Starting phenix.real_space_refine on Sat Sep 28 14:58:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oaa_0666/09_2024/6oaa_0666_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oaa_0666/09_2024/6oaa_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oaa_0666/09_2024/6oaa_0666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oaa_0666/09_2024/6oaa_0666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oaa_0666/09_2024/6oaa_0666_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oaa_0666/09_2024/6oaa_0666_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 10.73, per 1000 atoms: 0.55 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: 4.40 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.72 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: 4.76 Time building geometry restraints manager: 5.11 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 38.380 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.900 ------------------------------------------------------------------------------- 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 : 0.006 0.110 19893 Z= 0.362 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP G 211 HIS 0.004 0.001 HIS C 236 PHE 0.015 0.001 PHE E 462 TYR 0.012 0.001 TYR E 527 ARG 0.012 0.000 ARG E 372 *********************** 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 fitting. rotamer outliers: 7 poor density : 586 time to evaluate : 2.287 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: 0.8009 (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: 0.8438 (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: 0.3744 time to fit residues: 314.7501 Evaluate side-chains 365 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 361 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 0.0170 chunk 186 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 192 optimal weight: 0.0370 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 B 634 ASN C 280 ASN C 337 GLN C 612 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 491 ASN H 2 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19893 Z= 0.203 Angle : 0.786 12.727 26931 Z= 0.376 Chirality : 0.047 0.280 3009 Planarity : 0.006 0.089 3512 Dihedral : 12.550 160.645 2774 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Rotamer: Outliers : 0.14 % Allowed : 4.81 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.13), residues: 2468 helix: -3.47 (0.11), residues: 915 sheet: -1.53 (0.31), residues: 251 loop : -2.80 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 486 HIS 0.010 0.001 HIS G 166 PHE 0.017 0.001 PHE G 231 TYR 0.024 0.001 TYR G 172 ARG 0.006 0.001 ARG D 645 *********************** 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 442 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 439 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 MET cc_start: 0.8054 (mmt) cc_final: 0.7346 (mmt) REVERT: B 314 ASP cc_start: 0.7969 (t0) cc_final: 0.7626 (t0) REVERT: B 315 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6705 (mt-10) REVERT: B 342 MET cc_start: 0.8098 (ttm) cc_final: 0.7480 (tpt) REVERT: B 345 MET cc_start: 0.7179 (ppp) cc_final: 0.6721 (ppp) REVERT: B 370 PHE cc_start: 0.6371 (m-80) cc_final: 0.5877 (m-80) REVERT: B 437 MET cc_start: 0.8357 (tpp) cc_final: 0.7920 (tpp) REVERT: B 527 TYR cc_start: 0.7548 (p90) cc_final: 0.7126 (p90) REVERT: B 564 GLU cc_start: 0.8117 (tt0) cc_final: 0.7881 (tt0) REVERT: B 652 LEU cc_start: 0.8832 (mt) cc_final: 0.8440 (mt) REVERT: C 264 MET cc_start: 0.8292 (tpt) cc_final: 0.8036 (tpp) REVERT: C 301 GLU cc_start: 0.8162 (pt0) cc_final: 0.7941 (tt0) REVERT: C 412 GLU cc_start: 0.7785 (pt0) cc_final: 0.7551 (pt0) REVERT: C 500 LYS cc_start: 0.9293 (tppp) cc_final: 0.8959 (ttmt) REVERT: C 661 ASN cc_start: 0.8411 (t0) cc_final: 0.8164 (t0) REVERT: D 341 LEU cc_start: 0.9168 (mt) cc_final: 0.8962 (mt) REVERT: D 400 LEU cc_start: 0.8508 (mp) cc_final: 0.7877 (tt) REVERT: D 483 ASN cc_start: 0.6574 (p0) cc_final: 0.6319 (p0) REVERT: D 617 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8011 (mm-30) REVERT: D 687 LYS cc_start: 0.7655 (mmtm) cc_final: 0.7292 (mmtp) REVERT: E 229 MET cc_start: 0.7908 (tmm) cc_final: 0.7297 (tpp) REVERT: E 331 GLU cc_start: 0.8508 (mp0) cc_final: 0.7993 (mp0) REVERT: E 378 ASP cc_start: 0.8098 (m-30) cc_final: 0.7617 (m-30) REVERT: E 462 PHE cc_start: 0.6665 (m-80) cc_final: 0.6424 (m-80) REVERT: E 548 ASN cc_start: 0.7521 (p0) cc_final: 0.7271 (m-40) REVERT: E 582 THR cc_start: 0.7619 (t) cc_final: 0.6864 (t) REVERT: E 594 LYS cc_start: 0.7647 (tttt) cc_final: 0.7226 (tttm) REVERT: E 617 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6744 (mm-30) REVERT: E 618 MET cc_start: 0.7030 (tpt) cc_final: 0.6740 (tpt) REVERT: G 233 MET cc_start: 0.6292 (mmm) cc_final: 0.5607 (mmm) REVERT: G 263 MET cc_start: 0.8840 (mtm) cc_final: 0.8615 (mtp) REVERT: G 312 ARG cc_start: 0.8036 (tmm-80) cc_final: 0.7812 (tpp-160) REVERT: G 399 TYR cc_start: 0.7234 (m-80) cc_final: 0.6846 (m-80) REVERT: G 569 TRP cc_start: 0.8334 (t-100) cc_final: 0.8064 (t-100) REVERT: H 42 ARG cc_start: 0.5686 (mmm-85) cc_final: 0.5412 (mmm-85) outliers start: 3 outliers final: 0 residues processed: 441 average time/residue: 0.3328 time to fit residues: 216.3873 Evaluate side-chains 308 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 0.8980 chunk 69 optimal weight: 0.0170 chunk 185 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 61 optimal weight: 0.3980 chunk 223 optimal weight: 20.0000 chunk 241 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 221 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 HIS C 613 GLN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN D 394 HIS D 432 GLN ** 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** E 612 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN G 313 GLN ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19893 Z= 0.184 Angle : 0.733 10.177 26931 Z= 0.347 Chirality : 0.046 0.223 3009 Planarity : 0.005 0.111 3512 Dihedral : 12.295 157.505 2774 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Rotamer: Outliers : 0.05 % Allowed : 4.62 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.15), residues: 2468 helix: -2.32 (0.14), residues: 901 sheet: -1.40 (0.31), residues: 247 loop : -2.51 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 544 HIS 0.004 0.001 HIS D 757 PHE 0.020 0.001 PHE D 585 TYR 0.023 0.001 TYR G 172 ARG 0.015 0.001 ARG D 375 *********************** 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 406 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 405 time to evaluate : 2.149 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: 0.8450 (tp) cc_final: 0.8093 (tp) REVERT: B 264 MET cc_start: 0.7967 (mmt) cc_final: 0.7372 (mmt) REVERT: B 331 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7149 (mt-10) REVERT: B 370 PHE cc_start: 0.6261 (m-80) cc_final: 0.5724 (m-80) REVERT: B 437 MET cc_start: 0.8481 (tpp) cc_final: 0.8066 (tpp) REVERT: B 459 MET cc_start: 0.8444 (tpp) cc_final: 0.8096 (tpp) REVERT: B 527 TYR cc_start: 0.7358 (p90) cc_final: 0.7026 (p90) REVERT: B 564 GLU cc_start: 0.7941 (tt0) cc_final: 0.7725 (tt0) REVERT: B 611 VAL cc_start: 0.9105 (t) cc_final: 0.8850 (p) REVERT: B 652 LEU cc_start: 0.8932 (mt) cc_final: 0.8670 (mp) REVERT: C 293 GLU cc_start: 0.7428 (mp0) cc_final: 0.7208 (mp0) REVERT: C 500 LYS cc_start: 0.9142 (tppp) cc_final: 0.8807 (ttmt) REVERT: C 618 MET cc_start: 0.8227 (mmt) cc_final: 0.7985 (mmt) REVERT: C 661 ASN cc_start: 0.8468 (t0) cc_final: 0.8254 (t0) REVERT: D 245 ILE cc_start: 0.6842 (tp) cc_final: 0.6620 (tp) REVERT: D 285 MET cc_start: 0.8201 (mmm) cc_final: 0.7489 (mmm) REVERT: D 379 ILE cc_start: 0.7808 (mm) cc_final: 0.7254 (mt) REVERT: D 400 LEU cc_start: 0.8496 (mp) cc_final: 0.7832 (tt) REVERT: D 433 ILE cc_start: 0.9025 (pt) cc_final: 0.8788 (mt) REVERT: D 483 ASN cc_start: 0.6181 (p0) cc_final: 0.5825 (p0) REVERT: D 539 LYS cc_start: 0.8619 (mmtp) cc_final: 0.8336 (mmmt) REVERT: D 645 ARG cc_start: 0.8534 (ppt170) cc_final: 0.7835 (ttm170) REVERT: E 229 MET cc_start: 0.7892 (tmm) cc_final: 0.7316 (tpp) REVERT: E 331 GLU cc_start: 0.8449 (mp0) cc_final: 0.7992 (mp0) REVERT: E 462 PHE cc_start: 0.6757 (m-80) cc_final: 0.6413 (m-80) REVERT: E 548 ASN cc_start: 0.7553 (p0) cc_final: 0.7286 (m-40) REVERT: E 582 THR cc_start: 0.7559 (t) cc_final: 0.6993 (t) REVERT: E 594 LYS cc_start: 0.7542 (tttt) cc_final: 0.7109 (tttm) REVERT: G 233 MET cc_start: 0.6322 (mmm) cc_final: 0.5759 (mmm) REVERT: G 246 ASN cc_start: 0.8845 (t0) cc_final: 0.8627 (m-40) REVERT: G 263 MET cc_start: 0.8771 (mtm) cc_final: 0.8100 (mtp) REVERT: G 462 LEU cc_start: 0.8221 (mt) cc_final: 0.7902 (tp) REVERT: G 569 TRP cc_start: 0.8380 (t-100) cc_final: 0.8099 (t-100) REVERT: H 7 THR cc_start: 0.8016 (p) cc_final: 0.7778 (t) outliers start: 1 outliers final: 0 residues processed: 406 average time/residue: 0.3065 time to fit residues: 190.5357 Evaluate side-chains 307 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 24 optimal weight: 0.0570 chunk 106 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 224 optimal weight: 0.6980 chunk 237 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 212 optimal weight: 30.0000 chunk 64 optimal weight: 4.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 GLN ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 HIS ** D 432 GLN ** 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 205 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 502 GLN H 2 GLN H 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19893 Z= 0.242 Angle : 0.767 9.800 26931 Z= 0.365 Chirality : 0.047 0.220 3009 Planarity : 0.005 0.099 3512 Dihedral : 12.324 174.829 2774 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.71 % Favored : 91.21 % Rotamer: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.15), residues: 2468 helix: -1.77 (0.15), residues: 916 sheet: -1.11 (0.32), residues: 245 loop : -2.30 (0.16), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 544 HIS 0.008 0.001 HIS C 236 PHE 0.026 0.002 PHE D 585 TYR 0.026 0.002 TYR D 213 ARG 0.008 0.001 ARG E 645 *********************** 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 401 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 399 time to evaluate : 2.133 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: B 226 ILE cc_start: 0.8415 (tp) cc_final: 0.8035 (tp) REVERT: B 331 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7346 (mt-10) REVERT: B 345 MET cc_start: 0.7090 (ppp) cc_final: 0.6791 (ppp) REVERT: B 370 PHE cc_start: 0.6101 (m-80) cc_final: 0.5499 (m-80) REVERT: B 395 THR cc_start: 0.8807 (p) cc_final: 0.8495 (t) REVERT: B 437 MET cc_start: 0.8458 (tpp) cc_final: 0.8047 (tpp) REVERT: B 527 TYR cc_start: 0.7613 (p90) cc_final: 0.7366 (p90) REVERT: C 213 TYR cc_start: 0.7913 (m-80) cc_final: 0.7516 (m-80) REVERT: C 480 GLU cc_start: 0.6919 (pt0) cc_final: 0.6689 (pt0) REVERT: C 500 LYS cc_start: 0.9126 (tppp) cc_final: 0.8926 (ttpt) REVERT: C 618 MET cc_start: 0.8169 (mmt) cc_final: 0.7927 (mmt) REVERT: C 762 MET cc_start: 0.8933 (mmm) cc_final: 0.8655 (mmm) REVERT: D 283 GLU cc_start: 0.8368 (pp20) cc_final: 0.7973 (pt0) REVERT: D 379 ILE cc_start: 0.7985 (mm) cc_final: 0.7406 (mt) REVERT: D 400 LEU cc_start: 0.8560 (mp) cc_final: 0.7833 (tt) REVERT: D 483 ASN cc_start: 0.5801 (p0) cc_final: 0.5302 (p0) REVERT: D 485 THR cc_start: 0.7128 (m) cc_final: 0.6910 (p) REVERT: D 539 LYS cc_start: 0.8731 (mmtp) cc_final: 0.8454 (mmmt) REVERT: D 687 LYS cc_start: 0.7743 (mptt) cc_final: 0.7465 (mmtp) REVERT: D 690 GLN cc_start: 0.6935 (mm110) cc_final: 0.6536 (mp10) REVERT: E 229 MET cc_start: 0.8007 (tmm) cc_final: 0.7438 (tpp) REVERT: E 313 ILE cc_start: 0.9187 (tp) cc_final: 0.8950 (mt) REVERT: E 331 GLU cc_start: 0.8562 (mp0) cc_final: 0.8193 (mp0) REVERT: E 548 ASN cc_start: 0.7648 (p0) cc_final: 0.7272 (m-40) REVERT: E 582 THR cc_start: 0.7786 (t) cc_final: 0.7200 (t) REVERT: E 617 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7337 (mm-30) REVERT: G 263 MET cc_start: 0.8934 (mtm) cc_final: 0.8573 (mtm) REVERT: G 298 MET cc_start: 0.5303 (pmm) cc_final: 0.5064 (pmm) REVERT: G 312 ARG cc_start: 0.7990 (tmm-80) cc_final: 0.7740 (tpp-160) REVERT: G 569 TRP cc_start: 0.8478 (t-100) cc_final: 0.8221 (t-100) REVERT: H 45 PHE cc_start: 0.4921 (m-10) cc_final: 0.4628 (m-10) outliers start: 2 outliers final: 1 residues processed: 400 average time/residue: 0.3299 time to fit residues: 198.2429 Evaluate side-chains 313 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 312 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 177 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 GLN ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN D 394 HIS ** D 432 GLN ** 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** G 208 HIS G 246 ASN ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19893 Z= 0.228 Angle : 0.745 12.242 26931 Z= 0.353 Chirality : 0.047 0.281 3009 Planarity : 0.005 0.091 3512 Dihedral : 12.230 171.715 2774 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.63 % Favored : 91.29 % Rotamer: Outliers : 0.10 % Allowed : 3.18 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.16), residues: 2468 helix: -1.38 (0.16), residues: 930 sheet: -1.02 (0.32), residues: 247 loop : -2.27 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 544 HIS 0.007 0.001 HIS C 236 PHE 0.025 0.002 PHE D 585 TYR 0.024 0.001 TYR D 699 ARG 0.009 0.001 ARG E 645 *********************** 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 388 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 386 time to evaluate : 2.363 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: B 226 ILE cc_start: 0.8454 (tp) cc_final: 0.8089 (tp) REVERT: B 331 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7145 (mt-10) REVERT: B 363 ILE cc_start: 0.7339 (mm) cc_final: 0.7075 (mm) REVERT: B 388 LEU cc_start: 0.8303 (tt) cc_final: 0.7888 (tt) REVERT: B 420 ASP cc_start: 0.8825 (m-30) cc_final: 0.8534 (p0) REVERT: B 527 TYR cc_start: 0.7828 (p90) cc_final: 0.7627 (p90) REVERT: B 611 VAL cc_start: 0.9212 (t) cc_final: 0.8981 (p) REVERT: C 213 TYR cc_start: 0.7908 (m-80) cc_final: 0.7698 (m-80) REVERT: C 500 LYS cc_start: 0.9156 (tppp) cc_final: 0.8895 (ttpt) REVERT: C 564 GLU cc_start: 0.8190 (pt0) cc_final: 0.7941 (pt0) REVERT: C 618 MET cc_start: 0.8138 (mmt) cc_final: 0.7873 (mmt) REVERT: D 283 GLU cc_start: 0.8398 (pp20) cc_final: 0.8072 (pt0) REVERT: D 376 GLU cc_start: 0.7684 (tt0) cc_final: 0.7410 (mt-10) REVERT: D 400 LEU cc_start: 0.8563 (mp) cc_final: 0.7990 (tt) REVERT: D 483 ASN cc_start: 0.5941 (p0) cc_final: 0.5549 (p0) REVERT: D 485 THR cc_start: 0.6937 (m) cc_final: 0.6729 (p) REVERT: D 687 LYS cc_start: 0.7786 (mptt) cc_final: 0.7439 (mmtp) REVERT: D 690 GLN cc_start: 0.6940 (mm110) cc_final: 0.6562 (mp10) REVERT: D 771 ASP cc_start: 0.7232 (t0) cc_final: 0.7026 (t0) REVERT: E 229 MET cc_start: 0.7942 (tmm) cc_final: 0.7367 (tpp) REVERT: E 313 ILE cc_start: 0.9173 (tp) cc_final: 0.8962 (mt) REVERT: E 331 GLU cc_start: 0.8529 (mp0) cc_final: 0.8173 (mp0) REVERT: E 548 ASN cc_start: 0.7692 (p0) cc_final: 0.7457 (m-40) REVERT: E 582 THR cc_start: 0.7735 (t) cc_final: 0.7106 (t) REVERT: E 594 LYS cc_start: 0.7450 (tttt) cc_final: 0.6994 (tttm) REVERT: E 617 GLU cc_start: 0.8111 (mm-30) cc_final: 0.6990 (mm-30) REVERT: G 257 MET cc_start: 0.5011 (tpp) cc_final: 0.4468 (tpp) REVERT: G 263 MET cc_start: 0.8905 (mtm) cc_final: 0.8579 (mtm) REVERT: G 298 MET cc_start: 0.5336 (pmm) cc_final: 0.5067 (pmm) REVERT: G 569 TRP cc_start: 0.8466 (t-100) cc_final: 0.8265 (t-100) REVERT: H 8 LEU cc_start: 0.6691 (mm) cc_final: 0.6472 (mm) outliers start: 2 outliers final: 1 residues processed: 388 average time/residue: 0.3195 time to fit residues: 190.5351 Evaluate side-chains 305 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 197 optimal weight: 0.4980 chunk 110 optimal weight: 0.0870 chunk 19 optimal weight: 0.0570 chunk 78 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 HIS D 468 ASN E 327 ASN ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN G 426 ASN ** G 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN H 2 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19893 Z= 0.173 Angle : 0.721 8.722 26931 Z= 0.339 Chirality : 0.046 0.212 3009 Planarity : 0.005 0.088 3512 Dihedral : 12.083 164.935 2774 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.71 % Favored : 91.21 % Rotamer: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 1.56 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.16), residues: 2468 helix: -1.12 (0.16), residues: 926 sheet: -1.08 (0.31), residues: 258 loop : -2.24 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 544 HIS 0.010 0.001 HIS G 365 PHE 0.041 0.001 PHE E 312 TYR 0.025 0.001 TYR D 416 ARG 0.008 0.000 ARG E 645 *********************** 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 389 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 387 time to evaluate : 2.049 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: 0.8434 (tp) cc_final: 0.8103 (tp) REVERT: B 345 MET cc_start: 0.6986 (ppp) cc_final: 0.6169 (ppp) REVERT: B 369 ARG cc_start: 0.5171 (tpt170) cc_final: 0.4931 (tpt170) REVERT: B 420 ASP cc_start: 0.8603 (m-30) cc_final: 0.7975 (p0) REVERT: B 437 MET cc_start: 0.8226 (tpp) cc_final: 0.8012 (tpp) REVERT: B 458 THR cc_start: 0.6598 (p) cc_final: 0.5147 (p) REVERT: C 213 TYR cc_start: 0.7820 (m-80) cc_final: 0.7543 (m-80) REVERT: C 301 GLU cc_start: 0.8514 (tt0) cc_final: 0.8171 (tm-30) REVERT: C 339 LEU cc_start: 0.8982 (mp) cc_final: 0.8732 (mp) REVERT: C 564 GLU cc_start: 0.8105 (pt0) cc_final: 0.7817 (pt0) REVERT: C 713 ILE cc_start: 0.7809 (pt) cc_final: 0.7363 (mm) REVERT: C 762 MET cc_start: 0.8997 (mmm) cc_final: 0.8590 (mmm) REVERT: D 283 GLU cc_start: 0.8407 (pp20) cc_final: 0.8022 (pt0) REVERT: D 337 GLN cc_start: 0.9046 (tp40) cc_final: 0.8771 (tp-100) REVERT: D 341 LEU cc_start: 0.9312 (mt) cc_final: 0.8846 (mt) REVERT: D 376 GLU cc_start: 0.7717 (tt0) cc_final: 0.7498 (mt-10) REVERT: D 400 LEU cc_start: 0.8536 (mp) cc_final: 0.7980 (tt) REVERT: D 661 ASN cc_start: 0.8678 (m-40) cc_final: 0.8390 (m-40) REVERT: D 687 LYS cc_start: 0.7840 (mptt) cc_final: 0.7528 (mmtp) REVERT: D 690 GLN cc_start: 0.6897 (mm110) cc_final: 0.6562 (mp10) REVERT: E 229 MET cc_start: 0.7945 (tmm) cc_final: 0.7305 (tpp) REVERT: E 331 GLU cc_start: 0.8625 (mp0) cc_final: 0.8318 (mp0) REVERT: E 582 THR cc_start: 0.7621 (t) cc_final: 0.6989 (t) REVERT: E 594 LYS cc_start: 0.7370 (tttt) cc_final: 0.6921 (tttm) REVERT: G 257 MET cc_start: 0.5018 (tpp) cc_final: 0.4690 (tpp) REVERT: G 298 MET cc_start: 0.5321 (pmm) cc_final: 0.5042 (pmm) REVERT: G 495 MET cc_start: 0.8639 (pmm) cc_final: 0.8334 (pmm) REVERT: G 569 TRP cc_start: 0.8447 (t-100) cc_final: 0.8247 (t-100) outliers start: 2 outliers final: 0 residues processed: 389 average time/residue: 0.3018 time to fit residues: 179.0340 Evaluate side-chains 297 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 173 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 200 optimal weight: 0.0570 chunk 132 optimal weight: 8.9990 chunk 237 optimal weight: 0.0370 chunk 148 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN D 394 HIS E 327 ASN E 613 GLN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 ASN G 526 ASN H 2 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19893 Z= 0.213 Angle : 0.748 8.416 26931 Z= 0.353 Chirality : 0.047 0.210 3009 Planarity : 0.005 0.085 3512 Dihedral : 11.989 165.338 2774 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.04 % Favored : 90.88 % Rotamer: Outliers : 0.05 % Allowed : 1.73 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.78 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.16), residues: 2468 helix: -0.95 (0.16), residues: 934 sheet: -1.13 (0.31), residues: 267 loop : -2.22 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 544 HIS 0.007 0.001 HIS C 236 PHE 0.026 0.002 PHE D 585 TYR 0.022 0.001 TYR C 505 ARG 0.012 0.001 ARG E 645 *********************** 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 373 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 ILE cc_start: 0.8476 (tp) cc_final: 0.8082 (tp) REVERT: B 331 GLU cc_start: 0.7797 (mt-10) cc_final: 0.6997 (mt-10) REVERT: B 345 MET cc_start: 0.7071 (ppp) cc_final: 0.6378 (ppp) REVERT: B 363 ILE cc_start: 0.7498 (mm) cc_final: 0.7276 (mm) REVERT: B 369 ARG cc_start: 0.5095 (tpt170) cc_final: 0.4884 (tpt170) REVERT: B 420 ASP cc_start: 0.8632 (m-30) cc_final: 0.8398 (p0) REVERT: B 611 VAL cc_start: 0.9208 (t) cc_final: 0.9000 (p) REVERT: C 301 GLU cc_start: 0.8421 (tt0) cc_final: 0.8215 (tm-30) REVERT: C 713 ILE cc_start: 0.7883 (pt) cc_final: 0.7453 (mm) REVERT: C 762 MET cc_start: 0.8969 (mmm) cc_final: 0.8467 (mmm) REVERT: D 229 MET cc_start: 0.8384 (ttp) cc_final: 0.8046 (ppp) REVERT: D 245 ILE cc_start: 0.7348 (tp) cc_final: 0.7128 (tp) REVERT: D 283 GLU cc_start: 0.8431 (pp20) cc_final: 0.8118 (pt0) REVERT: D 337 GLN cc_start: 0.9058 (tp40) cc_final: 0.8739 (tp-100) REVERT: D 341 LEU cc_start: 0.9331 (mt) cc_final: 0.8801 (mt) REVERT: D 364 ASP cc_start: 0.8587 (t0) cc_final: 0.8345 (t70) REVERT: D 376 GLU cc_start: 0.7821 (tt0) cc_final: 0.7276 (mt-10) REVERT: D 400 LEU cc_start: 0.8650 (mp) cc_final: 0.7999 (tt) REVERT: D 661 ASN cc_start: 0.8680 (m-40) cc_final: 0.8392 (m-40) REVERT: D 687 LYS cc_start: 0.7902 (mptt) cc_final: 0.7578 (mmtp) REVERT: D 690 GLN cc_start: 0.7024 (mm110) cc_final: 0.6633 (mp10) REVERT: E 229 MET cc_start: 0.7978 (tmm) cc_final: 0.7361 (tpp) REVERT: E 331 GLU cc_start: 0.8688 (mp0) cc_final: 0.8348 (mp0) REVERT: E 594 LYS cc_start: 0.7493 (tttt) cc_final: 0.6918 (tttm) REVERT: G 257 MET cc_start: 0.4823 (tpp) cc_final: 0.4413 (tpp) REVERT: G 298 MET cc_start: 0.5332 (pmm) cc_final: 0.4974 (pmm) REVERT: G 462 LEU cc_start: 0.8536 (mm) cc_final: 0.8140 (mt) REVERT: H 42 ARG cc_start: 0.6825 (mmm160) cc_final: 0.6076 (tpt170) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.3127 time to fit residues: 176.7990 Evaluate side-chains 293 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 186 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 HIS E 327 ASN E 613 GLN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 499 GLN H 2 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19893 Z= 0.187 Angle : 0.732 9.287 26931 Z= 0.347 Chirality : 0.046 0.213 3009 Planarity : 0.005 0.085 3512 Dihedral : 11.853 162.795 2774 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.83 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.78 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.16), residues: 2468 helix: -0.82 (0.17), residues: 932 sheet: -0.97 (0.31), residues: 267 loop : -2.24 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 544 HIS 0.009 0.001 HIS C 236 PHE 0.025 0.001 PHE D 585 TYR 0.011 0.001 TYR B 416 ARG 0.010 0.001 ARG E 645 *********************** 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 372 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 2.187 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: 0.8513 (tp) cc_final: 0.8092 (tp) REVERT: B 345 MET cc_start: 0.7142 (ppp) cc_final: 0.6480 (ppp) REVERT: B 363 ILE cc_start: 0.7504 (mm) cc_final: 0.7291 (mm) REVERT: B 369 ARG cc_start: 0.5084 (tpt170) cc_final: 0.4843 (tpt170) REVERT: B 420 ASP cc_start: 0.8488 (m-30) cc_final: 0.8265 (p0) REVERT: B 459 MET cc_start: 0.7023 (mmp) cc_final: 0.6661 (tpp) REVERT: C 301 GLU cc_start: 0.8490 (tt0) cc_final: 0.7976 (tm-30) REVERT: C 713 ILE cc_start: 0.7887 (pt) cc_final: 0.7466 (mm) REVERT: C 762 MET cc_start: 0.8927 (mmm) cc_final: 0.8435 (mmm) REVERT: D 337 GLN cc_start: 0.9015 (tp40) cc_final: 0.8742 (tp-100) REVERT: D 341 LEU cc_start: 0.9319 (mt) cc_final: 0.8763 (mt) REVERT: D 376 GLU cc_start: 0.7935 (tt0) cc_final: 0.7319 (mt-10) REVERT: D 400 LEU cc_start: 0.8563 (mp) cc_final: 0.8021 (tt) REVERT: D 661 ASN cc_start: 0.8516 (m-40) cc_final: 0.8262 (m-40) REVERT: D 687 LYS cc_start: 0.7868 (mptt) cc_final: 0.7524 (mmtp) REVERT: D 690 GLN cc_start: 0.6954 (mm110) cc_final: 0.6621 (mp10) REVERT: D 771 ASP cc_start: 0.6862 (t0) cc_final: 0.6610 (t0) REVERT: E 229 MET cc_start: 0.7909 (tmm) cc_final: 0.7305 (tpp) REVERT: E 331 GLU cc_start: 0.8676 (mp0) cc_final: 0.8258 (mp0) REVERT: E 594 LYS cc_start: 0.7496 (tttt) cc_final: 0.6896 (tttm) REVERT: G 257 MET cc_start: 0.4753 (tpp) cc_final: 0.4325 (tpp) REVERT: G 298 MET cc_start: 0.5310 (pmm) cc_final: 0.4949 (pmm) REVERT: G 462 LEU cc_start: 0.8443 (mm) cc_final: 0.8042 (mt) REVERT: G 495 MET cc_start: 0.8740 (pmm) cc_final: 0.7971 (pmm) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.3091 time to fit residues: 174.2269 Evaluate side-chains 283 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 220 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 173 optimal weight: 0.0050 chunk 67 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN D 394 HIS E 327 ASN H 2 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19893 Z= 0.198 Angle : 0.750 10.279 26931 Z= 0.354 Chirality : 0.047 0.221 3009 Planarity : 0.005 0.084 3512 Dihedral : 11.805 163.535 2774 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.24 % Favored : 90.68 % Rotamer: Outliers : 0.05 % Allowed : 0.72 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.16), residues: 2468 helix: -0.80 (0.17), residues: 930 sheet: -0.93 (0.32), residues: 262 loop : -2.21 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 544 HIS 0.008 0.001 HIS C 236 PHE 0.026 0.001 PHE D 585 TYR 0.020 0.001 TYR B 505 ARG 0.011 0.001 ARG E 645 *********************** 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 367 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 366 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 ILE cc_start: 0.8503 (tp) cc_final: 0.8011 (tp) REVERT: B 331 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7011 (mt-10) REVERT: B 345 MET cc_start: 0.7152 (ppp) cc_final: 0.6534 (ppp) REVERT: B 395 THR cc_start: 0.8993 (p) cc_final: 0.8562 (t) REVERT: B 459 MET cc_start: 0.6941 (mmp) cc_final: 0.6717 (tpp) REVERT: C 301 GLU cc_start: 0.8448 (tt0) cc_final: 0.7967 (tm-30) REVERT: C 713 ILE cc_start: 0.7945 (pt) cc_final: 0.7543 (mm) REVERT: C 762 MET cc_start: 0.8852 (mmm) cc_final: 0.8331 (mmm) REVERT: D 337 GLN cc_start: 0.9051 (tp40) cc_final: 0.8802 (tp-100) REVERT: D 341 LEU cc_start: 0.9338 (mt) cc_final: 0.8826 (mt) REVERT: D 400 LEU cc_start: 0.8654 (mp) cc_final: 0.8071 (tt) REVERT: D 661 ASN cc_start: 0.8668 (m-40) cc_final: 0.8414 (m-40) REVERT: D 687 LYS cc_start: 0.7866 (mptt) cc_final: 0.7529 (mmtp) REVERT: D 690 GLN cc_start: 0.7033 (mm110) cc_final: 0.6698 (mp10) REVERT: D 771 ASP cc_start: 0.6845 (t0) cc_final: 0.6579 (t0) REVERT: E 331 GLU cc_start: 0.8710 (mp0) cc_final: 0.8298 (mp0) REVERT: E 342 MET cc_start: 0.8243 (mtm) cc_final: 0.8007 (mtm) REVERT: E 594 LYS cc_start: 0.7522 (tttt) cc_final: 0.6921 (tttm) REVERT: E 618 MET cc_start: 0.6739 (ppp) cc_final: 0.6307 (ppp) REVERT: G 298 MET cc_start: 0.5319 (pmm) cc_final: 0.4949 (pmm) REVERT: G 462 LEU cc_start: 0.8434 (mm) cc_final: 0.8171 (mt) outliers start: 1 outliers final: 0 residues processed: 367 average time/residue: 0.3092 time to fit residues: 175.0581 Evaluate side-chains 286 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 10.0000 chunk 142 optimal weight: 0.4980 chunk 110 optimal weight: 0.8980 chunk 162 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 225 optimal weight: 0.6980 chunk 195 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 155 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 HIS ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 ASN C 612 ASN D 394 HIS H 2 GLN H 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19893 Z= 0.187 Angle : 0.746 9.518 26931 Z= 0.351 Chirality : 0.047 0.217 3009 Planarity : 0.005 0.083 3512 Dihedral : 11.724 161.461 2774 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.87 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.16), residues: 2468 helix: -0.72 (0.17), residues: 939 sheet: -1.11 (0.31), residues: 268 loop : -2.17 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 544 HIS 0.008 0.001 HIS C 236 PHE 0.024 0.001 PHE D 585 TYR 0.018 0.001 TYR C 505 ARG 0.009 0.001 ARG E 645 ********************** 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 367 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 2.134 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: 0.8442 (tp) cc_final: 0.8222 (tp) REVERT: B 345 MET cc_start: 0.7131 (ppp) cc_final: 0.6553 (ppp) REVERT: B 363 ILE cc_start: 0.7594 (mm) cc_final: 0.7388 (mm) REVERT: B 395 THR cc_start: 0.9012 (p) cc_final: 0.8636 (t) REVERT: B 459 MET cc_start: 0.7128 (mmp) cc_final: 0.6914 (mmm) REVERT: C 301 GLU cc_start: 0.8454 (tt0) cc_final: 0.7976 (tm-30) REVERT: C 713 ILE cc_start: 0.7941 (pt) cc_final: 0.7534 (mm) REVERT: C 762 MET cc_start: 0.8820 (mmm) cc_final: 0.8303 (mmm) REVERT: D 245 ILE cc_start: 0.7358 (tp) cc_final: 0.7025 (tp) REVERT: D 341 LEU cc_start: 0.9406 (mt) cc_final: 0.8877 (mt) REVERT: D 400 LEU cc_start: 0.8625 (mp) cc_final: 0.8093 (tt) REVERT: D 493 ASP cc_start: 0.7606 (p0) cc_final: 0.7265 (t0) REVERT: D 661 ASN cc_start: 0.8641 (m-40) cc_final: 0.8359 (m-40) REVERT: D 687 LYS cc_start: 0.7866 (mptt) cc_final: 0.7504 (mmtp) REVERT: D 690 GLN cc_start: 0.6956 (mm110) cc_final: 0.6688 (mp10) REVERT: D 771 ASP cc_start: 0.6869 (t0) cc_final: 0.6601 (t0) REVERT: E 331 GLU cc_start: 0.8736 (mp0) cc_final: 0.8290 (mp0) REVERT: E 594 LYS cc_start: 0.7493 (tttt) cc_final: 0.6882 (tttm) REVERT: E 618 MET cc_start: 0.6753 (ppp) cc_final: 0.6297 (ppp) REVERT: G 257 MET cc_start: 0.4554 (tpp) cc_final: 0.4275 (tpp) REVERT: G 298 MET cc_start: 0.5295 (pmm) cc_final: 0.4950 (pmm) REVERT: G 444 GLU cc_start: 0.8618 (mp0) cc_final: 0.8392 (pm20) REVERT: G 462 LEU cc_start: 0.8519 (mm) cc_final: 0.8209 (mt) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.3192 time to fit residues: 183.1101 Evaluate side-chains 289 residues out of total 2077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 179 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 0.0670 chunk 195 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 24 optimal weight: 0.0030 chunk 36 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 overall best weight: 1.2932 ------------------------------------------------------------------------------- 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 ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN G 315 GLN G 400 GLN H 2 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.149892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.121974 restraints weight = 46086.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.122395 restraints weight = 33145.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.123058 restraints weight = 23085.669| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19893 Z= 0.210 Angle : 0.754 9.832 26931 Z= 0.355 Chirality : 0.047 0.206 3009 Planarity : 0.005 0.083 3512 Dihedral : 11.746 163.007 2774 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.36 % Favored : 90.56 % Rotamer: Outliers : 0.05 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.47 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.16), residues: 2468 helix: -0.62 (0.17), residues: 931 sheet: -0.98 (0.31), residues: 269 loop : -2.15 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 561 HIS 0.008 0.001 HIS C 236 PHE 0.028 0.001 PHE H 45 TYR 0.014 0.001 TYR C 505 ARG 0.015 0.001 ARG B 635 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4276.66 seconds wall clock time: 76 minutes 45.01 seconds (4605.01 seconds total)