Starting phenix.real_space_refine on Thu Mar 5 17:58:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ip2_9698/03_2026/6ip2_9698.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ip2_9698/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ip2_9698/03_2026/6ip2_9698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ip2_9698/03_2026/6ip2_9698.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ip2_9698/03_2026/6ip2_9698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ip2_9698/03_2026/6ip2_9698.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.23, per 1000 atoms: 0.21 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: 1.99 Conformation dependent library (CDL) restraints added in 1.0 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: 0.74 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: 3.46 Time building geometry restraints manager: 2.67 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: 15199 26.65 - 53.31: 479 53.31 - 79.96: 56 79.96 - 106.61: 9 106.61 - 133.27: 1 Dihedral angle restraints: 15744 sinusoidal: 6816 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 15741 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: 0.01 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: 0.210 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.250 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 12.869 133.268 9972 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 covalent geometry : bond 0.00774 (25032) covalent geometry : angle 1.38020 (33798) hydrogen bonds : bond 0.30648 ( 725) hydrogen bonds : angle 10.14223 ( 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 : 0.919 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: 0.1904 time to fit residues: 244.9078 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 : 0.946 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 E 323 HIS E 363 GLN E 405 GLN ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 ASN E 546 HIS E 659 ASN F 405 GLN 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 410 HIS A 454 ASN ** 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.167166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130821 restraints weight = 42897.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134223 restraints weight = 23337.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.136377 restraints weight = 15831.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137688 restraints weight = 12539.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.138394 restraints weight = 10949.936| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3247 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= 0.178 Angle : 0.827 12.879 33798 Z= 0.435 Chirality : 0.049 0.241 3876 Planarity : 0.006 0.117 4308 Dihedral : 12.668 89.038 3737 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.10 % Favored : 89.77 % Rotamer: Outliers : 3.45 % Allowed : 10.96 % 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: -4.27 (0.13), residues: 3108 helix: -2.87 (0.11), residues: 1363 sheet: -2.03 (0.26), residues: 352 loop : -2.93 (0.15), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 516 TYR 0.009 0.001 TYR C 499 PHE 0.026 0.002 PHE D 231 TRP 0.012 0.001 TRP A 510 HIS 0.012 0.002 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00395 (25032) covalent geometry : angle 0.82664 (33798) hydrogen bonds : bond 0.04890 ( 725) hydrogen bonds : angle 5.74942 ( 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 633 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 541 time to evaluate : 0.738 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 227 PHE cc_start: 0.8077 (t80) cc_final: 0.7816 (t80) REVERT: B 256 ILE cc_start: 0.8889 (mt) cc_final: 0.8573 (mt) REVERT: B 329 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6107 (mp0) REVERT: B 519 ASP cc_start: 0.7272 (p0) cc_final: 0.6328 (t0) REVERT: C 276 MET cc_start: 0.6024 (tpt) cc_final: 0.5539 (tpt) REVERT: C 283 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7195 (mttp) REVERT: C 435 ASN cc_start: 0.8543 (t0) cc_final: 0.7972 (t0) REVERT: C 682 LEU cc_start: 0.8750 (mt) cc_final: 0.8355 (mt) REVERT: D 440 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7596 (mm-30) REVERT: D 516 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7868 (ttp80) REVERT: D 565 ILE cc_start: 0.8969 (mt) cc_final: 0.8733 (tp) REVERT: D 678 GLU cc_start: 0.8196 (tp30) cc_final: 0.7959 (tp30) REVERT: E 229 ASP cc_start: 0.8549 (t70) cc_final: 0.8318 (t0) REVERT: E 312 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6737 (tm-30) REVERT: E 498 ASP cc_start: 0.5891 (m-30) cc_final: 0.5522 (m-30) REVERT: E 561 ASN cc_start: 0.8123 (m110) cc_final: 0.7727 (t0) REVERT: E 590 ASP cc_start: 0.8548 (t0) cc_final: 0.8289 (t0) REVERT: E 624 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8247 (mm-40) REVERT: E 657 MET cc_start: 0.8096 (ttp) cc_final: 0.7753 (ttp) REVERT: E 712 MET cc_start: 0.7438 (mmm) cc_final: 0.7046 (mtt) REVERT: E 727 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7414 (ttm110) REVERT: F 248 MET cc_start: 0.5563 (ptt) cc_final: 0.5243 (tmm) REVERT: F 276 MET cc_start: 0.5001 (mmm) cc_final: 0.3884 (tpp) REVERT: F 322 LEU cc_start: 0.6797 (tp) cc_final: 0.6483 (tp) REVERT: F 329 GLU cc_start: 0.7417 (tt0) cc_final: 0.7052 (pp20) REVERT: F 340 MET cc_start: 0.5020 (ptm) cc_final: 0.3354 (mmt) REVERT: F 414 MET cc_start: 0.8098 (ttp) cc_final: 0.7703 (tpt) REVERT: F 496 GLN cc_start: 0.4771 (tt0) cc_final: 0.4229 (mp10) REVERT: F 655 MET cc_start: 0.8148 (mtm) cc_final: 0.7841 (mtm) REVERT: F 716 MET cc_start: 0.8373 (mtp) cc_final: 0.7532 (mpp) REVERT: A 233 ARG cc_start: 0.7186 (mtt90) cc_final: 0.6945 (mmm160) REVERT: A 276 MET cc_start: 0.6993 (mmm) cc_final: 0.6172 (mtm) REVERT: A 467 MET cc_start: 0.0939 (mtm) cc_final: 0.0100 (mmt) REVERT: A 567 ILE cc_start: 0.8664 (mt) cc_final: 0.8192 (tt) REVERT: A 674 GLU cc_start: 0.8199 (mp0) cc_final: 0.7969 (mp0) outliers start: 92 outliers final: 42 residues processed: 601 average time/residue: 0.1637 time to fit residues: 155.6854 Evaluate side-chains 459 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 417 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 429 LEU 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 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 358 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: 9.9990 chunk 212 optimal weight: 30.0000 chunk 257 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 221 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 43 optimal weight: 0.1980 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 247 GLN ** 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** E 435 ASN ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 GLN ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 319 ASN ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.161925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125657 restraints weight = 43092.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.128834 restraints weight = 24322.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.130838 restraints weight = 16850.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.132058 restraints weight = 13529.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.132641 restraints weight = 11892.876| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 25032 Z= 0.252 Angle : 0.836 13.321 33798 Z= 0.436 Chirality : 0.050 0.265 3876 Planarity : 0.006 0.114 4308 Dihedral : 12.554 88.608 3737 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.68 % Favored : 88.22 % Rotamer: Outliers : 4.43 % Allowed : 14.41 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.11 % Twisted Proline : 3.03 % Twisted General : 0.34 % 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: -3.68 (0.14), residues: 3108 helix: -2.12 (0.12), residues: 1384 sheet: -2.05 (0.26), residues: 366 loop : -2.82 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 691 TYR 0.017 0.002 TYR C 499 PHE 0.041 0.002 PHE D 231 TRP 0.018 0.002 TRP B 510 HIS 0.009 0.002 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00581 (25032) covalent geometry : angle 0.83600 (33798) hydrogen bonds : bond 0.04384 ( 725) hydrogen bonds : angle 5.41386 ( 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: 118 poor density : 437 time to evaluate : 0.834 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 227 PHE cc_start: 0.8118 (t80) cc_final: 0.7898 (t80) REVERT: B 256 ILE cc_start: 0.9239 (mt) cc_final: 0.8910 (mt) REVERT: B 399 ASP cc_start: 0.8323 (p0) cc_final: 0.8103 (p0) REVERT: B 453 MET cc_start: 0.8730 (mmt) cc_final: 0.8006 (mmm) REVERT: B 712 MET cc_start: 0.8752 (tpp) cc_final: 0.8222 (tpp) REVERT: C 238 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7615 (ttm-80) REVERT: C 283 LYS cc_start: 0.8298 (mmmt) cc_final: 0.7578 (mttp) REVERT: C 435 ASN cc_start: 0.8780 (t0) cc_final: 0.8402 (t0) REVERT: C 520 ASP cc_start: 0.7894 (t0) cc_final: 0.7618 (t70) REVERT: D 340 MET cc_start: 0.2367 (ptm) cc_final: 0.1395 (mpp) REVERT: D 565 ILE cc_start: 0.9033 (mt) cc_final: 0.8753 (tp) REVERT: D 621 LEU cc_start: 0.9006 (tp) cc_final: 0.8673 (tp) REVERT: D 678 GLU cc_start: 0.8158 (tp30) cc_final: 0.7886 (tp30) REVERT: D 712 MET cc_start: 0.8851 (tpp) cc_final: 0.8598 (tpp) REVERT: E 264 CYS cc_start: 0.8432 (m) cc_final: 0.8217 (t) REVERT: E 312 GLU cc_start: 0.8018 (mm-30) cc_final: 0.6630 (tm-30) REVERT: E 337 ARG cc_start: 0.4836 (OUTLIER) cc_final: 0.4273 (ptp90) REVERT: E 561 ASN cc_start: 0.8195 (m110) cc_final: 0.7706 (t0) REVERT: E 573 MET cc_start: 0.8138 (mtp) cc_final: 0.7879 (mtp) REVERT: E 624 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8476 (mm-40) REVERT: E 712 MET cc_start: 0.7506 (mmm) cc_final: 0.7270 (mtt) REVERT: E 727 ARG cc_start: 0.7399 (mtm-85) cc_final: 0.7157 (ttm110) REVERT: F 276 MET cc_start: 0.4937 (mmm) cc_final: 0.4718 (mmm) REVERT: F 329 GLU cc_start: 0.7477 (tt0) cc_final: 0.7049 (pp20) REVERT: F 340 MET cc_start: 0.5481 (ptm) cc_final: 0.3767 (mmt) REVERT: F 394 GLU cc_start: 0.7372 (tp30) cc_final: 0.6353 (pm20) REVERT: F 414 MET cc_start: 0.8245 (ttp) cc_final: 0.7994 (ptm) REVERT: F 496 GLN cc_start: 0.4725 (tt0) cc_final: 0.4343 (mp10) REVERT: F 720 MET cc_start: 0.7699 (mmm) cc_final: 0.7276 (mtp) REVERT: A 233 ARG cc_start: 0.7380 (mtt90) cc_final: 0.7086 (mmm160) REVERT: A 276 MET cc_start: 0.7038 (mmm) cc_final: 0.6177 (mtm) REVERT: A 297 GLU cc_start: 0.5464 (mp0) cc_final: 0.4860 (mm-30) REVERT: A 467 MET cc_start: 0.0916 (mtm) cc_final: -0.0053 (mmt) REVERT: A 567 ILE cc_start: 0.8904 (mt) cc_final: 0.8452 (tt) outliers start: 118 outliers final: 71 residues processed: 516 average time/residue: 0.1514 time to fit residues: 126.3794 Evaluate side-chains 471 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 398 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 361 VAL 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 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 429 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 528 THR 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 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 358 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 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 524 LEU Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 713 LEU Chi-restraints excluded: chain F residue 363 GLN 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 574 ILE 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 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 730 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 207 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 23 optimal weight: 10.0000 chunk 282 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 149 optimal weight: 0.0570 chunk 294 optimal weight: 7.9990 chunk 302 optimal weight: 10.0000 overall best weight: 2.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 HIS ** 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 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 252 HIS ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.165333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129373 restraints weight = 42891.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.132683 restraints weight = 24070.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.134746 restraints weight = 16606.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136045 restraints weight = 13253.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.136689 restraints weight = 11579.070| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4236 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= 0.149 Angle : 0.735 13.531 33798 Z= 0.384 Chirality : 0.047 0.209 3876 Planarity : 0.005 0.106 4308 Dihedral : 11.975 89.945 3737 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.36 % Favored : 89.58 % Rotamer: Outliers : 3.64 % Allowed : 16.18 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.11 % Twisted Proline : 2.27 % 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: -3.14 (0.14), residues: 3108 helix: -1.59 (0.13), residues: 1370 sheet: -1.93 (0.26), residues: 364 loop : -2.58 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 516 TYR 0.010 0.001 TYR D 502 PHE 0.044 0.002 PHE D 231 TRP 0.014 0.001 TRP B 510 HIS 0.008 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00330 (25032) covalent geometry : angle 0.73461 (33798) hydrogen bonds : bond 0.03538 ( 725) hydrogen bonds : angle 4.99463 ( 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 546 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 449 time to evaluate : 0.987 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: B 227 PHE cc_start: 0.7924 (t80) cc_final: 0.7648 (t80) REVERT: B 240 PHE cc_start: 0.5375 (m-80) cc_final: 0.4936 (m-80) REVERT: B 256 ILE cc_start: 0.9180 (mt) cc_final: 0.8831 (mt) REVERT: B 399 ASP cc_start: 0.8345 (p0) cc_final: 0.8111 (p0) REVERT: B 458 LYS cc_start: 0.1087 (OUTLIER) cc_final: 0.0273 (ptpp) REVERT: B 519 ASP cc_start: 0.7323 (p0) cc_final: 0.6417 (t0) REVERT: B 662 SER cc_start: 0.8738 (m) cc_final: 0.8510 (m) REVERT: B 712 MET cc_start: 0.8692 (tpp) cc_final: 0.8336 (tpp) REVERT: C 283 LYS cc_start: 0.8013 (mmmt) cc_final: 0.7070 (mttp) REVERT: C 435 ASN cc_start: 0.8680 (t0) cc_final: 0.8307 (t0) REVERT: C 442 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7366 (tm-30) REVERT: C 720 MET cc_start: 0.7682 (mmm) cc_final: 0.7161 (mtp) REVERT: D 315 ARG cc_start: 0.5152 (mmm-85) cc_final: 0.4821 (mmm-85) REVERT: D 340 MET cc_start: 0.2330 (ptm) cc_final: 0.2064 (mpp) REVERT: D 453 MET cc_start: 0.7743 (mmm) cc_final: 0.7532 (tpp) REVERT: D 516 ARG cc_start: 0.7984 (ttp-110) cc_final: 0.7587 (ttp80) REVERT: D 565 ILE cc_start: 0.8968 (mt) cc_final: 0.8730 (tp) REVERT: D 712 MET cc_start: 0.8791 (tpp) cc_final: 0.8521 (tpp) REVERT: E 226 GLU cc_start: 0.8020 (mp0) cc_final: 0.7467 (mp0) REVERT: E 441 LEU cc_start: 0.8649 (tt) cc_final: 0.8431 (mt) REVERT: E 498 ASP cc_start: 0.6302 (m-30) cc_final: 0.5849 (m-30) REVERT: E 561 ASN cc_start: 0.8093 (m110) cc_final: 0.7679 (t0) REVERT: E 727 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.7311 (ttm110) REVERT: F 276 MET cc_start: 0.4864 (mmm) cc_final: 0.4611 (mmm) REVERT: F 329 GLU cc_start: 0.7422 (tt0) cc_final: 0.7049 (pp20) REVERT: F 340 MET cc_start: 0.5557 (ptm) cc_final: 0.3836 (mmt) REVERT: F 394 GLU cc_start: 0.7377 (tp30) cc_final: 0.6298 (pm20) REVERT: F 414 MET cc_start: 0.8226 (ttp) cc_final: 0.8002 (tmm) REVERT: F 453 MET cc_start: 0.6150 (mmm) cc_final: 0.5911 (mmm) REVERT: F 455 ARG cc_start: 0.7435 (mmm-85) cc_final: 0.7057 (mmm-85) REVERT: F 496 GLN cc_start: 0.4848 (tt0) cc_final: 0.4190 (mp10) REVERT: F 650 ASP cc_start: 0.7972 (p0) cc_final: 0.7730 (t0) REVERT: F 655 MET cc_start: 0.8250 (mtm) cc_final: 0.7737 (mtm) REVERT: F 720 MET cc_start: 0.7840 (mmm) cc_final: 0.7467 (mtp) REVERT: A 230 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7602 (pt) REVERT: A 276 MET cc_start: 0.7001 (mmm) cc_final: 0.6178 (mtm) REVERT: A 297 GLU cc_start: 0.5617 (mp0) cc_final: 0.5368 (mp0) REVERT: A 405 GLN cc_start: 0.5934 (tm-30) cc_final: 0.5463 (tm-30) REVERT: A 467 MET cc_start: 0.0955 (mtm) cc_final: -0.0032 (mmt) REVERT: A 567 ILE cc_start: 0.8866 (mt) cc_final: 0.8401 (tt) outliers start: 97 outliers final: 58 residues processed: 517 average time/residue: 0.1617 time to fit residues: 133.9991 Evaluate side-chains 458 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 398 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 239 VAL 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 295 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 483 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 LEU 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 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 467 MET 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 391 VAL Chi-restraints excluded: chain E residue 397 LEU 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 650 ASP Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 363 GLN 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 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 373 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 683 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 73 optimal weight: 6.9990 chunk 278 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 291 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 294 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN B 418 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 ASN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN D 292 ASN ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN D 505 ASN ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 HIS ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 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 = 0.4032 r_free = 0.4032 target = 0.164099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128437 restraints weight = 42948.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.131679 restraints weight = 24052.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.133743 restraints weight = 16620.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.134759 restraints weight = 13244.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135671 restraints weight = 11739.551| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4529 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 : 0.729 13.527 33798 Z= 0.383 Chirality : 0.047 0.204 3876 Planarity : 0.005 0.105 4308 Dihedral : 11.803 89.914 3737 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.55 % Favored : 88.38 % Rotamer: Outliers : 4.35 % Allowed : 17.42 % Favored : 78.23 % 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: -2.85 (0.15), residues: 3108 helix: -1.31 (0.14), residues: 1363 sheet: -1.88 (0.26), residues: 365 loop : -2.44 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 385 TYR 0.018 0.001 TYR F 259 PHE 0.030 0.002 PHE D 231 TRP 0.013 0.001 TRP B 510 HIS 0.009 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00385 (25032) covalent geometry : angle 0.72933 (33798) hydrogen bonds : bond 0.03449 ( 725) hydrogen bonds : angle 4.89098 ( 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 528 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 412 time to evaluate : 0.966 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 227 PHE cc_start: 0.7792 (t80) cc_final: 0.7562 (t80) REVERT: B 240 PHE cc_start: 0.5433 (m-80) cc_final: 0.5079 (m-80) REVERT: B 256 ILE cc_start: 0.9232 (mt) cc_final: 0.8844 (mt) REVERT: B 399 ASP cc_start: 0.8312 (p0) cc_final: 0.8108 (p0) REVERT: B 453 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8423 (mtp) REVERT: B 519 ASP cc_start: 0.7428 (p0) cc_final: 0.6556 (t0) REVERT: B 712 MET cc_start: 0.8686 (tpp) cc_final: 0.8319 (tpp) REVERT: B 715 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7466 (mt-10) REVERT: C 238 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7506 (ttm-80) REVERT: C 283 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7170 (mttp) REVERT: C 397 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8348 (pp) REVERT: C 435 ASN cc_start: 0.8705 (t0) cc_final: 0.8192 (t0) REVERT: C 440 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7398 (mt-10) REVERT: C 442 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7371 (tm-30) REVERT: C 720 MET cc_start: 0.7686 (mmm) cc_final: 0.7193 (mtp) REVERT: D 315 ARG cc_start: 0.5105 (mmm-85) cc_final: 0.4810 (mmm-85) REVERT: D 565 ILE cc_start: 0.8973 (mt) cc_final: 0.8719 (tp) REVERT: D 712 MET cc_start: 0.8802 (tpp) cc_final: 0.8563 (tpp) REVERT: E 226 GLU cc_start: 0.7951 (mp0) cc_final: 0.7461 (mp0) REVERT: E 498 ASP cc_start: 0.6235 (m-30) cc_final: 0.5865 (m-30) REVERT: E 561 ASN cc_start: 0.8077 (m110) cc_final: 0.7710 (t0) REVERT: F 276 MET cc_start: 0.4957 (mmm) cc_final: 0.4754 (mmm) REVERT: F 329 GLU cc_start: 0.7373 (tt0) cc_final: 0.7069 (pp20) REVERT: F 340 MET cc_start: 0.5683 (ptm) cc_final: 0.3715 (mmt) REVERT: F 394 GLU cc_start: 0.7291 (tp30) cc_final: 0.6255 (pm20) REVERT: F 453 MET cc_start: 0.6197 (mmm) cc_final: 0.5913 (mmm) REVERT: F 496 GLN cc_start: 0.4861 (tt0) cc_final: 0.4136 (mp10) REVERT: F 510 TRP cc_start: 0.7868 (p-90) cc_final: 0.7094 (p-90) REVERT: F 650 ASP cc_start: 0.8056 (p0) cc_final: 0.7817 (t0) REVERT: F 666 HIS cc_start: 0.7273 (t70) cc_final: 0.7001 (t-90) REVERT: F 720 MET cc_start: 0.7860 (mmm) cc_final: 0.7546 (mtp) REVERT: A 230 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7586 (pt) REVERT: A 276 MET cc_start: 0.6972 (mmm) cc_final: 0.6189 (mtm) REVERT: A 297 GLU cc_start: 0.5759 (mp0) cc_final: 0.5549 (mp0) REVERT: A 405 GLN cc_start: 0.6015 (tm-30) cc_final: 0.5588 (tm-30) REVERT: A 467 MET cc_start: 0.0932 (mtm) cc_final: -0.0123 (mmt) REVERT: A 567 ILE cc_start: 0.8938 (mt) cc_final: 0.8460 (tt) outliers start: 116 outliers final: 73 residues processed: 493 average time/residue: 0.1595 time to fit residues: 126.4283 Evaluate side-chains 460 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 383 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 248 MET Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 355 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 453 MET 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 238 ARG Chi-restraints excluded: chain C residue 239 VAL 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 295 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 585 MET 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 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 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 264 CYS Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 325 ILE 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 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 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 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 364 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 391 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 658 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 686 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 182 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 249 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 295 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 243 optimal weight: 8.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN B 418 GLN B 474 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** 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 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.164478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129011 restraints weight = 43236.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132298 restraints weight = 24321.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134348 restraints weight = 16683.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135618 restraints weight = 13315.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.136182 restraints weight = 11612.810| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4749 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= 0.157 Angle : 0.724 14.004 33798 Z= 0.376 Chirality : 0.047 0.208 3876 Planarity : 0.005 0.102 4308 Dihedral : 11.698 89.800 3737 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.00 % Favored : 88.93 % Rotamer: Outliers : 3.68 % Allowed : 17.98 % Favored : 78.34 % 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: -2.64 (0.15), residues: 3108 helix: -1.06 (0.14), residues: 1370 sheet: -1.81 (0.26), residues: 362 loop : -2.40 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 516 TYR 0.014 0.001 TYR F 259 PHE 0.024 0.002 PHE D 231 TRP 0.013 0.001 TRP B 510 HIS 0.008 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00354 (25032) covalent geometry : angle 0.72406 (33798) hydrogen bonds : bond 0.03274 ( 725) hydrogen bonds : angle 4.77940 ( 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 521 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 423 time to evaluate : 0.872 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 240 PHE cc_start: 0.5602 (m-80) cc_final: 0.5260 (m-80) REVERT: B 256 ILE cc_start: 0.9226 (mt) cc_final: 0.8847 (mt) REVERT: B 399 ASP cc_start: 0.8390 (p0) cc_final: 0.8051 (p0) REVERT: B 519 ASP cc_start: 0.7053 (p0) cc_final: 0.6526 (t0) REVERT: B 712 MET cc_start: 0.8620 (tpp) cc_final: 0.8228 (tpp) REVERT: B 715 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7606 (mt-10) REVERT: C 238 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7517 (ttm-80) REVERT: C 283 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7137 (mttp) REVERT: C 397 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8352 (pp) REVERT: C 435 ASN cc_start: 0.8690 (t0) cc_final: 0.8136 (t0) REVERT: C 440 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7334 (mt-10) REVERT: C 442 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7314 (tm-30) REVERT: C 720 MET cc_start: 0.7712 (mmm) cc_final: 0.7209 (mtp) REVERT: D 232 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8129 (ttm170) REVERT: D 281 GLU cc_start: 0.8413 (mp0) cc_final: 0.8125 (mp0) REVERT: D 315 ARG cc_start: 0.5097 (mmm-85) cc_final: 0.4805 (mmm-85) REVERT: D 453 MET cc_start: 0.8492 (tpp) cc_final: 0.8057 (tpt) REVERT: D 565 ILE cc_start: 0.8944 (mt) cc_final: 0.8697 (tp) REVERT: D 712 MET cc_start: 0.8808 (tpp) cc_final: 0.8602 (tpp) REVERT: E 226 GLU cc_start: 0.7989 (mp0) cc_final: 0.7521 (mp0) REVERT: E 498 ASP cc_start: 0.6072 (m-30) cc_final: 0.5675 (m-30) REVERT: E 561 ASN cc_start: 0.8038 (m110) cc_final: 0.7648 (t0) REVERT: F 329 GLU cc_start: 0.7316 (tt0) cc_final: 0.7003 (pp20) REVERT: F 340 MET cc_start: 0.5509 (ptm) cc_final: 0.3656 (mmt) REVERT: F 394 GLU cc_start: 0.7696 (tp30) cc_final: 0.6667 (pm20) REVERT: F 453 MET cc_start: 0.6266 (mmm) cc_final: 0.5962 (mmm) REVERT: F 496 GLN cc_start: 0.5165 (tt0) cc_final: 0.4452 (mp10) REVERT: F 510 TRP cc_start: 0.7854 (p-90) cc_final: 0.7138 (p-90) REVERT: F 666 HIS cc_start: 0.7256 (t70) cc_final: 0.6947 (t-90) REVERT: F 720 MET cc_start: 0.7982 (mmm) cc_final: 0.7739 (mtp) REVERT: A 230 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7592 (pt) REVERT: A 276 MET cc_start: 0.7158 (mmm) cc_final: 0.6314 (mtm) REVERT: A 297 GLU cc_start: 0.5986 (mp0) cc_final: 0.5749 (mp0) REVERT: A 405 GLN cc_start: 0.5988 (tm-30) cc_final: 0.5554 (tm-30) REVERT: A 467 MET cc_start: 0.0824 (mtm) cc_final: -0.0083 (mmt) REVERT: A 567 ILE cc_start: 0.8944 (mt) cc_final: 0.8429 (tt) REVERT: A 638 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7783 (mmm-85) REVERT: A 716 MET cc_start: 0.7705 (ttt) cc_final: 0.7415 (ttm) outliers start: 98 outliers final: 70 residues processed: 488 average time/residue: 0.1580 time to fit residues: 124.2290 Evaluate side-chains 455 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 380 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 344 THR 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 474 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 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 253 VAL 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 295 VAL Chi-restraints excluded: chain C residue 323 HIS 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 574 ILE Chi-restraints excluded: chain C residue 585 MET 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 467 MET Chi-restraints excluded: chain D residue 586 LYS Chi-restraints excluded: chain D residue 688 ASP 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 325 ILE 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 650 ASP Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 713 LEU Chi-restraints excluded: chain F residue 285 VAL 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 230 ILE 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 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 683 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: 6.9990 chunk 186 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 296 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 266 optimal weight: 0.0040 chunk 288 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 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 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN D 685 ASN ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.164269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.128789 restraints weight = 43091.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132028 restraints weight = 24091.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134054 restraints weight = 16666.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.135322 restraints weight = 13295.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.135791 restraints weight = 11611.076| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4908 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 : 0.719 13.744 33798 Z= 0.374 Chirality : 0.047 0.207 3876 Planarity : 0.005 0.099 4308 Dihedral : 11.643 88.134 3737 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.20 % Favored : 88.74 % Rotamer: Outliers : 4.02 % Allowed : 18.62 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.11 % Twisted Proline : 1.52 % 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: -2.49 (0.15), residues: 3108 helix: -0.88 (0.14), residues: 1363 sheet: -1.85 (0.26), residues: 370 loop : -2.36 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 516 TYR 0.013 0.001 TYR C 259 PHE 0.034 0.002 PHE D 231 TRP 0.012 0.001 TRP B 510 HIS 0.009 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00356 (25032) covalent geometry : angle 0.71891 (33798) hydrogen bonds : bond 0.03200 ( 725) hydrogen bonds : angle 4.71540 ( 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 510 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 403 time to evaluate : 0.925 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: 0.5622 (m-80) cc_final: 0.5222 (m-80) REVERT: B 256 ILE cc_start: 0.9238 (mt) cc_final: 0.8850 (mt) REVERT: B 399 ASP cc_start: 0.8304 (p0) cc_final: 0.7980 (p0) REVERT: B 409 ILE cc_start: 0.8728 (mt) cc_final: 0.8476 (tp) REVERT: B 451 THR cc_start: 0.8587 (m) cc_final: 0.8254 (p) REVERT: B 519 ASP cc_start: 0.7012 (p0) cc_final: 0.6536 (t0) REVERT: B 712 MET cc_start: 0.8593 (tpp) cc_final: 0.8224 (tpp) REVERT: C 238 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7528 (ttm-80) REVERT: C 283 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7139 (mttp) REVERT: C 397 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8356 (pp) REVERT: C 435 ASN cc_start: 0.8691 (t0) cc_final: 0.8138 (t0) REVERT: C 440 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7320 (mt-10) REVERT: C 442 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7283 (tm-30) REVERT: C 720 MET cc_start: 0.7717 (mmm) cc_final: 0.7221 (mtp) REVERT: D 232 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8155 (ttm170) REVERT: D 248 MET cc_start: 0.5132 (mtt) cc_final: 0.4906 (mtp) REVERT: D 281 GLU cc_start: 0.8351 (mp0) cc_final: 0.8123 (mp0) REVERT: D 315 ARG cc_start: 0.5077 (mmm-85) cc_final: 0.4795 (mmm-85) REVERT: D 409 ILE cc_start: 0.8955 (mt) cc_final: 0.8589 (mt) REVERT: D 453 MET cc_start: 0.8557 (tpp) cc_final: 0.8101 (tpt) REVERT: D 528 THR cc_start: 0.9338 (m) cc_final: 0.9049 (p) REVERT: D 565 ILE cc_start: 0.8938 (mt) cc_final: 0.8675 (tp) REVERT: E 226 GLU cc_start: 0.8032 (mp0) cc_final: 0.7656 (mp0) REVERT: E 561 ASN cc_start: 0.8116 (m110) cc_final: 0.7682 (t0) REVERT: F 329 GLU cc_start: 0.7330 (tt0) cc_final: 0.7103 (pp20) REVERT: F 340 MET cc_start: 0.5611 (ptm) cc_final: 0.3835 (mmm) REVERT: F 394 GLU cc_start: 0.7651 (tp30) cc_final: 0.6608 (pm20) REVERT: F 453 MET cc_start: 0.6236 (mmm) cc_final: 0.5921 (mmm) REVERT: F 496 GLN cc_start: 0.5023 (tt0) cc_final: 0.4484 (mp10) REVERT: F 510 TRP cc_start: 0.7867 (p-90) cc_final: 0.7169 (p-90) REVERT: F 655 MET cc_start: 0.8355 (mtm) cc_final: 0.7708 (mtm) REVERT: F 666 HIS cc_start: 0.7237 (t70) cc_final: 0.6845 (t-90) REVERT: F 720 MET cc_start: 0.7984 (mmm) cc_final: 0.7604 (mtp) REVERT: A 218 MET cc_start: 0.7056 (pmm) cc_final: 0.5705 (ppp) REVERT: A 230 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7557 (pt) REVERT: A 276 MET cc_start: 0.7086 (mmm) cc_final: 0.6187 (mtm) REVERT: A 297 GLU cc_start: 0.6093 (mp0) cc_final: 0.5868 (mp0) REVERT: A 405 GLN cc_start: 0.5983 (tm-30) cc_final: 0.5540 (tm-30) REVERT: A 467 MET cc_start: 0.0968 (mtm) cc_final: -0.0012 (mmt) REVERT: A 567 ILE cc_start: 0.8939 (mt) cc_final: 0.8402 (tt) REVERT: A 638 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7771 (mmm-85) REVERT: A 715 GLU cc_start: 0.8388 (tp30) cc_final: 0.8079 (tp30) REVERT: A 716 MET cc_start: 0.7706 (ttt) cc_final: 0.7432 (ttm) outliers start: 107 outliers final: 74 residues processed: 478 average time/residue: 0.1591 time to fit residues: 122.6403 Evaluate side-chains 463 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 384 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 248 MET 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 344 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 253 VAL 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 295 VAL Chi-restraints excluded: chain C residue 323 HIS 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 585 MET 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 292 ASN 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 467 MET 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 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 645 THR Chi-restraints excluded: chain E residue 650 ASP Chi-restraints excluded: chain E residue 680 LEU 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 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 373 THR Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 683 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: 2.9990 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: 0.0020 chunk 0 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 ASN B 374 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN D 685 ASN E 313 GLN E 353 GLN ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.166219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130584 restraints weight = 43368.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133818 restraints weight = 24441.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135920 restraints weight = 16912.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137151 restraints weight = 13485.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137735 restraints weight = 11846.473| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25032 Z= 0.137 Angle : 0.722 13.331 33798 Z= 0.372 Chirality : 0.047 0.221 3876 Planarity : 0.005 0.089 4308 Dihedral : 11.435 89.939 3737 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.30 % Favored : 89.64 % Rotamer: Outliers : 3.42 % Allowed : 19.86 % Favored : 76.73 % 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: -2.30 (0.15), residues: 3108 helix: -0.72 (0.14), residues: 1383 sheet: -1.67 (0.27), residues: 357 loop : -2.31 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 516 TYR 0.015 0.001 TYR C 259 PHE 0.026 0.001 PHE D 231 TRP 0.012 0.001 TRP B 510 HIS 0.006 0.001 HIS F 456 Details of bonding type rmsd covalent geometry : bond 0.00305 (25032) covalent geometry : angle 0.72246 (33798) hydrogen bonds : bond 0.03018 ( 725) hydrogen bonds : angle 4.60242 ( 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 506 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 415 time to evaluate : 0.998 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: 0.5539 (m-80) cc_final: 0.5293 (m-80) REVERT: B 256 ILE cc_start: 0.9228 (mt) cc_final: 0.8853 (mt) REVERT: B 409 ILE cc_start: 0.8720 (mt) cc_final: 0.8498 (tp) REVERT: B 451 THR cc_start: 0.8483 (m) cc_final: 0.8206 (p) REVERT: B 519 ASP cc_start: 0.6989 (p0) cc_final: 0.6602 (t0) REVERT: B 712 MET cc_start: 0.8594 (tpp) cc_final: 0.8215 (tpp) REVERT: C 238 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7463 (ttm-80) REVERT: C 283 LYS cc_start: 0.7971 (mmmt) cc_final: 0.6928 (mttp) REVERT: C 397 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8335 (pp) REVERT: C 435 ASN cc_start: 0.8658 (t0) cc_final: 0.8108 (t0) REVERT: C 440 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7316 (mt-10) REVERT: C 442 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7331 (tm-30) REVERT: C 720 MET cc_start: 0.7642 (mmm) cc_final: 0.7322 (mtp) REVERT: D 232 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8018 (ttm170) REVERT: D 266 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8898 (mtmm) REVERT: D 276 MET cc_start: 0.5664 (tpt) cc_final: 0.5277 (tpt) REVERT: D 315 ARG cc_start: 0.5123 (mmm-85) cc_final: 0.4846 (mmm-85) REVERT: D 352 ASN cc_start: 0.8041 (p0) cc_final: 0.7814 (m-40) REVERT: D 409 ILE cc_start: 0.8836 (mt) cc_final: 0.8433 (mt) REVERT: D 453 MET cc_start: 0.8606 (tpp) cc_final: 0.8397 (tpt) REVERT: D 481 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8462 (mm) REVERT: D 528 THR cc_start: 0.9304 (m) cc_final: 0.9009 (p) REVERT: D 565 ILE cc_start: 0.8880 (mt) cc_final: 0.8645 (tp) REVERT: E 226 GLU cc_start: 0.7974 (mp0) cc_final: 0.7623 (mp0) REVERT: E 434 LYS cc_start: 0.7216 (ptpt) cc_final: 0.7011 (tppt) REVERT: E 561 ASN cc_start: 0.8098 (m110) cc_final: 0.7683 (t0) REVERT: F 329 GLU cc_start: 0.7310 (tt0) cc_final: 0.7055 (pp20) REVERT: F 340 MET cc_start: 0.5409 (ptm) cc_final: 0.3686 (mmm) REVERT: F 394 GLU cc_start: 0.7706 (tp30) cc_final: 0.6613 (pm20) REVERT: F 414 MET cc_start: 0.8132 (tmm) cc_final: 0.7871 (tmm) REVERT: F 453 MET cc_start: 0.6279 (mmm) cc_final: 0.5856 (mmm) REVERT: F 496 GLN cc_start: 0.4983 (tt0) cc_final: 0.4381 (mp10) REVERT: F 621 LEU cc_start: 0.8982 (tp) cc_final: 0.8727 (tt) REVERT: F 666 HIS cc_start: 0.7190 (t70) cc_final: 0.6765 (t-90) REVERT: F 720 MET cc_start: 0.7927 (mmm) cc_final: 0.7461 (mtp) REVERT: A 230 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7602 (pt) REVERT: A 276 MET cc_start: 0.7083 (mmm) cc_final: 0.6243 (mtm) REVERT: A 405 GLN cc_start: 0.5979 (tm-30) cc_final: 0.5520 (tm-30) REVERT: A 467 MET cc_start: 0.0918 (mtm) cc_final: 0.0004 (mmt) REVERT: A 585 MET cc_start: 0.8359 (mtp) cc_final: 0.8001 (ttp) REVERT: A 638 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7964 (mtt-85) REVERT: A 715 GLU cc_start: 0.8400 (tp30) cc_final: 0.8103 (tp30) REVERT: A 716 MET cc_start: 0.7659 (ttt) cc_final: 0.7392 (ttm) outliers start: 91 outliers final: 61 residues processed: 478 average time/residue: 0.1514 time to fit residues: 116.2442 Evaluate side-chains 446 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 379 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 356 SER Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 253 VAL 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 295 VAL Chi-restraints excluded: chain C residue 323 HIS 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 574 ILE Chi-restraints excluded: chain C residue 585 MET 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 467 MET Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 586 LYS Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain E residue 285 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 565 ILE 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 466 ASP Chi-restraints excluded: chain F residue 536 LEU 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 F residue 664 THR Chi-restraints excluded: chain F residue 665 ILE 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 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 638 ARG 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: 10.0000 chunk 89 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 259 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 274 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 HIS ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 697 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.164072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127836 restraints weight = 43324.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131245 restraints weight = 23902.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.133371 restraints weight = 16268.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.134648 restraints weight = 12924.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.135269 restraints weight = 11290.656| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5207 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= 0.176 Angle : 0.748 12.788 33798 Z= 0.384 Chirality : 0.048 0.257 3876 Planarity : 0.005 0.085 4308 Dihedral : 11.483 87.919 3737 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.33 % Favored : 88.61 % Rotamer: Outliers : 3.15 % Allowed : 20.42 % Favored : 76.43 % 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: -2.26 (0.15), residues: 3108 helix: -0.67 (0.14), residues: 1373 sheet: -1.66 (0.27), residues: 357 loop : -2.27 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 233 TYR 0.030 0.002 TYR B 611 PHE 0.029 0.002 PHE D 231 TRP 0.012 0.001 TRP B 510 HIS 0.011 0.001 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00403 (25032) covalent geometry : angle 0.74815 (33798) hydrogen bonds : bond 0.03148 ( 725) hydrogen bonds : angle 4.65967 ( 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 476 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 392 time to evaluate : 0.839 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: B 233 ARG cc_start: 0.7066 (ptp-170) cc_final: 0.6571 (ptp-170) REVERT: B 235 PHE cc_start: 0.7530 (m-80) cc_final: 0.7288 (m-80) REVERT: B 256 ILE cc_start: 0.9286 (mt) cc_final: 0.8909 (mt) REVERT: B 399 ASP cc_start: 0.8326 (p0) cc_final: 0.7980 (p0) REVERT: B 409 ILE cc_start: 0.8704 (mt) cc_final: 0.8479 (tp) REVERT: B 451 THR cc_start: 0.8561 (m) cc_final: 0.8239 (p) REVERT: B 519 ASP cc_start: 0.7047 (p0) cc_final: 0.6631 (t0) REVERT: B 712 MET cc_start: 0.8593 (tpp) cc_final: 0.8138 (tpp) REVERT: B 715 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7371 (mt-10) REVERT: C 238 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7529 (ttm-80) REVERT: C 283 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7151 (mttp) REVERT: C 356 SER cc_start: 0.8322 (p) cc_final: 0.8059 (p) REVERT: C 397 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8364 (pp) REVERT: C 435 ASN cc_start: 0.8701 (t0) cc_final: 0.8251 (t0) REVERT: C 440 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7238 (mt-10) REVERT: C 442 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7317 (tm-30) REVERT: C 720 MET cc_start: 0.7679 (mmm) cc_final: 0.7392 (mtp) REVERT: D 232 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8071 (ttm170) REVERT: D 266 LYS cc_start: 0.9253 (mtmm) cc_final: 0.8942 (mtmm) REVERT: D 315 ARG cc_start: 0.5158 (mmm-85) cc_final: 0.4899 (mmm-85) REVERT: D 409 ILE cc_start: 0.8787 (mt) cc_final: 0.8367 (mt) REVERT: D 453 MET cc_start: 0.8531 (tpp) cc_final: 0.8125 (tpt) REVERT: D 481 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8479 (mm) REVERT: D 528 THR cc_start: 0.9340 (m) cc_final: 0.9029 (p) REVERT: D 565 ILE cc_start: 0.8907 (mt) cc_final: 0.8639 (tp) REVERT: E 467 MET cc_start: 0.3868 (mmp) cc_final: 0.3661 (mmp) REVERT: E 561 ASN cc_start: 0.8108 (m110) cc_final: 0.7677 (t0) REVERT: F 329 GLU cc_start: 0.7340 (tt0) cc_final: 0.7099 (pp20) REVERT: F 340 MET cc_start: 0.5563 (ptm) cc_final: 0.3804 (mmm) REVERT: F 394 GLU cc_start: 0.7755 (tp30) cc_final: 0.7232 (tm-30) REVERT: F 453 MET cc_start: 0.6188 (mmm) cc_final: 0.5814 (mmm) REVERT: F 496 GLN cc_start: 0.5152 (tt0) cc_final: 0.4483 (mp10) REVERT: F 510 TRP cc_start: 0.7861 (p-90) cc_final: 0.7152 (p-90) REVERT: F 621 LEU cc_start: 0.9016 (tp) cc_final: 0.8752 (tt) REVERT: F 666 HIS cc_start: 0.7285 (t70) cc_final: 0.6838 (t-90) REVERT: F 720 MET cc_start: 0.7918 (mmm) cc_final: 0.7577 (mtp) REVERT: A 230 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7550 (pt) REVERT: A 276 MET cc_start: 0.7114 (mmm) cc_final: 0.6241 (mtm) REVERT: A 297 GLU cc_start: 0.5814 (mp0) cc_final: 0.5424 (mm-30) REVERT: A 405 GLN cc_start: 0.5999 (tm-30) cc_final: 0.5542 (tm-30) REVERT: A 467 MET cc_start: 0.0956 (mtm) cc_final: 0.0016 (mmt) REVERT: A 550 THR cc_start: 0.7286 (m) cc_final: 0.7050 (m) REVERT: A 585 MET cc_start: 0.8411 (mtp) cc_final: 0.8065 (ttp) REVERT: A 638 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7779 (mmm-85) REVERT: A 674 GLU cc_start: 0.7891 (mp0) cc_final: 0.6977 (pp20) outliers start: 84 outliers final: 62 residues processed: 450 average time/residue: 0.1517 time to fit residues: 110.6311 Evaluate side-chains 449 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 381 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 356 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 662 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 238 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 253 VAL 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 295 VAL Chi-restraints excluded: chain C residue 323 HIS 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 467 MET Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain E residue 285 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 E residue 680 LEU Chi-restraints excluded: chain E residue 713 LEU 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 664 THR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 393 MET 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 638 ARG Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 683 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: 0.0470 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 chunk 297 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 84 optimal weight: 0.0010 chunk 34 optimal weight: 0.5980 chunk 95 optimal weight: 7.9990 chunk 87 optimal weight: 0.0070 overall best weight: 0.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C 435 ASN C 454 ASN D 374 ASN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN E 435 ASN ** F 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 374 ASN A 456 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.170887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135238 restraints weight = 43319.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.138789 restraints weight = 23702.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.141043 restraints weight = 16052.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.142465 restraints weight = 12608.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143132 restraints weight = 10908.088| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25032 Z= 0.126 Angle : 0.732 20.654 33798 Z= 0.372 Chirality : 0.046 0.215 3876 Planarity : 0.005 0.068 4308 Dihedral : 10.916 85.101 3737 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.40 % Favored : 90.54 % Rotamer: Outliers : 2.21 % Allowed : 21.40 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.14 % Twisted Proline : 0.76 % 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: -2.02 (0.15), residues: 3108 helix: -0.36 (0.15), residues: 1353 sheet: -1.47 (0.28), residues: 344 loop : -2.28 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 413 TYR 0.012 0.001 TYR C 259 PHE 0.021 0.001 PHE B 235 TRP 0.012 0.001 TRP E 510 HIS 0.007 0.001 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00261 (25032) covalent geometry : angle 0.73151 (33798) hydrogen bonds : bond 0.02807 ( 725) hydrogen bonds : angle 4.46302 ( 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 517 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 458 time to evaluate : 0.884 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: 0.9268 (mt) cc_final: 0.8905 (mt) REVERT: B 519 ASP cc_start: 0.6721 (p0) cc_final: 0.6473 (t0) REVERT: B 712 MET cc_start: 0.8502 (tpp) cc_final: 0.8156 (tpp) REVERT: B 715 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7275 (mt-10) REVERT: C 283 LYS cc_start: 0.7559 (mmmt) cc_final: 0.6552 (mttp) REVERT: C 356 SER cc_start: 0.8021 (p) cc_final: 0.7700 (p) REVERT: C 435 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.7974 (t0) REVERT: C 440 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7166 (mt-10) REVERT: C 720 MET cc_start: 0.7596 (mmm) cc_final: 0.7297 (mtp) REVERT: D 232 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7885 (ttm170) REVERT: D 409 ILE cc_start: 0.8402 (mt) cc_final: 0.7883 (mt) REVERT: D 496 GLN cc_start: 0.3007 (tp-100) cc_final: 0.2762 (tp-100) REVERT: D 498 ASP cc_start: 0.5938 (m-30) cc_final: 0.5550 (m-30) REVERT: D 528 THR cc_start: 0.9190 (m) cc_final: 0.8875 (p) REVERT: E 335 LYS cc_start: 0.7508 (mtpt) cc_final: 0.7103 (mtpp) REVERT: E 561 ASN cc_start: 0.8092 (m110) cc_final: 0.7603 (t0) REVERT: E 624 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8239 (mm-40) REVERT: E 657 MET cc_start: 0.8452 (ttp) cc_final: 0.8162 (ttp) REVERT: F 323 HIS cc_start: 0.5497 (OUTLIER) cc_final: 0.4510 (t-90) REVERT: F 340 MET cc_start: 0.5458 (ptm) cc_final: 0.3593 (mmm) REVERT: F 394 GLU cc_start: 0.7708 (tp30) cc_final: 0.6370 (pm20) REVERT: F 414 MET cc_start: 0.7977 (tmm) cc_final: 0.7570 (tmm) REVERT: F 453 MET cc_start: 0.6335 (mmm) cc_final: 0.5967 (mmm) REVERT: F 496 GLN cc_start: 0.5076 (tt0) cc_final: 0.4491 (mp10) REVERT: F 621 LEU cc_start: 0.8906 (tp) cc_final: 0.8592 (tt) REVERT: F 623 LEU cc_start: 0.9207 (tp) cc_final: 0.8930 (tt) REVERT: F 655 MET cc_start: 0.8477 (mtm) cc_final: 0.7847 (mtm) REVERT: F 666 HIS cc_start: 0.7067 (t70) cc_final: 0.6613 (t-90) REVERT: F 720 MET cc_start: 0.7916 (mmm) cc_final: 0.7706 (mtp) REVERT: A 218 MET cc_start: 0.6450 (pmm) cc_final: 0.5137 (ppp) REVERT: A 230 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7657 (pt) REVERT: A 276 MET cc_start: 0.6850 (mmm) cc_final: 0.6078 (mtm) REVERT: A 297 GLU cc_start: 0.5873 (mp0) cc_final: 0.5109 (mm-30) REVERT: A 405 GLN cc_start: 0.5902 (tm-30) cc_final: 0.5461 (tm-30) REVERT: A 415 ARG cc_start: 0.7642 (mtt90) cc_final: 0.7442 (mpt90) REVERT: A 440 GLU cc_start: 0.5220 (tm-30) cc_final: 0.5000 (tm-30) REVERT: A 467 MET cc_start: 0.1234 (mtm) cc_final: 0.0389 (mmt) REVERT: A 585 MET cc_start: 0.8297 (mtp) cc_final: 0.7947 (ttp) REVERT: A 680 LEU cc_start: 0.7833 (mp) cc_final: 0.6834 (tp) REVERT: A 715 GLU cc_start: 0.8355 (tp30) cc_final: 0.8136 (tp30) REVERT: A 720 MET cc_start: 0.7862 (mpp) cc_final: 0.6032 (ppp) outliers start: 59 outliers final: 42 residues processed: 499 average time/residue: 0.1512 time to fit residues: 121.8108 Evaluate side-chains 446 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 400 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 VAL 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 264 CYS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 435 ASN 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 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 467 MET Chi-restraints excluded: chain D residue 688 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 414 MET 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 285 VAL Chi-restraints excluded: chain F residue 323 HIS Chi-restraints excluded: chain F residue 536 LEU 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 664 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 614 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 165 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 218 optimal weight: 30.0000 chunk 295 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 ASN E 435 ASN ** 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 = 0.4046 r_free = 0.4046 target = 0.165109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129138 restraints weight = 43203.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.132515 restraints weight = 23758.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.134671 restraints weight = 16236.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.136017 restraints weight = 12843.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.136765 restraints weight = 11179.221| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25032 Z= 0.182 Angle : 0.770 12.334 33798 Z= 0.393 Chirality : 0.049 0.250 3876 Planarity : 0.005 0.065 4308 Dihedral : 11.022 84.784 3737 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.71 % Favored : 89.22 % Rotamer: Outliers : 2.10 % Allowed : 22.64 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.14 % Twisted Proline : 0.76 % 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: -2.08 (0.15), residues: 3108 helix: -0.44 (0.14), residues: 1385 sheet: -1.53 (0.27), residues: 351 loop : -2.32 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 516 TYR 0.014 0.001 TYR C 499 PHE 0.028 0.002 PHE D 231 TRP 0.011 0.001 TRP B 510 HIS 0.012 0.001 HIS D 410 Details of bonding type rmsd covalent geometry : bond 0.00417 (25032) covalent geometry : angle 0.76999 (33798) hydrogen bonds : bond 0.03126 ( 725) hydrogen bonds : angle 4.66168 ( 2097) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4758.53 seconds wall clock time: 82 minutes 50.75 seconds (4970.75 seconds total)