Starting phenix.real_space_refine on Thu Mar 5 05:23:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oaa_0666/03_2026/6oaa_0666_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oaa_0666/03_2026/6oaa_0666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oaa_0666/03_2026/6oaa_0666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oaa_0666/03_2026/6oaa_0666.map" model { file = "/net/cci-nas-00/data/ceres_data/6oaa_0666/03_2026/6oaa_0666_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oaa_0666/03_2026/6oaa_0666_neut.cif" } resolution = 4.1 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= 0.014 sd= 0.092 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: 7 Type Number sf(0) Gaussians P 16 5.49 5 S 87 5.16 5 Be 6 3.05 5 C 12228 2.51 5 N 3381 2.21 5 O 3810 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 213 residue(s): 0.02s 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: 19546 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3897 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 481} Chain: "C" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4088 Classifications: {'peptide': 532} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 27, 'TRANS': 500} Chain breaks: 2 Chain: "D" Number of atoms: 4130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4130 Classifications: {'peptide': 537} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 507} Chain breaks: 2 Chain: "E" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3383 Classifications: {'peptide': 442} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 23, 'TRANS': 415} Chain breaks: 1 Chain: "G" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3432 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain breaks: 2 Chain: "H" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {'ADP': 2, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {'ADP': 2, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'BEF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 108 Unusual residues: {'ADP': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.47, per 1000 atoms: 0.23 Number of scatterers: 19546 At special positions: 0 Unit cell: (140.3, 128.8, 164.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 16 15.00 F 18 9.00 O 3810 8.00 N 3381 7.00 C 12228 6.00 Be 6 4.00 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 Atom "HETATM19363 O3A ADP B 904 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=19, symmetry=0 Number of additional bonds: simple=19, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 979.2 milliseconds 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4620 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 39.4% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'B' and resid 219 through 228 removed outlier: 4.457A pdb=" N GLN B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.787A pdb=" N ALA B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 266 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 330 through 345 removed outlier: 3.534A pdb=" N VAL B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.622A pdb=" N ILE B 363 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.856A pdb=" N ARG B 369 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 395 removed outlier: 3.702A pdb=" N ILE B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 413 removed outlier: 3.742A pdb=" N ALA B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 436 removed outlier: 3.620A pdb=" N ALA B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 468 removed outlier: 3.808A pdb=" N PHE B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.605A pdb=" N GLU B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 502 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Proline residue: B 506 - end of helix removed outlier: 3.716A pdb=" N HIS B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 517 Processing helix chain 'B' and resid 536 through 544 removed outlier: 3.564A pdb=" N ALA B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 571 through 579 Processing helix chain 'B' and resid 589 through 594 removed outlier: 3.749A pdb=" N LYS B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 597 No H-bonds generated for 'chain 'B' and resid 595 through 597' Processing helix chain 'B' and resid 608 through 620 removed outlier: 3.624A pdb=" N ASN B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 613 " --> pdb=" O ARG B 609 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 614 " --> pdb=" O VAL B 610 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 616 " --> pdb=" O ASN B 612 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 617 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 671 removed outlier: 4.110A pdb=" N SER B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 667 " --> pdb=" O ARG B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 689 Processing helix chain 'B' and resid 695 through 716 removed outlier: 3.554A pdb=" N ILE B 700 " --> pdb=" O ASP B 696 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.803A pdb=" N GLN C 225 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 226 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 293 through 304 removed outlier: 3.702A pdb=" N ALA C 299 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 343 removed outlier: 3.570A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 340 " --> pdb=" O SER C 336 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.673A pdb=" N ARG C 369 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 394 removed outlier: 3.847A pdb=" N LEU C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 removed outlier: 3.788A pdb=" N LEU C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 436 removed outlier: 3.620A pdb=" N CYS C 425 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 429 " --> pdb=" O CYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 492 through 509 removed outlier: 3.552A pdb=" N THR C 502 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Proline residue: C 506 - end of helix Processing helix chain 'C' and resid 509 through 517 removed outlier: 4.329A pdb=" N TYR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 514 " --> pdb=" O PRO C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 563 through 579 removed outlier: 3.501A pdb=" N SER C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE C 569 " --> pdb=" O SER C 565 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG C 570 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 572 " --> pdb=" O ASN C 568 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS C 575 " --> pdb=" O ASP C 571 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 576 " --> pdb=" O ILE C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 619 removed outlier: 3.691A pdb=" N LEU C 614 " --> pdb=" O VAL C 610 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP C 619 " --> pdb=" O LEU C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 672 removed outlier: 4.085A pdb=" N SER C 665 " --> pdb=" O ASN C 661 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 669 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 671 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 672 " --> pdb=" O ASN C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 688 Processing helix chain 'C' and resid 695 through 711 removed outlier: 3.724A pdb=" N ILE C 700 " --> pdb=" O ASP C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 760 removed outlier: 3.787A pdb=" N PHE C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU C 760 " --> pdb=" O GLU C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 779 removed outlier: 3.565A pdb=" N ARG C 775 " --> pdb=" O ASP C 771 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG C 776 " --> pdb=" O ALA C 772 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR C 777 " --> pdb=" O GLU C 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.765A pdb=" N GLN D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE D 226 " --> pdb=" O GLN D 222 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL D 230 " --> pdb=" O ILE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 281 through 285 removed outlier: 4.274A pdb=" N VAL D 284 " --> pdb=" O GLY D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 302 removed outlier: 3.539A pdb=" N GLU D 302 " --> pdb=" O LYS D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.821A pdb=" N ARG D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 368 removed outlier: 3.968A pdb=" N ARG D 368 " --> pdb=" O PRO D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 392 removed outlier: 3.711A pdb=" N LEU D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 392 " --> pdb=" O LEU D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 387 through 392' Processing helix chain 'D' and resid 407 through 412 removed outlier: 3.682A pdb=" N ALA D 411 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU D 412 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 436 removed outlier: 3.627A pdb=" N GLU D 435 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS D 436 " --> pdb=" O GLN D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 467 removed outlier: 3.611A pdb=" N PHE D 462 " --> pdb=" O THR D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 475 removed outlier: 3.940A pdb=" N ARG D 475 " --> pdb=" O SER D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 504 removed outlier: 3.557A pdb=" N THR D 502 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 503 " --> pdb=" O LEU D 499 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 510 through 517 removed outlier: 3.748A pdb=" N THR D 514 " --> pdb=" O PRO D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 545 removed outlier: 3.527A pdb=" N LYS D 539 " --> pdb=" O THR D 535 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR D 543 " --> pdb=" O LYS D 539 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU D 544 " --> pdb=" O ALA D 540 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 580 removed outlier: 3.819A pdb=" N PHE D 573 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 594 removed outlier: 3.938A pdb=" N ILE D 592 " --> pdb=" O GLU D 588 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 619 removed outlier: 3.687A pdb=" N LEU D 614 " --> pdb=" O VAL D 610 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP D 619 " --> pdb=" O LEU D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 639 removed outlier: 4.336A pdb=" N GLN D 638 " --> pdb=" O ARG D 635 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE D 639 " --> pdb=" O PRO D 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 635 through 639' Processing helix chain 'D' and resid 661 through 671 removed outlier: 3.662A pdb=" N SER D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 666 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 667 " --> pdb=" O ARG D 663 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 669 " --> pdb=" O SER D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 689 removed outlier: 3.550A pdb=" N ALA D 688 " --> pdb=" O ALA D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 698 removed outlier: 3.619A pdb=" N LEU D 698 " --> pdb=" O GLY D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 708 Processing helix chain 'D' and resid 712 through 716 removed outlier: 4.033A pdb=" N HIS D 716 " --> pdb=" O ILE D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 778 removed outlier: 3.549A pdb=" N LEU D 774 " --> pdb=" O SER D 770 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG D 775 " --> pdb=" O ASP D 771 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR D 777 " --> pdb=" O GLU D 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 228 Processing helix chain 'E' and resid 230 through 236 removed outlier: 3.591A pdb=" N HIS E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 273 removed outlier: 3.537A pdb=" N ARG E 266 " --> pdb=" O THR E 262 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 303 removed outlier: 3.634A pdb=" N PHE E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 343 removed outlier: 3.633A pdb=" N VAL E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 341 " --> pdb=" O GLN E 337 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET E 342 " --> pdb=" O LEU E 338 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 removed outlier: 3.619A pdb=" N ARG E 368 " --> pdb=" O PRO E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 395 removed outlier: 3.507A pdb=" N ILE E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 413 removed outlier: 3.507A pdb=" N ALA E 411 " --> pdb=" O GLU E 407 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR E 413 " --> pdb=" O LEU E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 436 removed outlier: 3.586A pdb=" N CYS E 425 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE E 433 " --> pdb=" O ALA E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 468 removed outlier: 3.623A pdb=" N PHE E 462 " --> pdb=" O THR E 458 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY E 467 " --> pdb=" O ARG E 463 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN E 468 " --> pdb=" O PHE E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 503 removed outlier: 3.854A pdb=" N GLU E 497 " --> pdb=" O ASP E 493 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 503 " --> pdb=" O LEU E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 517 removed outlier: 4.349A pdb=" N TYR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR E 514 " --> pdb=" O PRO E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 545 removed outlier: 3.619A pdb=" N ALA E 538 " --> pdb=" O LYS E 534 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 541 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA E 542 " --> pdb=" O ALA E 538 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU E 544 " --> pdb=" O ALA E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 579 removed outlier: 3.566A pdb=" N SER E 567 " --> pdb=" O GLY E 563 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE E 569 " --> pdb=" O SER E 565 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG E 570 " --> pdb=" O GLU E 566 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE E 572 " --> pdb=" O ASN E 568 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE E 573 " --> pdb=" O ILE E 569 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS E 575 " --> pdb=" O ASP E 571 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA E 576 " --> pdb=" O ILE E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 592 Processing helix chain 'E' and resid 608 through 617 removed outlier: 3.647A pdb=" N ASN E 612 " --> pdb=" O ASP E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 659 through 668 removed outlier: 3.544A pdb=" N LEU E 664 " --> pdb=" O GLU E 660 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER E 665 " --> pdb=" O ASN E 661 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 666 " --> pdb=" O ALA E 662 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN E 668 " --> pdb=" O LEU E 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 125 removed outlier: 3.747A pdb=" N LEU G 122 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU G 123 " --> pdb=" O ASP G 119 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU G 125 " --> pdb=" O GLU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 160 removed outlier: 3.666A pdb=" N HIS G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 176 removed outlier: 3.681A pdb=" N LYS G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU G 176 " --> pdb=" O TYR G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 220 removed outlier: 3.898A pdb=" N GLN G 220 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 256 removed outlier: 4.326A pdb=" N ILE G 245 " --> pdb=" O LYS G 241 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA G 251 " --> pdb=" O GLU G 247 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP G 252 " --> pdb=" O PHE G 248 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 313 removed outlier: 3.609A pdb=" N LYS G 304 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU G 306 " --> pdb=" O GLN G 302 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU G 308 " --> pdb=" O LYS G 304 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN G 309 " --> pdb=" O ASN G 305 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE G 310 " --> pdb=" O GLU G 306 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP G 311 " --> pdb=" O MET G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 removed outlier: 3.871A pdb=" N ILE G 356 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET G 357 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS G 361 " --> pdb=" O MET G 357 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN G 362 " --> pdb=" O ALA G 358 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR G 363 " --> pdb=" O ALA G 359 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG G 364 " --> pdb=" O ARG G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 500 through 508 removed outlier: 4.120A pdb=" N LEU G 504 " --> pdb=" O ASP G 500 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS G 505 " --> pdb=" O TYR G 501 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU G 508 " --> pdb=" O LEU G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 517 through 525 removed outlier: 3.733A pdb=" N GLU G 522 " --> pdb=" O ASN G 518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER G 525 " --> pdb=" O HIS G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 536 removed outlier: 3.656A pdb=" N LEU G 530 " --> pdb=" O ASN G 526 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU G 531 " --> pdb=" O PHE G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 550 Processing helix chain 'G' and resid 556 through 565 removed outlier: 3.556A pdb=" N LEU G 561 " --> pdb=" O GLU G 557 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS G 562 " --> pdb=" O GLU G 558 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G 563 " --> pdb=" O SER G 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 566 through 579 removed outlier: 3.777A pdb=" N GLN G 570 " --> pdb=" O SER G 566 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR G 571 " --> pdb=" O ALA G 567 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU G 572 " --> pdb=" O GLY G 568 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL G 573 " --> pdb=" O TRP G 569 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU G 578 " --> pdb=" O MET G 574 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER G 579 " --> pdb=" O ILE G 575 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 30 Processing sheet with id=AA1, first strand: chain 'B' and resid 277 through 279 removed outlier: 6.813A pdb=" N PHE B 277 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ASP B 314 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE B 279 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ALA B 356 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE B 313 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU B 252 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 549 through 552 removed outlier: 6.729A pdb=" N ILE B 550 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASP B 587 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B 552 " --> pdb=" O ASP B 587 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 525 " --> pdb=" O GLN B 651 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 527 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 252 through 253 removed outlier: 6.715A pdb=" N ALA C 309 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE C 354 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE C 311 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ALA C 356 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE C 313 " --> pdb=" O ALA C 356 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 275 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N PHE C 312 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE C 277 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASP C 314 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE C 279 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 548 through 553 removed outlier: 5.969A pdb=" N ASN C 548 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE C 585 " --> pdb=" O ASN C 548 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE C 550 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASP C 587 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 552 " --> pdb=" O ASP C 587 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C 653 " --> pdb=" O LEU C 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 311 through 312 removed outlier: 6.978A pdb=" N ILE D 311 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ALA D 356 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL D 251 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 524 through 526 removed outlier: 6.018A pdb=" N ASN D 548 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE D 585 " --> pdb=" O ASN D 548 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE D 550 " --> pdb=" O PHE D 585 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASP D 587 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL D 552 " --> pdb=" O ASP D 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 313 through 314 removed outlier: 7.117A pdb=" N ILE E 313 " --> pdb=" O ALA E 356 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL E 251 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR E 357 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N MET E 253 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY E 250 " --> pdb=" O ARG E 375 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL E 377 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU E 252 " --> pdb=" O VAL E 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 275 through 276 removed outlier: 6.299A pdb=" N PHE E 275 " --> pdb=" O ILE E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 548 through 551 removed outlier: 3.595A pdb=" N VAL E 583 " --> pdb=" O ASN E 548 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL E 524 " --> pdb=" O GLY E 631 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR E 633 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE E 526 " --> pdb=" O THR E 633 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN E 651 " --> pdb=" O GLY E 523 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 236 through 238 removed outlier: 4.094A pdb=" N HIS G 236 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY G 276 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR G 264 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE G 284 " --> pdb=" O TYR G 262 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR G 262 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY G 323 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY G 265 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ARG G 321 " --> pdb=" O GLY G 265 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N VAL G 382 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE G 322 " --> pdb=" O VAL G 382 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N CYS G 384 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU G 324 " --> pdb=" O CYS G 384 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE G 386 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE G 326 " --> pdb=" O ILE G 386 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 414 through 415 436 hydrogen bonds defined for protein. 1251 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: 2.81 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3401 1.29 - 1.43: 4664 1.43 - 1.56: 11641 1.56 - 1.70: 26 1.70 - 1.83: 161 Bond restraints: 19893 Sorted by residual: bond pdb=" C ALA D 269 " pdb=" O ALA D 269 " ideal model delta sigma weight residual 1.235 1.160 0.075 1.26e-02 6.30e+03 3.53e+01 bond pdb=" C4 ADP E 903 " pdb=" C5 ADP E 903 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP B 904 " pdb=" C5 ADP B 904 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP C 903 " pdb=" C5 ADP C 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP E 904 " pdb=" C5 ADP E 904 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 ... (remaining 19888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 26232 2.65 - 5.30: 487 5.30 - 7.95: 138 7.95 - 10.60: 53 10.60 - 13.25: 21 Bond angle restraints: 26931 Sorted by residual: angle pdb=" C LEU D 239 " pdb=" N PHE D 240 " pdb=" CA PHE D 240 " ideal model delta sigma weight residual 120.58 107.60 12.98 1.71e+00 3.42e-01 5.76e+01 angle pdb=" C VAL D 268 " pdb=" CA VAL D 268 " pdb=" CB VAL D 268 " ideal model delta sigma weight residual 111.29 122.55 -11.26 1.64e+00 3.72e-01 4.71e+01 angle pdb=" C ALA D 267 " pdb=" N VAL D 268 " pdb=" CA VAL D 268 " ideal model delta sigma weight residual 121.97 109.94 12.03 1.80e+00 3.09e-01 4.47e+01 angle pdb=" CA PHE D 240 " pdb=" CB PHE D 240 " pdb=" CG PHE D 240 " ideal model delta sigma weight residual 113.80 107.24 6.56 1.00e+00 1.00e+00 4.31e+01 angle pdb=" C LYS E 594 " pdb=" N ALA E 595 " pdb=" CA ALA E 595 " ideal model delta sigma weight residual 121.54 133.74 -12.20 1.91e+00 2.74e-01 4.08e+01 ... (remaining 26926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.43: 11646 30.43 - 60.86: 442 60.86 - 91.29: 41 91.29 - 121.72: 11 121.72 - 152.15: 12 Dihedral angle restraints: 12152 sinusoidal: 4989 harmonic: 7163 Sorted by residual: dihedral pdb=" CA ALA B 580 " pdb=" C ALA B 580 " pdb=" N PRO B 581 " pdb=" CA PRO B 581 " ideal model delta harmonic sigma weight residual -180.00 -127.23 -52.77 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA ARG E 596 " pdb=" C ARG E 596 " pdb=" N GLY E 597 " pdb=" CA GLY E 597 " ideal model delta harmonic sigma weight residual 180.00 -135.70 -44.30 0 5.00e+00 4.00e-02 7.85e+01 dihedral pdb=" CA ALA E 595 " pdb=" C ALA E 595 " pdb=" N ARG E 596 " pdb=" CA ARG E 596 " ideal model delta harmonic sigma weight residual 180.00 139.76 40.24 0 5.00e+00 4.00e-02 6.48e+01 ... (remaining 12149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2684 0.086 - 0.172: 294 0.172 - 0.257: 27 0.257 - 0.343: 2 0.343 - 0.429: 2 Chirality restraints: 3009 Sorted by residual: chirality pdb=" CB ILE E 216 " pdb=" CA ILE E 216 " pdb=" CG1 ILE E 216 " pdb=" CG2 ILE E 216 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CB ILE C 666 " pdb=" CA ILE C 666 " pdb=" CG1 ILE C 666 " pdb=" CG2 ILE C 666 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB THR H 7 " pdb=" CA THR H 7 " pdb=" OG1 THR H 7 " pdb=" CG2 THR H 7 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3006 not shown) Planarity restraints: 3512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 269 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C ALA D 269 " 0.069 2.00e-02 2.50e+03 pdb=" O ALA D 269 " -0.028 2.00e-02 2.50e+03 pdb=" N ASN D 270 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO H 37 " 0.064 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO H 38 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO H 38 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO H 38 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 232 " -0.048 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO E 233 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 233 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 233 " -0.040 5.00e-02 4.00e+02 ... (remaining 3509 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 20 2.03 - 2.75: 2255 2.75 - 3.47: 27170 3.47 - 4.18: 45374 4.18 - 4.90: 76610 Nonbonded interactions: 151429 Sorted by model distance: nonbonded pdb=" CG2 THR C 535 " pdb=" F2 BEF C 902 " model vdw 1.317 3.410 nonbonded pdb=" CG2 THR D 535 " pdb=" F3 BEF D 902 " model vdw 1.369 3.410 nonbonded pdb=" O PRO B 257 " pdb=" O1B ADP B 904 " model vdw 1.386 3.040 nonbonded pdb=" OD1 ASP G 395 " pdb=" CD1 LEU H 43 " model vdw 1.504 3.460 nonbonded pdb=" OG1 THR C 262 " pdb=" O3A ADP C 903 " model vdw 1.539 3.040 ... (remaining 151424 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 209 through 436 or resid 457 through 670)) selection = (chain 'C' and (resid 209 through 436 or resid 457 through 670)) selection = (chain 'D' and (resid 209 through 436 or resid 457 through 670)) selection = (chain 'E' and resid 209 through 670) } 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: 1.170 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.310 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 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 : 0.018 0.786 19912 Z= 1.700 Angle : 1.064 13.250 26931 Z= 0.535 Chirality : 0.055 0.429 3009 Planarity : 0.006 0.097 3512 Dihedral : 16.651 152.147 7532 Min Nonbonded Distance : 1.317 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.27 % Favored : 91.45 % Rotamer: Outliers : 0.34 % Allowed : 9.05 % Favored : 90.61 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.21 % 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: -5.52 (0.12), residues: 2468 helix: -4.96 (0.05), residues: 838 sheet: -2.12 (0.29), residues: 262 loop : -3.17 (0.13), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 372 TYR 0.012 0.001 TYR E 527 PHE 0.015 0.001 PHE E 462 TRP 0.009 0.001 TRP G 211 HIS 0.004 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00563 (19893) covalent geometry : angle 1.06420 (26931) hydrogen bonds : bond 0.32604 ( 436) hydrogen bonds : angle 10.24505 ( 1251) Misc. bond : bond 0.54178 ( 19) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 586 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 ARG cc_start: 0.6363 (ptm160) cc_final: 0.6102 (ptm160) REVERT: B 314 ASP cc_start: 0.7896 (t0) cc_final: 0.7159 (t0) REVERT: B 315 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6478 (mt-10) REVERT: B 332 ARG cc_start: 0.8010 (ptm160) cc_final: 0.7723 (ttm110) REVERT: B 437 MET cc_start: 0.8362 (tpp) cc_final: 0.8061 (tpp) REVERT: B 513 TYR cc_start: 0.7420 (m-80) cc_final: 0.7114 (m-10) REVERT: B 556 GLU cc_start: 0.8484 (pp20) cc_final: 0.8228 (pp20) REVERT: B 562 TYR cc_start: 0.8192 (t80) cc_final: 0.7983 (t80) REVERT: B 564 GLU cc_start: 0.8531 (tt0) cc_final: 0.8127 (tp30) REVERT: B 652 LEU cc_start: 0.8894 (mt) cc_final: 0.8664 (mt) REVERT: C 236 HIS cc_start: 0.6057 (t-90) cc_final: 0.5763 (t-90) REVERT: C 239 LEU cc_start: 0.9007 (mt) cc_final: 0.8743 (mt) REVERT: C 301 GLU cc_start: 0.7913 (pt0) cc_final: 0.7563 (pt0) REVERT: C 433 ILE cc_start: 0.9183 (mt) cc_final: 0.8927 (mm) REVERT: C 568 ASN cc_start: 0.8078 (m-40) cc_final: 0.7869 (m-40) REVERT: C 572 ILE cc_start: 0.8651 (tt) cc_final: 0.8439 (tp) REVERT: C 661 ASN cc_start: 0.8265 (t0) cc_final: 0.8052 (t0) REVERT: D 285 MET cc_start: 0.7840 (mmm) cc_final: 0.7256 (mmm) REVERT: D 400 LEU cc_start: 0.8388 (mp) cc_final: 0.7861 (tt) REVERT: D 571 ASP cc_start: 0.7222 (p0) cc_final: 0.6406 (t70) REVERT: E 229 MET cc_start: 0.8009 (tmm) cc_final: 0.7307 (tpp) REVERT: E 331 GLU cc_start: 0.8463 (mp0) cc_final: 0.8170 (mp0) REVERT: E 333 ARG cc_start: 0.7924 (mtm180) cc_final: 0.6936 (mtm180) REVERT: E 462 PHE cc_start: 0.6777 (m-80) cc_final: 0.6406 (m-80) REVERT: E 464 PHE cc_start: 0.3437 (t80) cc_final: 0.3134 (t80) REVERT: E 548 ASN cc_start: 0.7399 (p0) cc_final: 0.6971 (m-40) REVERT: G 156 LYS cc_start: 0.8197 (mttt) cc_final: 0.7858 (mmtm) REVERT: G 263 MET cc_start: 0.8967 (mtm) cc_final: 0.8683 (mtp) REVERT: G 296 LEU cc_start: 0.7612 (pp) cc_final: 0.6739 (pp) REVERT: G 298 MET cc_start: 0.5426 (pmm) cc_final: 0.5136 (pmm) REVERT: G 302 GLN cc_start: 0.8445 (pp30) cc_final: 0.8232 (pp30) REVERT: G 312 ARG cc_start: 0.8101 (tmm-80) cc_final: 0.7798 (tpp-160) REVERT: G 399 TYR cc_start: 0.7256 (m-80) cc_final: 0.6670 (m-80) REVERT: G 443 ASN cc_start: 0.7446 (t0) cc_final: 0.7120 (t0) REVERT: G 569 TRP cc_start: 0.8414 (t-100) cc_final: 0.7909 (t-100) REVERT: H 16 GLU cc_start: 0.6919 (pm20) cc_final: 0.6698 (pm20) outliers start: 7 outliers final: 4 residues processed: 592 average time/residue: 0.1609 time to fit residues: 135.8712 Evaluate side-chains 365 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 361 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.3980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 ASN B 394 HIS C 280 ASN C 337 GLN C 612 ASN C 613 GLN C 638 GLN C 757 HIS D 568 ASN ** D 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN E 295 ASN ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN G 166 HIS G 170 HIS G 201 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN G 240 GLN G 272 ASN G 313 GLN G 315 GLN G 491 ASN H 2 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.161158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.134483 restraints weight = 46770.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.135423 restraints weight = 31108.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.136106 restraints weight = 21311.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.136585 restraints weight = 20541.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.136688 restraints weight = 18657.869| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19912 Z= 0.143 Angle : 0.787 12.432 26931 Z= 0.376 Chirality : 0.047 0.261 3009 Planarity : 0.006 0.098 3512 Dihedral : 12.500 159.231 2774 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.86 % Favored : 92.06 % Rotamer: Outliers : 0.24 % Allowed : 5.01 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.13 % 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: -4.33 (0.13), residues: 2468 helix: -3.39 (0.11), residues: 918 sheet: -1.51 (0.31), residues: 251 loop : -2.77 (0.15), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 387 TYR 0.023 0.001 TYR G 172 PHE 0.020 0.001 PHE G 231 TRP 0.025 0.002 TRP C 486 HIS 0.010 0.001 HIS G 166 Details of bonding type rmsd covalent geometry : bond 0.00316 (19893) covalent geometry : angle 0.78683 (26931) hydrogen bonds : bond 0.04471 ( 436) hydrogen bonds : angle 6.00248 ( 1251) Misc. bond : bond 0.00416 ( 19) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 434 time to evaluate : 0.730 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: B 264 MET cc_start: 0.8267 (mmt) cc_final: 0.7486 (mmt) REVERT: B 314 ASP cc_start: 0.7972 (t0) cc_final: 0.7610 (t0) REVERT: B 315 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6825 (mt-10) REVERT: B 342 MET cc_start: 0.7891 (ttm) cc_final: 0.7645 (tpt) REVERT: B 370 PHE cc_start: 0.6027 (m-80) cc_final: 0.5803 (m-80) REVERT: B 437 MET cc_start: 0.8117 (tpp) cc_final: 0.7667 (tpp) REVERT: B 527 TYR cc_start: 0.7279 (p90) cc_final: 0.6990 (p90) REVERT: B 564 GLU cc_start: 0.7954 (tt0) cc_final: 0.7588 (tt0) REVERT: B 652 LEU cc_start: 0.8703 (mt) cc_final: 0.8337 (mt) REVERT: C 236 HIS cc_start: 0.6471 (t-90) cc_final: 0.6166 (t70) REVERT: C 238 GLN cc_start: 0.6994 (pm20) cc_final: 0.6786 (pm20) REVERT: C 264 MET cc_start: 0.8088 (tpt) cc_final: 0.7866 (tpp) REVERT: C 301 GLU cc_start: 0.8002 (pt0) cc_final: 0.7784 (tt0) REVERT: C 348 ARG cc_start: 0.6803 (tpp80) cc_final: 0.5957 (tpp80) REVERT: C 351 VAL cc_start: 0.8829 (p) cc_final: 0.8358 (p) REVERT: C 412 GLU cc_start: 0.7569 (pt0) cc_final: 0.7358 (pt0) REVERT: D 400 LEU cc_start: 0.8455 (mp) cc_final: 0.7793 (tt) REVERT: D 539 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8292 (mmtp) REVERT: D 617 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7826 (mm-30) REVERT: D 687 LYS cc_start: 0.7701 (mmtm) cc_final: 0.7335 (mmtp) REVERT: E 229 MET cc_start: 0.7664 (tmm) cc_final: 0.7167 (tpp) REVERT: E 331 GLU cc_start: 0.8359 (mp0) cc_final: 0.7972 (mp0) REVERT: E 378 ASP cc_start: 0.7925 (m-30) cc_final: 0.7435 (m-30) REVERT: E 462 PHE cc_start: 0.6678 (m-80) cc_final: 0.6386 (m-80) REVERT: E 582 THR cc_start: 0.7710 (t) cc_final: 0.7025 (t) REVERT: E 594 LYS cc_start: 0.7687 (tttt) cc_final: 0.7273 (tttm) REVERT: E 617 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6726 (mm-30) REVERT: G 233 MET cc_start: 0.6215 (mmm) cc_final: 0.5597 (mmm) REVERT: G 399 TYR cc_start: 0.7153 (m-80) cc_final: 0.6798 (m-80) REVERT: G 574 MET cc_start: 0.8139 (ptm) cc_final: 0.7914 (ptt) outliers start: 5 outliers final: 0 residues processed: 437 average time/residue: 0.1421 time to fit residues: 92.8585 Evaluate side-chains 302 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 182 optimal weight: 0.7980 chunk 236 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 ASN C 270 ASN C 509 HIS C 612 ASN D 394 HIS ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN G 272 ASN G 313 GLN G 491 ASN G 526 ASN H 2 GLN H 31 GLN H 40 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.145188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116294 restraints weight = 47370.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.116211 restraints weight = 36253.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117246 restraints weight = 27490.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.117843 restraints weight = 22632.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117959 restraints weight = 20309.350| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 19912 Z= 0.319 Angle : 0.962 13.241 26931 Z= 0.472 Chirality : 0.053 0.352 3009 Planarity : 0.007 0.108 3512 Dihedral : 12.676 159.011 2774 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.64 % Favored : 90.28 % Rotamer: Outliers : 0.10 % Allowed : 7.70 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.21 % 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: -3.52 (0.15), residues: 2468 helix: -2.24 (0.14), residues: 956 sheet: -1.60 (0.30), residues: 264 loop : -2.58 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG D 375 TYR 0.034 0.003 TYR C 505 PHE 0.030 0.003 PHE H 45 TRP 0.024 0.002 TRP C 561 HIS 0.014 0.002 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00711 (19893) covalent geometry : angle 0.96210 (26931) hydrogen bonds : bond 0.04814 ( 436) hydrogen bonds : angle 5.74719 ( 1251) Misc. bond : bond 0.00556 ( 19) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 372 time to evaluate : 0.705 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: B 264 MET cc_start: 0.8377 (mmt) cc_final: 0.7641 (mmt) REVERT: B 331 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7496 (mt-10) REVERT: B 345 MET cc_start: 0.7172 (ppp) cc_final: 0.6802 (ppp) REVERT: B 437 MET cc_start: 0.7895 (tpp) cc_final: 0.7524 (tpp) REVERT: C 339 LEU cc_start: 0.8685 (mp) cc_final: 0.8357 (mp) REVERT: C 379 ILE cc_start: 0.8867 (mp) cc_final: 0.8587 (mt) REVERT: C 762 MET cc_start: 0.9018 (mmm) cc_final: 0.8655 (mmm) REVERT: D 215 ASP cc_start: 0.7526 (t0) cc_final: 0.7323 (t70) REVERT: D 245 ILE cc_start: 0.7115 (tp) cc_final: 0.6812 (tp) REVERT: D 283 GLU cc_start: 0.8294 (pp20) cc_final: 0.8060 (pt0) REVERT: D 285 MET cc_start: 0.8222 (mmm) cc_final: 0.7855 (mmm) REVERT: D 379 ILE cc_start: 0.8458 (mm) cc_final: 0.7897 (mt) REVERT: D 400 LEU cc_start: 0.8698 (mp) cc_final: 0.8064 (tt) REVERT: D 771 ASP cc_start: 0.7295 (t0) cc_final: 0.7075 (t0) REVERT: E 229 MET cc_start: 0.7847 (tmm) cc_final: 0.7316 (tpp) REVERT: E 313 ILE cc_start: 0.9357 (tp) cc_final: 0.9074 (mt) REVERT: E 331 GLU cc_start: 0.8458 (mp0) cc_final: 0.8237 (mp0) REVERT: E 594 LYS cc_start: 0.7783 (tttt) cc_final: 0.7353 (tttm) REVERT: E 617 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7475 (mm-30) REVERT: G 443 ASN cc_start: 0.7763 (t0) cc_final: 0.7555 (t0) REVERT: H 23 ILE cc_start: 0.7156 (tp) cc_final: 0.6811 (tp) outliers start: 2 outliers final: 2 residues processed: 374 average time/residue: 0.1357 time to fit residues: 77.5374 Evaluate side-chains 292 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 290 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 140 optimal weight: 7.9990 chunk 163 optimal weight: 0.0980 chunk 141 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 110 optimal weight: 0.7980 chunk 225 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 394 HIS ** D 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 ASN E 613 GLN G 166 HIS G 170 HIS G 497 GLN G 502 GLN H 2 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.149195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.120474 restraints weight = 46693.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120602 restraints weight = 35156.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.121712 restraints weight = 26996.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.122321 restraints weight = 21744.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.122323 restraints weight = 20022.226| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19912 Z= 0.140 Angle : 0.765 11.482 26931 Z= 0.363 Chirality : 0.048 0.272 3009 Planarity : 0.005 0.088 3512 Dihedral : 12.580 163.616 2774 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.47 % Favored : 91.45 % Rotamer: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.17 % 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: -3.08 (0.15), residues: 2468 helix: -1.67 (0.15), residues: 952 sheet: -1.38 (0.30), residues: 267 loop : -2.51 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 432 TYR 0.015 0.001 TYR B 213 PHE 0.021 0.001 PHE D 585 TRP 0.010 0.001 TRP C 561 HIS 0.009 0.001 HIS G 166 Details of bonding type rmsd covalent geometry : bond 0.00321 (19893) covalent geometry : angle 0.76550 (26931) hydrogen bonds : bond 0.03357 ( 436) hydrogen bonds : angle 5.29366 ( 1251) Misc. bond : bond 0.00369 ( 19) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 0.617 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: B 264 MET cc_start: 0.8386 (mmt) cc_final: 0.7688 (mmt) REVERT: B 331 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 333 ARG cc_start: 0.4678 (tpt-90) cc_final: 0.4290 (mmm160) REVERT: B 345 MET cc_start: 0.6978 (ppp) cc_final: 0.6492 (ppp) REVERT: B 437 MET cc_start: 0.7881 (tpp) cc_final: 0.7527 (tpp) REVERT: C 229 MET cc_start: 0.8366 (tpp) cc_final: 0.8041 (tpp) REVERT: C 348 ARG cc_start: 0.6472 (tpp80) cc_final: 0.6136 (tpp80) REVERT: C 402 ASP cc_start: 0.6749 (p0) cc_final: 0.6406 (m-30) REVERT: C 484 VAL cc_start: 0.8179 (m) cc_final: 0.7910 (m) REVERT: C 488 ASP cc_start: 0.7086 (m-30) cc_final: 0.6743 (m-30) REVERT: C 527 TYR cc_start: 0.7662 (p90) cc_final: 0.7201 (p90) REVERT: C 762 MET cc_start: 0.8953 (mmm) cc_final: 0.8616 (mmm) REVERT: D 245 ILE cc_start: 0.7154 (tp) cc_final: 0.6924 (tp) REVERT: D 283 GLU cc_start: 0.8305 (pp20) cc_final: 0.8033 (pt0) REVERT: D 337 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8489 (tp-100) REVERT: D 341 LEU cc_start: 0.9299 (mt) cc_final: 0.9062 (mt) REVERT: D 379 ILE cc_start: 0.7983 (mm) cc_final: 0.7510 (mt) REVERT: D 400 LEU cc_start: 0.8666 (mp) cc_final: 0.8127 (tt) REVERT: D 645 ARG cc_start: 0.8491 (ptt90) cc_final: 0.7897 (tmm160) REVERT: E 229 MET cc_start: 0.7699 (tmm) cc_final: 0.7301 (tpp) REVERT: E 263 LEU cc_start: 0.4704 (pt) cc_final: 0.3806 (pp) REVERT: E 313 ILE cc_start: 0.9262 (tp) cc_final: 0.9036 (mt) REVERT: E 505 TYR cc_start: 0.6599 (m-10) cc_final: 0.6371 (m-10) REVERT: E 594 LYS cc_start: 0.7525 (tttt) cc_final: 0.7087 (tttm) REVERT: G 436 GLU cc_start: 0.6635 (tm-30) cc_final: 0.6387 (tm-30) outliers start: 1 outliers final: 0 residues processed: 380 average time/residue: 0.1318 time to fit residues: 76.4298 Evaluate side-chains 286 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 165 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 229 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN B 470 ASN C 716 HIS D 225 GLN D 394 HIS ** D 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 GLN D 702 GLN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 HIS G 361 HIS ** G 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.137898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108918 restraints weight = 46552.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108550 restraints weight = 33579.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.109519 restraints weight = 26501.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110074 restraints weight = 22825.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110094 restraints weight = 21287.362| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 19912 Z= 0.337 Angle : 1.013 13.378 26931 Z= 0.496 Chirality : 0.056 0.337 3009 Planarity : 0.007 0.075 3512 Dihedral : 13.083 174.234 2774 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.07 % Favored : 87.84 % Rotamer: Outliers : 0.10 % Allowed : 5.39 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.78 % Twisted General : 0.25 % 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: -3.27 (0.15), residues: 2468 helix: -1.67 (0.15), residues: 968 sheet: -1.72 (0.30), residues: 262 loop : -2.71 (0.16), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 213 TYR 0.025 0.002 TYR C 505 PHE 0.064 0.003 PHE C 573 TRP 0.028 0.003 TRP C 561 HIS 0.014 0.002 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00769 (19893) covalent geometry : angle 1.01296 (26931) hydrogen bonds : bond 0.04647 ( 436) hydrogen bonds : angle 5.82607 ( 1251) Misc. bond : bond 0.00478 ( 19) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 345 time to evaluate : 0.568 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: B 264 MET cc_start: 0.8587 (mmt) cc_final: 0.7674 (mmt) REVERT: B 310 ILE cc_start: 0.8508 (tp) cc_final: 0.8292 (tt) REVERT: B 315 GLU cc_start: 0.7887 (tt0) cc_final: 0.7673 (tt0) REVERT: B 331 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7440 (mt-10) REVERT: B 333 ARG cc_start: 0.4963 (tpt-90) cc_final: 0.4177 (mmm160) REVERT: B 345 MET cc_start: 0.7061 (ppp) cc_final: 0.6572 (ppp) REVERT: B 459 MET cc_start: 0.8817 (tpp) cc_final: 0.8530 (tpp) REVERT: C 402 ASP cc_start: 0.7566 (p0) cc_final: 0.7062 (m-30) REVERT: C 543 THR cc_start: 0.8674 (p) cc_final: 0.8400 (m) REVERT: C 713 ILE cc_start: 0.8151 (pt) cc_final: 0.7701 (mt) REVERT: C 762 MET cc_start: 0.8893 (mmm) cc_final: 0.8481 (mmm) REVERT: D 229 MET cc_start: 0.8698 (ttp) cc_final: 0.8265 (ppp) REVERT: D 245 ILE cc_start: 0.7720 (tp) cc_final: 0.7459 (tp) REVERT: D 337 GLN cc_start: 0.8897 (tp-100) cc_final: 0.8586 (tp-100) REVERT: D 341 LEU cc_start: 0.9321 (mt) cc_final: 0.9096 (mt) REVERT: D 400 LEU cc_start: 0.8877 (mp) cc_final: 0.8300 (tt) REVERT: E 263 LEU cc_start: 0.4986 (pt) cc_final: 0.4473 (pp) REVERT: E 331 GLU cc_start: 0.8841 (mp0) cc_final: 0.8532 (mp0) REVERT: E 594 LYS cc_start: 0.7783 (tttt) cc_final: 0.7331 (tttm) REVERT: G 212 PRO cc_start: 0.2445 (Cg_endo) cc_final: 0.2126 (Cg_exo) REVERT: G 257 MET cc_start: 0.5504 (tpp) cc_final: 0.5172 (tpp) REVERT: H 23 ILE cc_start: 0.7055 (tp) cc_final: 0.6730 (tp) REVERT: H 43 LEU cc_start: 0.7172 (tp) cc_final: 0.6485 (tp) outliers start: 2 outliers final: 1 residues processed: 347 average time/residue: 0.1356 time to fit residues: 71.8146 Evaluate side-chains 277 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 40 optimal weight: 0.8980 chunk 239 optimal weight: 30.0000 chunk 131 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN D 468 ASN ** D 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 HIS ** G 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.144969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.115997 restraints weight = 45209.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.116043 restraints weight = 29922.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.116675 restraints weight = 23072.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.117100 restraints weight = 22031.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.117375 restraints weight = 18468.838| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19912 Z= 0.147 Angle : 0.807 12.968 26931 Z= 0.384 Chirality : 0.049 0.265 3009 Planarity : 0.005 0.094 3512 Dihedral : 12.745 171.698 2774 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.32 % Favored : 90.60 % Rotamer: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.78 % Twisted General : 0.17 % 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: -2.95 (0.16), residues: 2468 helix: -1.33 (0.16), residues: 959 sheet: -1.64 (0.30), residues: 269 loop : -2.58 (0.16), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 475 TYR 0.022 0.002 TYR E 505 PHE 0.039 0.002 PHE E 312 TRP 0.012 0.001 TRP C 561 HIS 0.006 0.001 HIS G 166 Details of bonding type rmsd covalent geometry : bond 0.00341 (19893) covalent geometry : angle 0.80731 (26931) hydrogen bonds : bond 0.03307 ( 436) hydrogen bonds : angle 5.27027 ( 1251) Misc. bond : bond 0.00380 ( 19) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 MET cc_start: 0.8594 (mmt) cc_final: 0.7580 (mmt) REVERT: B 333 ARG cc_start: 0.5030 (tpt-90) cc_final: 0.4462 (mmm160) REVERT: B 345 MET cc_start: 0.6926 (ppp) cc_final: 0.6500 (ppp) REVERT: C 345 MET cc_start: 0.6802 (tpp) cc_final: 0.6545 (tpt) REVERT: C 402 ASP cc_start: 0.7423 (p0) cc_final: 0.7031 (m-30) REVERT: C 504 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7773 (mm-30) REVERT: C 527 TYR cc_start: 0.7650 (p90) cc_final: 0.7124 (p90) REVERT: C 543 THR cc_start: 0.8395 (p) cc_final: 0.7872 (m) REVERT: C 560 MET cc_start: 0.7529 (ptt) cc_final: 0.7302 (ptt) REVERT: C 566 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8723 (mm-30) REVERT: C 713 ILE cc_start: 0.8042 (pt) cc_final: 0.7520 (mt) REVERT: C 762 MET cc_start: 0.8884 (mmm) cc_final: 0.8603 (mmm) REVERT: D 245 ILE cc_start: 0.7724 (tp) cc_final: 0.7447 (tp) REVERT: D 264 MET cc_start: 0.8244 (tpp) cc_final: 0.7968 (tpp) REVERT: D 285 MET cc_start: 0.7795 (ttm) cc_final: 0.7380 (ttm) REVERT: D 337 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8566 (tp-100) REVERT: D 341 LEU cc_start: 0.9274 (mt) cc_final: 0.9007 (mt) REVERT: D 345 MET cc_start: 0.7282 (tpp) cc_final: 0.5124 (ppp) REVERT: D 369 ARG cc_start: 0.8607 (ttp80) cc_final: 0.7942 (ttp80) REVERT: D 400 LEU cc_start: 0.8738 (mp) cc_final: 0.8413 (tt) REVERT: E 331 GLU cc_start: 0.8681 (mp0) cc_final: 0.8274 (mp0) REVERT: E 342 MET cc_start: 0.8362 (mtm) cc_final: 0.8155 (mtm) REVERT: E 505 TYR cc_start: 0.6652 (m-10) cc_final: 0.6383 (m-80) REVERT: E 594 LYS cc_start: 0.7531 (tttt) cc_final: 0.7085 (ttmm) REVERT: E 609 ARG cc_start: 0.7457 (mtm-85) cc_final: 0.6896 (mtm110) REVERT: G 122 LEU cc_start: 0.8861 (mp) cc_final: 0.8239 (tt) REVERT: G 212 PRO cc_start: 0.2089 (Cg_endo) cc_final: 0.1805 (Cg_exo) REVERT: G 495 MET cc_start: 0.8778 (pmm) cc_final: 0.8064 (pmm) outliers start: 1 outliers final: 0 residues processed: 379 average time/residue: 0.1373 time to fit residues: 79.4699 Evaluate side-chains 276 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 24 optimal weight: 0.0870 chunk 154 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 241 optimal weight: 0.0030 chunk 145 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 231 optimal weight: 0.0870 chunk 46 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 overall best weight: 0.5548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS B 470 ASN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN G 166 HIS H 2 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.146847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117752 restraints weight = 46012.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.118236 restraints weight = 32168.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.119413 restraints weight = 23962.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.120003 restraints weight = 19153.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.119999 restraints weight = 18003.898| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19912 Z= 0.128 Angle : 0.770 12.347 26931 Z= 0.363 Chirality : 0.048 0.262 3009 Planarity : 0.005 0.073 3512 Dihedral : 12.377 170.613 2774 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.01 % Favored : 89.91 % Rotamer: Outliers : 0.05 % Allowed : 2.07 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.78 % Twisted General : 0.17 % 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: -2.71 (0.16), residues: 2468 helix: -1.08 (0.16), residues: 956 sheet: -1.50 (0.32), residues: 258 loop : -2.47 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 332 TYR 0.025 0.001 TYR C 416 PHE 0.024 0.001 PHE C 692 TRP 0.015 0.001 TRP G 211 HIS 0.010 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00291 (19893) covalent geometry : angle 0.77027 (26931) hydrogen bonds : bond 0.03049 ( 436) hydrogen bonds : angle 5.08133 ( 1251) Misc. bond : bond 0.00345 ( 19) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 0.729 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 226 ILE cc_start: 0.8870 (tp) cc_final: 0.8406 (tp) REVERT: B 264 MET cc_start: 0.8472 (mmt) cc_final: 0.7592 (mmt) REVERT: B 333 ARG cc_start: 0.4982 (tpt-90) cc_final: 0.4459 (mmm160) REVERT: B 345 MET cc_start: 0.6844 (ppp) cc_final: 0.6586 (ppp) REVERT: B 395 THR cc_start: 0.8929 (p) cc_final: 0.8478 (t) REVERT: B 564 GLU cc_start: 0.7852 (tt0) cc_final: 0.7524 (tt0) REVERT: C 210 GLU cc_start: 0.7123 (pm20) cc_final: 0.6716 (pm20) REVERT: C 398 MET cc_start: 0.8522 (mtm) cc_final: 0.8119 (mtt) REVERT: C 402 ASP cc_start: 0.6983 (p0) cc_final: 0.6707 (m-30) REVERT: C 488 ASP cc_start: 0.7434 (m-30) cc_final: 0.6901 (m-30) REVERT: C 713 ILE cc_start: 0.7980 (pt) cc_final: 0.7544 (mm) REVERT: C 762 MET cc_start: 0.8867 (mmm) cc_final: 0.8573 (mmm) REVERT: D 264 MET cc_start: 0.8185 (tpp) cc_final: 0.7845 (tpp) REVERT: D 337 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8517 (tp-100) REVERT: D 341 LEU cc_start: 0.9299 (mt) cc_final: 0.8995 (mt) REVERT: D 345 MET cc_start: 0.7057 (tpp) cc_final: 0.4972 (ppp) REVERT: D 400 LEU cc_start: 0.8646 (mp) cc_final: 0.8256 (tt) REVERT: D 413 THR cc_start: 0.7034 (t) cc_final: 0.6749 (t) REVERT: D 590 ASP cc_start: 0.8025 (m-30) cc_final: 0.7787 (m-30) REVERT: E 331 GLU cc_start: 0.8659 (mp0) cc_final: 0.8102 (mp0) REVERT: E 594 LYS cc_start: 0.7588 (tttt) cc_final: 0.7052 (tttm) REVERT: E 609 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.6758 (ptp90) REVERT: E 618 MET cc_start: 0.7212 (ppp) cc_final: 0.6932 (ppp) REVERT: G 122 LEU cc_start: 0.8798 (mp) cc_final: 0.8132 (tt) REVERT: G 212 PRO cc_start: 0.1844 (Cg_endo) cc_final: 0.1622 (Cg_exo) REVERT: G 257 MET cc_start: 0.4721 (tpp) cc_final: 0.4479 (tpp) outliers start: 1 outliers final: 0 residues processed: 380 average time/residue: 0.1411 time to fit residues: 82.5022 Evaluate side-chains 300 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 0.0270 chunk 116 optimal weight: 0.3980 chunk 190 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS B 470 ASN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.146472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.117896 restraints weight = 45705.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.118403 restraints weight = 31262.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.119452 restraints weight = 23231.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.119817 restraints weight = 19773.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.119970 restraints weight = 17943.716| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19912 Z= 0.136 Angle : 0.775 11.360 26931 Z= 0.366 Chirality : 0.048 0.281 3009 Planarity : 0.005 0.073 3512 Dihedral : 12.216 169.990 2774 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.89 % Favored : 90.03 % Rotamer: Outliers : 0.05 % Allowed : 0.91 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.57 (0.16), residues: 2468 helix: -0.93 (0.16), residues: 961 sheet: -1.37 (0.31), residues: 272 loop : -2.45 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 369 TYR 0.021 0.001 TYR C 416 PHE 0.025 0.002 PHE C 692 TRP 0.011 0.001 TRP G 544 HIS 0.012 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00316 (19893) covalent geometry : angle 0.77484 (26931) hydrogen bonds : bond 0.02956 ( 436) hydrogen bonds : angle 5.03954 ( 1251) Misc. bond : bond 0.00394 ( 19) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 ILE cc_start: 0.8802 (tp) cc_final: 0.8540 (tp) REVERT: B 264 MET cc_start: 0.8497 (mmt) cc_final: 0.7591 (mmt) REVERT: B 333 ARG cc_start: 0.4732 (tpt-90) cc_final: 0.4250 (mmm160) REVERT: B 345 MET cc_start: 0.6768 (ppp) cc_final: 0.6495 (ppp) REVERT: B 564 GLU cc_start: 0.7871 (tt0) cc_final: 0.7533 (tt0) REVERT: C 210 GLU cc_start: 0.6826 (pm20) cc_final: 0.6333 (pm20) REVERT: C 301 GLU cc_start: 0.8027 (tt0) cc_final: 0.7817 (tt0) REVERT: C 398 MET cc_start: 0.8459 (mtm) cc_final: 0.8101 (mtt) REVERT: C 402 ASP cc_start: 0.6936 (p0) cc_final: 0.6699 (m-30) REVERT: C 488 ASP cc_start: 0.7402 (m-30) cc_final: 0.6904 (m-30) REVERT: C 527 TYR cc_start: 0.7591 (p90) cc_final: 0.7109 (p90) REVERT: C 713 ILE cc_start: 0.7982 (pt) cc_final: 0.7561 (mm) REVERT: C 762 MET cc_start: 0.8849 (mmm) cc_final: 0.8550 (mmm) REVERT: D 264 MET cc_start: 0.8295 (tpp) cc_final: 0.7906 (tpp) REVERT: D 337 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8587 (tp-100) REVERT: D 341 LEU cc_start: 0.9247 (mt) cc_final: 0.8961 (mt) REVERT: D 400 LEU cc_start: 0.8614 (mp) cc_final: 0.8230 (tt) REVERT: D 413 THR cc_start: 0.7205 (t) cc_final: 0.6904 (t) REVERT: D 590 ASP cc_start: 0.7966 (m-30) cc_final: 0.7700 (m-30) REVERT: E 331 GLU cc_start: 0.8665 (mp0) cc_final: 0.8087 (mp0) REVERT: E 565 SER cc_start: 0.8686 (p) cc_final: 0.8415 (m) REVERT: E 594 LYS cc_start: 0.7502 (tttt) cc_final: 0.6997 (tttm) REVERT: E 618 MET cc_start: 0.7361 (ppp) cc_final: 0.6880 (ppp) REVERT: G 122 LEU cc_start: 0.8812 (mp) cc_final: 0.8074 (tt) REVERT: G 212 PRO cc_start: 0.2232 (Cg_endo) cc_final: 0.1992 (Cg_exo) REVERT: G 257 MET cc_start: 0.4910 (tpp) cc_final: 0.4683 (tpp) REVERT: G 443 ASN cc_start: 0.7758 (t0) cc_final: 0.7535 (t0) REVERT: G 495 MET cc_start: 0.8260 (pmm) cc_final: 0.7190 (pmm) outliers start: 1 outliers final: 0 residues processed: 369 average time/residue: 0.1322 time to fit residues: 75.5879 Evaluate side-chains 294 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 169 optimal weight: 0.0770 chunk 105 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 229 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 ASN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 HIS ** D 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 499 GLN H 2 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.147391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.118104 restraints weight = 45451.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.118858 restraints weight = 30335.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.119439 restraints weight = 22141.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.120059 restraints weight = 20127.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.120367 restraints weight = 18110.818| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19912 Z= 0.129 Angle : 0.774 11.278 26931 Z= 0.365 Chirality : 0.048 0.270 3009 Planarity : 0.005 0.071 3512 Dihedral : 12.142 170.228 2774 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.17 % Favored : 89.75 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.52 (0.16), residues: 2468 helix: -0.86 (0.16), residues: 955 sheet: -1.32 (0.31), residues: 268 loop : -2.46 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 332 TYR 0.019 0.001 TYR C 416 PHE 0.029 0.001 PHE H 45 TRP 0.014 0.002 TRP G 569 HIS 0.012 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00299 (19893) covalent geometry : angle 0.77449 (26931) hydrogen bonds : bond 0.02830 ( 436) hydrogen bonds : angle 4.96211 ( 1251) Misc. bond : bond 0.00367 ( 19) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.613 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 226 ILE cc_start: 0.8797 (tp) cc_final: 0.8437 (tp) REVERT: B 264 MET cc_start: 0.8515 (mmt) cc_final: 0.7509 (mmt) REVERT: B 295 ASN cc_start: 0.7716 (p0) cc_final: 0.7290 (t0) REVERT: B 333 ARG cc_start: 0.4750 (tpt-90) cc_final: 0.4289 (mmm160) REVERT: B 345 MET cc_start: 0.6666 (ppp) cc_final: 0.6301 (ppp) REVERT: C 210 GLU cc_start: 0.6665 (pm20) cc_final: 0.6239 (pm20) REVERT: C 398 MET cc_start: 0.8378 (mtm) cc_final: 0.8042 (mtt) REVERT: C 402 ASP cc_start: 0.7008 (p0) cc_final: 0.6712 (m-30) REVERT: C 488 ASP cc_start: 0.7526 (m-30) cc_final: 0.6963 (m-30) REVERT: C 527 TYR cc_start: 0.7698 (p90) cc_final: 0.7275 (p90) REVERT: C 713 ILE cc_start: 0.8027 (pt) cc_final: 0.7591 (mm) REVERT: C 762 MET cc_start: 0.8850 (mmm) cc_final: 0.8570 (mmm) REVERT: D 264 MET cc_start: 0.8155 (tpp) cc_final: 0.7783 (tpp) REVERT: D 337 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8605 (tp-100) REVERT: D 341 LEU cc_start: 0.9236 (mt) cc_final: 0.8941 (mt) REVERT: D 345 MET cc_start: 0.7019 (tpt) cc_final: 0.5871 (ppp) REVERT: D 400 LEU cc_start: 0.8562 (mp) cc_final: 0.8198 (tt) REVERT: D 590 ASP cc_start: 0.7908 (m-30) cc_final: 0.7696 (m-30) REVERT: E 331 GLU cc_start: 0.8631 (mp0) cc_final: 0.7652 (mp0) REVERT: E 462 PHE cc_start: 0.8127 (m-80) cc_final: 0.7609 (m-80) REVERT: E 565 SER cc_start: 0.8672 (p) cc_final: 0.8250 (m) REVERT: E 594 LYS cc_start: 0.7516 (tttt) cc_final: 0.6956 (tttm) REVERT: G 122 LEU cc_start: 0.8907 (mp) cc_final: 0.8283 (tt) REVERT: G 212 PRO cc_start: 0.2024 (Cg_endo) cc_final: 0.1804 (Cg_exo) REVERT: G 284 ILE cc_start: 0.8754 (mm) cc_final: 0.8152 (tp) REVERT: G 443 ASN cc_start: 0.7654 (t0) cc_final: 0.7426 (t0) REVERT: G 448 THR cc_start: 0.7081 (t) cc_final: 0.6832 (t) REVERT: H 16 GLU cc_start: 0.6650 (pm20) cc_final: 0.5910 (pm20) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.1324 time to fit residues: 75.7359 Evaluate side-chains 291 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 50 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 181 optimal weight: 0.0060 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 243 optimal weight: 8.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS C 394 HIS ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 GLN H 2 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.143149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.115456 restraints weight = 45925.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114794 restraints weight = 31443.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.115403 restraints weight = 24241.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.115837 restraints weight = 22209.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116044 restraints weight = 20097.131| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 19912 Z= 0.193 Angle : 0.840 11.631 26931 Z= 0.402 Chirality : 0.050 0.259 3009 Planarity : 0.005 0.070 3512 Dihedral : 12.268 170.921 2774 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.78 % Favored : 89.14 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.56 (0.16), residues: 2468 helix: -0.93 (0.16), residues: 967 sheet: -1.46 (0.31), residues: 278 loop : -2.43 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 312 TYR 0.020 0.002 TYR C 416 PHE 0.025 0.002 PHE E 300 TRP 0.032 0.002 TRP C 561 HIS 0.012 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00450 (19893) covalent geometry : angle 0.84039 (26931) hydrogen bonds : bond 0.03244 ( 436) hydrogen bonds : angle 5.09226 ( 1251) Misc. bond : bond 0.00393 ( 19) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 ILE cc_start: 0.8882 (tp) cc_final: 0.8546 (tp) REVERT: B 264 MET cc_start: 0.8568 (mmt) cc_final: 0.7446 (mmt) REVERT: B 295 ASN cc_start: 0.7950 (p0) cc_final: 0.7562 (t0) REVERT: B 333 ARG cc_start: 0.4928 (tpt-90) cc_final: 0.4396 (mmm160) REVERT: B 345 MET cc_start: 0.6850 (ppp) cc_final: 0.6567 (ppp) REVERT: B 560 MET cc_start: 0.8724 (ttp) cc_final: 0.8502 (ttp) REVERT: C 210 GLU cc_start: 0.6892 (pm20) cc_final: 0.6443 (pm20) REVERT: C 402 ASP cc_start: 0.7343 (p0) cc_final: 0.6953 (m-30) REVERT: C 488 ASP cc_start: 0.7619 (m-30) cc_final: 0.7247 (m-30) REVERT: C 527 TYR cc_start: 0.7769 (p90) cc_final: 0.7232 (p90) REVERT: C 543 THR cc_start: 0.8455 (p) cc_final: 0.7888 (m) REVERT: C 713 ILE cc_start: 0.8148 (pt) cc_final: 0.7749 (mt) REVERT: C 762 MET cc_start: 0.8877 (mmm) cc_final: 0.8562 (mmm) REVERT: D 223 MET cc_start: 0.7898 (mmm) cc_final: 0.7385 (tpp) REVERT: D 337 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8612 (tp-100) REVERT: D 341 LEU cc_start: 0.9234 (mt) cc_final: 0.8946 (mt) REVERT: D 400 LEU cc_start: 0.8583 (mp) cc_final: 0.8241 (tt) REVERT: D 590 ASP cc_start: 0.8119 (m-30) cc_final: 0.7862 (m-30) REVERT: E 331 GLU cc_start: 0.8524 (mp0) cc_final: 0.7715 (mp0) REVERT: E 462 PHE cc_start: 0.8043 (m-80) cc_final: 0.7530 (m-80) REVERT: E 594 LYS cc_start: 0.7607 (tttt) cc_final: 0.6996 (tttm) REVERT: G 122 LEU cc_start: 0.8819 (mp) cc_final: 0.8256 (tt) REVERT: G 212 PRO cc_start: 0.2413 (Cg_endo) cc_final: 0.2178 (Cg_exo) REVERT: G 284 ILE cc_start: 0.8662 (mm) cc_final: 0.8227 (tp) REVERT: H 16 GLU cc_start: 0.6532 (pm20) cc_final: 0.5867 (pm20) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.1248 time to fit residues: 69.6274 Evaluate side-chains 287 residues out of total 2077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 75 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 185 optimal weight: 0.2980 chunk 27 optimal weight: 0.0060 chunk 154 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 127 optimal weight: 0.5980 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 ASN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 HIS H 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.143570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.115663 restraints weight = 45753.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.114796 restraints weight = 31869.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115712 restraints weight = 26537.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.116158 restraints weight = 22778.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.116389 restraints weight = 19908.098| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.6425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19912 Z= 0.167 Angle : 0.815 11.496 26931 Z= 0.388 Chirality : 0.050 0.251 3009 Planarity : 0.005 0.071 3512 Dihedral : 12.239 173.744 2774 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.78 % Favored : 89.14 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.55 (0.16), residues: 2468 helix: -0.89 (0.16), residues: 966 sheet: -1.44 (0.31), residues: 275 loop : -2.46 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 369 TYR 0.020 0.002 TYR C 505 PHE 0.028 0.002 PHE D 585 TRP 0.014 0.002 TRP G 544 HIS 0.011 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00391 (19893) covalent geometry : angle 0.81497 (26931) hydrogen bonds : bond 0.03108 ( 436) hydrogen bonds : angle 5.05199 ( 1251) Misc. bond : bond 0.00378 ( 19) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2906.60 seconds wall clock time: 51 minutes 48.72 seconds (3108.72 seconds total)