Starting phenix.real_space_refine on Sun Sep 13 15:48:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ip2_9698/09_2026/6ip2_9698.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ip2_9698/09_2026/6ip2_9698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ip2_9698/09_2026/6ip2_9698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ip2_9698/09_2026/6ip2_9698.map" model { file = "/net/cci-nas-00/data/ceres_data/6ip2_9698/09_2026/6ip2_9698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ip2_9698/09_2026/6ip2_9698.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ip2_9698/09_2026/6ip2_9698.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ip2_9698/09_2026/6ip2_9698.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 36 5.49 5 S 138 5.16 5 C 15486 2.51 5 N 4302 2.21 5 O 4698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24660 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 11, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 486} Chain: "C" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 493} Chain: "D" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 493} Chain: "E" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 492} Chain: "F" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 6, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 491} Chain: "A" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 493} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.44, per 1000 atoms: 0.22 Number of scatterers: 24660 At special positions: 0 Unit cell: (143.719, 141.106, 112.362, 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 138 16.00 P 36 15.00 O 4698 8.00 N 4302 7.00 C 15486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.2 seconds 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5772 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 14 sheets defined 43.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.830A pdb=" N SER B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASP B 229 " --> pdb=" O LYS B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.520A pdb=" N GLN B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 348 through 358 removed outlier: 4.047A pdb=" N ASN B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.588A pdb=" N LEU B 378 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 411 removed outlier: 3.583A pdb=" N ILE B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 removed outlier: 4.178A pdb=" N VAL B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 432 " --> pdb=" O GLU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 455 removed outlier: 3.560A pdb=" N GLY B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 484 removed outlier: 3.606A pdb=" N PHE B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 482 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 531 removed outlier: 4.537A pdb=" N THR B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.540A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 593 removed outlier: 4.091A pdb=" N LYS B 587 " --> pdb=" O GLN B 583 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 589 " --> pdb=" O MET B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.576A pdb=" N LEU B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 654 " --> pdb=" O ASP B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 684 removed outlier: 3.987A pdb=" N LEU B 682 " --> pdb=" O GLU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 699 removed outlier: 3.762A pdb=" N GLN B 697 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 719 removed outlier: 3.771A pdb=" N GLU B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN B 719 " --> pdb=" O GLU B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 730 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 230 through 235 Processing helix chain 'C' and resid 243 through 248 removed outlier: 3.608A pdb=" N GLN C 247 " --> pdb=" O GLU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 296 through 299 removed outlier: 4.601A pdb=" N GLU C 299 " --> pdb=" O GLY C 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 296 through 299' Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 329 through 333 removed outlier: 3.829A pdb=" N ALA C 332 " --> pdb=" O GLU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.661A pdb=" N LEU C 354 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 414 removed outlier: 3.524A pdb=" N ARG C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 412 " --> pdb=" O HIS C 408 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 433 removed outlier: 4.042A pdb=" N VAL C 431 " --> pdb=" O LYS C 427 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 432 " --> pdb=" O GLU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 457 removed outlier: 3.535A pdb=" N GLY C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'C' and resid 482 through 485 removed outlier: 3.588A pdb=" N GLU C 485 " --> pdb=" O ALA C 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 482 through 485' Processing helix chain 'C' and resid 511 through 531 removed outlier: 4.552A pdb=" N VAL C 517 " --> pdb=" O PRO C 513 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 520 " --> pdb=" O ARG C 516 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 Processing helix chain 'C' and resid 569 through 573 removed outlier: 3.761A pdb=" N LYS C 572 " --> pdb=" O SER C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 593 removed outlier: 3.882A pdb=" N CYS C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 619 through 625 removed outlier: 3.521A pdb=" N LEU C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 655 Processing helix chain 'C' and resid 672 through 684 removed outlier: 3.524A pdb=" N LEU C 682 " --> pdb=" O GLU C 678 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 698 Processing helix chain 'C' and resid 706 through 719 removed outlier: 3.739A pdb=" N GLU C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 733 removed outlier: 4.334A pdb=" N ALA C 731 " --> pdb=" O ARG C 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 240 through 243 removed outlier: 4.600A pdb=" N GLU D 243 " --> pdb=" O PHE D 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 243' Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 265 through 277 removed outlier: 3.838A pdb=" N LEU D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 270 " --> pdb=" O LYS D 266 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 removed outlier: 4.023A pdb=" N ARG D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 311 removed outlier: 3.636A pdb=" N GLU D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'D' and resid 348 through 356 removed outlier: 3.827A pdb=" N LEU D 354 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 356 " --> pdb=" O ASN D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 379 removed outlier: 3.945A pdb=" N LEU D 378 " --> pdb=" O ARG D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 399 through 411 removed outlier: 3.797A pdb=" N LEU D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN D 405 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 432 removed outlier: 3.510A pdb=" N VAL D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 427 through 432' Processing helix chain 'D' and resid 437 through 452 Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 476 through 484 removed outlier: 3.875A pdb=" N PHE D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.603A pdb=" N SER D 501 " --> pdb=" O ASP D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 530 removed outlier: 3.851A pdb=" N THR D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL D 517 " --> pdb=" O PRO D 513 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP D 520 " --> pdb=" O ARG D 516 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 524 " --> pdb=" O ASP D 520 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.757A pdb=" N LEU D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 574 removed outlier: 3.524A pdb=" N LYS D 572 " --> pdb=" O SER D 569 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE D 574 " --> pdb=" O ASP D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 592 removed outlier: 3.800A pdb=" N CYS D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 584 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS D 587 " --> pdb=" O GLN D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 609 Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.519A pdb=" N LEU D 623 " --> pdb=" O SER D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 653 removed outlier: 3.682A pdb=" N LEU D 652 " --> pdb=" O ARG D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 684 removed outlier: 3.523A pdb=" N LEU D 683 " --> pdb=" O ALA D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 699 removed outlier: 3.535A pdb=" N THR D 693 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE D 694 " --> pdb=" O GLU D 690 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS D 699 " --> pdb=" O ALA D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 718 Processing helix chain 'D' and resid 726 through 733 Processing helix chain 'E' and resid 223 through 228 removed outlier: 3.533A pdb=" N SER E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 234 removed outlier: 3.564A pdb=" N ARG E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA E 234 " --> pdb=" O ILE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 265 through 273 removed outlier: 3.537A pdb=" N ALA E 270 " --> pdb=" O LYS E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 276 No H-bonds generated for 'chain 'E' and resid 274 through 276' Processing helix chain 'E' and resid 296 through 301 removed outlier: 3.814A pdb=" N ASN E 301 " --> pdb=" O GLU E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 306 through 312 Processing helix chain 'E' and resid 329 through 333 removed outlier: 3.717A pdb=" N ALA E 332 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 359 removed outlier: 3.673A pdb=" N ASN E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE E 358 " --> pdb=" O LEU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 411 removed outlier: 3.549A pdb=" N ILE E 406 " --> pdb=" O GLY E 402 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE E 409 " --> pdb=" O GLN E 405 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS E 410 " --> pdb=" O ILE E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 433 Processing helix chain 'E' and resid 437 through 455 removed outlier: 3.686A pdb=" N VAL E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA E 447 " --> pdb=" O GLY E 443 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER E 450 " --> pdb=" O ARG E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.826A pdb=" N PHE E 480 " --> pdb=" O THR E 476 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E 482 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 removed outlier: 3.599A pdb=" N SER E 501 " --> pdb=" O ASP E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 531 removed outlier: 4.179A pdb=" N THR E 515 " --> pdb=" O GLY E 511 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG E 516 " --> pdb=" O ASP E 512 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP E 520 " --> pdb=" O ARG E 516 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 522 " --> pdb=" O LEU E 518 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 526 " --> pdb=" O GLU E 522 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN E 527 " --> pdb=" O LEU E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 560 Processing helix chain 'E' and resid 569 through 573 Processing helix chain 'E' and resid 579 through 587 Processing helix chain 'E' and resid 604 through 609 removed outlier: 3.507A pdb=" N LEU E 608 " --> pdb=" O ASP E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 624 Processing helix chain 'E' and resid 648 through 655 removed outlier: 3.517A pdb=" N LEU E 652 " --> pdb=" O ARG E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 682 removed outlier: 3.670A pdb=" N LEU E 682 " --> pdb=" O GLU E 678 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 699 removed outlier: 3.747A pdb=" N LYS E 699 " --> pdb=" O ALA E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 718 removed outlier: 3.550A pdb=" N ILE E 714 " --> pdb=" O LEU E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 734 Processing helix chain 'F' and resid 266 through 276 removed outlier: 3.824A pdb=" N GLN F 272 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS F 275 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 292 removed outlier: 3.834A pdb=" N ASN F 292 " --> pdb=" O GLU F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 306 removed outlier: 3.739A pdb=" N ARG F 303 " --> pdb=" O GLU F 299 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 334 removed outlier: 3.834A pdb=" N ILE F 333 " --> pdb=" O GLU F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 349 Processing helix chain 'F' and resid 350 through 355 Processing helix chain 'F' and resid 399 through 414 removed outlier: 3.837A pdb=" N ILE F 406 " --> pdb=" O GLY F 402 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG F 413 " --> pdb=" O ILE F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 431 Processing helix chain 'F' and resid 437 through 456 Processing helix chain 'F' and resid 498 through 503 removed outlier: 3.651A pdb=" N TYR F 502 " --> pdb=" O ASP F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 530 removed outlier: 3.614A pdb=" N THR F 515 " --> pdb=" O GLY F 511 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP F 520 " --> pdb=" O ARG F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 559 Processing helix chain 'F' and resid 569 through 573 removed outlier: 3.773A pdb=" N LYS F 572 " --> pdb=" O SER F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 592 removed outlier: 3.503A pdb=" N MET F 585 " --> pdb=" O LYS F 581 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE F 588 " --> pdb=" O ALA F 584 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 591 " --> pdb=" O LYS F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 609 Processing helix chain 'F' and resid 619 through 628 removed outlier: 3.934A pdb=" N VAL F 628 " --> pdb=" O GLN F 624 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 655 removed outlier: 3.658A pdb=" N LEU F 652 " --> pdb=" O ARG F 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 682 Processing helix chain 'F' and resid 687 through 699 removed outlier: 3.708A pdb=" N VAL F 698 " --> pdb=" O ILE F 694 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 719 removed outlier: 3.727A pdb=" N GLN F 719 " --> pdb=" O GLU F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 733 Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.517A pdb=" N SER A 228 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.604A pdb=" N LEU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.574A pdb=" N LEU A 291 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 292 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 removed outlier: 3.535A pdb=" N LEU A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.574A pdb=" N LEU A 378 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 379 " --> pdb=" O PRO A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 375 through 379' Processing helix chain 'A' and resid 399 through 410 removed outlier: 3.529A pdb=" N ILE A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 437 through 452 removed outlier: 3.876A pdb=" N LEU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 511 through 530 removed outlier: 3.540A pdb=" N THR A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.551A pdb=" N ALA A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.909A pdb=" N LYS A 572 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 573 " --> pdb=" O PRO A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 569 through 573' Processing helix chain 'A' and resid 577 through 592 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 619 through 630 removed outlier: 3.543A pdb=" N LEU A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.661A pdb=" N LEU A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 684 removed outlier: 3.510A pdb=" N LEU A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.809A pdb=" N GLN A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 removed outlier: 3.642A pdb=" N LEU A 711 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 734 removed outlier: 3.526A pdb=" N LYS A 728 " --> pdb=" O TYR A 724 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 282 through 285 removed outlier: 6.838A pdb=" N LYS B 283 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET B 372 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE B 256 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 391 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 564 through 568 removed outlier: 6.440A pdb=" N PHE B 564 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL B 601 " --> pdb=" O PHE B 564 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS B 566 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 645 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 663 " --> pdb=" O SER B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 670 through 672 removed outlier: 4.010A pdb=" N ALA B 671 " --> pdb=" O VAL B 703 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 283 through 285 removed outlier: 3.653A pdb=" N ILE C 326 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 391 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 564 through 568 removed outlier: 6.645A pdb=" N PHE C 564 " --> pdb=" O CYS C 599 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL C 601 " --> pdb=" O PHE C 564 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LYS C 566 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER C 598 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE C 643 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL C 600 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N THR C 645 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL C 602 " --> pdb=" O THR C 645 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR C 663 " --> pdb=" O SER C 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 282 through 284 removed outlier: 7.081A pdb=" N LYS D 283 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE D 325 " --> pdb=" O ILE D 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 564 through 568 removed outlier: 6.096A pdb=" N PHE D 564 " --> pdb=" O CYS D 599 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL D 601 " --> pdb=" O PHE D 564 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS D 566 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR D 645 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N THR D 663 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER D 538 " --> pdb=" O THR D 663 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ILE D 665 " --> pdb=" O SER D 538 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU D 540 " --> pdb=" O ILE D 665 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 284 through 285 removed outlier: 5.653A pdb=" N ILE E 256 " --> pdb=" O GLY E 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 565 through 568 removed outlier: 7.076A pdb=" N LYS E 566 " --> pdb=" O VAL E 601 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N THR E 663 " --> pdb=" O LEU E 536 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER E 538 " --> pdb=" O THR E 663 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE E 665 " --> pdb=" O SER E 538 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU E 540 " --> pdb=" O ILE E 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 255 through 258 Processing sheet with id=AB2, first strand: chain 'F' and resid 283 through 285 removed outlier: 6.180A pdb=" N LYS F 283 " --> pdb=" O ILE F 326 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 564 through 568 removed outlier: 3.634A pdb=" N LYS F 566 " --> pdb=" O CYS F 599 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N THR F 663 " --> pdb=" O LEU F 536 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER F 538 " --> pdb=" O THR F 663 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE F 665 " --> pdb=" O SER F 538 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU F 540 " --> pdb=" O ILE F 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 255 through 258 removed outlier: 6.182A pdb=" N ILE A 325 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N MET A 372 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE A 327 " --> pdb=" O MET A 372 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS A 283 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 565 through 568 removed outlier: 6.543A pdb=" N LYS A 566 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR A 663 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER A 538 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE A 665 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU A 540 " --> pdb=" O ILE A 665 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 2097 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: 3.96 Time building geometry restraints manager: 2.78 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: 7206 1.33 - 1.45: 3428 1.45 - 1.57: 14098 1.57 - 1.69: 60 1.69 - 1.81: 240 Bond restraints: 25032 Sorted by residual: bond pdb=" C4 ATP F 801 " pdb=" C5 ATP F 801 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.79e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.62e+01 bond pdb=" C4 ATP F 802 " pdb=" C5 ATP F 802 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.44e+01 bond pdb=" C4 ATP E 801 " pdb=" C5 ATP E 801 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C4 ATP E 802 " pdb=" C5 ATP E 802 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.16e+01 ... (remaining 25027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 33345 4.58 - 9.16: 379 9.16 - 13.73: 40 13.73 - 18.31: 12 18.31 - 22.89: 22 Bond angle restraints: 33798 Sorted by residual: angle pdb=" PB ATP D 802 " pdb=" O3B ATP D 802 " pdb=" PG ATP D 802 " ideal model delta sigma weight residual 139.87 116.98 22.89 1.00e+00 1.00e+00 5.24e+02 angle pdb=" PB ATP F 802 " pdb=" O3B ATP F 802 " pdb=" PG ATP F 802 " ideal model delta sigma weight residual 139.87 117.75 22.12 1.00e+00 1.00e+00 4.89e+02 angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 118.33 21.54 1.00e+00 1.00e+00 4.64e+02 angle pdb=" PB ATP C 802 " pdb=" O3B ATP C 802 " pdb=" PG ATP C 802 " ideal model delta sigma weight residual 139.87 118.51 21.36 1.00e+00 1.00e+00 4.56e+02 angle pdb=" PB ATP B 802 " pdb=" O3B ATP B 802 " pdb=" PG ATP B 802 " ideal model delta sigma weight residual 139.87 119.18 20.69 1.00e+00 1.00e+00 4.28e+02 ... (remaining 33793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.65: 14948 26.65 - 53.31: 383 53.31 - 79.96: 38 79.96 - 106.61: 2 106.61 - 133.27: 1 Dihedral angle restraints: 15372 sinusoidal: 6444 harmonic: 8928 Sorted by residual: dihedral pdb=" CA HIS B 417 " pdb=" C HIS B 417 " pdb=" N GLN B 418 " pdb=" CA GLN B 418 " ideal model delta harmonic sigma weight residual 180.00 46.73 133.27 0 5.00e+00 4.00e-02 7.10e+02 dihedral pdb=" CA GLY D 615 " pdb=" C GLY D 615 " pdb=" N PRO D 616 " pdb=" CA PRO D 616 " ideal model delta harmonic sigma weight residual 180.00 -130.37 -49.63 0 5.00e+00 4.00e-02 9.85e+01 dihedral pdb=" CA LYS D 462 " pdb=" C LYS D 462 " pdb=" N VAL D 463 " pdb=" CA VAL D 463 " ideal model delta harmonic sigma weight residual -180.00 -132.29 -47.71 0 5.00e+00 4.00e-02 9.11e+01 ... (remaining 15369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2940 0.067 - 0.133: 798 0.133 - 0.200: 113 0.200 - 0.267: 22 0.267 - 0.333: 3 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CB ILE C 302 " pdb=" CA ILE C 302 " pdb=" CG1 ILE C 302 " pdb=" CG2 ILE C 302 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB THR B 494 " pdb=" CA THR B 494 " pdb=" OG1 THR B 494 " pdb=" CG2 THR B 494 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CG LEU D 473 " pdb=" CB LEU D 473 " pdb=" CD1 LEU D 473 " pdb=" CD2 LEU D 473 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 3873 not shown) Planarity restraints: 4308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 489 " 0.084 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO B 490 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO B 490 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 490 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 287 " -0.062 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO C 288 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 288 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 288 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 287 " -0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO E 288 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 288 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 288 " -0.045 5.00e-02 4.00e+02 ... (remaining 4305 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4558 2.77 - 3.30: 23389 3.30 - 3.83: 39655 3.83 - 4.37: 48621 4.37 - 4.90: 78615 Nonbonded interactions: 194838 Sorted by model distance: nonbonded pdb=" OG SER A 421 " pdb=" OD1 ASP A 423 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR C 267 " pdb=" O3G ATP C 801 " model vdw 2.245 3.040 nonbonded pdb=" OE2 GLU D 468 " pdb=" OG SER D 472 " model vdw 2.278 3.040 nonbonded pdb=" O ARG C 232 " pdb=" OG SER D 450 " model vdw 2.281 3.040 nonbonded pdb=" OG SER F 569 " pdb=" OD1 ASP F 571 " model vdw 2.300 3.040 ... (remaining 194833 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.020 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 25032 Z= 0.441 Angle : 1.380 22.891 33798 Z= 0.896 Chirality : 0.061 0.333 3876 Planarity : 0.008 0.127 4308 Dihedral : 11.730 133.268 9600 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.19 % Favored : 87.68 % Rotamer: Outliers : 0.26 % Allowed : 2.97 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.11 % Twisted Proline : 3.03 % Twisted General : 0.77 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.47 (0.11), residues: 3108 helix: -4.28 (0.07), residues: 1294 sheet: -2.35 (0.26), residues: 355 loop : -3.26 (0.14), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 233 TYR 0.024 0.002 TYR F 259 PHE 0.025 0.003 PHE C 436 TRP 0.010 0.002 TRP B 510 HIS 0.014 0.002 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.44 (25032) covalent geometry : angle 1.38020 / 0.90 (33798) hydrogen bonds : bond 0.30648 / 20.22 ( 725) hydrogen bonds : angle 10.14223 / 7.01 ( 2097) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 861 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 ILE cc_start: 0.8943 (mt) cc_final: 0.8618 (mt) REVERT: B 285 VAL cc_start: 0.9367 (p) cc_final: 0.9090 (t) REVERT: B 510 TRP cc_start: 0.8092 (p-90) cc_final: 0.7891 (p90) REVERT: B 649 LYS cc_start: 0.8442 (tttp) cc_final: 0.8230 (ttpt) REVERT: C 268 LEU cc_start: 0.9087 (tp) cc_final: 0.8629 (tp) REVERT: C 283 LYS cc_start: 0.8373 (mmmt) cc_final: 0.7820 (mttp) REVERT: C 284 VAL cc_start: 0.9194 (t) cc_final: 0.8986 (p) REVERT: C 435 ASN cc_start: 0.8577 (t0) cc_final: 0.8062 (t0) REVERT: D 273 ILE cc_start: 0.9083 (tp) cc_final: 0.8877 (tt) REVERT: D 390 GLU cc_start: 0.7356 (tp30) cc_final: 0.7010 (mt-10) REVERT: D 397 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8748 (pt) REVERT: D 649 LYS cc_start: 0.8644 (tttm) cc_final: 0.8163 (ttpt) REVERT: E 312 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7041 (tm-30) REVERT: E 362 GLU cc_start: 0.7309 (pm20) cc_final: 0.7047 (tp30) REVERT: E 496 GLN cc_start: 0.5869 (mm-40) cc_final: 0.5644 (tm-30) REVERT: E 498 ASP cc_start: 0.6172 (m-30) cc_final: 0.5881 (m-30) REVERT: E 542 GLU cc_start: 0.7780 (pt0) cc_final: 0.7469 (pt0) REVERT: E 561 ASN cc_start: 0.7882 (m110) cc_final: 0.7608 (t0) REVERT: E 624 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8022 (mm-40) REVERT: E 721 ASP cc_start: 0.7428 (m-30) cc_final: 0.7224 (m-30) REVERT: E 727 ARG cc_start: 0.7651 (mtm-85) cc_final: 0.7343 (ttm110) REVERT: F 322 LEU cc_start: 0.6394 (tp) cc_final: 0.6085 (tt) REVERT: F 340 MET cc_start: 0.5259 (ptm) cc_final: 0.3820 (mmt) REVERT: F 496 GLN cc_start: 0.4546 (tt0) cc_final: 0.4257 (mp10) REVERT: F 607 ARG cc_start: 0.8117 (mmt-90) cc_final: 0.7836 (tpp-160) REVERT: F 651 VAL cc_start: 0.8898 (t) cc_final: 0.8661 (p) REVERT: F 655 MET cc_start: 0.8123 (mtm) cc_final: 0.7906 (mtm) REVERT: A 233 ARG cc_start: 0.7429 (mtt90) cc_final: 0.6787 (mmm160) REVERT: A 276 MET cc_start: 0.6921 (mmm) cc_final: 0.6215 (mtp) REVERT: A 368 LEU cc_start: 0.7477 (tp) cc_final: 0.7226 (mp) REVERT: A 446 ARG cc_start: 0.8482 (tpp80) cc_final: 0.8000 (tpp-160) REVERT: A 467 MET cc_start: 0.0346 (mtm) cc_final: -0.0566 (mmt) REVERT: A 523 LEU cc_start: 0.8269 (mt) cc_final: 0.7883 (mt) REVERT: A 527 GLN cc_start: 0.7716 (tt0) cc_final: 0.7480 (tt0) REVERT: A 567 ILE cc_start: 0.8697 (mt) cc_final: 0.8305 (tt) REVERT: A 621 LEU cc_start: 0.8729 (tp) cc_final: 0.8407 (mt) outliers start: 7 outliers final: 3 residues processed: 867 average time/residue: 0.1988 time to fit residues: 257.6484 Evaluate side-chains 475 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 471 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 397 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 323 HIS ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN B 365 ASN B 366 ASN B 418 GLN B 505 ASN B 546 HIS ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 301 ASN ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN ** D 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS E 363 GLN E 405 GLN ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 ASN E 659 ASN F 417 HIS F 449 GLN F 486 ASN F 526 GLN ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS A 319 ASN A 323 HIS ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN A 505 ASN A 653 GLN A 659 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.167076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130716 restraints weight = 42922.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.133969 restraints weight = 23807.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135997 restraints weight = 16443.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137298 restraints weight = 13205.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.137898 restraints weight = 11550.263| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25032 Z= 0.184 Angle : 0.833 12.896 33798 Z= 0.438 Chirality : 0.049 0.245 3876 Planarity : 0.006 0.116 4308 Dihedral : 9.149 89.594 3365 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.17 % Favored : 89.70 % Rotamer: Outliers : 3.23 % Allowed : 11.19 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.11 % Twisted Proline : 3.03 % Twisted General : 0.40 % 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: -4.29 (0.13), residues: 3108 helix: -2.88 (0.11), residues: 1365 sheet: -2.04 (0.26), residues: 353 loop : -2.94 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 516 TYR 0.009 0.001 TYR C 499 PHE 0.031 0.002 PHE D 231 TRP 0.011 0.001 TRP A 510 HIS 0.013 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (25032) covalent geometry : angle 0.83281 / 0.44 (33798) hydrogen bonds : bond 0.05159 / 3.46 ( 725) hydrogen bonds : angle 5.80139 / 3.98 ( 2097) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 538 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 PHE cc_start: 0.8081 (t80) cc_final: 0.7839 (t80) REVERT: B 256 ILE cc_start: 0.8883 (mt) cc_final: 0.8562 (mt) REVERT: B 329 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6111 (mp0) REVERT: B 453 MET cc_start: 0.8550 (mmt) cc_final: 0.7528 (mmm) REVERT: C 247 GLN cc_start: 0.7410 (mt0) cc_final: 0.7059 (mp10) REVERT: C 276 MET cc_start: 0.6094 (tpt) cc_final: 0.5559 (tpt) REVERT: C 283 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7236 (mttp) REVERT: C 435 ASN cc_start: 0.8543 (t0) cc_final: 0.7982 (t0) REVERT: C 520 ASP cc_start: 0.7637 (t0) cc_final: 0.7366 (t0) REVERT: C 682 LEU cc_start: 0.8760 (mt) cc_final: 0.8340 (mt) REVERT: D 440 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7573 (mm-30) REVERT: D 565 ILE cc_start: 0.8995 (mt) cc_final: 0.8757 (tp) REVERT: D 678 GLU cc_start: 0.8264 (tp30) cc_final: 0.8042 (tp30) REVERT: E 229 ASP cc_start: 0.8561 (t70) cc_final: 0.8326 (t0) REVERT: E 312 GLU cc_start: 0.7654 (mm-30) cc_final: 0.6732 (tm-30) REVERT: E 498 ASP cc_start: 0.5935 (m-30) cc_final: 0.5541 (m-30) REVERT: E 561 ASN cc_start: 0.8064 (m110) cc_final: 0.7717 (t0) REVERT: E 590 ASP cc_start: 0.8473 (t0) cc_final: 0.8200 (t0) REVERT: E 624 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8240 (mm-40) REVERT: E 657 MET cc_start: 0.8089 (ttp) cc_final: 0.7728 (ttp) REVERT: E 712 MET cc_start: 0.7430 (mmm) cc_final: 0.7005 (mtt) REVERT: E 727 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7413 (ttm110) REVERT: F 248 MET cc_start: 0.5409 (ptt) cc_final: 0.5206 (tmm) REVERT: F 276 MET cc_start: 0.4950 (mmm) cc_final: 0.3873 (tpp) REVERT: F 322 LEU cc_start: 0.6778 (tp) cc_final: 0.6457 (tp) REVERT: F 329 GLU cc_start: 0.7164 (tt0) cc_final: 0.6818 (pp20) REVERT: F 340 MET cc_start: 0.5003 (ptm) cc_final: 0.3345 (mmt) REVERT: F 414 MET cc_start: 0.8043 (ttp) cc_final: 0.7651 (tpt) REVERT: F 496 GLN cc_start: 0.4775 (tt0) cc_final: 0.4219 (mp10) REVERT: F 655 MET cc_start: 0.8207 (mtm) cc_final: 0.7920 (mtm) REVERT: F 712 MET cc_start: 0.8286 (mmm) cc_final: 0.7522 (mpp) REVERT: F 716 MET cc_start: 0.8360 (mtp) cc_final: 0.7520 (mpp) REVERT: A 233 ARG cc_start: 0.7178 (mtt90) cc_final: 0.6938 (mmm160) REVERT: A 276 MET cc_start: 0.6995 (mmm) cc_final: 0.6174 (mtm) REVERT: A 467 MET cc_start: 0.0916 (mtm) cc_final: 0.0098 (mmt) REVERT: A 567 ILE cc_start: 0.8692 (mt) cc_final: 0.8222 (tt) REVERT: A 674 GLU cc_start: 0.8205 (mp0) cc_final: 0.7974 (mp0) outliers start: 86 outliers final: 41 residues processed: 594 average time/residue: 0.1681 time to fit residues: 158.7697 Evaluate side-chains 457 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 416 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain F residue 363 GLN Chi-restraints excluded: chain F residue 427 LYS Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 730 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 10 optimal weight: 1.9990 chunk 212 optimal weight: 30.0000 chunk 257 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 221 optimal weight: 0.0970 chunk 172 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN B 449 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 319 ASN A 454 ASN ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.167422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131068 restraints weight = 43044.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134396 restraints weight = 23930.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136465 restraints weight = 16519.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.137741 restraints weight = 13244.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138361 restraints weight = 11608.956| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25032 Z= 0.151 Angle : 0.754 12.608 33798 Z= 0.394 Chirality : 0.047 0.227 3876 Planarity : 0.006 0.103 4308 Dihedral : 8.626 89.679 3365 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.46 % Favored : 89.45 % Rotamer: Outliers : 3.38 % Allowed : 14.64 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.11 % Twisted Proline : 2.27 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.14), residues: 3108 helix: -2.11 (0.12), residues: 1385 sheet: -1.87 (0.26), residues: 364 loop : -2.78 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 446 TYR 0.012 0.001 TYR D 502 PHE 0.031 0.002 PHE D 231 TRP 0.015 0.001 TRP B 510 HIS 0.006 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (25032) covalent geometry : angle 0.75408 / 0.39 (33798) hydrogen bonds : bond 0.03958 / 2.66 ( 725) hydrogen bonds : angle 5.16953 / 3.54 ( 2097) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 465 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 PHE cc_start: 0.8019 (t80) cc_final: 0.7780 (t80) REVERT: B 256 ILE cc_start: 0.9024 (mt) cc_final: 0.8699 (mt) REVERT: B 329 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6427 (mt-10) REVERT: B 519 ASP cc_start: 0.7163 (p0) cc_final: 0.6241 (t0) REVERT: B 655 MET cc_start: 0.8981 (mtt) cc_final: 0.8691 (mtt) REVERT: C 247 GLN cc_start: 0.7286 (mt0) cc_final: 0.6943 (mp10) REVERT: C 276 MET cc_start: 0.5871 (tpt) cc_final: 0.5654 (tpt) REVERT: C 283 LYS cc_start: 0.7838 (mmmt) cc_final: 0.7020 (mttp) REVERT: C 435 ASN cc_start: 0.8633 (t0) cc_final: 0.8095 (t0) REVERT: C 442 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7375 (tm-30) REVERT: C 453 MET cc_start: 0.7611 (mmm) cc_final: 0.7357 (tpt) REVERT: C 590 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8400 (t0) REVERT: D 712 MET cc_start: 0.8837 (tpp) cc_final: 0.8589 (tpp) REVERT: E 561 ASN cc_start: 0.8157 (m110) cc_final: 0.7634 (t0) REVERT: E 573 MET cc_start: 0.7919 (mtp) cc_final: 0.7660 (mtp) REVERT: E 712 MET cc_start: 0.7319 (mmm) cc_final: 0.7055 (mtt) REVERT: E 713 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8696 (mt) REVERT: F 276 MET cc_start: 0.4815 (mmm) cc_final: 0.4597 (mmm) REVERT: F 329 GLU cc_start: 0.7430 (tt0) cc_final: 0.7028 (pp20) REVERT: F 340 MET cc_start: 0.5402 (ptm) cc_final: 0.3684 (mmt) REVERT: F 414 MET cc_start: 0.8090 (ttp) cc_final: 0.7832 (tmm) REVERT: F 496 GLN cc_start: 0.4572 (tt0) cc_final: 0.4243 (mp10) REVERT: F 650 ASP cc_start: 0.7926 (p0) cc_final: 0.7384 (t0) REVERT: F 712 MET cc_start: 0.8226 (mmm) cc_final: 0.7595 (mpp) REVERT: F 720 MET cc_start: 0.7663 (mmm) cc_final: 0.7322 (mtp) REVERT: A 233 ARG cc_start: 0.7355 (mtt90) cc_final: 0.7149 (mmm160) REVERT: A 276 MET cc_start: 0.6993 (mmm) cc_final: 0.6161 (mtm) REVERT: A 467 MET cc_start: 0.0689 (mtm) cc_final: -0.0201 (mmt) REVERT: A 567 ILE cc_start: 0.8743 (mt) cc_final: 0.8301 (tt) outliers start: 90 outliers final: 43 residues processed: 528 average time/residue: 0.1559 time to fit residues: 133.8892 Evaluate side-chains 443 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 398 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 713 LEU Chi-restraints excluded: chain F residue 427 LYS Chi-restraints excluded: chain F residue 466 ASP Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 207 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 282 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 chunk 302 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN B 456 HIS ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 ASN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 GLN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN D 505 ASN ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN F 495 ASN ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.162165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125848 restraints weight = 43159.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.129016 restraints weight = 24501.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130982 restraints weight = 17102.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132264 restraints weight = 13766.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132874 restraints weight = 12068.349| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 25032 Z= 0.240 Angle : 0.800 13.601 33798 Z= 0.417 Chirality : 0.050 0.238 3876 Planarity : 0.006 0.105 4308 Dihedral : 8.605 85.149 3365 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.84 % Favored : 88.10 % Rotamer: Outliers : 4.58 % Allowed : 15.28 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.11 % Twisted Proline : 3.03 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.14), residues: 3108 helix: -1.68 (0.13), residues: 1382 sheet: -1.93 (0.26), residues: 365 loop : -2.62 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 385 TYR 0.016 0.002 TYR C 499 PHE 0.030 0.002 PHE D 231 TRP 0.015 0.002 TRP B 510 HIS 0.010 0.002 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 (25032) covalent geometry : angle 0.79970 / 0.42 (33798) hydrogen bonds : bond 0.03859 / 2.59 ( 725) hydrogen bonds : angle 5.16025 / 3.53 ( 2097) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 417 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 PHE cc_start: 0.8174 (t80) cc_final: 0.7786 (t80) REVERT: B 256 ILE cc_start: 0.9240 (mt) cc_final: 0.8892 (mt) REVERT: B 285 VAL cc_start: 0.9176 (p) cc_final: 0.8956 (m) REVERT: B 399 ASP cc_start: 0.8392 (p0) cc_final: 0.8043 (p0) REVERT: B 458 LYS cc_start: 0.0755 (OUTLIER) cc_final: 0.0068 (ptpp) REVERT: C 238 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7590 (ttm-80) REVERT: C 283 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7449 (mttp) REVERT: C 435 ASN cc_start: 0.8696 (t0) cc_final: 0.8473 (t0) REVERT: C 442 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7265 (tm-30) REVERT: C 520 ASP cc_start: 0.7940 (t0) cc_final: 0.7656 (t70) REVERT: D 315 ARG cc_start: 0.5224 (mmm-85) cc_final: 0.5001 (mmm-85) REVERT: D 340 MET cc_start: 0.2320 (ptm) cc_final: 0.1987 (mpp) REVERT: D 621 LEU cc_start: 0.9034 (tp) cc_final: 0.8715 (tp) REVERT: E 226 GLU cc_start: 0.8058 (mp0) cc_final: 0.7607 (mp0) REVERT: E 337 ARG cc_start: 0.4824 (OUTLIER) cc_final: 0.4526 (ptp90) REVERT: E 403 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8219 (mtm110) REVERT: E 498 ASP cc_start: 0.6328 (m-30) cc_final: 0.5889 (m-30) REVERT: E 561 ASN cc_start: 0.8103 (m110) cc_final: 0.7668 (t0) REVERT: E 624 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8113 (mm-40) REVERT: E 657 MET cc_start: 0.8094 (ttp) cc_final: 0.7880 (ttp) REVERT: E 712 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7250 (mtt) REVERT: E 713 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8745 (mt) REVERT: F 276 MET cc_start: 0.4876 (mmm) cc_final: 0.4670 (mmm) REVERT: F 329 GLU cc_start: 0.7463 (tt0) cc_final: 0.7047 (pp20) REVERT: F 340 MET cc_start: 0.5568 (ptm) cc_final: 0.3852 (mmt) REVERT: F 394 GLU cc_start: 0.7388 (tp30) cc_final: 0.6335 (pm20) REVERT: F 414 MET cc_start: 0.8233 (ttp) cc_final: 0.8004 (tmm) REVERT: F 453 MET cc_start: 0.6188 (mmm) cc_final: 0.5958 (mmm) REVERT: F 496 GLN cc_start: 0.4938 (tt0) cc_final: 0.4232 (mp10) REVERT: F 510 TRP cc_start: 0.7868 (p-90) cc_final: 0.7063 (p-90) REVERT: F 650 ASP cc_start: 0.8008 (p0) cc_final: 0.7621 (t0) REVERT: F 655 MET cc_start: 0.8378 (mtm) cc_final: 0.7796 (mtm) REVERT: F 720 MET cc_start: 0.7816 (mmm) cc_final: 0.7440 (mtp) REVERT: A 230 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7485 (pt) REVERT: A 233 ARG cc_start: 0.7390 (mtt90) cc_final: 0.7137 (mmm160) REVERT: A 276 MET cc_start: 0.7005 (mmm) cc_final: 0.6198 (mtm) REVERT: A 299 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6897 (pm20) REVERT: A 424 VAL cc_start: 0.3862 (OUTLIER) cc_final: 0.3650 (m) REVERT: A 467 MET cc_start: 0.0965 (mtm) cc_final: -0.0011 (mmt) REVERT: A 567 ILE cc_start: 0.8922 (mt) cc_final: 0.8470 (tt) REVERT: A 683 LEU cc_start: 0.7988 (tp) cc_final: 0.7753 (tp) outliers start: 122 outliers final: 81 residues processed: 500 average time/residue: 0.1642 time to fit residues: 132.2474 Evaluate side-chains 472 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 383 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 467 MET Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 417 HIS Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain E residue 650 ASP Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 712 MET Chi-restraints excluded: chain E residue 713 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 427 LYS Chi-restraints excluded: chain F residue 466 ASP Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 528 THR Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 680 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 73 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 291 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 294 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 GLN ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS ** A 456 HIS ** 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 = 0.4040 r_free = 0.4040 target = 0.164675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128779 restraints weight = 42887.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131982 restraints weight = 24108.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134042 restraints weight = 16732.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.135329 restraints weight = 13372.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135982 restraints weight = 11709.858| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25032 Z= 0.160 Angle : 0.731 13.444 33798 Z= 0.381 Chirality : 0.047 0.197 3876 Planarity : 0.005 0.106 4308 Dihedral : 8.266 85.685 3365 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.91 % Favored : 89.03 % Rotamer: Outliers : 4.02 % Allowed : 17.19 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.11 % Twisted Proline : 2.27 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.15), residues: 3108 helix: -1.31 (0.14), residues: 1367 sheet: -1.85 (0.26), residues: 363 loop : -2.44 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 516 TYR 0.018 0.001 TYR F 259 PHE 0.039 0.002 PHE D 231 TRP 0.015 0.001 TRP B 510 HIS 0.010 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (25032) covalent geometry : angle 0.73149 / 0.38 (33798) hydrogen bonds : bond 0.03404 / 2.28 ( 725) hydrogen bonds : angle 4.87572 / 3.35 ( 2097) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 424 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 PHE cc_start: 0.7968 (t80) cc_final: 0.7675 (t80) REVERT: B 240 PHE cc_start: 0.5469 (m-80) cc_final: 0.5090 (m-80) REVERT: B 256 ILE cc_start: 0.9207 (mt) cc_final: 0.8848 (mt) REVERT: B 399 ASP cc_start: 0.8378 (p0) cc_final: 0.8056 (p0) REVERT: B 453 MET cc_start: 0.8724 (mtt) cc_final: 0.8457 (mtp) REVERT: B 519 ASP cc_start: 0.7414 (p0) cc_final: 0.6366 (t0) REVERT: B 655 MET cc_start: 0.8986 (mtt) cc_final: 0.8729 (mtt) REVERT: C 238 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7525 (ttm-80) REVERT: C 283 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7202 (mttp) REVERT: C 397 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8373 (pp) REVERT: C 414 MET cc_start: 0.6833 (ttt) cc_final: 0.6352 (ttm) REVERT: C 435 ASN cc_start: 0.8728 (t0) cc_final: 0.8234 (t0) REVERT: C 440 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7364 (mt-10) REVERT: C 442 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7286 (tm-30) REVERT: C 720 MET cc_start: 0.7662 (mmm) cc_final: 0.7141 (mtp) REVERT: D 340 MET cc_start: 0.2230 (ptm) cc_final: 0.1996 (mpp) REVERT: E 226 GLU cc_start: 0.7901 (mp0) cc_final: 0.7466 (mp0) REVERT: E 440 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8096 (mp0) REVERT: E 498 ASP cc_start: 0.6195 (m-30) cc_final: 0.5841 (m-30) REVERT: E 561 ASN cc_start: 0.7982 (m110) cc_final: 0.7604 (t0) REVERT: F 329 GLU cc_start: 0.7438 (tt0) cc_final: 0.7089 (pp20) REVERT: F 340 MET cc_start: 0.5660 (ptm) cc_final: 0.3715 (mmt) REVERT: F 394 GLU cc_start: 0.7286 (tp30) cc_final: 0.6255 (pm20) REVERT: F 453 MET cc_start: 0.6233 (mmm) cc_final: 0.5950 (mmm) REVERT: F 496 GLN cc_start: 0.4806 (tt0) cc_final: 0.4121 (mp10) REVERT: F 510 TRP cc_start: 0.7841 (p-90) cc_final: 0.7146 (p-90) REVERT: F 650 ASP cc_start: 0.8037 (p0) cc_final: 0.7812 (t0) REVERT: F 666 HIS cc_start: 0.7224 (t70) cc_final: 0.6973 (t-90) REVERT: F 720 MET cc_start: 0.7851 (mmm) cc_final: 0.7511 (mtp) REVERT: A 230 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7577 (pt) REVERT: A 276 MET cc_start: 0.7003 (mmm) cc_final: 0.6201 (mtm) REVERT: A 405 GLN cc_start: 0.6044 (tm-30) cc_final: 0.5616 (tm-30) REVERT: A 407 LEU cc_start: 0.7586 (mm) cc_final: 0.7322 (mt) REVERT: A 424 VAL cc_start: 0.3925 (OUTLIER) cc_final: 0.3682 (m) REVERT: A 467 MET cc_start: 0.0914 (mtm) cc_final: -0.0122 (mmt) REVERT: A 567 ILE cc_start: 0.8930 (mt) cc_final: 0.8437 (tt) outliers start: 107 outliers final: 65 residues processed: 500 average time/residue: 0.1552 time to fit residues: 126.3017 Evaluate side-chains 464 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 395 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 467 MET Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 586 LYS Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 492 PHE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 650 ASP Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 427 LYS Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 456 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 182 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 40 optimal weight: 4.9990 chunk 295 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 243 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.166638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131152 restraints weight = 43020.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134459 restraints weight = 24020.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136497 restraints weight = 16623.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.137810 restraints weight = 13269.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138395 restraints weight = 11570.871| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25032 Z= 0.130 Angle : 0.704 15.328 33798 Z= 0.365 Chirality : 0.046 0.183 3876 Planarity : 0.005 0.098 4308 Dihedral : 7.958 85.201 3365 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.65 % Favored : 89.29 % Rotamer: Outliers : 3.87 % Allowed : 17.68 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.11 % Twisted Proline : 3.03 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.15), residues: 3108 helix: -1.03 (0.14), residues: 1377 sheet: -1.80 (0.26), residues: 361 loop : -2.40 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 233 TYR 0.014 0.001 TYR F 259 PHE 0.025 0.001 PHE D 231 TRP 0.013 0.001 TRP B 510 HIS 0.014 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (25032) covalent geometry : angle 0.70437 / 0.37 (33798) hydrogen bonds : bond 0.03089 / 2.07 ( 725) hydrogen bonds : angle 4.67265 / 3.20 ( 2097) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 439 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 240 PHE cc_start: 0.5604 (m-80) cc_final: 0.5102 (m-80) REVERT: B 256 ILE cc_start: 0.9198 (mt) cc_final: 0.8875 (mt) REVERT: B 399 ASP cc_start: 0.8289 (p0) cc_final: 0.7973 (p0) REVERT: B 519 ASP cc_start: 0.7131 (p0) cc_final: 0.6578 (t0) REVERT: B 655 MET cc_start: 0.8938 (mtt) cc_final: 0.8654 (mtt) REVERT: B 712 MET cc_start: 0.8593 (tpp) cc_final: 0.8241 (tpp) REVERT: C 238 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7445 (ttm-80) REVERT: C 283 LYS cc_start: 0.7897 (mmmt) cc_final: 0.6921 (mttp) REVERT: C 397 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8334 (pp) REVERT: C 414 MET cc_start: 0.6704 (ttt) cc_final: 0.6326 (ttm) REVERT: C 435 ASN cc_start: 0.8672 (t0) cc_final: 0.8069 (t0) REVERT: C 440 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7277 (mt-10) REVERT: C 442 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7216 (tm-30) REVERT: C 720 MET cc_start: 0.7662 (mmm) cc_final: 0.7137 (mtp) REVERT: D 232 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8202 (ttm170) REVERT: D 267 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8624 (p) REVERT: D 453 MET cc_start: 0.8496 (tpp) cc_final: 0.8085 (tpt) REVERT: D 528 THR cc_start: 0.9312 (m) cc_final: 0.9040 (p) REVERT: E 226 GLU cc_start: 0.7797 (mp0) cc_final: 0.7472 (mp0) REVERT: E 337 ARG cc_start: 0.4964 (OUTLIER) cc_final: 0.3461 (pmt100) REVERT: E 363 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7981 (mm110) REVERT: E 498 ASP cc_start: 0.5962 (m-30) cc_final: 0.5583 (m-30) REVERT: E 561 ASN cc_start: 0.7931 (m110) cc_final: 0.7503 (t0) REVERT: E 624 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8530 (mm-40) REVERT: F 329 GLU cc_start: 0.7348 (tt0) cc_final: 0.7035 (pp20) REVERT: F 340 MET cc_start: 0.5536 (ptm) cc_final: 0.3616 (mmt) REVERT: F 394 GLU cc_start: 0.7292 (tp30) cc_final: 0.6232 (pm20) REVERT: F 453 MET cc_start: 0.6238 (mmm) cc_final: 0.5878 (mmm) REVERT: F 455 ARG cc_start: 0.7284 (mmm-85) cc_final: 0.6971 (mmm-85) REVERT: F 496 GLN cc_start: 0.5066 (tt0) cc_final: 0.4417 (mp10) REVERT: F 510 TRP cc_start: 0.7801 (p-90) cc_final: 0.7120 (p-90) REVERT: F 621 LEU cc_start: 0.8970 (tp) cc_final: 0.8717 (tt) REVERT: F 666 HIS cc_start: 0.7124 (t70) cc_final: 0.6808 (t-90) REVERT: F 720 MET cc_start: 0.7881 (mmm) cc_final: 0.7575 (mtp) REVERT: A 230 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7504 (pt) REVERT: A 240 PHE cc_start: 0.4179 (OUTLIER) cc_final: 0.3707 (m-10) REVERT: A 276 MET cc_start: 0.6946 (mmm) cc_final: 0.6124 (mtm) REVERT: A 297 GLU cc_start: 0.5636 (mp0) cc_final: 0.4824 (mm-30) REVERT: A 328 ASP cc_start: 0.4979 (m-30) cc_final: 0.4402 (t70) REVERT: A 405 GLN cc_start: 0.6004 (tm-30) cc_final: 0.5608 (tm-30) REVERT: A 424 VAL cc_start: 0.3537 (OUTLIER) cc_final: 0.3147 (m) REVERT: A 467 MET cc_start: 0.0928 (mtm) cc_final: -0.0020 (mmt) REVERT: A 567 ILE cc_start: 0.8913 (mt) cc_final: 0.8440 (tt) REVERT: A 638 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7745 (mmm-85) REVERT: A 716 MET cc_start: 0.7650 (ttt) cc_final: 0.7440 (ttm) outliers start: 103 outliers final: 59 residues processed: 510 average time/residue: 0.1624 time to fit residues: 132.8424 Evaluate side-chains 466 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 398 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 467 MET Chi-restraints excluded: chain D residue 586 LYS Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 492 PHE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 650 ASP Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 466 ASP Chi-restraints excluded: chain F residue 536 LEU Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 665 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 686 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 222 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 243 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 296 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 266 optimal weight: 10.0000 chunk 288 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN B 418 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 ASN F 486 ASN ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 456 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.164314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128597 restraints weight = 43045.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131839 restraints weight = 24293.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133900 restraints weight = 16840.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.135156 restraints weight = 13457.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135907 restraints weight = 11778.523| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25032 Z= 0.173 Angle : 0.736 13.288 33798 Z= 0.378 Chirality : 0.047 0.205 3876 Planarity : 0.005 0.097 4308 Dihedral : 7.915 87.029 3365 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.07 % Favored : 88.87 % Rotamer: Outliers : 3.87 % Allowed : 18.66 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.11 % Twisted Proline : 2.27 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.15), residues: 3108 helix: -0.93 (0.14), residues: 1389 sheet: -1.79 (0.26), residues: 355 loop : -2.35 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 516 TYR 0.012 0.001 TYR F 259 PHE 0.025 0.002 PHE D 231 TRP 0.013 0.001 TRP B 510 HIS 0.013 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (25032) covalent geometry : angle 0.73588 / 0.38 (33798) hydrogen bonds : bond 0.03217 / 2.15 ( 725) hydrogen bonds : angle 4.68884 / 3.22 ( 2097) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 409 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 ILE cc_start: 0.9254 (mt) cc_final: 0.8874 (mt) REVERT: B 399 ASP cc_start: 0.8358 (p0) cc_final: 0.8035 (p0) REVERT: B 409 ILE cc_start: 0.8669 (mt) cc_final: 0.8445 (tp) REVERT: B 453 MET cc_start: 0.8709 (mtt) cc_final: 0.8204 (ttm) REVERT: B 519 ASP cc_start: 0.7161 (p0) cc_final: 0.6507 (t0) REVERT: B 655 MET cc_start: 0.8969 (mtt) cc_final: 0.8715 (mtt) REVERT: B 712 MET cc_start: 0.8550 (tpp) cc_final: 0.8201 (tpp) REVERT: B 715 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7100 (mt-10) REVERT: C 238 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7572 (ttm-80) REVERT: C 283 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7198 (mttp) REVERT: C 397 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8365 (pp) REVERT: C 435 ASN cc_start: 0.8711 (t0) cc_final: 0.8304 (t0) REVERT: C 440 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7212 (mt-10) REVERT: C 442 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7175 (tm-30) REVERT: C 720 MET cc_start: 0.7692 (mmm) cc_final: 0.7177 (mtp) REVERT: D 232 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8226 (ttm170) REVERT: D 267 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8758 (p) REVERT: D 453 MET cc_start: 0.8510 (tpp) cc_final: 0.8151 (tpt) REVERT: D 712 MET cc_start: 0.8590 (tpp) cc_final: 0.8328 (tpp) REVERT: E 335 LYS cc_start: 0.7717 (mtpt) cc_final: 0.7433 (mtpt) REVERT: E 337 ARG cc_start: 0.5089 (OUTLIER) cc_final: 0.3586 (pmt100) REVERT: E 363 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8047 (mm110) REVERT: E 498 ASP cc_start: 0.5846 (m-30) cc_final: 0.5594 (m-30) REVERT: E 561 ASN cc_start: 0.7937 (m110) cc_final: 0.7543 (t0) REVERT: F 329 GLU cc_start: 0.7368 (tt0) cc_final: 0.7069 (pp20) REVERT: F 340 MET cc_start: 0.5528 (ptm) cc_final: 0.3731 (mmt) REVERT: F 394 GLU cc_start: 0.7543 (tp30) cc_final: 0.6523 (pm20) REVERT: F 453 MET cc_start: 0.6168 (mmm) cc_final: 0.5771 (mmm) REVERT: F 455 ARG cc_start: 0.6948 (mmm-85) cc_final: 0.6614 (mmm-85) REVERT: F 496 GLN cc_start: 0.5080 (tt0) cc_final: 0.4571 (mp10) REVERT: F 510 TRP cc_start: 0.7872 (p-90) cc_final: 0.7172 (p-90) REVERT: F 655 MET cc_start: 0.8346 (mtm) cc_final: 0.7715 (mtm) REVERT: F 666 HIS cc_start: 0.7271 (t70) cc_final: 0.6919 (t-90) REVERT: F 720 MET cc_start: 0.7957 (mmm) cc_final: 0.7597 (mtp) REVERT: A 218 MET cc_start: 0.6677 (pmm) cc_final: 0.5514 (ppp) REVERT: A 230 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7545 (pt) REVERT: A 240 PHE cc_start: 0.4079 (OUTLIER) cc_final: 0.3685 (m-10) REVERT: A 276 MET cc_start: 0.6778 (mmm) cc_final: 0.5940 (mtm) REVERT: A 405 GLN cc_start: 0.6024 (tm-30) cc_final: 0.5593 (tm-30) REVERT: A 424 VAL cc_start: 0.3551 (OUTLIER) cc_final: 0.3133 (m) REVERT: A 467 MET cc_start: 0.0980 (mtm) cc_final: -0.0009 (mmt) REVERT: A 638 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7791 (mmm-85) REVERT: A 716 MET cc_start: 0.7684 (ttt) cc_final: 0.7426 (ttm) outliers start: 103 outliers final: 69 residues processed: 484 average time/residue: 0.1635 time to fit residues: 127.0570 Evaluate side-chains 462 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 384 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 467 MET Chi-restraints excluded: chain D residue 604 ASP Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 492 PHE Chi-restraints excluded: chain E residue 520 ASP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 565 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 650 ASP Chi-restraints excluded: chain E residue 713 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 421 SER Chi-restraints excluded: chain F residue 466 ASP Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 686 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 296 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 264 optimal weight: 0.8980 chunk 275 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 365 ASN B 418 GLN B 449 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.165915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130271 restraints weight = 43110.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.133563 restraints weight = 24337.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135655 restraints weight = 16832.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.136924 restraints weight = 13435.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.137735 restraints weight = 11760.421| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25032 Z= 0.142 Angle : 0.723 12.874 33798 Z= 0.371 Chirality : 0.047 0.207 3876 Planarity : 0.005 0.091 4308 Dihedral : 7.760 87.272 3365 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.75 % Favored : 89.19 % Rotamer: Outliers : 3.60 % Allowed : 19.44 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.14 % Twisted Proline : 1.52 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.15), residues: 3108 helix: -0.79 (0.14), residues: 1394 sheet: -1.65 (0.27), residues: 350 loop : -2.34 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 516 TYR 0.012 0.001 TYR F 259 PHE 0.019 0.001 PHE D 231 TRP 0.012 0.001 TRP B 510 HIS 0.010 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (25032) covalent geometry : angle 0.72314 / 0.37 (33798) hydrogen bonds : bond 0.03042 / 2.03 ( 725) hydrogen bonds : angle 4.56567 / 3.13 ( 2097) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 411 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 ILE cc_start: 0.9248 (mt) cc_final: 0.8889 (mt) REVERT: B 399 ASP cc_start: 0.8367 (p0) cc_final: 0.8037 (p0) REVERT: B 453 MET cc_start: 0.8644 (mtt) cc_final: 0.8107 (ttm) REVERT: B 519 ASP cc_start: 0.7130 (p0) cc_final: 0.6596 (t0) REVERT: B 655 MET cc_start: 0.8934 (mtt) cc_final: 0.8708 (mtt) REVERT: B 712 MET cc_start: 0.8562 (tpp) cc_final: 0.8198 (tpp) REVERT: C 238 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7388 (ttm-80) REVERT: C 283 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7009 (mttp) REVERT: C 414 MET cc_start: 0.6628 (ttt) cc_final: 0.6174 (ttm) REVERT: C 435 ASN cc_start: 0.8651 (t0) cc_final: 0.8178 (t0) REVERT: C 440 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7324 (mt-10) REVERT: C 442 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7243 (tm-30) REVERT: C 720 MET cc_start: 0.7649 (mmm) cc_final: 0.7324 (mtp) REVERT: D 232 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8148 (ttm170) REVERT: D 267 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8735 (p) REVERT: D 453 MET cc_start: 0.8512 (tpp) cc_final: 0.8114 (tpt) REVERT: D 481 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8467 (mm) REVERT: D 528 THR cc_start: 0.9318 (m) cc_final: 0.9017 (p) REVERT: D 712 MET cc_start: 0.8514 (tpp) cc_final: 0.8250 (tpp) REVERT: E 226 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7984 (mp0) REVERT: E 229 ASP cc_start: 0.8858 (t0) cc_final: 0.8599 (t0) REVERT: E 335 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7508 (mtpt) REVERT: E 337 ARG cc_start: 0.5046 (OUTLIER) cc_final: 0.3595 (pmt100) REVERT: E 363 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8057 (mm110) REVERT: E 434 LYS cc_start: 0.7586 (ptpt) cc_final: 0.7325 (tppt) REVERT: E 561 ASN cc_start: 0.7940 (m110) cc_final: 0.7529 (t0) REVERT: F 329 GLU cc_start: 0.7348 (tt0) cc_final: 0.7077 (pp20) REVERT: F 340 MET cc_start: 0.5586 (ptm) cc_final: 0.3789 (mmt) REVERT: F 394 GLU cc_start: 0.7635 (tp30) cc_final: 0.6577 (pm20) REVERT: F 414 MET cc_start: 0.8112 (tmm) cc_final: 0.7849 (tmm) REVERT: F 453 MET cc_start: 0.6225 (mmm) cc_final: 0.5844 (mmm) REVERT: F 455 ARG cc_start: 0.7097 (mmm-85) cc_final: 0.6832 (mmm-85) REVERT: F 496 GLN cc_start: 0.5055 (tt0) cc_final: 0.4541 (mp10) REVERT: F 510 TRP cc_start: 0.7866 (p-90) cc_final: 0.7175 (p-90) REVERT: F 621 LEU cc_start: 0.8970 (tp) cc_final: 0.8715 (tt) REVERT: F 666 HIS cc_start: 0.7231 (t70) cc_final: 0.6840 (t-90) REVERT: F 720 MET cc_start: 0.7965 (mmm) cc_final: 0.7684 (mtp) REVERT: A 230 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7547 (pt) REVERT: A 240 PHE cc_start: 0.3998 (OUTLIER) cc_final: 0.2919 (m-10) REVERT: A 276 MET cc_start: 0.6840 (mmm) cc_final: 0.6018 (mtm) REVERT: A 297 GLU cc_start: 0.5714 (mp0) cc_final: 0.5099 (mm-30) REVERT: A 405 GLN cc_start: 0.5975 (tm-30) cc_final: 0.5573 (tm-30) REVERT: A 424 VAL cc_start: 0.3585 (OUTLIER) cc_final: 0.3077 (m) REVERT: A 467 MET cc_start: 0.0965 (mtm) cc_final: 0.0044 (mmt) REVERT: A 638 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7750 (mmm-85) REVERT: A 716 MET cc_start: 0.7697 (ttt) cc_final: 0.7437 (ttm) outliers start: 96 outliers final: 68 residues processed: 474 average time/residue: 0.1634 time to fit residues: 125.2182 Evaluate side-chains 468 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 391 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 467 MET Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 586 LYS Chi-restraints excluded: chain D residue 604 ASP Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 492 PHE Chi-restraints excluded: chain E residue 520 ASP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 650 ASP Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 466 ASP Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 609 LEU Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 665 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 686 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 230 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 274 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 408 HIS B 418 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.165078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129408 restraints weight = 43185.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.132665 restraints weight = 24451.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.134751 restraints weight = 16974.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.136050 restraints weight = 13553.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136509 restraints weight = 11832.518| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25032 Z= 0.158 Angle : 0.743 12.608 33798 Z= 0.378 Chirality : 0.047 0.243 3876 Planarity : 0.005 0.086 4308 Dihedral : 7.729 87.403 3365 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.04 % Favored : 88.90 % Rotamer: Outliers : 3.49 % Allowed : 19.74 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.11 % Twisted Proline : 2.27 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.15), residues: 3108 helix: -0.69 (0.14), residues: 1388 sheet: -1.64 (0.27), residues: 352 loop : -2.29 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 413 TYR 0.012 0.001 TYR F 259 PHE 0.033 0.002 PHE D 231 TRP 0.012 0.001 TRP B 510 HIS 0.014 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (25032) covalent geometry : angle 0.74327 / 0.38 (33798) hydrogen bonds : bond 0.03065 / 2.05 ( 725) hydrogen bonds : angle 4.54965 / 3.12 ( 2097) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 395 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 ILE cc_start: 0.9256 (mt) cc_final: 0.8881 (mt) REVERT: B 399 ASP cc_start: 0.8367 (p0) cc_final: 0.8048 (p0) REVERT: B 453 MET cc_start: 0.8662 (mtt) cc_final: 0.8234 (ttm) REVERT: B 519 ASP cc_start: 0.7103 (p0) cc_final: 0.6632 (t0) REVERT: B 655 MET cc_start: 0.8947 (mtt) cc_final: 0.8733 (mtt) REVERT: B 712 MET cc_start: 0.8575 (tpp) cc_final: 0.8206 (tpp) REVERT: B 715 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7019 (mt-10) REVERT: C 238 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7401 (ttm-80) REVERT: C 283 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7146 (mttp) REVERT: C 356 SER cc_start: 0.8210 (p) cc_final: 0.7925 (p) REVERT: C 414 MET cc_start: 0.6795 (ttt) cc_final: 0.6362 (ttm) REVERT: C 435 ASN cc_start: 0.8595 (t0) cc_final: 0.8287 (t0) REVERT: C 440 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7201 (mt-10) REVERT: C 442 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7243 (tm-30) REVERT: C 720 MET cc_start: 0.7664 (mmm) cc_final: 0.7350 (mtp) REVERT: D 232 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8149 (ttm170) REVERT: D 340 MET cc_start: 0.4379 (mpp) cc_final: 0.3270 (mpp) REVERT: D 453 MET cc_start: 0.8477 (tpp) cc_final: 0.8171 (tpt) REVERT: D 481 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8467 (mm) REVERT: D 528 THR cc_start: 0.9325 (m) cc_final: 0.9022 (p) REVERT: D 697 GLN cc_start: 0.7882 (mm110) cc_final: 0.7591 (mm-40) REVERT: D 712 MET cc_start: 0.8531 (tpp) cc_final: 0.8265 (tpp) REVERT: E 335 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7518 (mtpt) REVERT: E 337 ARG cc_start: 0.5127 (OUTLIER) cc_final: 0.3673 (pmt100) REVERT: E 363 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7961 (mm110) REVERT: E 434 LYS cc_start: 0.7474 (ptpt) cc_final: 0.7269 (tppt) REVERT: E 467 MET cc_start: 0.4221 (mmp) cc_final: 0.4006 (mmp) REVERT: E 561 ASN cc_start: 0.7933 (m110) cc_final: 0.7545 (t0) REVERT: F 329 GLU cc_start: 0.7410 (tt0) cc_final: 0.7175 (pp20) REVERT: F 340 MET cc_start: 0.5652 (ptm) cc_final: 0.3853 (mmt) REVERT: F 394 GLU cc_start: 0.7658 (tp30) cc_final: 0.7011 (tm-30) REVERT: F 453 MET cc_start: 0.5992 (mmm) cc_final: 0.5711 (mmm) REVERT: F 455 ARG cc_start: 0.7185 (mmm-85) cc_final: 0.6964 (mmm-85) REVERT: F 496 GLN cc_start: 0.5222 (tt0) cc_final: 0.4662 (mp10) REVERT: F 510 TRP cc_start: 0.7828 (p-90) cc_final: 0.7092 (p-90) REVERT: F 621 LEU cc_start: 0.8989 (tp) cc_final: 0.8732 (tt) REVERT: F 666 HIS cc_start: 0.7238 (t70) cc_final: 0.6800 (t-90) REVERT: F 720 MET cc_start: 0.7972 (mmm) cc_final: 0.7652 (mtp) REVERT: A 230 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7558 (pt) REVERT: A 276 MET cc_start: 0.6819 (mmm) cc_final: 0.6000 (mtm) REVERT: A 297 GLU cc_start: 0.5892 (mp0) cc_final: 0.5221 (mm-30) REVERT: A 328 ASP cc_start: 0.4692 (m-30) cc_final: 0.4189 (t70) REVERT: A 405 GLN cc_start: 0.5999 (tm-30) cc_final: 0.5585 (tm-30) REVERT: A 467 MET cc_start: 0.0981 (mtm) cc_final: 0.0052 (mmt) REVERT: A 528 THR cc_start: 0.8700 (m) cc_final: 0.8437 (t) REVERT: A 585 MET cc_start: 0.8376 (mtp) cc_final: 0.8031 (ttp) outliers start: 93 outliers final: 65 residues processed: 457 average time/residue: 0.1606 time to fit residues: 119.4695 Evaluate side-chains 454 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 384 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 586 LYS Chi-restraints excluded: chain D residue 604 ASP Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 492 PHE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 565 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 650 ASP Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 421 SER Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 609 LEU Chi-restraints excluded: chain F residue 612 VAL Chi-restraints excluded: chain F residue 663 THR Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 686 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 56 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 297 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 198 optimal weight: 6.9990 chunk 84 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.166814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130996 restraints weight = 43197.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134468 restraints weight = 23635.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.136669 restraints weight = 16064.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.138039 restraints weight = 12675.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.138922 restraints weight = 10993.593| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25032 Z= 0.133 Angle : 0.725 12.106 33798 Z= 0.370 Chirality : 0.047 0.219 3876 Planarity : 0.005 0.078 4308 Dihedral : 7.595 87.406 3365 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.36 % Favored : 89.58 % Rotamer: Outliers : 2.63 % Allowed : 20.53 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.14 % Twisted Proline : 2.27 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.15), residues: 3108 helix: -0.53 (0.14), residues: 1380 sheet: -1.52 (0.27), residues: 351 loop : -2.33 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 415 TYR 0.011 0.001 TYR F 259 PHE 0.036 0.001 PHE B 235 TRP 0.011 0.001 TRP B 510 HIS 0.022 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (25032) covalent geometry : angle 0.72546 / 0.37 (33798) hydrogen bonds : bond 0.02946 / 1.95 ( 725) hydrogen bonds : angle 4.48418 / 3.08 ( 2097) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 413 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 ILE cc_start: 0.9233 (mt) cc_final: 0.8822 (mt) REVERT: B 453 MET cc_start: 0.8621 (mtt) cc_final: 0.8336 (ttm) REVERT: B 519 ASP cc_start: 0.7042 (p0) cc_final: 0.6547 (t0) REVERT: B 712 MET cc_start: 0.8545 (tpp) cc_final: 0.8168 (tpp) REVERT: B 715 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7221 (mt-10) REVERT: C 283 LYS cc_start: 0.7954 (mmmt) cc_final: 0.6896 (mttp) REVERT: C 356 SER cc_start: 0.8212 (p) cc_final: 0.7914 (p) REVERT: C 414 MET cc_start: 0.6693 (ttt) cc_final: 0.6252 (ttm) REVERT: C 435 ASN cc_start: 0.8586 (t0) cc_final: 0.8298 (t0) REVERT: C 440 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7198 (mt-10) REVERT: C 442 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7166 (tm-30) REVERT: C 720 MET cc_start: 0.7638 (mmm) cc_final: 0.7323 (mtp) REVERT: D 232 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8041 (ttm170) REVERT: D 481 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8437 (mm) REVERT: D 528 THR cc_start: 0.9274 (m) cc_final: 0.8967 (p) REVERT: D 697 GLN cc_start: 0.7779 (mm110) cc_final: 0.7568 (mm-40) REVERT: D 712 MET cc_start: 0.8527 (tpp) cc_final: 0.8268 (tpp) REVERT: E 229 ASP cc_start: 0.8979 (t0) cc_final: 0.8625 (t0) REVERT: E 335 LYS cc_start: 0.7674 (mtpt) cc_final: 0.7425 (mtpt) REVERT: E 337 ARG cc_start: 0.5169 (OUTLIER) cc_final: 0.3724 (pmt100) REVERT: E 467 MET cc_start: 0.3586 (mmp) cc_final: 0.3087 (mmp) REVERT: E 561 ASN cc_start: 0.7938 (m110) cc_final: 0.7489 (t0) REVERT: E 624 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8147 (mm-40) REVERT: F 329 GLU cc_start: 0.7379 (tt0) cc_final: 0.7168 (pp20) REVERT: F 340 MET cc_start: 0.5577 (ptm) cc_final: 0.3802 (mmt) REVERT: F 394 GLU cc_start: 0.7677 (tp30) cc_final: 0.6548 (pm20) REVERT: F 453 MET cc_start: 0.6013 (mmm) cc_final: 0.5738 (mmm) REVERT: F 496 GLN cc_start: 0.5179 (tt0) cc_final: 0.4537 (mp10) REVERT: F 510 TRP cc_start: 0.7804 (p-90) cc_final: 0.7075 (p-90) REVERT: F 621 LEU cc_start: 0.8948 (tp) cc_final: 0.8708 (tt) REVERT: F 666 HIS cc_start: 0.7196 (t70) cc_final: 0.6779 (t-90) REVERT: F 720 MET cc_start: 0.7930 (mmm) cc_final: 0.7668 (mtp) REVERT: A 218 MET cc_start: 0.6674 (pmm) cc_final: 0.5434 (ppp) REVERT: A 230 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7665 (pt) REVERT: A 276 MET cc_start: 0.6668 (mmm) cc_final: 0.5889 (mtm) REVERT: A 297 GLU cc_start: 0.5932 (mp0) cc_final: 0.5174 (mm-30) REVERT: A 405 GLN cc_start: 0.5955 (tm-30) cc_final: 0.5347 (tm-30) REVERT: A 409 ILE cc_start: 0.7932 (mt) cc_final: 0.7283 (mm) REVERT: A 467 MET cc_start: 0.0972 (mtm) cc_final: 0.0089 (mmt) REVERT: A 528 THR cc_start: 0.8772 (m) cc_final: 0.8497 (t) REVERT: A 585 MET cc_start: 0.8372 (mtp) cc_final: 0.8042 (ttp) REVERT: A 715 GLU cc_start: 0.8421 (tp30) cc_final: 0.8143 (tp30) outliers start: 70 outliers final: 56 residues processed: 461 average time/residue: 0.1515 time to fit residues: 114.8249 Evaluate side-chains 454 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 394 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 586 LYS Chi-restraints excluded: chain D residue 604 ASP Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 492 PHE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 650 ASP Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 686 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 165 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 218 optimal weight: 0.9990 chunk 295 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 130 optimal weight: 0.0970 chunk 174 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 685 ASN ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 GLN ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.164368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128502 restraints weight = 43191.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131907 restraints weight = 23789.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.134113 restraints weight = 16185.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135479 restraints weight = 12756.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.136199 restraints weight = 11067.225| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25032 Z= 0.170 Angle : 0.750 12.481 33798 Z= 0.382 Chirality : 0.048 0.211 3876 Planarity : 0.005 0.075 4308 Dihedral : 7.646 87.847 3365 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.00 % Favored : 88.93 % Rotamer: Outliers : 2.89 % Allowed : 20.53 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.14 % Twisted Proline : 2.27 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.15), residues: 3108 helix: -0.51 (0.14), residues: 1385 sheet: -1.54 (0.27), residues: 353 loop : -2.32 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 403 TYR 0.031 0.002 TYR B 611 PHE 0.033 0.002 PHE B 235 TRP 0.012 0.001 TRP B 510 HIS 0.013 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (25032) covalent geometry : angle 0.75048 / 0.38 (33798) hydrogen bonds : bond 0.03069 / 2.04 ( 725) hydrogen bonds : angle 4.55255 / 3.13 ( 2097) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4994.15 seconds wall clock time: 86 minutes 58.88 seconds (5218.88 seconds total)