Starting phenix.real_space_refine on Fri Feb 16 09:23:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwc_35053/02_2024/8hwc_35053.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwc_35053/02_2024/8hwc_35053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwc_35053/02_2024/8hwc_35053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwc_35053/02_2024/8hwc_35053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwc_35053/02_2024/8hwc_35053.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwc_35053/02_2024/8hwc_35053.pdb" } resolution = 3.3 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= 0.005 sd= 0.081 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9564 2.51 5 N 2541 2.21 5 O 2754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 405": "OE1" <-> "OE2" Residue "F GLU 480": "OE1" <-> "OE2" Residue "D ASP 424": "OD1" <-> "OD2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B GLU 579": "OE1" <-> "OE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 637": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14943 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2313 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain breaks: 5 Chain: "F" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2514 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain breaks: 4 Chain: "D" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2178 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 10, 'TRANS': 255} Chain breaks: 6 Chain: "C" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2283 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 5 Chain: "B" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2610 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 4 Chain: "A" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3045 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 359} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 7.67, per 1000 atoms: 0.51 Number of scatterers: 14943 At special positions: 0 Unit cell: (101.835, 136.875, 135.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2754 8.00 N 2541 7.00 C 9564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 2.5 seconds 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3518 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 23 sheets defined 41.4% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.635A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 removed outlier: 3.916A pdb=" N LEU E 367 " --> pdb=" O LEU E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 374 No H-bonds generated for 'chain 'E' and resid 372 through 374' Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 387 through 400 removed outlier: 3.711A pdb=" N THR E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 435 removed outlier: 4.318A pdb=" N LYS E 435 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 removed outlier: 3.605A pdb=" N GLU E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE E 464 " --> pdb=" O GLU E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 488 Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 571 through 577 Processing helix chain 'E' and resid 617 through 621 removed outlier: 3.562A pdb=" N ARG E 620 " --> pdb=" O LEU E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 680 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.589A pdb=" N ASN F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 371 removed outlier: 3.871A pdb=" N LEU F 367 " --> pdb=" O LEU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 385 through 398 removed outlier: 3.674A pdb=" N LYS F 390 " --> pdb=" O PRO F 386 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 435 removed outlier: 4.393A pdb=" N ASP F 432 " --> pdb=" O SER F 429 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS F 435 " --> pdb=" O ASP F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 469 removed outlier: 3.662A pdb=" N GLU F 460 " --> pdb=" O PRO F 456 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 488 Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 572 through 577 Processing helix chain 'F' and resid 617 through 621 removed outlier: 3.922A pdb=" N ILE F 621 " --> pdb=" O MET F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 661 Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.669A pdb=" N ASN D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 removed outlier: 4.038A pdb=" N LEU D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 387 through 400 removed outlier: 3.594A pdb=" N THR D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 434 Processing helix chain 'D' and resid 455 through 469 removed outlier: 3.764A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 488 Processing helix chain 'D' and resid 510 through 521 Processing helix chain 'D' and resid 574 through 578 removed outlier: 3.610A pdb=" N LEU D 577 " --> pdb=" O ILE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 621 removed outlier: 4.062A pdb=" N ILE D 621 " --> pdb=" O MET D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.513A pdb=" N ASN C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 removed outlier: 3.736A pdb=" N LEU C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 390 through 398 Processing helix chain 'C' and resid 455 through 469 removed outlier: 4.071A pdb=" N GLU C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE C 464 " --> pdb=" O GLU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 617 through 621 removed outlier: 3.758A pdb=" N ILE C 621 " --> pdb=" O MET C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.618A pdb=" N ASN B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.931A pdb=" N LEU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.867A pdb=" N THR B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 4.358A pdb=" N LYS B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 removed outlier: 3.609A pdb=" N GLU B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 544 through 548 removed outlier: 3.649A pdb=" N HIS B 548 " --> pdb=" O ALA B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 577 removed outlier: 3.839A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.773A pdb=" N ILE B 621 " --> pdb=" O MET B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.779A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 4.002A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 386 through 398 removed outlier: 3.664A pdb=" N LYS A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 removed outlier: 4.179A pdb=" N ASP A 432 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.644A pdb=" N GLU A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.664A pdb=" N ASP A 534 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 617 through 621 removed outlier: 3.625A pdb=" N ILE A 621 " --> pdb=" O MET A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 680 Processing sheet with id=AA1, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AA3, first strand: chain 'E' and resid 500 through 503 removed outlier: 6.213A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE E 626 " --> pdb=" O PHE E 500 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE E 502 " --> pdb=" O PHE E 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 553 through 555 removed outlier: 6.425A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AA6, first strand: chain 'F' and resid 412 through 415 Processing sheet with id=AA7, first strand: chain 'F' and resid 500 through 503 removed outlier: 6.320A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 525 through 526 removed outlier: 6.794A pdb=" N VAL F 525 " --> pdb=" O PHE F 554 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AB1, first strand: chain 'D' and resid 412 through 415 Processing sheet with id=AB2, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB3, first strand: chain 'C' and resid 412 through 415 Processing sheet with id=AB4, first strand: chain 'C' and resid 500 through 503 removed outlier: 5.956A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 552 through 553 removed outlier: 3.825A pdb=" N VAL C 553 " --> pdb=" O THR C 599 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AB7, first strand: chain 'B' and resid 412 through 415 Processing sheet with id=AB8, first strand: chain 'B' and resid 500 through 502 removed outlier: 6.172A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 525 through 526 removed outlier: 6.444A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AC2, first strand: chain 'A' and resid 412 through 415 Processing sheet with id=AC3, first strand: chain 'A' and resid 500 through 502 removed outlier: 5.845A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 525 through 526 removed outlier: 6.939A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 628 through 630 removed outlier: 5.749A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 474 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.96 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4657 1.34 - 1.46: 2156 1.46 - 1.58: 8284 1.58 - 1.70: 1 1.70 - 1.81: 126 Bond restraints: 15224 Sorted by residual: bond pdb=" CB PRO B 690 " pdb=" CG PRO B 690 " ideal model delta sigma weight residual 1.492 1.617 -0.125 5.00e-02 4.00e+02 6.28e+00 bond pdb=" C LEU A 558 " pdb=" N PRO A 559 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.25e-02 6.40e+03 6.07e+00 bond pdb=" N ASP B 402 " pdb=" CA ASP B 402 " ideal model delta sigma weight residual 1.453 1.483 -0.030 1.22e-02 6.72e+03 5.91e+00 bond pdb=" N THR D 449 " pdb=" CA THR D 449 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.42e+00 bond pdb=" N LEU F 515 " pdb=" CA LEU F 515 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.23e+00 ... (remaining 15219 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.41: 360 106.41 - 113.32: 8317 113.32 - 120.23: 5479 120.23 - 127.14: 6227 127.14 - 134.06: 123 Bond angle restraints: 20506 Sorted by residual: angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 113.42 106.79 6.63 1.17e+00 7.31e-01 3.22e+01 angle pdb=" N TRP C 675 " pdb=" CA TRP C 675 " pdb=" CB TRP C 675 " ideal model delta sigma weight residual 109.94 102.38 7.56 1.49e+00 4.50e-01 2.57e+01 angle pdb=" CA PRO B 690 " pdb=" N PRO B 690 " pdb=" CD PRO B 690 " ideal model delta sigma weight residual 112.00 105.65 6.35 1.40e+00 5.10e-01 2.05e+01 angle pdb=" C LYS C 674 " pdb=" N TRP C 675 " pdb=" CA TRP C 675 " ideal model delta sigma weight residual 120.54 125.53 -4.99 1.35e+00 5.49e-01 1.37e+01 angle pdb=" CA MET B 462 " pdb=" CB MET B 462 " pdb=" CG MET B 462 " ideal model delta sigma weight residual 114.10 121.32 -7.22 2.00e+00 2.50e-01 1.30e+01 ... (remaining 20501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7953 17.95 - 35.91: 1084 35.91 - 53.86: 215 53.86 - 71.81: 34 71.81 - 89.77: 13 Dihedral angle restraints: 9299 sinusoidal: 3909 harmonic: 5390 Sorted by residual: dihedral pdb=" CA LYS D 677 " pdb=" C LYS D 677 " pdb=" N LYS D 678 " pdb=" CA LYS D 678 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASN B 594 " pdb=" CB ASN B 594 " pdb=" CG ASN B 594 " pdb=" OD1 ASN B 594 " ideal model delta sinusoidal sigma weight residual -90.00 -160.39 70.39 2 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CB GLU C 405 " pdb=" CG GLU C 405 " pdb=" CD GLU C 405 " pdb=" OE1 GLU C 405 " ideal model delta sinusoidal sigma weight residual 0.00 -89.77 89.77 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 9296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1935 0.056 - 0.111: 347 0.111 - 0.167: 31 0.167 - 0.223: 2 0.223 - 0.279: 1 Chirality restraints: 2316 Sorted by residual: chirality pdb=" CB ILE A 583 " pdb=" CA ILE A 583 " pdb=" CG1 ILE A 583 " pdb=" CG2 ILE A 583 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU A 461 " pdb=" CB LEU A 461 " pdb=" CD1 LEU A 461 " pdb=" CD2 LEU A 461 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA LEU A 515 " pdb=" N LEU A 515 " pdb=" C LEU A 515 " pdb=" CB LEU A 515 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 2313 not shown) Planarity restraints: 2583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 675 " -0.051 2.00e-02 2.50e+03 4.78e-02 5.72e+01 pdb=" CG TRP C 675 " 0.125 2.00e-02 2.50e+03 pdb=" CD1 TRP C 675 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 TRP C 675 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 675 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 675 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 675 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 675 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 675 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP C 675 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 681 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO D 682 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 682 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 682 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 361 " -0.048 5.00e-02 4.00e+02 7.18e-02 8.26e+00 pdb=" N PRO B 362 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 362 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 362 " -0.039 5.00e-02 4.00e+02 ... (remaining 2580 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3127 2.78 - 3.31: 14135 3.31 - 3.84: 23657 3.84 - 4.37: 27458 4.37 - 4.90: 47541 Nonbonded interactions: 115918 Sorted by model distance: nonbonded pdb=" N GLN E 660 " pdb=" OE1 GLN E 660 " model vdw 2.245 2.520 nonbonded pdb=" OD2 ASP F 346 " pdb=" OG SER F 359 " model vdw 2.254 2.440 nonbonded pdb=" OD2 ASP E 398 " pdb=" NH1 ARG D 389 " model vdw 2.254 2.520 nonbonded pdb=" O THR A 406 " pdb=" NH1 ARG A 595 " model vdw 2.256 2.520 nonbonded pdb=" OG1 THR C 342 " pdb=" O ASP C 346 " model vdw 2.258 2.440 ... (remaining 115913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 323 through 525 or resid 543 through 554 or resid 573 thro \ ugh 602 or resid 617 through 626 or resid 656 through 688)) selection = (chain 'C' and (resid 323 through 593 or resid 595 through 626 or resid 656 thro \ ugh 688)) selection = (chain 'E' and (resid 323 through 525 or resid 543 through 554 or resid 573 thro \ ugh 602 or resid 617 through 688)) selection = (chain 'F' and (resid 323 through 525 or resid 543 through 554 or resid 573 thro \ ugh 602 or resid 617 through 626 or resid 656 through 688)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.390 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 38.900 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 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 : 0.003 0.125 15224 Z= 0.211 Angle : 0.603 8.790 20506 Z= 0.334 Chirality : 0.042 0.279 2316 Planarity : 0.005 0.074 2583 Dihedral : 16.491 89.765 5781 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.30 % Allowed : 24.91 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.80 (0.21), residues: 1776 helix: -0.35 (0.20), residues: 699 sheet: -1.51 (0.34), residues: 251 loop : -1.79 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.125 0.003 TRP C 675 HIS 0.003 0.001 HIS E 548 PHE 0.013 0.001 PHE A 357 TYR 0.017 0.001 TYR C 482 ARG 0.009 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 449 THR cc_start: 0.6113 (OUTLIER) cc_final: 0.5769 (p) outliers start: 5 outliers final: 1 residues processed: 181 average time/residue: 0.2219 time to fit residues: 63.9757 Evaluate side-chains 169 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 478 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 105 optimal weight: 20.0000 chunk 164 optimal weight: 0.0470 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 660 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15224 Z= 0.280 Angle : 0.541 8.617 20506 Z= 0.274 Chirality : 0.042 0.190 2316 Planarity : 0.004 0.053 2583 Dihedral : 3.991 24.579 1977 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.66 % Allowed : 24.56 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.70 (0.21), residues: 1776 helix: -0.16 (0.21), residues: 698 sheet: -1.56 (0.32), residues: 267 loop : -1.80 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP C 675 HIS 0.004 0.001 HIS E 347 PHE 0.012 0.001 PHE A 357 TYR 0.014 0.001 TYR A 482 ARG 0.004 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 172 time to evaluate : 1.908 Fit side-chains revert: symmetry clash REVERT: F 497 CYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6716 (m) REVERT: D 436 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7625 (m-80) REVERT: D 679 TYR cc_start: 0.6458 (m-10) cc_final: 0.6186 (m-10) REVERT: B 458 MET cc_start: 0.7310 (mmm) cc_final: 0.7034 (tpt) outliers start: 45 outliers final: 20 residues processed: 207 average time/residue: 0.2182 time to fit residues: 72.2937 Evaluate side-chains 182 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 546 ASN Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 686 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 0.0470 chunk 164 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 660 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15224 Z= 0.133 Angle : 0.491 11.155 20506 Z= 0.245 Chirality : 0.040 0.287 2316 Planarity : 0.004 0.047 2583 Dihedral : 3.594 24.915 1974 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.95 % Allowed : 24.73 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.48 (0.21), residues: 1776 helix: 0.04 (0.20), residues: 708 sheet: -1.66 (0.32), residues: 275 loop : -1.61 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 675 HIS 0.002 0.000 HIS E 548 PHE 0.012 0.001 PHE B 543 TYR 0.018 0.001 TYR A 664 ARG 0.003 0.000 ARG F 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 382 GLU cc_start: 0.8194 (pt0) cc_final: 0.7963 (pt0) REVERT: F 497 CYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6753 (m) REVERT: D 436 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: D 679 TYR cc_start: 0.6571 (m-10) cc_final: 0.6360 (m-10) REVERT: C 497 CYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6445 (m) REVERT: C 579 GLU cc_start: 0.6968 (pt0) cc_final: 0.6269 (pt0) REVERT: B 612 ARG cc_start: 0.7597 (ttp80) cc_final: 0.7386 (ttp80) REVERT: A 382 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: A 497 CYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7396 (m) outliers start: 33 outliers final: 16 residues processed: 198 average time/residue: 0.2157 time to fit residues: 68.8818 Evaluate side-chains 180 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 489 CYS Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 546 ASN Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 603 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 660 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15224 Z= 0.243 Angle : 0.537 14.875 20506 Z= 0.265 Chirality : 0.042 0.237 2316 Planarity : 0.004 0.047 2583 Dihedral : 3.790 24.666 1974 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.20 % Allowed : 23.73 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.54 (0.21), residues: 1776 helix: -0.01 (0.20), residues: 711 sheet: -1.64 (0.32), residues: 280 loop : -1.67 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 675 HIS 0.003 0.001 HIS B 347 PHE 0.011 0.001 PHE A 357 TYR 0.015 0.001 TYR A 664 ARG 0.002 0.000 ARG F 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 175 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 351 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7696 (mt) REVERT: F 372 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8766 (ptt-90) REVERT: F 497 CYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6721 (m) REVERT: D 436 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: D 600 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7644 (pt) REVERT: C 497 CYS cc_start: 0.6591 (OUTLIER) cc_final: 0.6110 (m) REVERT: C 579 GLU cc_start: 0.7042 (pt0) cc_final: 0.6449 (pt0) REVERT: B 351 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7734 (mt) REVERT: B 432 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8143 (p0) REVERT: B 612 ARG cc_start: 0.7605 (ttp80) cc_final: 0.7375 (ttp80) REVERT: A 372 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8042 (ptt-90) REVERT: A 382 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: A 454 ASP cc_start: 0.6466 (t0) cc_final: 0.6127 (t0) REVERT: A 497 CYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7273 (m) outliers start: 54 outliers final: 28 residues processed: 219 average time/residue: 0.2259 time to fit residues: 76.7423 Evaluate side-chains 207 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 168 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 546 ASN Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 686 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 0.1980 chunk 149 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15224 Z= 0.164 Angle : 0.513 16.531 20506 Z= 0.253 Chirality : 0.040 0.192 2316 Planarity : 0.004 0.044 2583 Dihedral : 3.627 24.735 1974 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.31 % Allowed : 24.08 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.44 (0.21), residues: 1776 helix: 0.05 (0.20), residues: 717 sheet: -1.65 (0.32), residues: 280 loop : -1.58 (0.24), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP C 675 HIS 0.002 0.001 HIS A 680 PHE 0.008 0.001 PHE E 427 TYR 0.015 0.001 TYR E 664 ARG 0.003 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 179 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 382 GLU cc_start: 0.8251 (pt0) cc_final: 0.8023 (pt0) REVERT: F 372 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8726 (ptt-90) REVERT: F 497 CYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6583 (m) REVERT: D 436 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: C 497 CYS cc_start: 0.6682 (OUTLIER) cc_final: 0.6212 (m) REVERT: C 579 GLU cc_start: 0.6907 (pt0) cc_final: 0.6390 (pt0) REVERT: A 497 CYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7309 (m) REVERT: A 514 ARG cc_start: 0.7714 (ptp90) cc_final: 0.7449 (ptp90) outliers start: 56 outliers final: 35 residues processed: 219 average time/residue: 0.2208 time to fit residues: 75.5395 Evaluate side-chains 208 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 489 CYS Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 546 ASN Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 686 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15224 Z= 0.279 Angle : 0.565 17.796 20506 Z= 0.278 Chirality : 0.042 0.173 2316 Planarity : 0.004 0.046 2583 Dihedral : 3.879 24.793 1974 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.20 % Allowed : 24.44 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.54 (0.21), residues: 1776 helix: -0.08 (0.20), residues: 718 sheet: -1.66 (0.32), residues: 275 loop : -1.60 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP C 675 HIS 0.003 0.001 HIS B 347 PHE 0.013 0.001 PHE A 357 TYR 0.015 0.001 TYR A 482 ARG 0.003 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 174 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 501 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7144 (m-10) REVERT: F 351 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7694 (mt) REVERT: F 497 CYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6799 (m) REVERT: D 436 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: C 344 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7554 (mtp85) REVERT: C 497 CYS cc_start: 0.6649 (OUTLIER) cc_final: 0.6161 (m) REVERT: C 579 GLU cc_start: 0.6923 (pt0) cc_final: 0.6359 (pt0) REVERT: A 372 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8032 (ptt-90) REVERT: A 497 CYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7316 (m) REVERT: A 600 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8865 (mm) outliers start: 54 outliers final: 38 residues processed: 218 average time/residue: 0.2234 time to fit residues: 76.2417 Evaluate side-chains 211 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 165 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 546 ASN Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 686 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 147 optimal weight: 0.0040 chunk 97 optimal weight: 0.0770 chunk 174 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 overall best weight: 4.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 597 HIS D 466 ASN D 469 GLN D 478 ASN ** D 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 ASN A 597 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.093 15224 Z= 0.676 Angle : 0.795 18.061 20506 Z= 0.396 Chirality : 0.051 0.175 2316 Planarity : 0.006 0.061 2583 Dihedral : 4.918 24.747 1974 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 4.32 % Allowed : 23.61 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.11 (0.20), residues: 1776 helix: -0.55 (0.20), residues: 696 sheet: -1.84 (0.32), residues: 267 loop : -1.95 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.004 TRP C 675 HIS 0.005 0.002 HIS A 347 PHE 0.029 0.002 PHE A 357 TYR 0.020 0.002 TYR C 409 ARG 0.006 0.001 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 169 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 346 ASP cc_start: 0.7735 (m-30) cc_final: 0.7511 (p0) REVERT: E 501 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7382 (m-10) REVERT: F 497 CYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7183 (m) REVERT: D 426 MET cc_start: 0.7778 (tpp) cc_final: 0.7516 (tpp) REVERT: C 344 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7581 (mtp85) REVERT: C 497 CYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6145 (m) REVERT: B 612 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7295 (ttp80) REVERT: A 351 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7284 (mt) REVERT: A 372 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8179 (ptt-90) REVERT: A 497 CYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7475 (m) REVERT: A 600 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8909 (mm) REVERT: A 684 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7285 (tmm) outliers start: 73 outliers final: 40 residues processed: 229 average time/residue: 0.2223 time to fit residues: 80.1913 Evaluate side-chains 208 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 160 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 546 ASN Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 684 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 0.0060 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 596 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15224 Z= 0.162 Angle : 0.568 18.894 20506 Z= 0.280 Chirality : 0.041 0.153 2316 Planarity : 0.004 0.044 2583 Dihedral : 4.029 25.326 1974 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.19 % Allowed : 25.86 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.62 (0.21), residues: 1776 helix: -0.09 (0.21), residues: 693 sheet: -1.80 (0.31), residues: 275 loop : -1.61 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.003 TRP C 675 HIS 0.003 0.001 HIS D 597 PHE 0.009 0.001 PHE E 357 TYR 0.013 0.001 TYR C 679 ARG 0.004 0.000 ARG C 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 177 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 501 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: F 497 CYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7131 (m) REVERT: C 344 ARG cc_start: 0.7769 (mtp85) cc_final: 0.7528 (mtp85) REVERT: C 497 CYS cc_start: 0.6600 (OUTLIER) cc_final: 0.6018 (m) REVERT: B 351 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7666 (mt) REVERT: A 334 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8381 (tp) REVERT: A 344 ARG cc_start: 0.7404 (mtp85) cc_final: 0.6878 (mtm-85) REVERT: A 372 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8119 (ptt-90) REVERT: A 497 CYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7383 (m) REVERT: A 600 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8749 (mm) outliers start: 37 outliers final: 21 residues processed: 207 average time/residue: 0.2399 time to fit residues: 76.7156 Evaluate side-chains 188 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 546 ASN Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 603 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 0.0270 chunk 127 optimal weight: 0.0970 chunk 49 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15224 Z= 0.168 Angle : 0.577 19.084 20506 Z= 0.283 Chirality : 0.041 0.155 2316 Planarity : 0.004 0.046 2583 Dihedral : 3.916 27.096 1974 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.01 % Allowed : 26.27 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.52 (0.21), residues: 1776 helix: -0.04 (0.20), residues: 704 sheet: -1.77 (0.31), residues: 280 loop : -1.52 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.003 TRP C 675 HIS 0.002 0.001 HIS D 597 PHE 0.011 0.001 PHE F 554 TYR 0.013 0.001 TYR C 676 ARG 0.003 0.000 ARG C 663 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 501 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7227 (m-10) REVERT: F 497 CYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6756 (m) REVERT: C 344 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7520 (mtp85) REVERT: C 360 GLU cc_start: 0.6970 (pm20) cc_final: 0.6751 (pm20) REVERT: C 497 CYS cc_start: 0.6708 (OUTLIER) cc_final: 0.6163 (m) REVERT: B 351 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7720 (mt) REVERT: A 344 ARG cc_start: 0.7389 (mtp85) cc_final: 0.6806 (mtm-85) REVERT: A 372 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7776 (ptt-90) REVERT: A 458 MET cc_start: 0.6376 (ptm) cc_final: 0.6172 (ptm) REVERT: A 497 CYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7264 (m) REVERT: A 600 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8765 (mm) REVERT: A 684 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.6809 (tmm) outliers start: 34 outliers final: 23 residues processed: 197 average time/residue: 0.2364 time to fit residues: 73.1253 Evaluate side-chains 195 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 546 ASN Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 684 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 88 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15224 Z= 0.254 Angle : 0.603 18.769 20506 Z= 0.296 Chirality : 0.043 0.152 2316 Planarity : 0.004 0.046 2583 Dihedral : 4.053 27.572 1974 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.01 % Allowed : 26.27 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.55 (0.21), residues: 1776 helix: -0.08 (0.20), residues: 704 sheet: -1.74 (0.32), residues: 275 loop : -1.55 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.003 TRP C 675 HIS 0.003 0.001 HIS D 597 PHE 0.018 0.001 PHE E 357 TYR 0.014 0.001 TYR C 676 ARG 0.003 0.000 ARG C 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 501 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7270 (m-10) REVERT: F 497 CYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6939 (m) REVERT: C 344 ARG cc_start: 0.7714 (mtp85) cc_final: 0.7471 (mtp85) REVERT: C 360 GLU cc_start: 0.7043 (pm20) cc_final: 0.6800 (pm20) REVERT: C 497 CYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6110 (m) REVERT: B 612 ARG cc_start: 0.7538 (ttp80) cc_final: 0.7289 (ttp80) REVERT: A 372 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.7824 (ptt-90) REVERT: A 458 MET cc_start: 0.6361 (ptm) cc_final: 0.6121 (ptm) REVERT: A 497 CYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7275 (m) REVERT: A 600 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8794 (mm) REVERT: A 684 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6806 (tmm) outliers start: 34 outliers final: 27 residues processed: 188 average time/residue: 0.2300 time to fit residues: 68.2450 Evaluate side-chains 194 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 546 ASN Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 684 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 126 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.215146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.160014 restraints weight = 18366.510| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.54 r_work: 0.3175 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15224 Z= 0.225 Angle : 0.589 18.119 20506 Z= 0.289 Chirality : 0.042 0.149 2316 Planarity : 0.004 0.047 2583 Dihedral : 3.987 27.238 1974 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.25 % Allowed : 26.39 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.52 (0.21), residues: 1776 helix: -0.03 (0.21), residues: 703 sheet: -1.78 (0.32), residues: 280 loop : -1.53 (0.24), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.003 TRP C 675 HIS 0.002 0.001 HIS D 597 PHE 0.016 0.001 PHE E 357 TYR 0.014 0.001 TYR C 676 ARG 0.004 0.000 ARG C 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2876.61 seconds wall clock time: 53 minutes 21.16 seconds (3201.16 seconds total)