581 (OUTLIER) cc_final: 0.4990 (pmm) REVERT: C 607 LEU cc_start: 0.6501 (mt) cc_final: 0.6056 (pp) REVERT: C 699 LEU cc_start: 0.6499 (mt) cc_final: 0.6235 (tp) REVERT: D 146 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7632 (ttt-90) REVERT: D 170 ASN cc_start: 0.8481 (t0) cc_final: 0.8064 (t160) REVERT: D 322 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7505 (ptm160) REVERT: D 545 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5765 (ppp) REVERT: D 568 TYR cc_start: 0.7162 (p90) cc_final: 0.6731 (p90) REVERT: D 586 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7951 (mm) REVERT: D 612 MET cc_start: 0.6660 (mmm) cc_final: 0.6434 (mmm) REVERT: D 638 TRP cc_start: 0.5751 (m100) cc_final: 0.5352 (m100) REVERT: D 700 GLN cc_start: 0.6097 (mt0) cc_final: 0.5794 (mm-40) REVERT: E 98 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7298 (tt) REVERT: E 147 LEU cc_start: 0.8502 (tp) cc_final: 0.8186 (tt) REVERT: E 170 ASN cc_start: 0.8421 (t0) cc_final: 0.7939 (t160) REVERT: E 176 GLU cc_start: 0.7493 (mp0) cc_final: 0.7054 (tp30) REVERT: E 545 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.5404 (pmm) REVERT: E 609 GLN cc_start: 0.5787 (mp10) cc_final: 0.5261 (tp-100) REVERT: E 672 MET cc_start: 0.3761 (ptm) cc_final: 0.3354 (ppp) REVERT: E 699 LEU cc_start: 0.6145 (mt) cc_final: 0.5824 (tp) REVERT: F 264 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7169 (pt0) REVERT: F 322 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7062 (ptp-170) REVERT: F 575 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6649 (pt0) REVERT: F 612 MET cc_start: 0.7006 (mmt) cc_final: 0.6730 (mmm) REVERT: F 638 TRP cc_start: 0.6359 (m100) cc_final: 0.6097 (m100) REVERT: G 101 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6759 (mp0) REVERT: G 149 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7363 (tm-30) REVERT: G 176 GLU cc_start: 0.7566 (mp0) cc_final: 0.7096 (tp30) REVERT: G 259 PHE cc_start: 0.8748 (t80) cc_final: 0.8438 (t80) REVERT: G 609 GLN cc_start: 0.6177 (mp10) cc_final: 0.5382 (tp-100) REVERT: G 630 MET cc_start: 0.3927 (ttt) cc_final: 0.3523 (mtp) REVERT: G 699 LEU cc_start: 0.6174 (mt) cc_final: 0.5905 (tp) REVERT: H 170 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.7973 (t160) REVERT: H 245 MET cc_start: 0.8446 (mtp) cc_final: 0.8178 (mtp) REVERT: H 264 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7080 (pt0) REVERT: H 545 MET cc_start: 0.6055 (OUTLIER) cc_final: 0.5701 (ppp) REVERT: H 568 TYR cc_start: 0.7226 (p90) cc_final: 0.6843 (p90) REVERT: H 586 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8085 (mm) REVERT: H 638 TRP cc_start: 0.5680 (m100) cc_final: 0.5243 (m100) REVERT: H 657 ILE cc_start: 0.7205 (mp) cc_final: 0.6628 (tp) REVERT: H 699 LEU cc_start: 0.6497 (mt) cc_final: 0.6218 (tp) outliers start: 99 outliers final: 58 residues processed: 368 average time/residue: 0.6656 time to fit residues: 298.6595 Evaluate side-chains 346 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 271 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 586 LEU Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 323 optimal weight: 4.9990 chunk 311 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 128 optimal weight: 0.0870 chunk 312 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 383 optimal weight: 4.9990 chunk 382 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 616 ASN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN C 616 ASN D 280 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.152929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120437 restraints weight = 53750.410| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.56 r_work: 0.2985 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39336 Z= 0.139 Angle : 0.549 13.613 53224 Z= 0.274 Chirality : 0.039 0.146 6088 Planarity : 0.003 0.039 6848 Dihedral : 5.132 41.879 5754 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.28 % Allowed : 16.13 % Favored : 81.59 % 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: 1.11 (0.13), residues: 4824 helix: 1.12 (0.09), residues: 3424 sheet: -1.23 (0.43), residues: 152 loop : 0.20 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 249 TYR 0.011 0.001 TYR F 380 PHE 0.010 0.001 PHE D 466 TRP 0.009 0.001 TRP E 638 HIS 0.004 0.001 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00342 (39336) covalent geometry : angle 0.54948 (53224) hydrogen bonds : bond 0.03362 ( 1960) hydrogen bonds : angle 3.30323 ( 5784) ********************** 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: 93 poor density : 287 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.6819 (mtm110) cc_final: 0.6467 (tmm-80) REVERT: A 147 LEU cc_start: 0.8342 (tm) cc_final: 0.8096 (tp) REVERT: A 326 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: A 363 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7597 (tppp) REVERT: A 672 MET cc_start: 0.3957 (ptm) cc_final: 0.3556 (ppp) REVERT: A 699 LEU cc_start: 0.6438 (mt) cc_final: 0.6185 (tp) REVERT: B 586 LEU cc_start: 0.8295 (mm) cc_final: 0.8029 (mm) REVERT: B 638 TRP cc_start: 0.5680 (m100) cc_final: 0.5345 (m100) REVERT: B 700 GLN cc_start: 0.6025 (mt0) cc_final: 0.5813 (mm-40) REVERT: C 147 LEU cc_start: 0.8452 (tm) cc_final: 0.8206 (tp) REVERT: C 150 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7789 (mp10) REVERT: C 325 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7314 (p0) REVERT: C 607 LEU cc_start: 0.6499 (mt) cc_final: 0.5974 (pp) REVERT: C 609 GLN cc_start: 0.6420 (OUTLIER) cc_final: 0.6010 (pt0) REVERT: C 699 LEU cc_start: 0.6492 (mt) cc_final: 0.6230 (tp) REVERT: D 146 ARG cc_start: 0.7805 (ttp-170) cc_final: 0.7497 (ttt-90) REVERT: D 170 ASN cc_start: 0.8506 (t0) cc_final: 0.8077 (t160) REVERT: D 545 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5774 (ppp) REVERT: D 568 TYR cc_start: 0.7147 (p90) cc_final: 0.6709 (p90) REVERT: D 586 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7939 (mm) REVERT: D 638 TRP cc_start: 0.5854 (m100) cc_final: 0.5469 (m100) REVERT: D 700 GLN cc_start: 0.5944 (mt0) cc_final: 0.5735 (mm-40) REVERT: E 101 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6750 (mp0) REVERT: E 147 LEU cc_start: 0.8466 (tp) cc_final: 0.8145 (tt) REVERT: E 170 ASN cc_start: 0.8496 (t0) cc_final: 0.7956 (t160) REVERT: E 176 GLU cc_start: 0.7422 (mp0) cc_final: 0.7026 (tp30) REVERT: E 363 LYS cc_start: 0.8029 (tppp) cc_final: 0.7491 (tttp) REVERT: E 672 MET cc_start: 0.3766 (ptm) cc_final: 0.3355 (ppp) REVERT: E 699 LEU cc_start: 0.5895 (mt) cc_final: 0.5656 (tp) REVERT: F 264 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7094 (pt0) REVERT: F 322 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7269 (ptp-170) REVERT: F 545 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5672 (ppp) REVERT: F 575 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6767 (pt0) REVERT: F 612 MET cc_start: 0.6918 (mmt) cc_final: 0.6643 (mmm) REVERT: F 638 TRP cc_start: 0.6436 (m100) cc_final: 0.6166 (m100) REVERT: G 101 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6632 (mp0) REVERT: G 149 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7632 (tp30) REVERT: G 176 GLU cc_start: 0.7468 (mp0) cc_final: 0.7055 (tp30) REVERT: G 545 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5163 (pmm) REVERT: G 609 GLN cc_start: 0.5977 (mp10) cc_final: 0.5697 (mp10) REVERT: G 630 MET cc_start: 0.3867 (ttt) cc_final: 0.3438 (mtp) REVERT: G 699 LEU cc_start: 0.6187 (mt) cc_final: 0.5931 (tp) REVERT: H 101 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6205 (mp0) REVERT: H 170 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8343 (t0) REVERT: H 245 MET cc_start: 0.8474 (mtp) cc_final: 0.8203 (mtp) REVERT: H 264 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7058 (pt0) REVERT: H 322 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7494 (ptp-170) REVERT: H 545 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5732 (ppp) REVERT: H 568 TYR cc_start: 0.7227 (p90) cc_final: 0.7001 (p90) REVERT: H 638 TRP cc_start: 0.5616 (m100) cc_final: 0.5248 (m100) REVERT: H 686 GLU cc_start: 0.7951 (mp0) cc_final: 0.6533 (pt0) REVERT: H 699 LEU cc_start: 0.6606 (mt) cc_final: 0.6293 (tp) outliers start: 93 outliers final: 65 residues processed: 352 average time/residue: 0.6963 time to fit residues: 298.1821 Evaluate side-chains 356 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 275 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 545 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 545 MET Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain G residue 672 MET Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 468 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 630 MET Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 81 optimal weight: 6.9990 chunk 433 optimal weight: 7.9990 chunk 315 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 343 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 419 optimal weight: 3.9990 chunk 291 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN C 616 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN ** F 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.153064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120515 restraints weight = 53792.336| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.54 r_work: 0.2990 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.203 39336 Z= 0.143 Angle : 0.640 59.198 53224 Z= 0.339 Chirality : 0.039 0.470 6088 Planarity : 0.003 0.038 6848 Dihedral : 5.133 41.920 5754 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.40 % Allowed : 16.18 % Favored : 81.42 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.13), residues: 4824 helix: 1.13 (0.09), residues: 3424 sheet: -1.20 (0.43), residues: 152 loop : 0.21 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 307 TYR 0.011 0.001 TYR F 380 PHE 0.026 0.001 PHE G 259 TRP 0.007 0.001 TRP B 253 HIS 0.003 0.001 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00343 (39336) covalent geometry : angle 0.64003 (53224) hydrogen bonds : bond 0.03319 ( 1960) hydrogen bonds : angle 3.30234 ( 5784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11474.84 seconds wall clock time: 196 minutes 15.88 seconds (11775.88 seconds total)