Starting phenix.real_space_refine on Wed Jan 14 23:02:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z8j_14553/01_2026/7z8j_14553.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z8j_14553/01_2026/7z8j_14553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z8j_14553/01_2026/7z8j_14553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z8j_14553/01_2026/7z8j_14553.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z8j_14553/01_2026/7z8j_14553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z8j_14553/01_2026/7z8j_14553.map" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 82 5.16 5 C 12761 2.51 5 N 3625 2.21 5 O 3721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20189 Number of models: 1 Model: "" Number of chains: 9 Chain: "X" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 797 Classifications: {'peptide': 93} Link IDs: {'TRANS': 92} Chain: "f" Number of atoms: 5545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5545 Classifications: {'peptide': 674} Link IDs: {'PTRANS': 21, 'TRANS': 652} Chain breaks: 4 Chain: "h" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2804 Classifications: {'peptide': 358} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 340} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 1981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1981 Classifications: {'peptide': 247} Incomplete info: {'backbone_only': 13} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "m" Number of atoms: 4333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4333 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 13, 'TRANS': 510} Chain breaks: 3 Chain: "n" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1068 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 3 Chain: "o" Number of atoms: 2808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2808 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 17, 'TRANS': 340} Chain: "r" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 56 Classifications: {'peptide': 14} Incomplete info: {'backbone_only': 13} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "x" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 797 Classifications: {'peptide': 93} Link IDs: {'TRANS': 92} Time building chain proxies: 4.52, per 1000 atoms: 0.22 Number of scatterers: 20189 At special positions: 0 Unit cell: (184.186, 158.052, 146.851, 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 82 16.00 O 3721 8.00 N 3625 7.00 C 12761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 1.0 seconds 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4710 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 17 sheets defined 60.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'X' and resid 100 through 192 removed outlier: 3.856A pdb=" N ARG X 192 " --> pdb=" O GLN X 188 " (cutoff:3.500A) Processing helix chain 'f' and resid 270 through 283 Processing helix chain 'f' and resid 332 through 337 Processing helix chain 'f' and resid 340 through 347 Processing helix chain 'f' and resid 349 through 365 Processing helix chain 'f' and resid 366 through 370 Processing helix chain 'f' and resid 373 through 400 removed outlier: 3.826A pdb=" N THR f 398 " --> pdb=" O LYS f 394 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG f 399 " --> pdb=" O VAL f 395 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS f 400 " --> pdb=" O LEU f 396 " (cutoff:3.500A) Processing helix chain 'f' and resid 405 through 441 Processing helix chain 'f' and resid 454 through 484 removed outlier: 4.250A pdb=" N LYS f 458 " --> pdb=" O PRO f 454 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU f 459 " --> pdb=" O ALA f 455 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN f 472 " --> pdb=" O LYS f 468 " (cutoff:3.500A) Processing helix chain 'f' and resid 514 through 532 Processing helix chain 'f' and resid 539 through 575 removed outlier: 3.584A pdb=" N ALA f 545 " --> pdb=" O GLU f 541 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP f 554 " --> pdb=" O MET f 550 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU f 555 " --> pdb=" O LYS f 551 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG f 563 " --> pdb=" O ARG f 559 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG f 567 " --> pdb=" O ARG f 563 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP f 570 " --> pdb=" O ALA f 566 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN f 571 " --> pdb=" O ARG f 567 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU f 572 " --> pdb=" O LEU f 568 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY f 573 " --> pdb=" O ARG f 569 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR f 574 " --> pdb=" O ASP f 570 " (cutoff:3.500A) Processing helix chain 'f' and resid 577 through 588 removed outlier: 3.577A pdb=" N ILE f 584 " --> pdb=" O GLU f 580 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE f 588 " --> pdb=" O ILE f 584 " (cutoff:3.500A) Processing helix chain 'f' and resid 589 through 593 removed outlier: 3.872A pdb=" N PHE f 592 " --> pdb=" O ASN f 589 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL f 593 " --> pdb=" O ALA f 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 589 through 593' Processing helix chain 'f' and resid 597 through 625 removed outlier: 4.492A pdb=" N THR f 606 " --> pdb=" O ARG f 602 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLN f 607 " --> pdb=" O GLU f 603 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE f 609 " --> pdb=" O GLN f 605 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN f 610 " --> pdb=" O THR f 606 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL f 625 " --> pdb=" O ASP f 621 " (cutoff:3.500A) Processing helix chain 'f' and resid 630 through 639 removed outlier: 3.744A pdb=" N LYS f 634 " --> pdb=" O SER f 630 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL f 638 " --> pdb=" O LYS f 634 " (cutoff:3.500A) Processing helix chain 'f' and resid 642 through 670 removed outlier: 3.731A pdb=" N ILE f 654 " --> pdb=" O TRP f 650 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP f 667 " --> pdb=" O LYS f 663 " (cutoff:3.500A) Processing helix chain 'f' and resid 672 through 675 Processing helix chain 'f' and resid 676 through 693 removed outlier: 3.861A pdb=" N LYS f 681 " --> pdb=" O VAL f 677 " (cutoff:3.500A) Processing helix chain 'f' and resid 695 through 710 removed outlier: 3.675A pdb=" N GLN f 707 " --> pdb=" O ALA f 703 " (cutoff:3.500A) Processing helix chain 'f' and resid 740 through 757 removed outlier: 3.679A pdb=" N ILE f 744 " --> pdb=" O LEU f 740 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS f 748 " --> pdb=" O ILE f 744 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP f 755 " --> pdb=" O ARG f 751 " (cutoff:3.500A) Processing helix chain 'f' and resid 761 through 774 removed outlier: 3.927A pdb=" N LEU f 774 " --> pdb=" O GLN f 770 " (cutoff:3.500A) Processing helix chain 'f' and resid 774 through 798 removed outlier: 3.579A pdb=" N ARG f 798 " --> pdb=" O LYS f 794 " (cutoff:3.500A) Processing helix chain 'f' and resid 799 through 804 removed outlier: 4.344A pdb=" N LEU f 803 " --> pdb=" O THR f 800 " (cutoff:3.500A) Processing helix chain 'f' and resid 805 through 820 removed outlier: 3.554A pdb=" N GLU f 811 " --> pdb=" O GLY f 807 " (cutoff:3.500A) Processing helix chain 'f' and resid 828 through 864 removed outlier: 3.679A pdb=" N GLN f 834 " --> pdb=" O ASP f 830 " (cutoff:3.500A) Processing helix chain 'f' and resid 865 through 867 No H-bonds generated for 'chain 'f' and resid 865 through 867' Processing helix chain 'f' and resid 870 through 892 Processing helix chain 'f' and resid 895 through 927 Processing helix chain 'f' and resid 974 through 995 removed outlier: 3.606A pdb=" N CYS f 978 " --> pdb=" O PRO f 974 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL f 992 " --> pdb=" O ALA f 988 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL f 993 " --> pdb=" O TRP f 989 " (cutoff:3.500A) Processing helix chain 'f' and resid 1013 through 1018 Processing helix chain 'f' and resid 1019 through 1026 removed outlier: 3.769A pdb=" N LEU f1023 " --> pdb=" O ARG f1020 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET f1026 " --> pdb=" O LEU f1023 " (cutoff:3.500A) Processing helix chain 'f' and resid 1030 through 1048 Processing helix chain 'h' and resid 600 through 605 Processing helix chain 'h' and resid 609 through 621 Processing helix chain 'j' and resid 112 through 122 removed outlier: 4.728A pdb=" N GLY j 117 " --> pdb=" O TYR j 114 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS j 120 " --> pdb=" O GLY j 117 " (cutoff:3.500A) Processing helix chain 'j' and resid 141 through 143 No H-bonds generated for 'chain 'j' and resid 141 through 143' Processing helix chain 'j' and resid 144 through 164 removed outlier: 3.986A pdb=" N LYS j 164 " --> pdb=" O ILE j 160 " (cutoff:3.500A) Processing helix chain 'j' and resid 166 through 183 Processing helix chain 'j' and resid 233 through 235 No H-bonds generated for 'chain 'j' and resid 233 through 235' Processing helix chain 'j' and resid 236 through 244 removed outlier: 3.714A pdb=" N LYS j 242 " --> pdb=" O SER j 238 " (cutoff:3.500A) Processing helix chain 'j' and resid 247 through 266 Processing helix chain 'j' and resid 279 through 293 Processing helix chain 'j' and resid 316 through 327 removed outlier: 4.132A pdb=" N ILE j 322 " --> pdb=" O LYS j 318 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU j 323 " --> pdb=" O LYS j 319 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS j 324 " --> pdb=" O ILE j 320 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU j 325 " --> pdb=" O ALA j 321 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN j 326 " --> pdb=" O ILE j 322 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE j 327 " --> pdb=" O LEU j 323 " (cutoff:3.500A) Processing helix chain 'j' and resid 335 through 340 removed outlier: 3.745A pdb=" N PHE j 339 " --> pdb=" O ALA j 335 " (cutoff:3.500A) Processing helix chain 'j' and resid 358 through 373 Processing helix chain 'j' and resid 427 through 439 removed outlier: 3.882A pdb=" N LYS j 439 " --> pdb=" O SER j 435 " (cutoff:3.500A) Processing helix chain 'm' and resid 270 through 292 removed outlier: 3.513A pdb=" N GLU m 274 " --> pdb=" O THR m 270 " (cutoff:3.500A) Processing helix chain 'm' and resid 323 through 338 Proline residue: m 334 - end of helix removed outlier: 3.631A pdb=" N ASP m 338 " --> pdb=" O PRO m 334 " (cutoff:3.500A) Processing helix chain 'm' and resid 341 through 346 Processing helix chain 'm' and resid 349 through 365 Processing helix chain 'm' and resid 366 through 370 Processing helix chain 'm' and resid 373 through 399 Processing helix chain 'm' and resid 405 through 441 Processing helix chain 'm' and resid 442 through 445 Processing helix chain 'm' and resid 456 through 483 removed outlier: 3.757A pdb=" N ARG m 471 " --> pdb=" O ARG m 467 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU m 476 " --> pdb=" O GLN m 472 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL m 479 " --> pdb=" O GLN m 475 " (cutoff:3.500A) Processing helix chain 'm' and resid 514 through 533 removed outlier: 4.103A pdb=" N VAL m 533 " --> pdb=" O ASN m 529 " (cutoff:3.500A) Processing helix chain 'm' and resid 539 through 575 removed outlier: 3.862A pdb=" N ARG m 567 " --> pdb=" O ARG m 563 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU m 572 " --> pdb=" O LEU m 568 " (cutoff:3.500A) Processing helix chain 'm' and resid 577 through 588 Processing helix chain 'm' and resid 589 through 593 Processing helix chain 'm' and resid 594 through 601 removed outlier: 4.009A pdb=" N GLY m 599 " --> pdb=" O PRO m 595 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA m 600 " --> pdb=" O HIS m 596 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE m 601 " --> pdb=" O ILE m 597 " (cutoff:3.500A) Processing helix chain 'm' and resid 602 through 625 removed outlier: 3.580A pdb=" N THR m 606 " --> pdb=" O ARG m 602 " (cutoff:3.500A) Processing helix chain 'm' and resid 630 through 639 removed outlier: 3.815A pdb=" N LYS m 634 " --> pdb=" O SER m 630 " (cutoff:3.500A) Processing helix chain 'm' and resid 642 through 670 Processing helix chain 'm' and resid 672 through 676 removed outlier: 3.545A pdb=" N HIS m 676 " --> pdb=" O TRP m 673 " (cutoff:3.500A) Processing helix chain 'm' and resid 678 through 693 removed outlier: 3.636A pdb=" N LEU m 682 " --> pdb=" O GLU m 678 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS m 692 " --> pdb=" O SER m 688 " (cutoff:3.500A) Processing helix chain 'm' and resid 695 through 710 Processing helix chain 'm' and resid 741 through 757 removed outlier: 4.037A pdb=" N THR m 745 " --> pdb=" O PRO m 741 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU m 746 " --> pdb=" O GLU m 742 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER m 747 " --> pdb=" O ILE m 743 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU m 753 " --> pdb=" O GLU m 749 " (cutoff:3.500A) Processing helix chain 'm' and resid 761 through 798 Proline residue: m 776 - end of helix removed outlier: 3.546A pdb=" N ARG m 798 " --> pdb=" O LYS m 794 " (cutoff:3.500A) Processing helix chain 'm' and resid 799 through 804 removed outlier: 3.991A pdb=" N LEU m 803 " --> pdb=" O THR m 800 " (cutoff:3.500A) Processing helix chain 'm' and resid 805 through 821 removed outlier: 4.084A pdb=" N ALA m 821 " --> pdb=" O ALA m 817 " (cutoff:3.500A) Processing helix chain 'm' and resid 828 through 851 removed outlier: 3.615A pdb=" N TYR m 832 " --> pdb=" O LYS m 828 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN m 834 " --> pdb=" O ASP m 830 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL m 847 " --> pdb=" O PHE m 843 " (cutoff:3.500A) Processing helix chain 'n' and resid 466 through 481 removed outlier: 3.665A pdb=" N GLN n 475 " --> pdb=" O ARG n 471 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL n 481 " --> pdb=" O ARG n 477 " (cutoff:3.500A) Processing helix chain 'n' and resid 518 through 531 Processing helix chain 'n' and resid 547 through 575 removed outlier: 3.823A pdb=" N LEU n 572 " --> pdb=" O LEU n 568 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA n 575 " --> pdb=" O GLN n 571 " (cutoff:3.500A) Processing helix chain 'n' and resid 577 through 588 removed outlier: 3.705A pdb=" N MET n 581 " --> pdb=" O ASN n 577 " (cutoff:3.500A) Processing helix chain 'n' and resid 596 through 616 removed outlier: 4.433A pdb=" N ALA n 600 " --> pdb=" O HIS n 596 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR n 604 " --> pdb=" O ALA n 600 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN n 607 " --> pdb=" O GLU n 603 " (cutoff:3.500A) Processing helix chain 'n' and resid 662 through 667 Processing helix chain 'n' and resid 672 through 675 removed outlier: 3.597A pdb=" N ASN n 675 " --> pdb=" O GLY n 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 672 through 675' Processing helix chain 'n' and resid 676 through 681 removed outlier: 4.080A pdb=" N LYS n 681 " --> pdb=" O VAL n 677 " (cutoff:3.500A) Processing helix chain 'o' and resid 600 through 605 removed outlier: 3.515A pdb=" N VAL o 605 " --> pdb=" O GLU o 601 " (cutoff:3.500A) Processing helix chain 'o' and resid 609 through 621 Processing helix chain 'r' and resid 427 through 439 Processing helix chain 'x' and resid 101 through 192 removed outlier: 3.565A pdb=" N GLU x 160 " --> pdb=" O ARG x 156 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU x 165 " --> pdb=" O ASN x 161 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG x 192 " --> pdb=" O GLN x 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'f' and resid 718 through 724 removed outlier: 3.638A pdb=" N LYS f 736 " --> pdb=" O THR f 719 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'h' and resid 265 through 271 removed outlier: 6.718A pdb=" N ILE h 596 " --> pdb=" O ASN h 268 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN h 270 " --> pdb=" O ILE h 594 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE h 594 " --> pdb=" O GLN h 270 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG h 575 " --> pdb=" O GLY h 588 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'h' and resid 282 through 287 removed outlier: 3.952A pdb=" N CYS h 284 " --> pdb=" O SER h 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'h' and resid 335 through 340 Processing sheet with id=AA5, first strand: chain 'h' and resid 386 through 392 removed outlier: 3.585A pdb=" N CYS h 386 " --> pdb=" O ILE h 401 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'h' and resid 434 through 438 removed outlier: 6.686A pdb=" N GLY h 450 " --> pdb=" O THR h 435 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N MET h 437 " --> pdb=" O VAL h 448 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL h 448 " --> pdb=" O MET h 437 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N CYS h 460 " --> pdb=" O ILE h 468 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE h 468 " --> pdb=" O CYS h 460 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'h' and resid 479 through 484 removed outlier: 3.793A pdb=" N GLY h 481 " --> pdb=" O SER h 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 527 through 532 removed outlier: 3.835A pdb=" N ASP h 529 " --> pdb=" O VAL h 543 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG h 548 " --> pdb=" O ASP h 544 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'j' and resid 133 through 138 removed outlier: 6.506A pdb=" N VAL j 133 " --> pdb=" O LEU j 228 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL j 230 " --> pdb=" O VAL j 133 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE j 135 " --> pdb=" O VAL j 230 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR j 232 " --> pdb=" O PHE j 135 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA j 137 " --> pdb=" O THR j 232 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'm' and resid 718 through 719 Processing sheet with id=AB2, first strand: chain 'o' and resid 265 through 271 removed outlier: 5.746A pdb=" N LEU o 267 " --> pdb=" O ASP o 598 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ASP o 598 " --> pdb=" O LEU o 267 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG o 269 " --> pdb=" O ILE o 596 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'o' and resid 282 through 287 removed outlier: 4.006A pdb=" N CYS o 284 " --> pdb=" O SER o 298 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL o 312 " --> pdb=" O TYR o 299 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'o' and resid 338 through 340 removed outlier: 3.645A pdb=" N GLN o 371 " --> pdb=" O LEU o 359 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'o' and resid 384 through 392 removed outlier: 3.628A pdb=" N CYS o 386 " --> pdb=" O ILE o 401 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS o 406 " --> pdb=" O SER o 402 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'o' and resid 434 through 438 removed outlier: 6.621A pdb=" N GLY o 450 " --> pdb=" O THR o 435 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET o 437 " --> pdb=" O VAL o 448 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL o 448 " --> pdb=" O MET o 437 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL o 456 " --> pdb=" O MET o 471 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N MET o 471 " --> pdb=" O VAL o 456 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR o 458 " --> pdb=" O SER o 469 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'o' and resid 479 through 484 removed outlier: 6.603A pdb=" N SER o 500 " --> pdb=" O THR o 480 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE o 482 " --> pdb=" O VAL o 498 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL o 498 " --> pdb=" O ILE o 482 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N CYS o 484 " --> pdb=" O LEU o 496 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU o 496 " --> pdb=" O CYS o 484 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR o 505 " --> pdb=" O SER o 501 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'o' and resid 527 through 532 removed outlier: 3.901A pdb=" N ASP o 529 " --> pdb=" O VAL o 543 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG o 548 " --> pdb=" O ASP o 544 " (cutoff:3.500A) 1244 hydrogen bonds defined for protein. 3609 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: 3.79 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3840 1.33 - 1.45: 5037 1.45 - 1.57: 11571 1.57 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 20586 Sorted by residual: bond pdb=" N ASN o 570 " pdb=" CA ASN o 570 " ideal model delta sigma weight residual 1.458 1.491 -0.034 7.40e-03 1.83e+04 2.06e+01 bond pdb=" N ASN m 333 " pdb=" CA ASN m 333 " ideal model delta sigma weight residual 1.461 1.492 -0.031 9.20e-03 1.18e+04 1.12e+01 bond pdb=" C PHE m 739 " pdb=" N LEU m 740 " ideal model delta sigma weight residual 1.331 1.383 -0.052 1.59e-02 3.96e+03 1.08e+01 bond pdb=" N ASN f 333 " pdb=" CA ASN f 333 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.73e+00 bond pdb=" N ILE f 853 " pdb=" CA ILE f 853 " ideal model delta sigma weight residual 1.461 1.497 -0.037 1.19e-02 7.06e+03 9.50e+00 ... (remaining 20581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 26485 1.97 - 3.94: 1103 3.94 - 5.91: 178 5.91 - 7.88: 16 7.88 - 9.85: 4 Bond angle restraints: 27786 Sorted by residual: angle pdb=" N LEU X 145 " pdb=" CA LEU X 145 " pdb=" C LEU X 145 " ideal model delta sigma weight residual 111.28 105.85 5.43 1.09e+00 8.42e-01 2.48e+01 angle pdb=" C ILE o 594 " pdb=" N VAL o 595 " pdb=" CA VAL o 595 " ideal model delta sigma weight residual 122.93 116.81 6.12 1.26e+00 6.30e-01 2.36e+01 angle pdb=" N ASP n 558 " pdb=" CA ASP n 558 " pdb=" C ASP n 558 " ideal model delta sigma weight residual 111.82 106.35 5.47 1.16e+00 7.43e-01 2.22e+01 angle pdb=" CA ASN f 453 " pdb=" C ASN f 453 " pdb=" N PRO f 454 " ideal model delta sigma weight residual 117.59 122.44 -4.85 1.03e+00 9.43e-01 2.22e+01 angle pdb=" N LYS x 144 " pdb=" CA LYS x 144 " pdb=" C LYS x 144 " ideal model delta sigma weight residual 111.28 106.26 5.02 1.09e+00 8.42e-01 2.12e+01 ... (remaining 27781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 10767 17.75 - 35.50: 1313 35.50 - 53.25: 307 53.25 - 71.00: 59 71.00 - 88.75: 28 Dihedral angle restraints: 12474 sinusoidal: 5226 harmonic: 7248 Sorted by residual: dihedral pdb=" CA THR o 505 " pdb=" C THR o 505 " pdb=" N VAL o 506 " pdb=" CA VAL o 506 " ideal model delta harmonic sigma weight residual 180.00 154.76 25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" C ASP f 887 " pdb=" N ASP f 887 " pdb=" CA ASP f 887 " pdb=" CB ASP f 887 " ideal model delta harmonic sigma weight residual -122.60 -133.05 10.45 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" CA PHE f 469 " pdb=" C PHE f 469 " pdb=" N ARG f 470 " pdb=" CA ARG f 470 " ideal model delta harmonic sigma weight residual 180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 12471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2472 0.058 - 0.116: 434 0.116 - 0.173: 101 0.173 - 0.231: 21 0.231 - 0.289: 11 Chirality restraints: 3039 Sorted by residual: chirality pdb=" CA ASP f 887 " pdb=" N ASP f 887 " pdb=" C ASP f 887 " pdb=" CB ASP f 887 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA ILE o 594 " pdb=" N ILE o 594 " pdb=" C ILE o 594 " pdb=" CB ILE o 594 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB THR m 362 " pdb=" CA THR m 362 " pdb=" OG1 THR m 362 " pdb=" CG2 THR m 362 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 3036 not shown) Planarity restraints: 3590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS X 139 " -0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C LYS X 139 " 0.058 2.00e-02 2.50e+03 pdb=" O LYS X 139 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU X 140 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP n 673 " -0.016 2.00e-02 2.50e+03 1.93e-02 9.35e+00 pdb=" CG TRP n 673 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP n 673 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP n 673 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP n 673 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP n 673 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP n 673 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP n 673 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP n 673 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP n 673 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU f 890 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C LEU f 890 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU f 890 " 0.014 2.00e-02 2.50e+03 pdb=" N HIS f 891 " 0.013 2.00e-02 2.50e+03 ... (remaining 3587 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3211 2.76 - 3.30: 20269 3.30 - 3.83: 33269 3.83 - 4.37: 39714 4.37 - 4.90: 66147 Nonbonded interactions: 162610 Sorted by model distance: nonbonded pdb=" O VAL m 395 " pdb=" OG1 THR m 398 " model vdw 2.229 3.040 nonbonded pdb=" OG SER o 402 " pdb=" OD1 ASP o 404 " model vdw 2.234 3.040 nonbonded pdb=" O GLU m 382 " pdb=" OG SER m 385 " model vdw 2.236 3.040 nonbonded pdb=" O GLU f 418 " pdb=" OG1 THR f 422 " model vdw 2.243 3.040 nonbonded pdb=" O PRO j 142 " pdb=" OH TYR j 336 " model vdw 2.252 3.040 ... (remaining 162605 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 'X' selection = chain 'x' } ncs_group { reference = chain 'h' selection = (chain 'o' and (resid 264 through 524 or (resid 525 and (name N or name CA or na \ me C or name O )) or resid 526 through 621)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 43.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.910 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 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 0.052 20586 Z= 0.358 Angle : 0.867 9.852 27786 Z= 0.541 Chirality : 0.052 0.289 3039 Planarity : 0.005 0.086 3590 Dihedral : 16.588 88.746 7764 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.78 % Allowed : 15.65 % Favored : 83.57 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2445 helix: 1.51 (0.14), residues: 1307 sheet: -1.01 (0.26), residues: 334 loop : 0.18 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG f 435 TYR 0.026 0.002 TYR h 327 PHE 0.030 0.002 PHE o 343 TRP 0.052 0.002 TRP n 673 HIS 0.016 0.001 HIS m 363 Details of bonding type rmsd covalent geometry : bond 0.00605 (20586) covalent geometry : angle 0.86736 (27786) hydrogen bonds : bond 0.17194 ( 1244) hydrogen bonds : angle 6.31309 ( 3609) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 389 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 465 GLN cc_start: 0.7609 (tt0) cc_final: 0.7278 (tt0) REVERT: f 684 GLN cc_start: 0.7855 (mt0) cc_final: 0.7646 (mt0) REVERT: f 789 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6766 (mp0) REVERT: f 824 TRP cc_start: 0.8883 (m100) cc_final: 0.8645 (m100) REVERT: f 848 ASP cc_start: 0.5975 (t0) cc_final: 0.5610 (m-30) REVERT: f 883 LYS cc_start: 0.7843 (mttt) cc_final: 0.7385 (mttp) REVERT: h 548 ARG cc_start: 0.7448 (ttp-110) cc_final: 0.7215 (ttp-110) REVERT: j 103 ARG cc_start: 0.4712 (ttt-90) cc_final: 0.1263 (mmp80) REVERT: j 135 PHE cc_start: 0.7009 (m-10) cc_final: 0.6769 (m-80) REVERT: j 152 TRP cc_start: 0.7480 (m100) cc_final: 0.7184 (m-10) REVERT: j 251 LEU cc_start: 0.7551 (mp) cc_final: 0.7339 (tt) REVERT: m 337 LYS cc_start: 0.7515 (tttt) cc_final: 0.7308 (tmtt) REVERT: m 425 ASP cc_start: 0.7626 (m-30) cc_final: 0.7124 (p0) REVERT: m 466 MET cc_start: 0.7838 (mpp) cc_final: 0.7610 (mpp) REVERT: m 550 MET cc_start: 0.7472 (mmm) cc_final: 0.7058 (mmt) REVERT: m 558 ASP cc_start: 0.7934 (t0) cc_final: 0.7663 (t70) REVERT: m 567 ARG cc_start: 0.6414 (tpt90) cc_final: 0.6081 (mmm160) REVERT: m 598 ARG cc_start: 0.7641 (ttm110) cc_final: 0.7193 (ptm160) REVERT: m 764 ILE cc_start: 0.7957 (mm) cc_final: 0.7727 (mt) REVERT: m 782 ILE cc_start: 0.8077 (mt) cc_final: 0.7844 (mm) REVERT: m 842 ASN cc_start: 0.8497 (m-40) cc_final: 0.8281 (t0) REVERT: n 466 MET cc_start: 0.7470 (mmt) cc_final: 0.7107 (tpp) REVERT: n 563 ARG cc_start: 0.6797 (tmm160) cc_final: 0.6561 (ptm160) REVERT: n 564 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7035 (mt) REVERT: n 570 ASP cc_start: 0.6726 (t70) cc_final: 0.6488 (t0) REVERT: n 605 GLN cc_start: 0.7608 (mt0) cc_final: 0.7178 (mt0) REVERT: o 266 SER cc_start: 0.8263 (t) cc_final: 0.7994 (p) REVERT: o 342 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8146 (tptt) REVERT: o 406 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8198 (ttmt) REVERT: o 430 LYS cc_start: 0.7957 (tttt) cc_final: 0.7475 (mmtt) REVERT: x 146 GLU cc_start: 0.6661 (tp30) cc_final: 0.6368 (tp30) REVERT: x 163 GLU cc_start: 0.7311 (tt0) cc_final: 0.6667 (tt0) REVERT: x 174 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6068 (tm-30) outliers start: 17 outliers final: 7 residues processed: 400 average time/residue: 0.1807 time to fit residues: 102.7524 Evaluate side-chains 369 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 361 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain f residue 850 LEU Chi-restraints excluded: chain m residue 273 GLN Chi-restraints excluded: chain n residue 564 ILE Chi-restraints excluded: chain n residue 601 ILE Chi-restraints excluded: chain o residue 281 VAL Chi-restraints excluded: chain o residue 407 ILE Chi-restraints excluded: chain x residue 145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.0570 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.4980 chunk 227 optimal weight: 0.0670 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.8980 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 161 ASN f 280 ASN f 342 ASN f 456 HIS f 889 ASN h 279 HIS h 365 ASN ** h 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 593 GLN j 366 GLN n 529 ASN o 356 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.173220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141661 restraints weight = 35006.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141339 restraints weight = 27695.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143130 restraints weight = 24923.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143522 restraints weight = 15773.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144027 restraints weight = 15328.931| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20586 Z= 0.182 Angle : 0.560 10.933 27786 Z= 0.302 Chirality : 0.040 0.197 3039 Planarity : 0.004 0.047 3590 Dihedral : 4.880 60.236 2736 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.06 % Allowed : 15.10 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.17), residues: 2445 helix: 1.96 (0.14), residues: 1330 sheet: -0.88 (0.26), residues: 332 loop : 0.22 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG n 567 TYR 0.017 0.002 TYR f 553 PHE 0.017 0.002 PHE j 253 TRP 0.019 0.002 TRP n 673 HIS 0.014 0.001 HIS h 279 Details of bonding type rmsd covalent geometry : bond 0.00386 (20586) covalent geometry : angle 0.56007 (27786) hydrogen bonds : bond 0.05444 ( 1244) hydrogen bonds : angle 4.67563 ( 3609) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 382 time to evaluate : 0.790 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: f 465 GLN cc_start: 0.7431 (tt0) cc_final: 0.7205 (tt0) REVERT: f 469 PHE cc_start: 0.6635 (t80) cc_final: 0.6349 (t80) REVERT: f 553 TYR cc_start: 0.7676 (t80) cc_final: 0.7405 (t80) REVERT: f 749 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6946 (mm-30) REVERT: f 883 LYS cc_start: 0.7675 (mttt) cc_final: 0.7250 (mttp) REVERT: f 922 TRP cc_start: 0.7323 (t60) cc_final: 0.6733 (t60) REVERT: h 269 ARG cc_start: 0.7534 (mtp180) cc_final: 0.7237 (mtp180) REVERT: h 308 GLU cc_start: 0.7068 (mp0) cc_final: 0.6464 (mp0) REVERT: h 484 CYS cc_start: 0.8119 (t) cc_final: 0.7557 (m) REVERT: h 607 ARG cc_start: 0.6649 (mtt180) cc_final: 0.6000 (mtt180) REVERT: j 103 ARG cc_start: 0.4256 (ttt-90) cc_final: 0.0195 (mmm160) REVERT: j 135 PHE cc_start: 0.7045 (m-10) cc_final: 0.6705 (m-80) REVERT: j 251 LEU cc_start: 0.7344 (mp) cc_final: 0.7031 (tt) REVERT: m 273 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7152 (mt0) REVERT: m 324 GLN cc_start: 0.7256 (mp10) cc_final: 0.7014 (mp10) REVERT: m 332 TYR cc_start: 0.6582 (m-10) cc_final: 0.6341 (m-10) REVERT: m 352 LYS cc_start: 0.8347 (mmmt) cc_final: 0.7813 (tppt) REVERT: m 372 TYR cc_start: 0.8171 (t80) cc_final: 0.7901 (t80) REVERT: m 407 GLU cc_start: 0.7601 (pm20) cc_final: 0.7226 (pm20) REVERT: m 425 ASP cc_start: 0.7546 (m-30) cc_final: 0.7124 (p0) REVERT: m 466 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7026 (mpp) REVERT: m 540 LYS cc_start: 0.7511 (tppt) cc_final: 0.7146 (tppt) REVERT: m 550 MET cc_start: 0.7471 (mmm) cc_final: 0.7060 (mmt) REVERT: m 558 ASP cc_start: 0.7913 (t0) cc_final: 0.7500 (t0) REVERT: m 567 ARG cc_start: 0.6020 (tpt90) cc_final: 0.5633 (mmm160) REVERT: m 782 ILE cc_start: 0.8335 (mt) cc_final: 0.8047 (mm) REVERT: n 466 MET cc_start: 0.7537 (mmt) cc_final: 0.7120 (tpp) REVERT: n 556 ARG cc_start: 0.7130 (ttm-80) cc_final: 0.6926 (ttm110) REVERT: n 570 ASP cc_start: 0.6947 (t70) cc_final: 0.6647 (t0) REVERT: n 605 GLN cc_start: 0.7624 (mt0) cc_final: 0.7262 (mt0) REVERT: o 274 GLU cc_start: 0.7435 (tp30) cc_final: 0.7205 (tp30) REVERT: o 342 LYS cc_start: 0.8306 (ttpt) cc_final: 0.8094 (tptt) REVERT: o 430 LYS cc_start: 0.7938 (tttt) cc_final: 0.7612 (mmtm) REVERT: x 130 MET cc_start: 0.6269 (mmm) cc_final: 0.5744 (mmp) REVERT: x 140 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6469 (mp0) REVERT: x 146 GLU cc_start: 0.6480 (tp30) cc_final: 0.6004 (tp30) REVERT: x 152 LYS cc_start: 0.7889 (tptp) cc_final: 0.6971 (tmtt) REVERT: x 163 GLU cc_start: 0.7469 (tt0) cc_final: 0.7256 (tt0) REVERT: x 174 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6158 (tm-30) outliers start: 45 outliers final: 24 residues processed: 405 average time/residue: 0.1795 time to fit residues: 103.7678 Evaluate side-chains 378 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 352 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain f residue 341 LEU Chi-restraints excluded: chain f residue 613 LYS Chi-restraints excluded: chain f residue 852 ILE Chi-restraints excluded: chain f residue 978 CYS Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain h residue 368 THR Chi-restraints excluded: chain h residue 407 ILE Chi-restraints excluded: chain h residue 551 LEU Chi-restraints excluded: chain h residue 576 VAL Chi-restraints excluded: chain h residue 593 GLN Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain m residue 273 GLN Chi-restraints excluded: chain m residue 466 MET Chi-restraints excluded: chain m residue 572 LEU Chi-restraints excluded: chain m residue 666 GLU Chi-restraints excluded: chain m residue 808 LEU Chi-restraints excluded: chain n residue 550 MET Chi-restraints excluded: chain n residue 564 ILE Chi-restraints excluded: chain n residue 601 ILE Chi-restraints excluded: chain o residue 281 VAL Chi-restraints excluded: chain o residue 328 VAL Chi-restraints excluded: chain o residue 386 CYS Chi-restraints excluded: chain o residue 407 ILE Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain x residue 145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 178 optimal weight: 0.0870 chunk 135 optimal weight: 0.0270 chunk 230 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 218 optimal weight: 0.6980 chunk 100 optimal weight: 0.2980 chunk 115 optimal weight: 0.5980 chunk 211 optimal weight: 0.0980 chunk 54 optimal weight: 0.3980 overall best weight: 0.1416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 161 ASN h 382 HIS ** h 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 273 GLN m 844 GLN o 290 GLN x 147 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.174040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141716 restraints weight = 34870.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142835 restraints weight = 25813.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144349 restraints weight = 18884.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144429 restraints weight = 12898.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144710 restraints weight = 13361.679| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20586 Z= 0.129 Angle : 0.511 8.290 27786 Z= 0.273 Chirality : 0.039 0.162 3039 Planarity : 0.003 0.043 3590 Dihedral : 4.510 55.672 2734 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.38 % Allowed : 14.97 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.17), residues: 2445 helix: 2.27 (0.14), residues: 1309 sheet: -0.73 (0.26), residues: 330 loop : 0.31 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG x 156 TYR 0.022 0.001 TYR f 980 PHE 0.013 0.001 PHE f 409 TRP 0.017 0.001 TRP o 509 HIS 0.003 0.001 HIS X 153 Details of bonding type rmsd covalent geometry : bond 0.00272 (20586) covalent geometry : angle 0.51148 (27786) hydrogen bonds : bond 0.04579 ( 1244) hydrogen bonds : angle 4.29758 ( 3609) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 368 time to evaluate : 0.784 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: X 150 GLN cc_start: 0.8143 (tp-100) cc_final: 0.7940 (tp-100) REVERT: X 191 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6747 (mm) REVERT: f 465 GLN cc_start: 0.7500 (tt0) cc_final: 0.7183 (tt0) REVERT: f 469 PHE cc_start: 0.6481 (t80) cc_final: 0.6004 (t80) REVERT: f 553 TYR cc_start: 0.7632 (t80) cc_final: 0.7382 (t80) REVERT: f 721 GLU cc_start: 0.7062 (pt0) cc_final: 0.6377 (pm20) REVERT: f 736 LYS cc_start: 0.7867 (mmtp) cc_final: 0.6948 (mmtt) REVERT: f 749 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6774 (mm-30) REVERT: f 883 LYS cc_start: 0.7628 (mttt) cc_final: 0.7203 (mttp) REVERT: f 922 TRP cc_start: 0.7397 (t60) cc_final: 0.7140 (t60) REVERT: f 987 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6572 (t80) REVERT: h 279 HIS cc_start: 0.7745 (m90) cc_final: 0.7382 (m90) REVERT: h 308 GLU cc_start: 0.7137 (mp0) cc_final: 0.6501 (mp0) REVERT: h 422 MET cc_start: 0.7452 (pmm) cc_final: 0.6885 (pmm) REVERT: h 471 MET cc_start: 0.8048 (tmm) cc_final: 0.7832 (ttt) REVERT: j 135 PHE cc_start: 0.6955 (m-10) cc_final: 0.6598 (m-80) REVERT: j 251 LEU cc_start: 0.7287 (mp) cc_final: 0.7013 (tt) REVERT: j 364 MET cc_start: 0.6869 (tmm) cc_final: 0.6642 (tmm) REVERT: m 274 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7267 (tt0) REVERT: m 324 GLN cc_start: 0.7244 (mp10) cc_final: 0.6940 (mp10) REVERT: m 327 GLU cc_start: 0.6480 (mm-30) cc_final: 0.5941 (mm-30) REVERT: m 332 TYR cc_start: 0.6689 (m-10) cc_final: 0.6419 (m-10) REVERT: m 352 LYS cc_start: 0.8314 (mmmt) cc_final: 0.7789 (tppt) REVERT: m 425 ASP cc_start: 0.7451 (m-30) cc_final: 0.7145 (p0) REVERT: m 540 LYS cc_start: 0.7449 (tppt) cc_final: 0.6912 (tppt) REVERT: m 544 GLU cc_start: 0.6510 (mm-30) cc_final: 0.6229 (mm-30) REVERT: m 550 MET cc_start: 0.7382 (mmm) cc_final: 0.7086 (mmp) REVERT: m 558 ASP cc_start: 0.7920 (t0) cc_final: 0.7501 (t0) REVERT: m 567 ARG cc_start: 0.6080 (tpt90) cc_final: 0.5779 (mmm160) REVERT: m 598 ARG cc_start: 0.7418 (ttm110) cc_final: 0.7179 (ttm110) REVERT: m 750 VAL cc_start: 0.8332 (t) cc_final: 0.8043 (t) REVERT: n 466 MET cc_start: 0.7481 (mmt) cc_final: 0.7051 (tpp) REVERT: n 556 ARG cc_start: 0.7132 (ttm-80) cc_final: 0.6822 (ttm-80) REVERT: n 570 ASP cc_start: 0.7101 (t70) cc_final: 0.6833 (t0) REVERT: n 602 ARG cc_start: 0.6589 (mtp-110) cc_final: 0.5968 (mtp-110) REVERT: n 605 GLN cc_start: 0.7644 (mt0) cc_final: 0.7343 (mt0) REVERT: o 274 GLU cc_start: 0.7474 (tp30) cc_final: 0.7177 (tm-30) REVERT: o 573 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8253 (mp) REVERT: x 130 MET cc_start: 0.6607 (mmm) cc_final: 0.6048 (tpp) REVERT: x 140 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6495 (mp0) REVERT: x 146 GLU cc_start: 0.6420 (tp30) cc_final: 0.5950 (tp30) REVERT: x 156 ARG cc_start: 0.6216 (ttp-110) cc_final: 0.5858 (ttm110) outliers start: 52 outliers final: 31 residues processed: 399 average time/residue: 0.1813 time to fit residues: 103.0945 Evaluate side-chains 366 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 332 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 161 ASN Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 191 LEU Chi-restraints excluded: chain f residue 396 LEU Chi-restraints excluded: chain f residue 463 LEU Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 697 GLU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 792 CYS Chi-restraints excluded: chain f residue 852 ILE Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain h residue 321 LYS Chi-restraints excluded: chain h residue 368 THR Chi-restraints excluded: chain h residue 407 ILE Chi-restraints excluded: chain h residue 551 LEU Chi-restraints excluded: chain h residue 576 VAL Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain m residue 353 ILE Chi-restraints excluded: chain m residue 653 GLN Chi-restraints excluded: chain m residue 666 GLU Chi-restraints excluded: chain m residue 740 LEU Chi-restraints excluded: chain m residue 779 ILE Chi-restraints excluded: chain m residue 808 LEU Chi-restraints excluded: chain n residue 550 MET Chi-restraints excluded: chain n residue 564 ILE Chi-restraints excluded: chain n residue 593 VAL Chi-restraints excluded: chain o residue 281 VAL Chi-restraints excluded: chain o residue 318 MET Chi-restraints excluded: chain o residue 386 CYS Chi-restraints excluded: chain o residue 407 ILE Chi-restraints excluded: chain o residue 460 CYS Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 573 LEU Chi-restraints excluded: chain x residue 145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 90 optimal weight: 0.0570 chunk 103 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.0980 chunk 184 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 475 GLN ** h 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 593 GLN m 473 HIS m 620 HIS m 844 GLN n 475 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.174128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141265 restraints weight = 35095.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142201 restraints weight = 25990.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.143564 restraints weight = 19602.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.144212 restraints weight = 14689.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144466 restraints weight = 13301.363| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20586 Z= 0.201 Angle : 0.524 11.872 27786 Z= 0.280 Chirality : 0.039 0.139 3039 Planarity : 0.004 0.044 3590 Dihedral : 4.214 38.799 2729 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.93 % Allowed : 15.88 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.17), residues: 2445 helix: 2.38 (0.14), residues: 1311 sheet: -0.64 (0.26), residues: 330 loop : 0.26 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 156 TYR 0.025 0.002 TYR f 980 PHE 0.023 0.002 PHE m 277 TRP 0.016 0.001 TRP o 410 HIS 0.010 0.001 HIS m 363 Details of bonding type rmsd covalent geometry : bond 0.00428 (20586) covalent geometry : angle 0.52428 (27786) hydrogen bonds : bond 0.04480 ( 1244) hydrogen bonds : angle 4.25847 ( 3609) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 343 time to evaluate : 0.783 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: X 191 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.6707 (mm) REVERT: f 465 GLN cc_start: 0.7497 (tt0) cc_final: 0.7184 (tt0) REVERT: f 469 PHE cc_start: 0.6452 (t80) cc_final: 0.6009 (t80) REVERT: f 553 TYR cc_start: 0.7639 (t80) cc_final: 0.7424 (t80) REVERT: f 617 GLU cc_start: 0.6882 (tp30) cc_final: 0.6333 (tp30) REVERT: f 708 GLN cc_start: 0.7125 (mm-40) cc_final: 0.6905 (mm-40) REVERT: f 713 VAL cc_start: 0.8374 (p) cc_final: 0.8095 (t) REVERT: f 721 GLU cc_start: 0.7078 (pt0) cc_final: 0.6797 (pt0) REVERT: f 736 LYS cc_start: 0.7799 (mmtp) cc_final: 0.7371 (mmtm) REVERT: f 749 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6752 (mm-30) REVERT: f 883 LYS cc_start: 0.7743 (mttt) cc_final: 0.7198 (mttp) REVERT: f 987 PHE cc_start: 0.6862 (OUTLIER) cc_final: 0.6638 (t80) REVERT: h 269 ARG cc_start: 0.7621 (mtp180) cc_final: 0.7360 (mtp180) REVERT: h 308 GLU cc_start: 0.7286 (mp0) cc_final: 0.6577 (mp0) REVERT: h 471 MET cc_start: 0.8064 (tmm) cc_final: 0.7862 (ttt) REVERT: h 594 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7713 (mt) REVERT: j 135 PHE cc_start: 0.7030 (m-10) cc_final: 0.6618 (m-80) REVERT: j 251 LEU cc_start: 0.7324 (mp) cc_final: 0.6887 (tt) REVERT: j 364 MET cc_start: 0.6913 (tmm) cc_final: 0.6629 (tmm) REVERT: m 273 GLN cc_start: 0.7539 (mt0) cc_final: 0.7060 (mp10) REVERT: m 324 GLN cc_start: 0.7267 (mp10) cc_final: 0.7060 (mp10) REVERT: m 332 TYR cc_start: 0.6785 (m-10) cc_final: 0.6574 (m-10) REVERT: m 352 LYS cc_start: 0.8353 (mmmt) cc_final: 0.7828 (tppt) REVERT: m 407 GLU cc_start: 0.7409 (pm20) cc_final: 0.6921 (pm20) REVERT: m 425 ASP cc_start: 0.7522 (m-30) cc_final: 0.7045 (p0) REVERT: m 426 GLU cc_start: 0.7136 (pt0) cc_final: 0.6848 (pt0) REVERT: m 466 MET cc_start: 0.7569 (mtm) cc_final: 0.7099 (mpp) REVERT: m 468 LYS cc_start: 0.7551 (ttmt) cc_final: 0.7251 (ttmt) REVERT: m 540 LYS cc_start: 0.7464 (tppt) cc_final: 0.7102 (tppt) REVERT: m 550 MET cc_start: 0.7327 (mmm) cc_final: 0.7099 (mmp) REVERT: m 558 ASP cc_start: 0.7945 (t0) cc_final: 0.7516 (t0) REVERT: m 567 ARG cc_start: 0.6046 (tpt90) cc_final: 0.5029 (mmm160) REVERT: m 598 ARG cc_start: 0.7417 (ttm110) cc_final: 0.7189 (ttp80) REVERT: m 782 ILE cc_start: 0.8298 (mt) cc_final: 0.8019 (mm) REVERT: m 810 LYS cc_start: 0.6670 (mptt) cc_final: 0.6322 (mptt) REVERT: m 846 LYS cc_start: 0.5527 (tptm) cc_final: 0.5223 (tptt) REVERT: n 466 MET cc_start: 0.7495 (mmt) cc_final: 0.7105 (tpp) REVERT: n 556 ARG cc_start: 0.7084 (ttm-80) cc_final: 0.6817 (ttm110) REVERT: n 563 ARG cc_start: 0.7021 (tmm160) cc_final: 0.6711 (ptm160) REVERT: n 570 ASP cc_start: 0.7164 (t70) cc_final: 0.6898 (t0) REVERT: n 588 PHE cc_start: 0.3728 (m-10) cc_final: 0.3451 (m-80) REVERT: o 274 GLU cc_start: 0.7507 (tp30) cc_final: 0.7249 (tm-30) REVERT: x 130 MET cc_start: 0.6685 (mmm) cc_final: 0.6114 (tpp) REVERT: x 148 LEU cc_start: 0.7810 (mp) cc_final: 0.7587 (tp) REVERT: x 156 ARG cc_start: 0.6260 (ttp-110) cc_final: 0.5941 (ttm110) outliers start: 64 outliers final: 39 residues processed: 384 average time/residue: 0.1834 time to fit residues: 100.7398 Evaluate side-chains 367 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 325 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 145 LEU Chi-restraints excluded: chain X residue 191 LEU Chi-restraints excluded: chain f residue 396 LEU Chi-restraints excluded: chain f residue 463 LEU Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 673 TRP Chi-restraints excluded: chain f residue 697 GLU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 792 CYS Chi-restraints excluded: chain f residue 852 ILE Chi-restraints excluded: chain f residue 978 CYS Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain f residue 1026 MET Chi-restraints excluded: chain h residue 321 LYS Chi-restraints excluded: chain h residue 368 THR Chi-restraints excluded: chain h residue 407 ILE Chi-restraints excluded: chain h residue 551 LEU Chi-restraints excluded: chain h residue 576 VAL Chi-restraints excluded: chain h residue 587 VAL Chi-restraints excluded: chain h residue 594 ILE Chi-restraints excluded: chain j residue 178 VAL Chi-restraints excluded: chain j residue 289 HIS Chi-restraints excluded: chain m residue 353 ILE Chi-restraints excluded: chain m residue 398 THR Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 572 LEU Chi-restraints excluded: chain m residue 653 GLN Chi-restraints excluded: chain m residue 666 GLU Chi-restraints excluded: chain m residue 713 VAL Chi-restraints excluded: chain m residue 740 LEU Chi-restraints excluded: chain m residue 779 ILE Chi-restraints excluded: chain m residue 808 LEU Chi-restraints excluded: chain n residue 475 GLN Chi-restraints excluded: chain n residue 550 MET Chi-restraints excluded: chain n residue 593 VAL Chi-restraints excluded: chain o residue 318 MET Chi-restraints excluded: chain o residue 386 CYS Chi-restraints excluded: chain o residue 407 ILE Chi-restraints excluded: chain o residue 422 MET Chi-restraints excluded: chain o residue 550 ASP Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain x residue 145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 27 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 chunk 74 optimal weight: 0.0370 chunk 106 optimal weight: 0.7980 chunk 210 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 91 optimal weight: 0.2980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 150 GLN X 161 ASN ** h 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 426 HIS m 844 GLN n 475 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.174303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142703 restraints weight = 34445.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143154 restraints weight = 24875.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144491 restraints weight = 20119.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145172 restraints weight = 15418.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145621 restraints weight = 14613.586| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20586 Z= 0.215 Angle : 0.533 14.383 27786 Z= 0.283 Chirality : 0.040 0.181 3039 Planarity : 0.003 0.042 3590 Dihedral : 4.158 39.002 2725 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.93 % Allowed : 16.34 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.17), residues: 2445 helix: 2.40 (0.14), residues: 1312 sheet: -0.67 (0.26), residues: 330 loop : 0.22 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 156 TYR 0.025 0.002 TYR f 980 PHE 0.017 0.002 PHE o 472 TRP 0.016 0.002 TRP o 410 HIS 0.006 0.001 HIS m 363 Details of bonding type rmsd covalent geometry : bond 0.00461 (20586) covalent geometry : angle 0.53347 (27786) hydrogen bonds : bond 0.04415 ( 1244) hydrogen bonds : angle 4.20529 ( 3609) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 345 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 130 MET cc_start: 0.5939 (ppp) cc_final: 0.5691 (ttt) REVERT: X 140 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6695 (tm-30) REVERT: X 167 GLU cc_start: 0.7440 (pt0) cc_final: 0.7217 (pt0) REVERT: X 191 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.6773 (mm) REVERT: f 465 GLN cc_start: 0.7492 (tt0) cc_final: 0.7177 (tt0) REVERT: f 469 PHE cc_start: 0.6398 (t80) cc_final: 0.5951 (t80) REVERT: f 553 TYR cc_start: 0.7595 (t80) cc_final: 0.7362 (t80) REVERT: f 617 GLU cc_start: 0.6911 (tp30) cc_final: 0.6432 (tp30) REVERT: f 665 VAL cc_start: 0.8137 (p) cc_final: 0.7711 (t) REVERT: f 713 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8079 (t) REVERT: f 721 GLU cc_start: 0.7100 (pt0) cc_final: 0.6885 (mp0) REVERT: f 736 LYS cc_start: 0.7810 (mmtp) cc_final: 0.7317 (mmtp) REVERT: f 749 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6794 (mm-30) REVERT: f 883 LYS cc_start: 0.7750 (mttt) cc_final: 0.7251 (mttp) REVERT: f 987 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6614 (t80) REVERT: h 279 HIS cc_start: 0.7803 (m90) cc_final: 0.7352 (m90) REVERT: h 308 GLU cc_start: 0.7302 (mp0) cc_final: 0.6522 (mp0) REVERT: h 471 MET cc_start: 0.8040 (tmm) cc_final: 0.7754 (ttt) REVERT: h 607 ARG cc_start: 0.6653 (mtt180) cc_final: 0.6091 (mtt180) REVERT: j 135 PHE cc_start: 0.6966 (m-10) cc_final: 0.6614 (m-80) REVERT: j 251 LEU cc_start: 0.7359 (mp) cc_final: 0.6920 (tt) REVERT: j 364 MET cc_start: 0.6895 (tmm) cc_final: 0.6619 (tmm) REVERT: m 273 GLN cc_start: 0.7571 (mt0) cc_final: 0.7358 (mt0) REVERT: m 352 LYS cc_start: 0.8334 (mmmt) cc_final: 0.7809 (tppt) REVERT: m 372 TYR cc_start: 0.8036 (t80) cc_final: 0.7672 (t80) REVERT: m 407 GLU cc_start: 0.7346 (pm20) cc_final: 0.6850 (pm20) REVERT: m 468 LYS cc_start: 0.7586 (ttmt) cc_final: 0.7296 (ttmt) REVERT: m 540 LYS cc_start: 0.7553 (tppt) cc_final: 0.7208 (tppt) REVERT: m 550 MET cc_start: 0.7388 (mmm) cc_final: 0.7148 (mmp) REVERT: m 558 ASP cc_start: 0.7934 (t0) cc_final: 0.7506 (t0) REVERT: m 567 ARG cc_start: 0.6041 (tpt90) cc_final: 0.5226 (mmm160) REVERT: m 598 ARG cc_start: 0.7410 (ttm110) cc_final: 0.6892 (ptm160) REVERT: m 754 LYS cc_start: 0.8467 (tppt) cc_final: 0.8224 (tptt) REVERT: m 782 ILE cc_start: 0.8310 (mt) cc_final: 0.8012 (mm) REVERT: m 810 LYS cc_start: 0.6448 (mptt) cc_final: 0.5900 (mptt) REVERT: n 466 MET cc_start: 0.7504 (mmt) cc_final: 0.7120 (tpp) REVERT: n 556 ARG cc_start: 0.7142 (ttm-80) cc_final: 0.6808 (ttm110) REVERT: n 563 ARG cc_start: 0.7115 (tmm160) cc_final: 0.6746 (ptm160) REVERT: n 570 ASP cc_start: 0.7211 (t70) cc_final: 0.6947 (t0) REVERT: n 605 GLN cc_start: 0.7652 (mt0) cc_final: 0.7401 (mt0) REVERT: o 274 GLU cc_start: 0.7516 (tp30) cc_final: 0.7270 (tm-30) REVERT: o 327 TYR cc_start: 0.7774 (m-80) cc_final: 0.6761 (m-80) REVERT: o 613 ARG cc_start: 0.7540 (mtt-85) cc_final: 0.7212 (mtt-85) REVERT: o 618 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7311 (tp) REVERT: x 130 MET cc_start: 0.6541 (mmm) cc_final: 0.6107 (tpp) REVERT: x 140 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6656 (mp0) REVERT: x 148 LEU cc_start: 0.7783 (mp) cc_final: 0.7554 (tp) REVERT: x 152 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8063 (tptt) REVERT: x 156 ARG cc_start: 0.6161 (ttp-110) cc_final: 0.5670 (ttp-110) outliers start: 64 outliers final: 45 residues processed: 384 average time/residue: 0.1789 time to fit residues: 98.3179 Evaluate side-chains 381 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 331 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 145 LEU Chi-restraints excluded: chain X residue 191 LEU Chi-restraints excluded: chain f residue 396 LEU Chi-restraints excluded: chain f residue 463 LEU Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 673 TRP Chi-restraints excluded: chain f residue 697 GLU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 792 CYS Chi-restraints excluded: chain f residue 852 ILE Chi-restraints excluded: chain f residue 978 CYS Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain f residue 1026 MET Chi-restraints excluded: chain h residue 321 LYS Chi-restraints excluded: chain h residue 322 LYS Chi-restraints excluded: chain h residue 368 THR Chi-restraints excluded: chain h residue 407 ILE Chi-restraints excluded: chain h residue 460 CYS Chi-restraints excluded: chain h residue 546 MET Chi-restraints excluded: chain h residue 551 LEU Chi-restraints excluded: chain h residue 576 VAL Chi-restraints excluded: chain h residue 587 VAL Chi-restraints excluded: chain h residue 599 VAL Chi-restraints excluded: chain j residue 178 VAL Chi-restraints excluded: chain j residue 289 HIS Chi-restraints excluded: chain m residue 445 ASN Chi-restraints excluded: chain m residue 449 VAL Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 572 LEU Chi-restraints excluded: chain m residue 653 GLN Chi-restraints excluded: chain m residue 666 GLU Chi-restraints excluded: chain m residue 713 VAL Chi-restraints excluded: chain m residue 740 LEU Chi-restraints excluded: chain m residue 779 ILE Chi-restraints excluded: chain m residue 808 LEU Chi-restraints excluded: chain n residue 475 GLN Chi-restraints excluded: chain n residue 593 VAL Chi-restraints excluded: chain n residue 662 MET Chi-restraints excluded: chain o residue 318 MET Chi-restraints excluded: chain o residue 386 CYS Chi-restraints excluded: chain o residue 407 ILE Chi-restraints excluded: chain o residue 422 MET Chi-restraints excluded: chain o residue 505 THR Chi-restraints excluded: chain o residue 520 PHE Chi-restraints excluded: chain o residue 543 VAL Chi-restraints excluded: chain o residue 550 ASP Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 618 LEU Chi-restraints excluded: chain x residue 145 LEU Chi-restraints excluded: chain x residue 152 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 172 optimal weight: 0.0970 chunk 174 optimal weight: 0.6980 chunk 167 optimal weight: 0.1980 chunk 207 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 188 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 161 ASN f 708 GLN ** h 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 426 HIS m 844 GLN n 475 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.173900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141971 restraints weight = 34542.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142518 restraints weight = 24514.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144039 restraints weight = 19277.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.144299 restraints weight = 14792.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144529 restraints weight = 13527.642| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20586 Z= 0.212 Angle : 0.534 14.675 27786 Z= 0.284 Chirality : 0.039 0.141 3039 Planarity : 0.004 0.042 3590 Dihedral : 4.165 39.001 2725 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.02 % Allowed : 16.61 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.17), residues: 2445 helix: 2.42 (0.14), residues: 1312 sheet: -0.64 (0.26), residues: 330 loop : 0.16 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 156 TYR 0.026 0.002 TYR f 980 PHE 0.017 0.002 PHE o 472 TRP 0.015 0.002 TRP h 509 HIS 0.010 0.001 HIS m 363 Details of bonding type rmsd covalent geometry : bond 0.00455 (20586) covalent geometry : angle 0.53430 (27786) hydrogen bonds : bond 0.04359 ( 1244) hydrogen bonds : angle 4.17585 ( 3609) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 341 time to evaluate : 0.818 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: X 130 MET cc_start: 0.6013 (ppp) cc_final: 0.5784 (ttt) REVERT: X 140 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6753 (tm-30) REVERT: X 147 HIS cc_start: 0.6580 (m-70) cc_final: 0.6304 (m-70) REVERT: X 150 GLN cc_start: 0.8243 (tp40) cc_final: 0.8011 (tp-100) REVERT: X 191 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7203 (mm) REVERT: f 465 GLN cc_start: 0.7492 (tt0) cc_final: 0.7127 (tt0) REVERT: f 469 PHE cc_start: 0.6381 (t80) cc_final: 0.5951 (t80) REVERT: f 553 TYR cc_start: 0.7585 (t80) cc_final: 0.7362 (t80) REVERT: f 617 GLU cc_start: 0.6877 (tp30) cc_final: 0.6376 (tp30) REVERT: f 665 VAL cc_start: 0.8125 (p) cc_final: 0.7700 (t) REVERT: f 708 GLN cc_start: 0.7172 (mm110) cc_final: 0.6919 (mm-40) REVERT: f 713 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8053 (t) REVERT: f 736 LYS cc_start: 0.7813 (mmtp) cc_final: 0.7258 (mtmm) REVERT: f 749 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6751 (mm-30) REVERT: f 883 LYS cc_start: 0.7776 (mttt) cc_final: 0.7209 (mttp) REVERT: f 987 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.6568 (t80) REVERT: f 1035 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6693 (mm-30) REVERT: h 278 LYS cc_start: 0.8288 (ttmm) cc_final: 0.8036 (ttmm) REVERT: h 279 HIS cc_start: 0.7726 (m90) cc_final: 0.7289 (m90) REVERT: h 308 GLU cc_start: 0.7319 (mp0) cc_final: 0.6608 (mp0) REVERT: h 353 TYR cc_start: 0.8108 (t80) cc_final: 0.7740 (t80) REVERT: h 363 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7836 (mtm110) REVERT: h 471 MET cc_start: 0.8007 (tmm) cc_final: 0.7742 (ttt) REVERT: h 607 ARG cc_start: 0.6670 (mtt180) cc_final: 0.6118 (mtt180) REVERT: j 135 PHE cc_start: 0.6905 (m-10) cc_final: 0.6537 (m-80) REVERT: j 251 LEU cc_start: 0.7357 (mp) cc_final: 0.6910 (tt) REVERT: j 364 MET cc_start: 0.6926 (tmm) cc_final: 0.6614 (tmm) REVERT: m 273 GLN cc_start: 0.7568 (mt0) cc_final: 0.7347 (mt0) REVERT: m 333 ASN cc_start: 0.6637 (t0) cc_final: 0.5944 (t0) REVERT: m 352 LYS cc_start: 0.8340 (mmmt) cc_final: 0.7818 (tppt) REVERT: m 372 TYR cc_start: 0.7925 (t80) cc_final: 0.7612 (t80) REVERT: m 407 GLU cc_start: 0.7319 (pm20) cc_final: 0.6827 (pm20) REVERT: m 468 LYS cc_start: 0.7552 (ttmt) cc_final: 0.7280 (ttmt) REVERT: m 540 LYS cc_start: 0.7590 (tppt) cc_final: 0.7126 (tppt) REVERT: m 550 MET cc_start: 0.7408 (mmm) cc_final: 0.7180 (mmp) REVERT: m 558 ASP cc_start: 0.7966 (t0) cc_final: 0.7763 (m-30) REVERT: m 567 ARG cc_start: 0.6007 (tpt90) cc_final: 0.5189 (mmm160) REVERT: m 598 ARG cc_start: 0.7438 (ttm110) cc_final: 0.6959 (ptm160) REVERT: m 629 GLN cc_start: 0.7321 (mp10) cc_final: 0.7098 (mp10) REVERT: m 782 ILE cc_start: 0.8306 (mt) cc_final: 0.8006 (mm) REVERT: m 810 LYS cc_start: 0.6349 (mptt) cc_final: 0.5645 (mmtt) REVERT: n 466 MET cc_start: 0.7521 (mmt) cc_final: 0.7045 (tpp) REVERT: n 556 ARG cc_start: 0.7153 (ttm-80) cc_final: 0.6843 (ttm110) REVERT: n 563 ARG cc_start: 0.7110 (tmm160) cc_final: 0.6806 (ptm160) REVERT: n 570 ASP cc_start: 0.7133 (t70) cc_final: 0.6875 (t0) REVERT: n 604 TYR cc_start: 0.6838 (m-10) cc_final: 0.6569 (m-10) REVERT: o 327 TYR cc_start: 0.7800 (m-80) cc_final: 0.6826 (m-80) REVERT: o 390 VAL cc_start: 0.8746 (t) cc_final: 0.8530 (m) REVERT: o 618 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7303 (tp) REVERT: x 130 MET cc_start: 0.6514 (mmm) cc_final: 0.6208 (tpp) REVERT: x 148 LEU cc_start: 0.7736 (mp) cc_final: 0.7515 (tp) REVERT: x 152 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7944 (tptt) outliers start: 66 outliers final: 43 residues processed: 384 average time/residue: 0.1818 time to fit residues: 99.8737 Evaluate side-chains 376 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 328 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 145 LEU Chi-restraints excluded: chain X residue 191 LEU Chi-restraints excluded: chain f residue 396 LEU Chi-restraints excluded: chain f residue 463 LEU Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 673 TRP Chi-restraints excluded: chain f residue 697 GLU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 792 CYS Chi-restraints excluded: chain f residue 852 ILE Chi-restraints excluded: chain f residue 978 CYS Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain h residue 321 LYS Chi-restraints excluded: chain h residue 368 THR Chi-restraints excluded: chain h residue 370 VAL Chi-restraints excluded: chain h residue 407 ILE Chi-restraints excluded: chain h residue 460 CYS Chi-restraints excluded: chain h residue 551 LEU Chi-restraints excluded: chain h residue 576 VAL Chi-restraints excluded: chain h residue 587 VAL Chi-restraints excluded: chain h residue 599 VAL Chi-restraints excluded: chain j residue 178 VAL Chi-restraints excluded: chain j residue 289 HIS Chi-restraints excluded: chain m residue 398 THR Chi-restraints excluded: chain m residue 431 GLN Chi-restraints excluded: chain m residue 445 ASN Chi-restraints excluded: chain m residue 449 VAL Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 653 GLN Chi-restraints excluded: chain m residue 666 GLU Chi-restraints excluded: chain m residue 713 VAL Chi-restraints excluded: chain m residue 740 LEU Chi-restraints excluded: chain m residue 779 ILE Chi-restraints excluded: chain m residue 808 LEU Chi-restraints excluded: chain n residue 475 GLN Chi-restraints excluded: chain n residue 550 MET Chi-restraints excluded: chain n residue 593 VAL Chi-restraints excluded: chain n residue 662 MET Chi-restraints excluded: chain o residue 318 MET Chi-restraints excluded: chain o residue 386 CYS Chi-restraints excluded: chain o residue 407 ILE Chi-restraints excluded: chain o residue 520 PHE Chi-restraints excluded: chain o residue 543 VAL Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain o residue 618 LEU Chi-restraints excluded: chain x residue 145 LEU Chi-restraints excluded: chain x residue 152 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 173 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 133 optimal weight: 0.2980 chunk 180 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 226 optimal weight: 0.2980 chunk 193 optimal weight: 0.0020 chunk 224 optimal weight: 0.1980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 161 ASN f 465 GLN ** h 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 844 GLN n 475 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.173389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140969 restraints weight = 34392.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.141976 restraints weight = 25878.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143431 restraints weight = 18165.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143576 restraints weight = 15326.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144267 restraints weight = 12820.261| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20586 Z= 0.167 Angle : 0.524 15.849 27786 Z= 0.276 Chirality : 0.039 0.245 3039 Planarity : 0.003 0.043 3590 Dihedral : 4.099 38.681 2725 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.47 % Allowed : 17.21 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.17), residues: 2445 helix: 2.50 (0.14), residues: 1314 sheet: -0.58 (0.27), residues: 330 loop : 0.20 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG n 598 TYR 0.025 0.001 TYR f 980 PHE 0.017 0.001 PHE o 343 TRP 0.014 0.002 TRP h 509 HIS 0.010 0.001 HIS m 363 Details of bonding type rmsd covalent geometry : bond 0.00363 (20586) covalent geometry : angle 0.52417 (27786) hydrogen bonds : bond 0.04167 ( 1244) hydrogen bonds : angle 4.09513 ( 3609) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 343 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 140 GLU cc_start: 0.6989 (tm-30) cc_final: 0.6751 (tm-30) REVERT: X 147 HIS cc_start: 0.6563 (m-70) cc_final: 0.6296 (m-70) REVERT: X 191 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7176 (mm) REVERT: f 465 GLN cc_start: 0.7483 (tt0) cc_final: 0.7173 (tt0) REVERT: f 469 PHE cc_start: 0.6424 (t80) cc_final: 0.6056 (t80) REVERT: f 550 MET cc_start: 0.7583 (tpp) cc_final: 0.6996 (mmp) REVERT: f 553 TYR cc_start: 0.7599 (t80) cc_final: 0.7346 (t80) REVERT: f 617 GLU cc_start: 0.6902 (tp30) cc_final: 0.6313 (tp30) REVERT: f 665 VAL cc_start: 0.8111 (p) cc_final: 0.7702 (t) REVERT: f 708 GLN cc_start: 0.7130 (mm110) cc_final: 0.6881 (mm-40) REVERT: f 713 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8054 (t) REVERT: f 736 LYS cc_start: 0.7825 (mmtp) cc_final: 0.7230 (mtmm) REVERT: f 749 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6737 (mm-30) REVERT: f 883 LYS cc_start: 0.7749 (mttt) cc_final: 0.7194 (mttp) REVERT: f 987 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.6542 (t80) REVERT: h 269 ARG cc_start: 0.7464 (mtp85) cc_final: 0.7258 (mtp180) REVERT: h 308 GLU cc_start: 0.7333 (mp0) cc_final: 0.6606 (mp0) REVERT: h 353 TYR cc_start: 0.8079 (t80) cc_final: 0.7679 (t80) REVERT: h 422 MET cc_start: 0.7351 (pmm) cc_final: 0.6954 (pmm) REVERT: h 471 MET cc_start: 0.8009 (tmm) cc_final: 0.7681 (ttt) REVERT: h 607 ARG cc_start: 0.6649 (mtt180) cc_final: 0.6122 (mtt180) REVERT: j 135 PHE cc_start: 0.6887 (m-10) cc_final: 0.6511 (m-80) REVERT: j 251 LEU cc_start: 0.7345 (mp) cc_final: 0.6884 (tt) REVERT: j 364 MET cc_start: 0.6939 (tmm) cc_final: 0.6616 (tmm) REVERT: m 273 GLN cc_start: 0.7565 (mt0) cc_final: 0.7347 (mt0) REVERT: m 333 ASN cc_start: 0.6804 (t0) cc_final: 0.6210 (t0) REVERT: m 337 LYS cc_start: 0.7712 (mmtt) cc_final: 0.7413 (mmtm) REVERT: m 352 LYS cc_start: 0.8330 (mmmt) cc_final: 0.7842 (tppt) REVERT: m 407 GLU cc_start: 0.7296 (pm20) cc_final: 0.6806 (pm20) REVERT: m 468 LYS cc_start: 0.7523 (ttmt) cc_final: 0.7278 (ttmt) REVERT: m 567 ARG cc_start: 0.6101 (tpt90) cc_final: 0.5446 (mmm160) REVERT: m 598 ARG cc_start: 0.7503 (ttm110) cc_final: 0.7014 (ptm160) REVERT: m 634 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7729 (ttmm) REVERT: m 754 LYS cc_start: 0.8378 (tptt) cc_final: 0.7945 (tppt) REVERT: m 782 ILE cc_start: 0.8282 (mt) cc_final: 0.7998 (mm) REVERT: m 810 LYS cc_start: 0.6119 (mptt) cc_final: 0.5642 (mptt) REVERT: n 466 MET cc_start: 0.7577 (mmt) cc_final: 0.6994 (tpp) REVERT: n 556 ARG cc_start: 0.7161 (ttm-80) cc_final: 0.6804 (ttm110) REVERT: n 563 ARG cc_start: 0.7092 (tmm160) cc_final: 0.6811 (ptm160) REVERT: n 570 ASP cc_start: 0.7128 (t70) cc_final: 0.6878 (t0) REVERT: n 604 TYR cc_start: 0.6846 (m-10) cc_final: 0.6558 (m-10) REVERT: n 605 GLN cc_start: 0.7052 (mt0) cc_final: 0.6427 (mt0) REVERT: o 327 TYR cc_start: 0.7694 (m-80) cc_final: 0.6634 (m-80) REVERT: o 390 VAL cc_start: 0.8722 (t) cc_final: 0.8481 (m) REVERT: o 559 GLU cc_start: 0.6686 (mp0) cc_final: 0.6399 (mp0) REVERT: x 130 MET cc_start: 0.6513 (mmm) cc_final: 0.5687 (mmp) REVERT: x 140 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6824 (mt-10) REVERT: x 152 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7934 (tptt) outliers start: 54 outliers final: 38 residues processed: 381 average time/residue: 0.1829 time to fit residues: 99.5616 Evaluate side-chains 377 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 335 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 145 LEU Chi-restraints excluded: chain X residue 191 LEU Chi-restraints excluded: chain f residue 396 LEU Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 673 TRP Chi-restraints excluded: chain f residue 697 GLU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 792 CYS Chi-restraints excluded: chain f residue 852 ILE Chi-restraints excluded: chain f residue 978 CYS Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain h residue 407 ILE Chi-restraints excluded: chain h residue 551 LEU Chi-restraints excluded: chain h residue 576 VAL Chi-restraints excluded: chain h residue 587 VAL Chi-restraints excluded: chain h residue 599 VAL Chi-restraints excluded: chain j residue 178 VAL Chi-restraints excluded: chain j residue 289 HIS Chi-restraints excluded: chain m residue 398 THR Chi-restraints excluded: chain m residue 431 GLN Chi-restraints excluded: chain m residue 445 ASN Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 653 GLN Chi-restraints excluded: chain m residue 666 GLU Chi-restraints excluded: chain m residue 688 SER Chi-restraints excluded: chain m residue 713 VAL Chi-restraints excluded: chain m residue 740 LEU Chi-restraints excluded: chain m residue 779 ILE Chi-restraints excluded: chain m residue 808 LEU Chi-restraints excluded: chain n residue 475 GLN Chi-restraints excluded: chain n residue 662 MET Chi-restraints excluded: chain o residue 318 MET Chi-restraints excluded: chain o residue 346 ASN Chi-restraints excluded: chain o residue 381 THR Chi-restraints excluded: chain o residue 386 CYS Chi-restraints excluded: chain o residue 407 ILE Chi-restraints excluded: chain o residue 517 LEU Chi-restraints excluded: chain o residue 520 PHE Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain x residue 145 LEU Chi-restraints excluded: chain x residue 152 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.0970 chunk 221 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 218 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 157 optimal weight: 0.0770 chunk 78 optimal weight: 0.8980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 150 GLN X 161 ASN f 465 GLN f 799 ASN ** h 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 426 HIS m 844 GLN n 475 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.172908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.140963 restraints weight = 34550.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141558 restraints weight = 25776.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.142913 restraints weight = 19228.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143479 restraints weight = 14497.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143873 restraints weight = 13198.788| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20586 Z= 0.236 Angle : 0.561 15.809 27786 Z= 0.296 Chirality : 0.040 0.191 3039 Planarity : 0.004 0.088 3590 Dihedral : 4.180 38.806 2725 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.70 % Allowed : 17.25 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.17), residues: 2445 helix: 2.44 (0.14), residues: 1315 sheet: -0.62 (0.27), residues: 330 loop : 0.16 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG n 598 TYR 0.027 0.002 TYR f 980 PHE 0.026 0.002 PHE m 277 TRP 0.023 0.002 TRP h 611 HIS 0.011 0.001 HIS m 363 Details of bonding type rmsd covalent geometry : bond 0.00507 (20586) covalent geometry : angle 0.56142 (27786) hydrogen bonds : bond 0.04320 ( 1244) hydrogen bonds : angle 4.16499 ( 3609) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 342 time to evaluate : 0.741 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: X 140 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6737 (tm-30) REVERT: X 147 HIS cc_start: 0.6605 (m-70) cc_final: 0.6345 (m-70) REVERT: X 191 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7110 (mm) REVERT: f 465 GLN cc_start: 0.7494 (tt0) cc_final: 0.6983 (tt0) REVERT: f 469 PHE cc_start: 0.6429 (t80) cc_final: 0.6075 (t80) REVERT: f 550 MET cc_start: 0.7576 (tpp) cc_final: 0.7018 (mmp) REVERT: f 553 TYR cc_start: 0.7577 (t80) cc_final: 0.7318 (t80) REVERT: f 580 GLU cc_start: 0.7400 (pt0) cc_final: 0.7046 (pt0) REVERT: f 617 GLU cc_start: 0.6948 (tp30) cc_final: 0.6314 (tp30) REVERT: f 665 VAL cc_start: 0.8049 (p) cc_final: 0.7636 (t) REVERT: f 708 GLN cc_start: 0.7157 (mm110) cc_final: 0.6901 (mm-40) REVERT: f 713 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8044 (t) REVERT: f 736 LYS cc_start: 0.7872 (mmtp) cc_final: 0.7432 (mtmm) REVERT: f 749 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6768 (mm-30) REVERT: f 883 LYS cc_start: 0.7777 (mttt) cc_final: 0.7219 (mttp) REVERT: f 987 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6541 (t80) REVERT: f 1035 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6752 (mm-30) REVERT: h 269 ARG cc_start: 0.7513 (mtp85) cc_final: 0.7288 (mtp180) REVERT: h 308 GLU cc_start: 0.7373 (mp0) cc_final: 0.6588 (mp0) REVERT: h 353 TYR cc_start: 0.8171 (t80) cc_final: 0.7741 (t80) REVERT: h 422 MET cc_start: 0.7339 (pmm) cc_final: 0.6948 (pmm) REVERT: h 471 MET cc_start: 0.7977 (tmm) cc_final: 0.7736 (ttt) REVERT: j 135 PHE cc_start: 0.6859 (m-10) cc_final: 0.6480 (m-80) REVERT: j 251 LEU cc_start: 0.7375 (mp) cc_final: 0.6917 (tt) REVERT: j 264 GLN cc_start: 0.3871 (tm-30) cc_final: 0.3525 (tm-30) REVERT: j 364 MET cc_start: 0.6960 (tmm) cc_final: 0.6639 (tmm) REVERT: m 273 GLN cc_start: 0.7588 (mt0) cc_final: 0.7349 (mt0) REVERT: m 333 ASN cc_start: 0.6925 (t0) cc_final: 0.6390 (t0) REVERT: m 337 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7492 (mmtt) REVERT: m 352 LYS cc_start: 0.8335 (mmmt) cc_final: 0.7802 (tppt) REVERT: m 407 GLU cc_start: 0.7283 (pm20) cc_final: 0.6785 (pm20) REVERT: m 453 ASN cc_start: 0.7762 (p0) cc_final: 0.7309 (p0) REVERT: m 466 MET cc_start: 0.7366 (mtm) cc_final: 0.7115 (mpp) REVERT: m 468 LYS cc_start: 0.7522 (ttmt) cc_final: 0.7223 (ttmt) REVERT: m 567 ARG cc_start: 0.6104 (tpt90) cc_final: 0.5428 (mmm160) REVERT: m 598 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7056 (ptm160) REVERT: m 614 ASP cc_start: 0.7179 (m-30) cc_final: 0.6802 (t0) REVERT: m 629 GLN cc_start: 0.7383 (mp10) cc_final: 0.7095 (mp10) REVERT: m 754 LYS cc_start: 0.8385 (tptt) cc_final: 0.7932 (tppt) REVERT: m 782 ILE cc_start: 0.8312 (mt) cc_final: 0.8048 (mm) REVERT: m 810 LYS cc_start: 0.6174 (mptt) cc_final: 0.5547 (mptt) REVERT: n 466 MET cc_start: 0.7615 (mmt) cc_final: 0.7118 (tpp) REVERT: n 550 MET cc_start: 0.6759 (mmt) cc_final: 0.6430 (tpp) REVERT: n 556 ARG cc_start: 0.7181 (ttm-80) cc_final: 0.6799 (ttm110) REVERT: n 563 ARG cc_start: 0.7073 (tmm160) cc_final: 0.6806 (ptm160) REVERT: n 570 ASP cc_start: 0.7173 (t70) cc_final: 0.6935 (t0) REVERT: n 604 TYR cc_start: 0.6871 (m-10) cc_final: 0.6561 (m-10) REVERT: o 327 TYR cc_start: 0.7826 (m-80) cc_final: 0.6800 (m-80) REVERT: o 390 VAL cc_start: 0.8736 (t) cc_final: 0.8473 (m) REVERT: o 613 ARG cc_start: 0.7722 (mtt-85) cc_final: 0.7238 (mtt-85) REVERT: x 140 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6816 (mt-10) REVERT: x 152 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7856 (tptt) REVERT: x 156 ARG cc_start: 0.6348 (ttp-110) cc_final: 0.5910 (ttp-110) outliers start: 59 outliers final: 44 residues processed: 383 average time/residue: 0.1823 time to fit residues: 99.7440 Evaluate side-chains 383 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 335 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 145 LEU Chi-restraints excluded: chain X residue 191 LEU Chi-restraints excluded: chain f residue 396 LEU Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 673 TRP Chi-restraints excluded: chain f residue 697 GLU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 792 CYS Chi-restraints excluded: chain f residue 852 ILE Chi-restraints excluded: chain f residue 978 CYS Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain h residue 322 LYS Chi-restraints excluded: chain h residue 370 VAL Chi-restraints excluded: chain h residue 407 ILE Chi-restraints excluded: chain h residue 460 CYS Chi-restraints excluded: chain h residue 551 LEU Chi-restraints excluded: chain h residue 576 VAL Chi-restraints excluded: chain h residue 587 VAL Chi-restraints excluded: chain h residue 599 VAL Chi-restraints excluded: chain j residue 178 VAL Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 289 HIS Chi-restraints excluded: chain m residue 398 THR Chi-restraints excluded: chain m residue 431 GLN Chi-restraints excluded: chain m residue 445 ASN Chi-restraints excluded: chain m residue 449 VAL Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 653 GLN Chi-restraints excluded: chain m residue 666 GLU Chi-restraints excluded: chain m residue 713 VAL Chi-restraints excluded: chain m residue 740 LEU Chi-restraints excluded: chain m residue 779 ILE Chi-restraints excluded: chain m residue 808 LEU Chi-restraints excluded: chain n residue 475 GLN Chi-restraints excluded: chain n residue 593 VAL Chi-restraints excluded: chain n residue 662 MET Chi-restraints excluded: chain o residue 281 VAL Chi-restraints excluded: chain o residue 318 MET Chi-restraints excluded: chain o residue 346 ASN Chi-restraints excluded: chain o residue 381 THR Chi-restraints excluded: chain o residue 386 CYS Chi-restraints excluded: chain o residue 407 ILE Chi-restraints excluded: chain o residue 517 LEU Chi-restraints excluded: chain o residue 543 VAL Chi-restraints excluded: chain o residue 550 ASP Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain x residue 145 LEU Chi-restraints excluded: chain x residue 152 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 13 optimal weight: 0.8980 chunk 138 optimal weight: 0.3980 chunk 155 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 233 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 0.0980 chunk 64 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 127 ASN X 161 ASN f 465 GLN ** h 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 426 HIS m 844 GLN n 475 GLN n 605 GLN x 133 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.172598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140844 restraints weight = 34490.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.141762 restraints weight = 25758.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.143317 restraints weight = 18689.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143554 restraints weight = 14605.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143874 restraints weight = 13131.079| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20586 Z= 0.215 Angle : 0.564 15.389 27786 Z= 0.296 Chirality : 0.040 0.168 3039 Planarity : 0.004 0.049 3590 Dihedral : 4.172 34.277 2725 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.61 % Allowed : 17.71 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.17), residues: 2445 helix: 2.45 (0.14), residues: 1316 sheet: -0.61 (0.27), residues: 330 loop : 0.14 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG n 598 TYR 0.027 0.002 TYR f 980 PHE 0.025 0.002 PHE m 582 TRP 0.024 0.002 TRP m 755 HIS 0.011 0.001 HIS m 363 Details of bonding type rmsd covalent geometry : bond 0.00463 (20586) covalent geometry : angle 0.56434 (27786) hydrogen bonds : bond 0.04280 ( 1244) hydrogen bonds : angle 4.15516 ( 3609) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 348 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 140 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6722 (tm-30) REVERT: X 147 HIS cc_start: 0.6601 (m-70) cc_final: 0.6355 (m-70) REVERT: X 191 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7160 (mm) REVERT: f 410 GLU cc_start: 0.7998 (tp30) cc_final: 0.7644 (tp30) REVERT: f 413 MET cc_start: 0.7532 (mmm) cc_final: 0.7294 (mmm) REVERT: f 465 GLN cc_start: 0.7312 (tt0) cc_final: 0.7083 (tt0) REVERT: f 469 PHE cc_start: 0.6431 (t80) cc_final: 0.6092 (t80) REVERT: f 550 MET cc_start: 0.7551 (tpp) cc_final: 0.6986 (mmp) REVERT: f 553 TYR cc_start: 0.7533 (t80) cc_final: 0.7273 (t80) REVERT: f 580 GLU cc_start: 0.7407 (pt0) cc_final: 0.7072 (pt0) REVERT: f 617 GLU cc_start: 0.6954 (tp30) cc_final: 0.6268 (tp30) REVERT: f 665 VAL cc_start: 0.8084 (p) cc_final: 0.7661 (t) REVERT: f 708 GLN cc_start: 0.7144 (mm110) cc_final: 0.6877 (mm-40) REVERT: f 713 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8028 (t) REVERT: f 721 GLU cc_start: 0.7165 (pt0) cc_final: 0.6871 (mp0) REVERT: f 736 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7265 (mmtp) REVERT: f 749 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6763 (mm-30) REVERT: f 755 TRP cc_start: 0.6557 (p-90) cc_final: 0.6121 (p-90) REVERT: f 883 LYS cc_start: 0.7767 (mttt) cc_final: 0.7183 (mttp) REVERT: f 987 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.6541 (t80) REVERT: f 1035 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6662 (mm-30) REVERT: h 269 ARG cc_start: 0.7505 (mtp85) cc_final: 0.7263 (mtp180) REVERT: h 308 GLU cc_start: 0.7322 (mp0) cc_final: 0.6764 (mp0) REVERT: h 353 TYR cc_start: 0.8177 (t80) cc_final: 0.7720 (t80) REVERT: h 471 MET cc_start: 0.7998 (tmm) cc_final: 0.7691 (ttt) REVERT: h 607 ARG cc_start: 0.6613 (mtt180) cc_final: 0.6096 (mtt180) REVERT: j 135 PHE cc_start: 0.6818 (m-10) cc_final: 0.6440 (m-80) REVERT: j 251 LEU cc_start: 0.7400 (mp) cc_final: 0.6927 (tt) REVERT: j 364 MET cc_start: 0.6948 (tmm) cc_final: 0.6666 (tmm) REVERT: m 273 GLN cc_start: 0.7581 (mt0) cc_final: 0.7348 (mt0) REVERT: m 324 GLN cc_start: 0.7126 (mp10) cc_final: 0.6909 (pm20) REVERT: m 333 ASN cc_start: 0.6913 (t0) cc_final: 0.6238 (t0) REVERT: m 337 LYS cc_start: 0.7756 (mmtt) cc_final: 0.7389 (mmtm) REVERT: m 352 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7804 (tppt) REVERT: m 407 GLU cc_start: 0.7273 (pm20) cc_final: 0.6794 (pm20) REVERT: m 453 ASN cc_start: 0.7751 (p0) cc_final: 0.7297 (p0) REVERT: m 466 MET cc_start: 0.7338 (mtm) cc_final: 0.7004 (mtm) REVERT: m 468 LYS cc_start: 0.7614 (ttmt) cc_final: 0.7330 (ttmt) REVERT: m 567 ARG cc_start: 0.6101 (tpt90) cc_final: 0.5383 (mmm160) REVERT: m 580 GLU cc_start: 0.7133 (tp30) cc_final: 0.6686 (tp30) REVERT: m 598 ARG cc_start: 0.7523 (ttm110) cc_final: 0.7065 (ptm160) REVERT: m 614 ASP cc_start: 0.7179 (m-30) cc_final: 0.6826 (t0) REVERT: m 629 GLN cc_start: 0.7366 (mp10) cc_final: 0.7078 (mp10) REVERT: m 754 LYS cc_start: 0.8388 (tptt) cc_final: 0.8077 (tppt) REVERT: m 782 ILE cc_start: 0.8314 (mt) cc_final: 0.8060 (mm) REVERT: m 810 LYS cc_start: 0.6210 (mptt) cc_final: 0.5721 (mptt) REVERT: n 466 MET cc_start: 0.7620 (mmt) cc_final: 0.7092 (tpp) REVERT: n 556 ARG cc_start: 0.7141 (ttm-80) cc_final: 0.6895 (ttm110) REVERT: n 563 ARG cc_start: 0.7050 (tmm160) cc_final: 0.6782 (ptm160) REVERT: n 570 ASP cc_start: 0.7160 (t70) cc_final: 0.6934 (t0) REVERT: n 605 GLN cc_start: 0.7349 (mt0) cc_final: 0.6846 (mt0) REVERT: o 327 TYR cc_start: 0.7804 (m-80) cc_final: 0.6761 (m-80) REVERT: o 390 VAL cc_start: 0.8725 (t) cc_final: 0.8468 (m) REVERT: o 613 ARG cc_start: 0.7722 (mtt-85) cc_final: 0.7239 (mtt-85) REVERT: x 140 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6774 (mt-10) REVERT: x 152 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7912 (tmtt) outliers start: 57 outliers final: 44 residues processed: 388 average time/residue: 0.1761 time to fit residues: 98.1253 Evaluate side-chains 390 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 342 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 145 LEU Chi-restraints excluded: chain X residue 191 LEU Chi-restraints excluded: chain f residue 396 LEU Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 673 TRP Chi-restraints excluded: chain f residue 697 GLU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 792 CYS Chi-restraints excluded: chain f residue 826 SER Chi-restraints excluded: chain f residue 852 ILE Chi-restraints excluded: chain f residue 978 CYS Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain h residue 322 LYS Chi-restraints excluded: chain h residue 370 VAL Chi-restraints excluded: chain h residue 407 ILE Chi-restraints excluded: chain h residue 460 CYS Chi-restraints excluded: chain h residue 546 MET Chi-restraints excluded: chain h residue 551 LEU Chi-restraints excluded: chain h residue 576 VAL Chi-restraints excluded: chain h residue 587 VAL Chi-restraints excluded: chain h residue 599 VAL Chi-restraints excluded: chain j residue 178 VAL Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain m residue 398 THR Chi-restraints excluded: chain m residue 431 GLN Chi-restraints excluded: chain m residue 445 ASN Chi-restraints excluded: chain m residue 449 VAL Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 653 GLN Chi-restraints excluded: chain m residue 666 GLU Chi-restraints excluded: chain m residue 688 SER Chi-restraints excluded: chain m residue 713 VAL Chi-restraints excluded: chain m residue 740 LEU Chi-restraints excluded: chain m residue 779 ILE Chi-restraints excluded: chain m residue 808 LEU Chi-restraints excluded: chain n residue 593 VAL Chi-restraints excluded: chain n residue 662 MET Chi-restraints excluded: chain o residue 318 MET Chi-restraints excluded: chain o residue 346 ASN Chi-restraints excluded: chain o residue 381 THR Chi-restraints excluded: chain o residue 386 CYS Chi-restraints excluded: chain o residue 407 ILE Chi-restraints excluded: chain o residue 517 LEU Chi-restraints excluded: chain o residue 520 PHE Chi-restraints excluded: chain o residue 543 VAL Chi-restraints excluded: chain o residue 550 ASP Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain x residue 152 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 242 optimal weight: 0.5980 chunk 185 optimal weight: 0.9990 chunk 169 optimal weight: 0.0970 chunk 104 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 chunk 223 optimal weight: 0.0980 chunk 158 optimal weight: 0.5980 chunk 218 optimal weight: 0.0970 chunk 211 optimal weight: 0.2980 chunk 94 optimal weight: 0.3980 chunk 173 optimal weight: 0.2980 overall best weight: 0.1376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 161 ASN f 620 HIS ** h 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 426 HIS j 159 HIS m 631 GLN m 844 GLN n 571 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.176141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144838 restraints weight = 34489.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145995 restraints weight = 26637.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146729 restraints weight = 18615.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.147457 restraints weight = 16674.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147825 restraints weight = 13998.004| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20586 Z= 0.128 Angle : 0.548 15.367 27786 Z= 0.286 Chirality : 0.039 0.168 3039 Planarity : 0.003 0.060 3590 Dihedral : 3.938 18.969 2723 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.24 % Allowed : 18.26 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.17), residues: 2445 helix: 2.55 (0.14), residues: 1321 sheet: -0.62 (0.26), residues: 330 loop : 0.24 (0.24), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG f 354 TYR 0.029 0.001 TYR n 604 PHE 0.018 0.001 PHE o 343 TRP 0.027 0.002 TRP m 755 HIS 0.019 0.001 HIS j 289 Details of bonding type rmsd covalent geometry : bond 0.00282 (20586) covalent geometry : angle 0.54824 (27786) hydrogen bonds : bond 0.03973 ( 1244) hydrogen bonds : angle 3.99360 ( 3609) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 353 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 137 MET cc_start: 0.7072 (mmm) cc_final: 0.6826 (mmm) REVERT: X 140 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6719 (tm-30) REVERT: X 147 HIS cc_start: 0.6588 (m-70) cc_final: 0.6323 (m-70) REVERT: X 153 HIS cc_start: 0.7804 (t-170) cc_final: 0.7496 (t-170) REVERT: X 191 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7094 (mm) REVERT: f 465 GLN cc_start: 0.7459 (tt0) cc_final: 0.7137 (tt0) REVERT: f 469 PHE cc_start: 0.6429 (t80) cc_final: 0.6067 (t80) REVERT: f 550 MET cc_start: 0.7541 (tpp) cc_final: 0.7065 (mmp) REVERT: f 553 TYR cc_start: 0.7573 (t80) cc_final: 0.7313 (t80) REVERT: f 580 GLU cc_start: 0.7445 (pt0) cc_final: 0.7064 (pt0) REVERT: f 617 GLU cc_start: 0.6951 (tp30) cc_final: 0.6354 (tp30) REVERT: f 665 VAL cc_start: 0.8022 (p) cc_final: 0.7651 (t) REVERT: f 708 GLN cc_start: 0.7123 (mm110) cc_final: 0.6862 (mm-40) REVERT: f 713 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.7999 (t) REVERT: f 749 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6628 (mm-30) REVERT: f 755 TRP cc_start: 0.6493 (p-90) cc_final: 0.6048 (p-90) REVERT: f 883 LYS cc_start: 0.7736 (mttt) cc_final: 0.7173 (mttp) REVERT: f 922 TRP cc_start: 0.7541 (t60) cc_final: 0.7239 (t60) REVERT: f 987 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6477 (t80) REVERT: f 1035 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6689 (mm-30) REVERT: h 269 ARG cc_start: 0.7403 (mtp85) cc_final: 0.7169 (mtp180) REVERT: h 308 GLU cc_start: 0.7315 (mp0) cc_final: 0.6773 (mp0) REVERT: h 353 TYR cc_start: 0.8038 (t80) cc_final: 0.7519 (t80) REVERT: h 471 MET cc_start: 0.7995 (tmm) cc_final: 0.7677 (ttt) REVERT: h 607 ARG cc_start: 0.6870 (mtt180) cc_final: 0.6327 (mtt180) REVERT: j 135 PHE cc_start: 0.6811 (m-10) cc_final: 0.6446 (m-80) REVERT: j 228 LEU cc_start: 0.7553 (mp) cc_final: 0.6992 (pt) REVERT: j 251 LEU cc_start: 0.7361 (mp) cc_final: 0.6875 (tt) REVERT: m 273 GLN cc_start: 0.7543 (mt0) cc_final: 0.7320 (mt0) REVERT: m 324 GLN cc_start: 0.7130 (mp10) cc_final: 0.6894 (pm20) REVERT: m 333 ASN cc_start: 0.6810 (t0) cc_final: 0.6090 (t0) REVERT: m 337 LYS cc_start: 0.7654 (mmtt) cc_final: 0.7156 (mmmt) REVERT: m 352 LYS cc_start: 0.8367 (mmmt) cc_final: 0.7857 (tppt) REVERT: m 407 GLU cc_start: 0.7039 (pm20) cc_final: 0.6595 (pm20) REVERT: m 453 ASN cc_start: 0.7733 (p0) cc_final: 0.7301 (p0) REVERT: m 466 MET cc_start: 0.7381 (mtm) cc_final: 0.7021 (mtm) REVERT: m 468 LYS cc_start: 0.7593 (ttmt) cc_final: 0.7305 (ttmt) REVERT: m 551 LYS cc_start: 0.8082 (tptt) cc_final: 0.7468 (mmmt) REVERT: m 580 GLU cc_start: 0.7170 (tp30) cc_final: 0.6615 (tp30) REVERT: m 598 ARG cc_start: 0.7445 (ttm110) cc_final: 0.6999 (ptm160) REVERT: m 629 GLN cc_start: 0.7358 (mp10) cc_final: 0.7059 (mp10) REVERT: m 754 LYS cc_start: 0.8305 (tptt) cc_final: 0.7987 (tppt) REVERT: m 782 ILE cc_start: 0.8274 (mt) cc_final: 0.8039 (mm) REVERT: m 810 LYS cc_start: 0.6194 (mptt) cc_final: 0.5663 (mmtt) REVERT: n 466 MET cc_start: 0.7551 (mmt) cc_final: 0.7042 (tpp) REVERT: n 563 ARG cc_start: 0.7063 (tmm160) cc_final: 0.6823 (ptm160) REVERT: n 570 ASP cc_start: 0.7053 (t70) cc_final: 0.6765 (t0) REVERT: n 605 GLN cc_start: 0.7383 (mt0) cc_final: 0.6890 (mt0) REVERT: o 327 TYR cc_start: 0.7645 (m-80) cc_final: 0.6455 (m-80) REVERT: o 390 VAL cc_start: 0.8706 (t) cc_final: 0.8416 (m) REVERT: o 613 ARG cc_start: 0.7574 (mtt-85) cc_final: 0.7126 (mtt-85) REVERT: x 140 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6806 (mt-10) REVERT: x 152 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7779 (tptt) REVERT: x 156 ARG cc_start: 0.6481 (ttp-110) cc_final: 0.6176 (ttp-110) outliers start: 49 outliers final: 38 residues processed: 385 average time/residue: 0.1785 time to fit residues: 98.7173 Evaluate side-chains 372 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 330 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 145 LEU Chi-restraints excluded: chain X residue 191 LEU Chi-restraints excluded: chain f residue 396 LEU Chi-restraints excluded: chain f residue 620 HIS Chi-restraints excluded: chain f residue 644 VAL Chi-restraints excluded: chain f residue 673 TRP Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 792 CYS Chi-restraints excluded: chain f residue 826 SER Chi-restraints excluded: chain f residue 852 ILE Chi-restraints excluded: chain f residue 978 CYS Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain h residue 322 LYS Chi-restraints excluded: chain h residue 370 VAL Chi-restraints excluded: chain h residue 407 ILE Chi-restraints excluded: chain h residue 460 CYS Chi-restraints excluded: chain h residue 546 MET Chi-restraints excluded: chain h residue 551 LEU Chi-restraints excluded: chain h residue 599 VAL Chi-restraints excluded: chain j residue 178 VAL Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain m residue 398 THR Chi-restraints excluded: chain m residue 445 ASN Chi-restraints excluded: chain m residue 449 VAL Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 653 GLN Chi-restraints excluded: chain m residue 666 GLU Chi-restraints excluded: chain m residue 688 SER Chi-restraints excluded: chain m residue 713 VAL Chi-restraints excluded: chain m residue 740 LEU Chi-restraints excluded: chain m residue 755 TRP Chi-restraints excluded: chain m residue 779 ILE Chi-restraints excluded: chain m residue 808 LEU Chi-restraints excluded: chain n residue 593 VAL Chi-restraints excluded: chain o residue 318 MET Chi-restraints excluded: chain o residue 346 ASN Chi-restraints excluded: chain o residue 386 CYS Chi-restraints excluded: chain o residue 407 ILE Chi-restraints excluded: chain o residue 520 PHE Chi-restraints excluded: chain o residue 543 VAL Chi-restraints excluded: chain o residue 560 VAL Chi-restraints excluded: chain x residue 152 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 126 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 186 optimal weight: 0.3980 chunk 235 optimal weight: 5.9990 chunk 82 optimal weight: 0.4980 chunk 39 optimal weight: 0.0770 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 161 ASN f 465 GLN f 620 HIS ** h 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 426 HIS m 844 GLN n 571 GLN x 133 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.172365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140207 restraints weight = 34676.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141161 restraints weight = 24794.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142463 restraints weight = 18252.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.142518 restraints weight = 16080.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142996 restraints weight = 13339.337| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20586 Z= 0.240 Angle : 0.598 14.750 27786 Z= 0.313 Chirality : 0.041 0.217 3039 Planarity : 0.004 0.060 3590 Dihedral : 4.092 20.458 2723 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.43 % Allowed : 18.31 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.17), residues: 2445 helix: 2.45 (0.14), residues: 1323 sheet: -0.64 (0.26), residues: 332 loop : 0.15 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG n 598 TYR 0.040 0.002 TYR n 604 PHE 0.032 0.002 PHE j 253 TRP 0.037 0.002 TRP h 611 HIS 0.022 0.001 HIS f 620 Details of bonding type rmsd covalent geometry : bond 0.00516 (20586) covalent geometry : angle 0.59775 (27786) hydrogen bonds : bond 0.04305 ( 1244) hydrogen bonds : angle 4.16483 ( 3609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4299.63 seconds wall clock time: 75 minutes 2.98 seconds (4502.98 seconds total)