Starting phenix.real_space_refine on Fri Mar 22 05:15:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqi_26695/03_2024/7uqi_26695_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqi_26695/03_2024/7uqi_26695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqi_26695/03_2024/7uqi_26695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqi_26695/03_2024/7uqi_26695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqi_26695/03_2024/7uqi_26695_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqi_26695/03_2024/7uqi_26695_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 122 5.16 5 C 20742 2.51 5 N 5529 2.21 5 O 6021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 506": "OE1" <-> "OE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A GLU 733": "OE1" <-> "OE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A GLU 865": "OE1" <-> "OE2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A GLU 1320": "OE1" <-> "OE2" Residue "A GLU 1326": "OE1" <-> "OE2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "A GLU 1373": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B GLU 632": "OE1" <-> "OE2" Residue "B GLU 757": "OE1" <-> "OE2" Residue "B GLU 764": "OE1" <-> "OE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "B GLU 847": "OE1" <-> "OE2" Residue "B GLU 873": "OE1" <-> "OE2" Residue "B GLU 914": "OE1" <-> "OE2" Residue "B GLU 935": "OE1" <-> "OE2" Residue "B GLU 1325": "OE1" <-> "OE2" Residue "C GLU 519": "OE1" <-> "OE2" Residue "C GLU 873": "OE1" <-> "OE2" Residue "D GLU 437": "OE1" <-> "OE2" Residue "D GLU 690": "OE1" <-> "OE2" Residue "D GLU 760": "OE1" <-> "OE2" Residue "D GLU 764": "OE1" <-> "OE2" Residue "D GLU 795": "OE1" <-> "OE2" Residue "D GLU 815": "OE1" <-> "OE2" Residue "D GLU 847": "OE1" <-> "OE2" Residue "D GLU 879": "OE1" <-> "OE2" Residue "D GLU 914": "OE1" <-> "OE2" Residue "D GLU 935": "OE1" <-> "OE2" Residue "D GLU 1325": "OE1" <-> "OE2" Residue "D GLU 1336": "OE1" <-> "OE2" Residue "D GLU 1347": "OE1" <-> "OE2" Residue "D GLU 1372": "OE1" <-> "OE2" Residue "E GLU 757": "OE1" <-> "OE2" Residue "E GLU 760": "OE1" <-> "OE2" Residue "E GLU 824": "OE1" <-> "OE2" Residue "E GLU 873": "OE1" <-> "OE2" Residue "E GLU 914": "OE1" <-> "OE2" Residue "E GLU 1336": "OE1" <-> "OE2" Residue "F GLU 437": "OE1" <-> "OE2" Residue "F GLU 497": "OE1" <-> "OE2" Residue "F GLU 760": "OE1" <-> "OE2" Residue "F GLU 764": "OE1" <-> "OE2" Residue "F GLU 794": "OE1" <-> "OE2" Residue "F GLU 795": "OE1" <-> "OE2" Residue "F GLU 824": "OE1" <-> "OE2" Residue "F GLU 903": "OE1" <-> "OE2" Residue "F GLU 914": "OE1" <-> "OE2" Residue "F GLU 1336": "OE1" <-> "OE2" Residue "F GLU 1347": "OE1" <-> "OE2" Residue "G ARG 993": "NH1" <-> "NH2" Residue "G GLU 1051": "OE1" <-> "OE2" Residue "G GLU 1060": "OE1" <-> "OE2" Residue "G GLU 1109": "OE1" <-> "OE2" Residue "H ASP 1117": "OD1" <-> "OD2" Residue "H GLU 1126": "OE1" <-> "OE2" Residue "I GLU 1082": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32424 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4591 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 32, 'TRANS': 543} Chain breaks: 2 Chain: "B" Number of atoms: 4612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4612 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 4607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4607 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 32, 'TRANS': 545} Chain breaks: 2 Chain: "D" Number of atoms: 4586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4586 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 32, 'TRANS': 543} Chain breaks: 2 Chain: "E" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4448 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 32, 'TRANS': 525} Chain breaks: 4 Chain: "F" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4519 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 32, 'TRANS': 534} Chain breaks: 3 Chain: "G" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1642 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 2 Chain: "H" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1642 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 2 Chain: "I" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1642 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.17, per 1000 atoms: 0.53 Number of scatterers: 32424 At special positions: 0 Unit cell: (160.425, 148.781, 183.713, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 122 16.00 P 10 15.00 O 6021 8.00 N 5529 7.00 C 20742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.73 Conformation dependent library (CDL) restraints added in 6.2 seconds 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7698 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 15 sheets defined 48.2% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.47 Creating SS restraints... Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 486 through 489 No H-bonds generated for 'chain 'A' and resid 486 through 489' Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 521 through 524 No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 535 through 546 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 589 through 599 Processing helix chain 'A' and resid 609 through 618 Processing helix chain 'A' and resid 624 through 642 Processing helix chain 'A' and resid 644 through 648 removed outlier: 4.038A pdb=" N ARG A 648 " --> pdb=" O GLN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 673 removed outlier: 3.890A pdb=" N LEU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 679 No H-bonds generated for 'chain 'A' and resid 677 through 679' Processing helix chain 'A' and resid 694 through 710 removed outlier: 5.486A pdb=" N ASP A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLN A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 755 through 762 removed outlier: 4.259A pdb=" N PHE A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.742A pdb=" N ALA A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 808 Processing helix chain 'A' and resid 815 through 828 Processing helix chain 'A' and resid 839 through 842 No H-bonds generated for 'chain 'A' and resid 839 through 842' Processing helix chain 'A' and resid 848 through 859 Processing helix chain 'A' and resid 878 through 883 Processing helix chain 'A' and resid 885 through 889 removed outlier: 4.257A pdb=" N ASP A 888 " --> pdb=" O ILE A 885 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 889 " --> pdb=" O LEU A 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 885 through 889' Processing helix chain 'A' and resid 903 through 911 removed outlier: 3.595A pdb=" N SER A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 1325 through 1338 Processing helix chain 'A' and resid 1344 through 1360 removed outlier: 3.626A pdb=" N ILE A1357 " --> pdb=" O SER A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1377 Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.611A pdb=" N ASP B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 424 " --> pdb=" O ASN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 460 through 470 Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.845A pdb=" N LEU B 500 " --> pdb=" O ALA B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 523 No H-bonds generated for 'chain 'B' and resid 520 through 523' Processing helix chain 'B' and resid 533 through 546 removed outlier: 4.355A pdb=" N ILE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 598 Processing helix chain 'B' and resid 608 through 617 Processing helix chain 'B' and resid 623 through 641 Processing helix chain 'B' and resid 643 through 646 Processing helix chain 'B' and resid 663 through 672 Processing helix chain 'B' and resid 676 through 679 No H-bonds generated for 'chain 'B' and resid 676 through 679' Processing helix chain 'B' and resid 692 through 709 removed outlier: 3.533A pdb=" N LEU B 696 " --> pdb=" O LYS B 693 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA B 697 " --> pdb=" O PRO B 694 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ASP B 698 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 700 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B 701 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN B 702 " --> pdb=" O GLN B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 753 through 766 removed outlier: 5.426A pdb=" N PHE B 758 " --> pdb=" O ARG B 754 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N PHE B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLN B 766 " --> pdb=" O MET B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 792 removed outlier: 3.710A pdb=" N ALA B 787 " --> pdb=" O GLN B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 808 Processing helix chain 'B' and resid 814 through 826 Processing helix chain 'B' and resid 838 through 844 removed outlier: 3.755A pdb=" N ASN B 843 " --> pdb=" O ASP B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 858 removed outlier: 3.585A pdb=" N LEU B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 882 Processing helix chain 'B' and resid 884 through 888 removed outlier: 4.274A pdb=" N ASP B 887 " --> pdb=" O ILE B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 916 Processing helix chain 'B' and resid 1324 through 1337 Processing helix chain 'B' and resid 1343 through 1359 Processing helix chain 'B' and resid 1367 through 1376 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 419 through 434 Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 436 through 439 Processing helix chain 'C' and resid 460 through 470 Processing helix chain 'C' and resid 495 through 509 Processing helix chain 'C' and resid 520 through 523 No H-bonds generated for 'chain 'C' and resid 520 through 523' Processing helix chain 'C' and resid 534 through 546 Processing helix chain 'C' and resid 564 through 566 No H-bonds generated for 'chain 'C' and resid 564 through 566' Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 588 through 598 Processing helix chain 'C' and resid 608 through 617 Processing helix chain 'C' and resid 623 through 641 Processing helix chain 'C' and resid 643 through 646 Processing helix chain 'C' and resid 663 through 670 Processing helix chain 'C' and resid 691 through 707 Proline residue: C 694 - end of helix removed outlier: 5.055A pdb=" N ALA C 697 " --> pdb=" O PRO C 694 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP C 698 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 700 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASN C 701 " --> pdb=" O ASP C 698 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN C 702 " --> pdb=" O GLN C 699 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS C 706 " --> pdb=" O LEU C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 753 through 766 removed outlier: 3.776A pdb=" N GLU C 757 " --> pdb=" O PHE C 753 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN C 766 " --> pdb=" O MET C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 792 Processing helix chain 'C' and resid 803 through 806 No H-bonds generated for 'chain 'C' and resid 803 through 806' Processing helix chain 'C' and resid 814 through 827 Processing helix chain 'C' and resid 838 through 844 removed outlier: 3.936A pdb=" N ASN C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 859 Processing helix chain 'C' and resid 877 through 881 removed outlier: 4.136A pdb=" N LYS C 881 " --> pdb=" O SER C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 removed outlier: 4.240A pdb=" N ASP C 887 " --> pdb=" O ILE C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 917 removed outlier: 4.015A pdb=" N LEU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU C 916 " --> pdb=" O LEU C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 1324 through 1337 Processing helix chain 'C' and resid 1343 through 1359 removed outlier: 3.632A pdb=" N ILE C1356 " --> pdb=" O SER C1352 " (cutoff:3.500A) Processing helix chain 'C' and resid 1367 through 1376 Processing helix chain 'D' and resid 419 through 429 removed outlier: 3.934A pdb=" N ASP D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLN D 424 " --> pdb=" O ASN D 420 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET D 428 " --> pdb=" O GLN D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 434 No H-bonds generated for 'chain 'D' and resid 431 through 434' Processing helix chain 'D' and resid 436 through 439 No H-bonds generated for 'chain 'D' and resid 436 through 439' Processing helix chain 'D' and resid 460 through 470 removed outlier: 3.638A pdb=" N ALA D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA D 469 " --> pdb=" O ARG D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 508 removed outlier: 3.524A pdb=" N LEU D 500 " --> pdb=" O ALA D 496 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU D 503 " --> pdb=" O GLN D 499 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS D 508 " --> pdb=" O PHE D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 522 No H-bonds generated for 'chain 'D' and resid 520 through 522' Processing helix chain 'D' and resid 533 through 545 removed outlier: 4.332A pdb=" N SER D 537 " --> pdb=" O GLN D 533 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 539 " --> pdb=" O HIS D 535 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA D 544 " --> pdb=" O SER D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 571 No H-bonds generated for 'chain 'D' and resid 569 through 571' Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 608 through 617 Processing helix chain 'D' and resid 623 through 641 Processing helix chain 'D' and resid 643 through 645 No H-bonds generated for 'chain 'D' and resid 643 through 645' Processing helix chain 'D' and resid 663 through 672 removed outlier: 4.373A pdb=" N LEU D 668 " --> pdb=" O SER D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 711 removed outlier: 5.133A pdb=" N ASP D 698 " --> pdb=" O PRO D 694 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLN D 699 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU D 703 " --> pdb=" O GLN D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 727 No H-bonds generated for 'chain 'D' and resid 725 through 727' Processing helix chain 'D' and resid 754 through 757 No H-bonds generated for 'chain 'D' and resid 754 through 757' Processing helix chain 'D' and resid 764 through 766 No H-bonds generated for 'chain 'D' and resid 764 through 766' Processing helix chain 'D' and resid 782 through 792 Processing helix chain 'D' and resid 803 through 805 No H-bonds generated for 'chain 'D' and resid 803 through 805' Processing helix chain 'D' and resid 814 through 827 Processing helix chain 'D' and resid 838 through 844 removed outlier: 3.709A pdb=" N ASN D 843 " --> pdb=" O ASP D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 858 Processing helix chain 'D' and resid 877 through 882 Processing helix chain 'D' and resid 884 through 888 removed outlier: 4.104A pdb=" N ASP D 887 " --> pdb=" O ILE D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 917 Processing helix chain 'D' and resid 1324 through 1337 Processing helix chain 'D' and resid 1343 through 1359 Processing helix chain 'D' and resid 1368 through 1376 Processing helix chain 'E' and resid 412 through 414 No H-bonds generated for 'chain 'E' and resid 412 through 414' Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 431 through 434 No H-bonds generated for 'chain 'E' and resid 431 through 434' Processing helix chain 'E' and resid 460 through 469 Processing helix chain 'E' and resid 496 through 508 Processing helix chain 'E' and resid 520 through 523 No H-bonds generated for 'chain 'E' and resid 520 through 523' Processing helix chain 'E' and resid 540 through 546 Processing helix chain 'E' and resid 564 through 566 No H-bonds generated for 'chain 'E' and resid 564 through 566' Processing helix chain 'E' and resid 569 through 571 No H-bonds generated for 'chain 'E' and resid 569 through 571' Processing helix chain 'E' and resid 590 through 596 Processing helix chain 'E' and resid 608 through 615 Processing helix chain 'E' and resid 623 through 641 removed outlier: 4.118A pdb=" N SER E 641 " --> pdb=" O ILE E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 645 No H-bonds generated for 'chain 'E' and resid 643 through 645' Processing helix chain 'E' and resid 663 through 672 removed outlier: 4.058A pdb=" N LYS E 672 " --> pdb=" O LEU E 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 711 removed outlier: 5.699A pdb=" N ASP E 698 " --> pdb=" O PRO E 694 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLN E 699 " --> pdb=" O LEU E 695 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN E 701 " --> pdb=" O ALA E 697 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN E 702 " --> pdb=" O ASP E 698 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 703 " --> pdb=" O GLN E 699 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 766 removed outlier: 4.161A pdb=" N GLN E 766 " --> pdb=" O MET E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 782 through 794 removed outlier: 3.669A pdb=" N GLU E 794 " --> pdb=" O LEU E 790 " (cutoff:3.500A) Processing helix chain 'E' and resid 803 through 806 No H-bonds generated for 'chain 'E' and resid 803 through 806' Processing helix chain 'E' and resid 814 through 827 Processing helix chain 'E' and resid 838 through 844 removed outlier: 4.423A pdb=" N ASN E 843 " --> pdb=" O ASP E 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 847 through 858 Processing helix chain 'E' and resid 877 through 881 Processing helix chain 'E' and resid 884 through 888 removed outlier: 4.199A pdb=" N ASP E 887 " --> pdb=" O ILE E 884 " (cutoff:3.500A) Processing helix chain 'E' and resid 902 through 916 removed outlier: 4.168A pdb=" N ASN E 911 " --> pdb=" O ARG E 907 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU E 912 " --> pdb=" O TYR E 908 " (cutoff:3.500A) Processing helix chain 'E' and resid 1324 through 1337 Processing helix chain 'E' and resid 1343 through 1360 removed outlier: 3.902A pdb=" N SER E1360 " --> pdb=" O ILE E1356 " (cutoff:3.500A) Processing helix chain 'E' and resid 1369 through 1376 Processing helix chain 'F' and resid 412 through 414 No H-bonds generated for 'chain 'F' and resid 412 through 414' Processing helix chain 'F' and resid 419 through 428 removed outlier: 3.749A pdb=" N LYS F 426 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU F 427 " --> pdb=" O ASP F 423 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET F 428 " --> pdb=" O GLN F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 434 Processing helix chain 'F' and resid 436 through 439 No H-bonds generated for 'chain 'F' and resid 436 through 439' Processing helix chain 'F' and resid 460 through 468 Processing helix chain 'F' and resid 493 through 509 removed outlier: 4.051A pdb=" N GLU F 497 " --> pdb=" O VAL F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 523 No H-bonds generated for 'chain 'F' and resid 520 through 523' Processing helix chain 'F' and resid 540 through 546 Processing helix chain 'F' and resid 564 through 566 No H-bonds generated for 'chain 'F' and resid 564 through 566' Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.577A pdb=" N THR F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 615 Processing helix chain 'F' and resid 625 through 641 Processing helix chain 'F' and resid 644 through 647 No H-bonds generated for 'chain 'F' and resid 644 through 647' Processing helix chain 'F' and resid 663 through 667 Processing helix chain 'F' and resid 690 through 710 Proline residue: F 694 - end of helix removed outlier: 5.289A pdb=" N ASP F 698 " --> pdb=" O PRO F 694 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN F 699 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU F 703 " --> pdb=" O GLN F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 730 Processing helix chain 'F' and resid 754 through 766 removed outlier: 3.536A pdb=" N SER F 761 " --> pdb=" O GLU F 757 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN F 766 " --> pdb=" O MET F 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 782 through 792 removed outlier: 3.740A pdb=" N ALA F 787 " --> pdb=" O GLN F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 803 through 806 No H-bonds generated for 'chain 'F' and resid 803 through 806' Processing helix chain 'F' and resid 814 through 827 Processing helix chain 'F' and resid 838 through 844 removed outlier: 3.839A pdb=" N ASN F 843 " --> pdb=" O ASP F 839 " (cutoff:3.500A) Processing helix chain 'F' and resid 847 through 858 Processing helix chain 'F' and resid 877 through 881 removed outlier: 4.148A pdb=" N LYS F 881 " --> pdb=" O SER F 878 " (cutoff:3.500A) Processing helix chain 'F' and resid 886 through 888 No H-bonds generated for 'chain 'F' and resid 886 through 888' Processing helix chain 'F' and resid 902 through 916 removed outlier: 3.516A pdb=" N TYR F 908 " --> pdb=" O ASN F 904 " (cutoff:3.500A) Processing helix chain 'F' and resid 1324 through 1337 Processing helix chain 'F' and resid 1343 through 1359 Processing helix chain 'F' and resid 1367 through 1376 Processing helix chain 'G' and resid 956 through 992 removed outlier: 4.315A pdb=" N GLY G 985 " --> pdb=" O ILE G 981 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU G 986 " --> pdb=" O LYS G 982 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU G 989 " --> pdb=" O GLY G 985 " (cutoff:3.500A) Processing helix chain 'G' and resid 996 through 998 No H-bonds generated for 'chain 'G' and resid 996 through 998' Processing helix chain 'G' and resid 1004 through 1008 Processing helix chain 'G' and resid 1048 through 1055 removed outlier: 3.648A pdb=" N ASN G1055 " --> pdb=" O GLU G1051 " (cutoff:3.500A) Processing helix chain 'G' and resid 1061 through 1077 Processing helix chain 'G' and resid 1081 through 1101 Processing helix chain 'G' and resid 1104 through 1130 Processing helix chain 'H' and resid 956 through 992 removed outlier: 3.991A pdb=" N GLY H 985 " --> pdb=" O ILE H 981 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU H 986 " --> pdb=" O LYS H 982 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU H 989 " --> pdb=" O GLY H 985 " (cutoff:3.500A) Processing helix chain 'H' and resid 996 through 998 No H-bonds generated for 'chain 'H' and resid 996 through 998' Processing helix chain 'H' and resid 1004 through 1008 Processing helix chain 'H' and resid 1048 through 1055 removed outlier: 3.673A pdb=" N ASN H1055 " --> pdb=" O GLU H1051 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1077 Processing helix chain 'H' and resid 1081 through 1101 Processing helix chain 'H' and resid 1104 through 1130 Processing helix chain 'I' and resid 956 through 992 removed outlier: 4.183A pdb=" N GLY I 985 " --> pdb=" O ILE I 981 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU I 986 " --> pdb=" O LYS I 982 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU I 989 " --> pdb=" O GLY I 985 " (cutoff:3.500A) Processing helix chain 'I' and resid 996 through 998 No H-bonds generated for 'chain 'I' and resid 996 through 998' Processing helix chain 'I' and resid 1004 through 1008 Processing helix chain 'I' and resid 1048 through 1055 Processing helix chain 'I' and resid 1061 through 1077 Processing helix chain 'I' and resid 1081 through 1101 Processing helix chain 'I' and resid 1104 through 1130 Processing sheet with id= A, first strand: chain 'A' and resid 580 through 584 removed outlier: 6.841A pdb=" N THR A 480 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE A 517 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE A 482 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP A 519 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG A 484 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 895 through 898 removed outlier: 7.544A pdb=" N PHE A 896 " --> pdb=" O ARG A 772 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU A 774 " --> pdb=" O PHE A 896 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 898 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN A 776 " --> pdb=" O LEU A 898 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU A 773 " --> pdb=" O ILE A 867 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 869 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE A 775 " --> pdb=" O LEU A 869 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS A 871 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N GLY A 777 " --> pdb=" O CYS A 871 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA A 873 " --> pdb=" O GLY A 777 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER A 832 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU A 870 " --> pdb=" O SER A 832 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL A 834 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU A 872 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE A 836 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLU A 874 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASN A 798 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 835 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN A 800 " --> pdb=" O PHE A 835 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 579 through 583 removed outlier: 3.640A pdb=" N GLY B 454 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER B 513 " --> pdb=" O ILE B 556 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE B 558 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE B 515 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ALA B 560 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE B 517 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR B 479 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE B 516 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE B 481 " --> pdb=" O PHE B 516 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 894 through 897 removed outlier: 7.904A pdb=" N PHE B 895 " --> pdb=" O ARG B 771 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 773 " --> pdb=" O PHE B 895 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU B 897 " --> pdb=" O LEU B 773 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN B 775 " --> pdb=" O LEU B 897 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU B 772 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU B 868 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE B 774 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N CYS B 870 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N GLY B 776 " --> pdb=" O CYS B 870 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 872 " --> pdb=" O GLY B 776 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N SER B 831 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU B 869 " --> pdb=" O SER B 831 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL B 833 " --> pdb=" O LEU B 869 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU B 871 " --> pdb=" O VAL B 833 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE B 835 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N GLU B 873 " --> pdb=" O ILE B 835 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN B 797 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE B 834 " --> pdb=" O ASN B 797 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLN B 799 " --> pdb=" O PHE B 834 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 579 through 583 removed outlier: 6.060A pdb=" N VAL C 557 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE C 452 " --> pdb=" O VAL C 557 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY C 559 " --> pdb=" O PHE C 452 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLY C 454 " --> pdb=" O GLY C 559 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR C 561 " --> pdb=" O GLY C 454 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N ILE C 558 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 515 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA C 560 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE C 517 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR C 479 " --> pdb=" O ILE C 514 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE C 516 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE C 481 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP C 518 " --> pdb=" O PHE C 481 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG C 483 " --> pdb=" O ASP C 518 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 894 through 897 removed outlier: 7.629A pdb=" N PHE C 895 " --> pdb=" O ARG C 771 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU C 773 " --> pdb=" O PHE C 895 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU C 897 " --> pdb=" O LEU C 773 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASN C 775 " --> pdb=" O LEU C 897 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU C 772 " --> pdb=" O ILE C 866 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 868 " --> pdb=" O LEU C 772 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 774 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N CYS C 870 " --> pdb=" O ILE C 774 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N GLY C 776 " --> pdb=" O CYS C 870 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA C 872 " --> pdb=" O GLY C 776 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER C 831 " --> pdb=" O LEU C 867 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU C 869 " --> pdb=" O SER C 831 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL C 833 " --> pdb=" O LEU C 869 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU C 871 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE C 835 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLU C 873 " --> pdb=" O ILE C 835 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN C 797 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHE C 834 " --> pdb=" O ASN C 797 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN C 799 " --> pdb=" O PHE C 834 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 579 through 582 removed outlier: 7.164A pdb=" N SER D 513 " --> pdb=" O ILE D 556 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE D 558 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE D 515 " --> pdb=" O ILE D 558 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ALA D 560 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE D 517 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE D 481 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP D 518 " --> pdb=" O PHE D 481 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG D 483 " --> pdb=" O ASP D 518 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 894 through 897 removed outlier: 7.663A pdb=" N PHE D 895 " --> pdb=" O ARG D 771 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU D 773 " --> pdb=" O PHE D 895 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU D 897 " --> pdb=" O LEU D 773 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN D 775 " --> pdb=" O LEU D 897 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU D 772 " --> pdb=" O ILE D 866 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU D 868 " --> pdb=" O LEU D 772 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE D 774 " --> pdb=" O LEU D 868 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N CYS D 870 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N GLY D 776 " --> pdb=" O CYS D 870 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA D 872 " --> pdb=" O GLY D 776 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER D 831 " --> pdb=" O LEU D 867 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU D 869 " --> pdb=" O SER D 831 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL D 833 " --> pdb=" O LEU D 869 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU D 871 " --> pdb=" O VAL D 833 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE D 835 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N GLU D 873 " --> pdb=" O ILE D 835 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASN D 797 " --> pdb=" O VAL D 832 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE D 834 " --> pdb=" O ASN D 797 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLN D 799 " --> pdb=" O PHE D 834 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'E' and resid 579 through 583 removed outlier: 6.407A pdb=" N VAL E 557 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE E 452 " --> pdb=" O VAL E 557 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY E 559 " --> pdb=" O PHE E 452 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLY E 454 " --> pdb=" O GLY E 559 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR E 561 " --> pdb=" O GLY E 454 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE E 515 " --> pdb=" O ILE E 558 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA E 560 " --> pdb=" O ILE E 515 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N PHE E 517 " --> pdb=" O ALA E 560 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 894 through 897 removed outlier: 7.678A pdb=" N PHE E 895 " --> pdb=" O ARG E 771 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU E 773 " --> pdb=" O PHE E 895 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU E 897 " --> pdb=" O LEU E 773 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN E 775 " --> pdb=" O LEU E 897 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LEU E 772 " --> pdb=" O ILE E 866 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU E 868 " --> pdb=" O LEU E 772 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE E 774 " --> pdb=" O LEU E 868 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N CYS E 870 " --> pdb=" O ILE E 774 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLY E 776 " --> pdb=" O CYS E 870 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA E 872 " --> pdb=" O GLY E 776 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER E 831 " --> pdb=" O LEU E 867 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU E 869 " --> pdb=" O SER E 831 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL E 833 " --> pdb=" O LEU E 869 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU E 871 " --> pdb=" O VAL E 833 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE E 835 " --> pdb=" O LEU E 871 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N GLU E 873 " --> pdb=" O ILE E 835 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN E 797 " --> pdb=" O VAL E 832 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE E 834 " --> pdb=" O ASN E 797 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN E 799 " --> pdb=" O PHE E 834 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'F' and resid 579 through 583 removed outlier: 6.850A pdb=" N SER F 513 " --> pdb=" O ILE F 556 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE F 558 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE F 515 " --> pdb=" O ILE F 558 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA F 560 " --> pdb=" O ILE F 515 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N PHE F 517 " --> pdb=" O ALA F 560 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR F 479 " --> pdb=" O ILE F 514 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE F 516 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE F 481 " --> pdb=" O PHE F 516 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 894 through 897 removed outlier: 7.634A pdb=" N PHE F 895 " --> pdb=" O ARG F 771 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU F 773 " --> pdb=" O PHE F 895 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU F 897 " --> pdb=" O LEU F 773 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN F 775 " --> pdb=" O LEU F 897 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LEU F 772 " --> pdb=" O ILE F 866 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU F 868 " --> pdb=" O LEU F 772 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE F 774 " --> pdb=" O LEU F 868 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N CYS F 870 " --> pdb=" O ILE F 774 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLY F 776 " --> pdb=" O CYS F 870 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA F 872 " --> pdb=" O GLY F 776 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER F 831 " --> pdb=" O LEU F 867 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU F 869 " --> pdb=" O SER F 831 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL F 833 " --> pdb=" O LEU F 869 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU F 871 " --> pdb=" O VAL F 833 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE F 835 " --> pdb=" O LEU F 871 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N GLU F 873 " --> pdb=" O ILE F 835 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASN F 797 " --> pdb=" O VAL F 832 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N PHE F 834 " --> pdb=" O ASN F 797 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN F 799 " --> pdb=" O PHE F 834 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'G' and resid 1025 through 1027 Processing sheet with id= N, first strand: chain 'H' and resid 1025 through 1027 Processing sheet with id= O, first strand: chain 'I' and resid 1025 through 1027 1158 hydrogen bonds defined for protein. 3333 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: 9.43 Time building geometry restraints manager: 13.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5404 1.30 - 1.43: 8013 1.43 - 1.56: 19411 1.56 - 1.69: 17 1.69 - 1.82: 205 Bond restraints: 33050 Sorted by residual: bond pdb=" C SER F 831 " pdb=" O SER F 831 " ideal model delta sigma weight residual 1.234 1.176 0.058 1.22e-02 6.72e+03 2.28e+01 bond pdb=" C LYS D 491 " pdb=" O LYS D 491 " ideal model delta sigma weight residual 1.235 1.287 -0.051 1.26e-02 6.30e+03 1.66e+01 bond pdb=" N ARG C 627 " pdb=" CA ARG C 627 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.19e-02 7.06e+03 1.33e+01 bond pdb=" CA SER F 831 " pdb=" CB SER F 831 " ideal model delta sigma weight residual 1.534 1.475 0.059 1.76e-02 3.23e+03 1.12e+01 bond pdb=" CA SER F 831 " pdb=" C SER F 831 " ideal model delta sigma weight residual 1.521 1.485 0.036 1.23e-02 6.61e+03 8.52e+00 ... (remaining 33045 not shown) Histogram of bond angle deviations from ideal: 93.69 - 102.13: 90 102.13 - 110.57: 9076 110.57 - 119.01: 18212 119.01 - 127.45: 16985 127.45 - 135.89: 248 Bond angle restraints: 44611 Sorted by residual: angle pdb=" N THR I1077 " pdb=" CA THR I1077 " pdb=" C THR I1077 " ideal model delta sigma weight residual 111.28 120.46 -9.18 1.09e+00 8.42e-01 7.09e+01 angle pdb=" N SER C 528 " pdb=" CA SER C 528 " pdb=" C SER C 528 " ideal model delta sigma weight residual 108.23 118.12 -9.89 1.72e+00 3.38e-01 3.30e+01 angle pdb=" N GLU H1119 " pdb=" CA GLU H1119 " pdb=" C GLU H1119 " ideal model delta sigma weight residual 112.38 106.07 6.31 1.22e+00 6.72e-01 2.67e+01 angle pdb=" N LYS C 508 " pdb=" CA LYS C 508 " pdb=" C LYS C 508 " ideal model delta sigma weight residual 113.12 107.20 5.92 1.25e+00 6.40e-01 2.24e+01 angle pdb=" CA LYS D 593 " pdb=" CB LYS D 593 " pdb=" CG LYS D 593 " ideal model delta sigma weight residual 114.10 123.43 -9.33 2.00e+00 2.50e-01 2.18e+01 ... (remaining 44606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.24: 18925 27.24 - 54.47: 1351 54.47 - 81.71: 107 81.71 - 108.95: 20 108.95 - 136.18: 2 Dihedral angle restraints: 20405 sinusoidal: 8617 harmonic: 11788 Sorted by residual: dihedral pdb=" C5' ADP E1401 " pdb=" O5' ADP E1401 " pdb=" PA ADP E1401 " pdb=" O2A ADP E1401 " ideal model delta sinusoidal sigma weight residual 300.00 163.82 136.18 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" O2A ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PA ADP A1401 " pdb=" PB ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 70.67 -130.67 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" CA ASN G 346 " pdb=" C ASN G 346 " pdb=" N PHE G 347 " pdb=" CA PHE G 347 " ideal model delta harmonic sigma weight residual 180.00 150.68 29.32 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 20402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 4450 0.068 - 0.137: 547 0.137 - 0.205: 15 0.205 - 0.274: 2 0.274 - 0.342: 4 Chirality restraints: 5018 Sorted by residual: chirality pdb=" CA THR F 716 " pdb=" N THR F 716 " pdb=" C THR F 716 " pdb=" CB THR F 716 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CG LEU H1125 " pdb=" CB LEU H1125 " pdb=" CD1 LEU H1125 " pdb=" CD2 LEU H1125 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA THR I1077 " pdb=" N THR I1077 " pdb=" C THR I1077 " pdb=" CB THR I1077 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 5015 not shown) Planarity restraints: 5713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 924 " 0.106 5.00e-02 4.00e+02 1.58e-01 4.00e+01 pdb=" N PRO A 925 " -0.274 5.00e-02 4.00e+02 pdb=" CA PRO A 925 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO A 925 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 655 " 0.090 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO B 656 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO B 656 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO B 656 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 923 " -0.089 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO C 924 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO C 924 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 924 " -0.068 5.00e-02 4.00e+02 ... (remaining 5710 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3894 2.75 - 3.29: 33742 3.29 - 3.82: 54553 3.82 - 4.36: 63907 4.36 - 4.90: 105993 Nonbonded interactions: 262089 Sorted by model distance: nonbonded pdb=" OG SER I1059 " pdb=" OD2 ASP I1117 " model vdw 2.210 2.440 nonbonded pdb=" N GLU A 848 " pdb=" OE1 GLU A 848 " model vdw 2.212 2.520 nonbonded pdb=" O ARG C 828 " pdb=" OG SER C 831 " model vdw 2.225 2.440 nonbonded pdb=" OG SER A1361 " pdb=" OG1 THR A1370 " model vdw 2.227 2.440 nonbonded pdb=" O PHE I 990 " pdb=" NH2 ARG I 998 " model vdw 2.233 2.520 ... (remaining 262084 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 410 through 487 or resid 496 through 526 or resid 539 thro \ ugh 733 or resid 752 through 1379)) selection = (chain 'B' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 732 or resid 751 through 1378)) selection = (chain 'C' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 732 or resid 751 through 1378)) selection = (chain 'D' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 1378)) selection = (chain 'E' and (resid 409 through 732 or resid 751 through 1378)) selection = (chain 'F' and (resid 409 through 486 or resid 495 through 525 or resid 538 thro \ ugh 732 or resid 751 through 1378)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.030 Extract box with map and model: 5.460 Check model and map are aligned: 0.530 Set scattering table: 0.310 Process input model: 83.480 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 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 : 0.004 0.069 33050 Z= 0.251 Angle : 0.777 15.636 44611 Z= 0.417 Chirality : 0.045 0.342 5018 Planarity : 0.006 0.158 5713 Dihedral : 17.303 136.184 12707 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.18 % Favored : 93.80 % Rotamer: Outliers : 0.86 % Allowed : 22.87 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 3965 helix: 0.06 (0.12), residues: 1952 sheet: -1.03 (0.27), residues: 368 loop : -1.69 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 841 HIS 0.004 0.001 HIS E 453 PHE 0.037 0.001 PHE I1042 TYR 0.041 0.001 TYR B 784 ARG 0.014 0.001 ARG C 627 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 651 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 581 GLU cc_start: 0.7059 (mp0) cc_final: 0.6758 (mt-10) REVERT: B 881 LYS cc_start: 0.7720 (tppt) cc_final: 0.7341 (mmmm) REVERT: C 435 TYR cc_start: 0.8109 (m-80) cc_final: 0.7806 (m-80) REVERT: D 421 TYR cc_start: 0.7789 (m-80) cc_final: 0.7465 (m-80) REVERT: D 632 GLU cc_start: 0.7206 (tp30) cc_final: 0.6981 (tp30) REVERT: D 1333 CYS cc_start: 0.7153 (p) cc_final: 0.6953 (t) REVERT: E 764 GLU cc_start: 0.6903 (pp20) cc_final: 0.6589 (pp20) REVERT: E 856 LEU cc_start: 0.8356 (tp) cc_final: 0.8052 (tp) REVERT: E 886 SER cc_start: 0.7899 (m) cc_final: 0.7689 (m) REVERT: F 427 GLU cc_start: 0.7705 (tt0) cc_final: 0.7316 (tm-30) REVERT: F 572 ARG cc_start: 0.7235 (mtm-85) cc_final: 0.6987 (mpp-170) REVERT: G 1033 LEU cc_start: 0.7055 (tp) cc_final: 0.6391 (pp) outliers start: 31 outliers final: 13 residues processed: 666 average time/residue: 0.5237 time to fit residues: 520.8610 Evaluate side-chains 659 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 646 time to evaluate : 3.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 511 GLN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain H residue 1111 LYS Chi-restraints excluded: chain H residue 1114 ARG Chi-restraints excluded: chain H residue 1116 ARG Chi-restraints excluded: chain I residue 1026 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 231 optimal weight: 0.6980 chunk 359 optimal weight: 30.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN A 830 GLN C 531 GLN C 699 GLN D 453 HIS ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 GLN E 775 ASN E 829 GLN E 896 GLN F 712 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 33050 Z= 0.404 Angle : 0.679 11.068 44611 Z= 0.334 Chirality : 0.045 0.204 5018 Planarity : 0.006 0.108 5713 Dihedral : 7.054 136.768 4397 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.94 % Favored : 93.04 % Rotamer: Outliers : 2.73 % Allowed : 21.71 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3965 helix: 0.05 (0.12), residues: 1976 sheet: -1.08 (0.27), residues: 379 loop : -1.68 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 841 HIS 0.005 0.001 HIS E 898 PHE 0.019 0.002 PHE D 480 TYR 0.032 0.002 TYR B 784 ARG 0.019 0.001 ARG D 576 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 660 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 GLU cc_start: 0.7037 (mp0) cc_final: 0.6758 (mp0) REVERT: A 611 PHE cc_start: 0.8365 (t80) cc_final: 0.8164 (t80) REVERT: A 912 ASN cc_start: 0.7719 (m-40) cc_final: 0.7366 (t0) REVERT: B 434 LEU cc_start: 0.8410 (mt) cc_final: 0.8102 (mp) REVERT: B 547 ASP cc_start: 0.6889 (t0) cc_final: 0.6493 (t0) REVERT: B 760 GLU cc_start: 0.6314 (tm-30) cc_final: 0.6085 (tm-30) REVERT: B 879 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: B 1325 GLU cc_start: 0.6651 (tm-30) cc_final: 0.6412 (tm-30) REVERT: C 435 TYR cc_start: 0.8143 (m-80) cc_final: 0.7942 (m-10) REVERT: C 499 GLN cc_start: 0.8202 (tp40) cc_final: 0.7860 (tp40) REVERT: C 665 ASP cc_start: 0.7747 (m-30) cc_final: 0.7316 (m-30) REVERT: C 769 LYS cc_start: 0.7461 (mmtp) cc_final: 0.7247 (mmtp) REVERT: C 887 ASP cc_start: 0.7172 (p0) cc_final: 0.6900 (p0) REVERT: C 925 MET cc_start: 0.5727 (tmm) cc_final: 0.5411 (tmm) REVERT: C 1358 TRP cc_start: 0.8060 (m100) cc_final: 0.7731 (t-100) REVERT: D 589 LYS cc_start: 0.8626 (mmmm) cc_final: 0.8004 (mmmm) REVERT: D 593 LYS cc_start: 0.8342 (mmmt) cc_final: 0.8071 (mmtp) REVERT: D 632 GLU cc_start: 0.7182 (tp30) cc_final: 0.6739 (tp30) REVERT: D 639 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: D 698 ASP cc_start: 0.7613 (p0) cc_final: 0.7378 (p0) REVERT: D 760 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7102 (tm-30) REVERT: D 1329 LYS cc_start: 0.8153 (tppt) cc_final: 0.7849 (tppt) REVERT: E 647 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.5607 (ptt-90) REVERT: E 764 GLU cc_start: 0.6768 (pp20) cc_final: 0.6494 (pp20) REVERT: E 824 GLU cc_start: 0.6824 (tp30) cc_final: 0.6608 (tp30) REVERT: E 863 ASN cc_start: 0.7869 (p0) cc_final: 0.7114 (p0) REVERT: E 933 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6721 (pp) REVERT: F 426 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7892 (ttpt) REVERT: F 427 GLU cc_start: 0.7860 (tt0) cc_final: 0.7313 (tm-30) REVERT: F 428 MET cc_start: 0.7007 (tpt) cc_final: 0.6040 (tpt) REVERT: F 463 MET cc_start: 0.6826 (tpp) cc_final: 0.6567 (tpp) REVERT: F 573 ARG cc_start: 0.7660 (mmm-85) cc_final: 0.7162 (ttm-80) REVERT: F 667 MET cc_start: 0.7191 (tpp) cc_final: 0.6958 (tpp) REVERT: F 863 ASN cc_start: 0.7066 (p0) cc_final: 0.6836 (p0) REVERT: G 1033 LEU cc_start: 0.7032 (tp) cc_final: 0.6419 (pp) REVERT: H 1116 ARG cc_start: -0.4069 (OUTLIER) cc_final: -0.4750 (tmm-80) outliers start: 99 outliers final: 59 residues processed: 717 average time/residue: 0.5034 time to fit residues: 542.8675 Evaluate side-chains 706 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 642 time to evaluate : 3.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1376 LYS Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 879 GLU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 914 GLU Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain C residue 1372 GLU Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 639 GLN Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 769 LYS Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 870 CYS Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 647 ARG Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 775 ASN Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 860 LEU Chi-restraints excluded: chain E residue 887 ASP Chi-restraints excluded: chain E residue 898 HIS Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 699 GLN Chi-restraints excluded: chain F residue 844 THR Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1127 ASP Chi-restraints excluded: chain H residue 1113 THR Chi-restraints excluded: chain H residue 1116 ARG Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1096 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 299 optimal weight: 0.0050 chunk 244 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 360 optimal weight: 50.0000 chunk 389 optimal weight: 30.0000 chunk 320 optimal weight: 0.6980 chunk 357 optimal weight: 10.0000 chunk 122 optimal weight: 0.0470 chunk 289 optimal weight: 6.9990 overall best weight: 0.7496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 896 GLN F 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33050 Z= 0.199 Angle : 0.600 10.851 44611 Z= 0.292 Chirality : 0.041 0.289 5018 Planarity : 0.005 0.082 5713 Dihedral : 6.555 137.234 4375 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.10 % Favored : 93.87 % Rotamer: Outliers : 2.95 % Allowed : 22.73 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3965 helix: 0.27 (0.12), residues: 1977 sheet: -0.97 (0.28), residues: 365 loop : -1.59 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I1054 HIS 0.004 0.001 HIS A1351 PHE 0.018 0.001 PHE F 581 TYR 0.017 0.001 TYR B 784 ARG 0.007 0.000 ARG F 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 659 time to evaluate : 3.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 GLU cc_start: 0.6946 (mp0) cc_final: 0.6691 (mp0) REVERT: A 614 LYS cc_start: 0.7370 (ttpt) cc_final: 0.7160 (ttpt) REVERT: A 661 LYS cc_start: 0.7845 (tptm) cc_final: 0.7572 (tptm) REVERT: A 1349 ASP cc_start: 0.6928 (t0) cc_final: 0.6696 (t0) REVERT: A 1377 PHE cc_start: 0.8201 (t80) cc_final: 0.7944 (t80) REVERT: B 483 ARG cc_start: 0.7376 (mmm-85) cc_final: 0.7140 (mmm-85) REVERT: B 547 ASP cc_start: 0.6900 (t0) cc_final: 0.6276 (t0) REVERT: B 601 LYS cc_start: 0.7838 (tmtt) cc_final: 0.7440 (tmtt) REVERT: B 879 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: C 410 VAL cc_start: 0.8098 (m) cc_final: 0.7804 (p) REVERT: C 435 TYR cc_start: 0.8088 (m-80) cc_final: 0.7814 (m-10) REVERT: C 499 GLN cc_start: 0.8165 (tp40) cc_final: 0.7793 (tp40) REVERT: C 505 GLU cc_start: 0.6602 (tp30) cc_final: 0.6342 (tp30) REVERT: C 508 LYS cc_start: 0.7999 (tppt) cc_final: 0.7612 (tppt) REVERT: C 665 ASP cc_start: 0.7748 (m-30) cc_final: 0.7300 (m-30) REVERT: C 858 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7832 (ttm170) REVERT: C 922 ASP cc_start: 0.6378 (t0) cc_final: 0.6143 (t0) REVERT: C 925 MET cc_start: 0.5743 (tmm) cc_final: 0.5382 (tmm) REVERT: C 1358 TRP cc_start: 0.8047 (m100) cc_final: 0.7732 (t-100) REVERT: D 480 PHE cc_start: 0.7793 (t80) cc_final: 0.7517 (t80) REVERT: D 589 LYS cc_start: 0.8509 (mmmm) cc_final: 0.7794 (mmmm) REVERT: D 593 LYS cc_start: 0.8331 (mmmt) cc_final: 0.8056 (mmtp) REVERT: D 594 ILE cc_start: 0.8307 (mt) cc_final: 0.8044 (tt) REVERT: D 616 PHE cc_start: 0.6904 (t80) cc_final: 0.6569 (t80) REVERT: D 698 ASP cc_start: 0.7639 (p0) cc_final: 0.7242 (p0) REVERT: D 760 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7136 (tm-30) REVERT: D 792 TYR cc_start: 0.7250 (t80) cc_final: 0.6878 (t80) REVERT: D 1329 LYS cc_start: 0.8062 (tppt) cc_final: 0.7773 (tppt) REVERT: E 428 MET cc_start: 0.7876 (mmm) cc_final: 0.7493 (mmp) REVERT: E 647 ARG cc_start: 0.5885 (OUTLIER) cc_final: 0.5612 (ptt-90) REVERT: E 764 GLU cc_start: 0.6805 (pp20) cc_final: 0.6445 (pp20) REVERT: E 814 ILE cc_start: 0.8361 (mm) cc_final: 0.8104 (mt) REVERT: E 824 GLU cc_start: 0.6902 (tp30) cc_final: 0.6560 (tp30) REVERT: E 827 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7321 (ttmm) REVERT: E 863 ASN cc_start: 0.7604 (p0) cc_final: 0.6791 (p0) REVERT: E 871 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8513 (mp) REVERT: E 873 GLU cc_start: 0.6993 (mp0) cc_final: 0.6630 (mp0) REVERT: F 424 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8067 (tm-30) REVERT: F 426 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7798 (ttpt) REVERT: F 427 GLU cc_start: 0.7680 (tt0) cc_final: 0.7196 (tm-30) REVERT: F 428 MET cc_start: 0.6466 (tpt) cc_final: 0.5944 (tpt) REVERT: F 463 MET cc_start: 0.6784 (tpp) cc_final: 0.6391 (tpp) REVERT: F 549 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.5052 (mtp) REVERT: F 573 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7264 (ttm-80) REVERT: F 579 ARG cc_start: 0.6500 (ttp-110) cc_final: 0.6046 (mtp-110) REVERT: F 614 LEU cc_start: 0.8607 (mm) cc_final: 0.8402 (mt) REVERT: F 667 MET cc_start: 0.7202 (tpp) cc_final: 0.6719 (tpp) REVERT: F 690 GLU cc_start: 0.6616 (tp30) cc_final: 0.6257 (tm-30) REVERT: F 863 ASN cc_start: 0.6945 (p0) cc_final: 0.6713 (p0) REVERT: G 1033 LEU cc_start: 0.7008 (tp) cc_final: 0.6393 (pp) REVERT: H 1116 ARG cc_start: -0.3627 (OUTLIER) cc_final: -0.4556 (tmm-80) REVERT: I 1031 MET cc_start: 0.2539 (tpp) cc_final: 0.0870 (tpp) outliers start: 107 outliers final: 64 residues processed: 716 average time/residue: 0.5134 time to fit residues: 553.2728 Evaluate side-chains 715 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 645 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1376 LYS Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 879 GLU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 858 ARG Chi-restraints excluded: chain C residue 914 GLU Chi-restraints excluded: chain D residue 441 ASN Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 465 ARG Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 769 LYS Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 870 CYS Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 647 ARG Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 871 LEU Chi-restraints excluded: chain E residue 887 ASP Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 844 THR Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 922 ASP Chi-restraints excluded: chain F residue 1336 GLU Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain G residue 1127 ASP Chi-restraints excluded: chain H residue 1113 THR Chi-restraints excluded: chain H residue 1116 ARG Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 8.9990 chunk 270 optimal weight: 2.9990 chunk 186 optimal weight: 0.0060 chunk 39 optimal weight: 0.6980 chunk 171 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 361 optimal weight: 40.0000 chunk 382 optimal weight: 30.0000 chunk 188 optimal weight: 3.9990 chunk 342 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 overall best weight: 1.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 GLN D 535 HIS D 639 GLN E 799 GLN F 712 ASN F 820 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33050 Z= 0.329 Angle : 0.628 8.845 44611 Z= 0.307 Chirality : 0.043 0.257 5018 Planarity : 0.005 0.080 5713 Dihedral : 6.562 136.170 4373 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.78 % Favored : 93.19 % Rotamer: Outliers : 3.70 % Allowed : 22.79 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 3965 helix: 0.22 (0.12), residues: 1978 sheet: -1.03 (0.28), residues: 368 loop : -1.61 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 842 HIS 0.005 0.001 HIS B 453 PHE 0.016 0.001 PHE D 480 TYR 0.021 0.001 TYR B 784 ARG 0.009 0.000 ARG D 576 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 658 time to evaluate : 3.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 LYS cc_start: 0.7267 (ttpt) cc_final: 0.6916 (ttpt) REVERT: A 661 LYS cc_start: 0.7800 (tptm) cc_final: 0.7580 (tptm) REVERT: A 912 ASN cc_start: 0.7677 (m-40) cc_final: 0.7289 (t0) REVERT: A 1349 ASP cc_start: 0.6926 (t0) cc_final: 0.6658 (t0) REVERT: A 1377 PHE cc_start: 0.8241 (t80) cc_final: 0.7950 (t80) REVERT: B 483 ARG cc_start: 0.7416 (mmm-85) cc_final: 0.7181 (mmm-85) REVERT: B 547 ASP cc_start: 0.7025 (t0) cc_final: 0.6209 (t0) REVERT: B 552 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8149 (ttp80) REVERT: B 601 LYS cc_start: 0.7996 (tmtt) cc_final: 0.7777 (tmtt) REVERT: B 760 GLU cc_start: 0.6683 (tp30) cc_final: 0.6412 (tp30) REVERT: B 879 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: B 1325 GLU cc_start: 0.6600 (tp30) cc_final: 0.6343 (tp30) REVERT: C 410 VAL cc_start: 0.8177 (m) cc_final: 0.7890 (p) REVERT: C 435 TYR cc_start: 0.8139 (m-80) cc_final: 0.7877 (m-10) REVERT: C 499 GLN cc_start: 0.8199 (tp40) cc_final: 0.7807 (tp40) REVERT: C 508 LYS cc_start: 0.8086 (tppt) cc_final: 0.7711 (tppt) REVERT: C 665 ASP cc_start: 0.7755 (m-30) cc_final: 0.7355 (m-30) REVERT: C 769 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7182 (mmtp) REVERT: C 858 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7163 (ptp-170) REVERT: C 879 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6688 (tm-30) REVERT: C 925 MET cc_start: 0.5741 (tmm) cc_final: 0.5348 (tmm) REVERT: D 546 MET cc_start: 0.5922 (ptt) cc_final: 0.5666 (ptt) REVERT: D 589 LYS cc_start: 0.8556 (mmmm) cc_final: 0.7763 (mmmm) REVERT: D 593 LYS cc_start: 0.8337 (mmmt) cc_final: 0.8063 (mmtp) REVERT: D 594 ILE cc_start: 0.8294 (mt) cc_final: 0.8043 (tt) REVERT: D 616 PHE cc_start: 0.6879 (t80) cc_final: 0.6575 (t80) REVERT: D 643 PRO cc_start: 0.8591 (Cg_endo) cc_final: 0.8304 (Cg_exo) REVERT: D 647 ARG cc_start: 0.7201 (mmp-170) cc_final: 0.6650 (mmp80) REVERT: D 686 GLN cc_start: 0.7587 (pm20) cc_final: 0.7225 (pm20) REVERT: D 698 ASP cc_start: 0.7641 (p0) cc_final: 0.7239 (p0) REVERT: D 760 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6929 (tm-30) REVERT: D 778 LYS cc_start: 0.8049 (tptm) cc_final: 0.7790 (tppt) REVERT: D 792 TYR cc_start: 0.7373 (t80) cc_final: 0.7028 (t80) REVERT: D 824 GLU cc_start: 0.6492 (tm-30) cc_final: 0.6187 (tm-30) REVERT: D 1329 LYS cc_start: 0.8118 (tppt) cc_final: 0.7830 (tppt) REVERT: E 428 MET cc_start: 0.8011 (mmm) cc_final: 0.7590 (mmp) REVERT: E 647 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.5636 (ptt-90) REVERT: E 764 GLU cc_start: 0.6798 (pp20) cc_final: 0.6431 (pp20) REVERT: E 812 ARG cc_start: 0.6348 (ttp-110) cc_final: 0.6067 (mtp-110) REVERT: E 824 GLU cc_start: 0.6919 (tp30) cc_final: 0.6485 (tp30) REVERT: E 827 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7581 (ttmt) REVERT: E 856 LEU cc_start: 0.8373 (tp) cc_final: 0.8121 (tp) REVERT: E 863 ASN cc_start: 0.7874 (p0) cc_final: 0.7068 (p0) REVERT: E 933 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6719 (pp) REVERT: F 424 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8084 (tm-30) REVERT: F 427 GLU cc_start: 0.7729 (tt0) cc_final: 0.7365 (tm-30) REVERT: F 428 MET cc_start: 0.6838 (tpt) cc_final: 0.6164 (tpt) REVERT: F 463 MET cc_start: 0.6726 (tpp) cc_final: 0.6216 (tpp) REVERT: F 547 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: F 549 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.5070 (mtp) REVERT: F 573 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.7232 (ttm-80) REVERT: F 667 MET cc_start: 0.7274 (tpp) cc_final: 0.6760 (tpp) REVERT: F 847 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: F 863 ASN cc_start: 0.7123 (p0) cc_final: 0.6840 (p0) REVERT: G 1062 LYS cc_start: -0.0118 (tptt) cc_final: -0.0478 (tptt) REVERT: G 1125 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8404 (pp) outliers start: 134 outliers final: 88 residues processed: 738 average time/residue: 0.5059 time to fit residues: 563.2203 Evaluate side-chains 748 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 651 time to evaluate : 3.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1329 LYS Chi-restraints excluded: chain A residue 1374 ILE Chi-restraints excluded: chain A residue 1376 LYS Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 876 ASP Chi-restraints excluded: chain B residue 879 GLU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 482 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 858 ARG Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 914 GLU Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 441 ASN Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 769 LYS Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 870 CYS Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 647 ARG Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 692 ILE Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 860 LEU Chi-restraints excluded: chain E residue 871 LEU Chi-restraints excluded: chain E residue 887 ASP Chi-restraints excluded: chain E residue 898 HIS Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 547 ASP Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 692 ILE Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 844 THR Chi-restraints excluded: chain F residue 847 GLU Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 987 MET Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain G residue 1127 ASP Chi-restraints excluded: chain H residue 1113 THR Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 0.9980 chunk 217 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 285 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 0 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 343 optimal weight: 20.0000 chunk 96 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 GLN D 639 GLN F 712 ASN F 820 GLN F 898 HIS ** I1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33050 Z= 0.204 Angle : 0.602 11.335 44611 Z= 0.292 Chirality : 0.042 0.246 5018 Planarity : 0.005 0.077 5713 Dihedral : 6.300 133.369 4369 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.00 % Rotamer: Outliers : 3.48 % Allowed : 23.37 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3965 helix: 0.39 (0.12), residues: 1974 sheet: -0.96 (0.28), residues: 365 loop : -1.54 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 842 HIS 0.004 0.001 HIS A1351 PHE 0.047 0.001 PHE G1042 TYR 0.020 0.001 TYR B 784 ARG 0.013 0.000 ARG D 573 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 659 time to evaluate : 3.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 581 GLU cc_start: 0.6983 (mp0) cc_final: 0.6711 (mp0) REVERT: A 614 LYS cc_start: 0.7294 (ttpt) cc_final: 0.6852 (ttpt) REVERT: A 648 ARG cc_start: 0.7708 (mmp-170) cc_final: 0.7459 (mmt180) REVERT: A 661 LYS cc_start: 0.7754 (tptm) cc_final: 0.7526 (tptm) REVERT: A 912 ASN cc_start: 0.7608 (m-40) cc_final: 0.7243 (t0) REVERT: A 1349 ASP cc_start: 0.6972 (t0) cc_final: 0.6666 (t0) REVERT: B 483 ARG cc_start: 0.7360 (mmm-85) cc_final: 0.7155 (mmm-85) REVERT: B 547 ASP cc_start: 0.6983 (t0) cc_final: 0.6234 (t0) REVERT: B 601 LYS cc_start: 0.7949 (tmtt) cc_final: 0.7666 (tmtt) REVERT: B 876 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7087 (p0) REVERT: B 1325 GLU cc_start: 0.6581 (tp30) cc_final: 0.6290 (tp30) REVERT: C 410 VAL cc_start: 0.8106 (m) cc_final: 0.7705 (p) REVERT: C 428 MET cc_start: 0.7743 (ptm) cc_final: 0.7349 (ttp) REVERT: C 435 TYR cc_start: 0.8104 (m-80) cc_final: 0.7839 (m-10) REVERT: C 499 GLN cc_start: 0.8164 (tp40) cc_final: 0.7854 (tp40) REVERT: C 508 LYS cc_start: 0.8026 (tppt) cc_final: 0.7595 (tppt) REVERT: C 557 VAL cc_start: 0.8585 (t) cc_final: 0.8359 (m) REVERT: C 562 ASN cc_start: 0.8009 (t160) cc_final: 0.7705 (t0) REVERT: C 665 ASP cc_start: 0.7758 (m-30) cc_final: 0.7335 (m-30) REVERT: C 782 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: C 858 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7704 (ttm170) REVERT: C 879 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6634 (tm-30) REVERT: C 925 MET cc_start: 0.5747 (tmm) cc_final: 0.5403 (tmm) REVERT: D 480 PHE cc_start: 0.7781 (t80) cc_final: 0.7579 (t80) REVERT: D 589 LYS cc_start: 0.8463 (mmmm) cc_final: 0.7694 (mmmm) REVERT: D 593 LYS cc_start: 0.8324 (mmmt) cc_final: 0.8006 (mmtp) REVERT: D 594 ILE cc_start: 0.8307 (mt) cc_final: 0.8063 (tt) REVERT: D 613 LYS cc_start: 0.7672 (ttmt) cc_final: 0.7368 (ttmt) REVERT: D 616 PHE cc_start: 0.6880 (t80) cc_final: 0.6547 (t80) REVERT: D 639 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7746 (mm110) REVERT: D 643 PRO cc_start: 0.8564 (Cg_endo) cc_final: 0.8277 (Cg_exo) REVERT: D 698 ASP cc_start: 0.7618 (p0) cc_final: 0.7082 (p0) REVERT: D 760 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7103 (tm-30) REVERT: D 778 LYS cc_start: 0.7977 (tptm) cc_final: 0.7769 (tppt) REVERT: D 792 TYR cc_start: 0.7428 (t80) cc_final: 0.7143 (t80) REVERT: D 824 GLU cc_start: 0.6522 (tm-30) cc_final: 0.6228 (tm-30) REVERT: D 1329 LYS cc_start: 0.8052 (tppt) cc_final: 0.7740 (tppt) REVERT: E 647 ARG cc_start: 0.5867 (OUTLIER) cc_final: 0.5660 (ptt-90) REVERT: E 757 GLU cc_start: 0.7164 (pm20) cc_final: 0.6955 (pm20) REVERT: E 764 GLU cc_start: 0.6792 (pp20) cc_final: 0.6390 (pp20) REVERT: E 812 ARG cc_start: 0.6289 (ttp-110) cc_final: 0.6025 (mtp-110) REVERT: E 824 GLU cc_start: 0.6973 (tp30) cc_final: 0.6566 (tp30) REVERT: E 827 LYS cc_start: 0.8054 (ttmt) cc_final: 0.7380 (ttmm) REVERT: E 856 LEU cc_start: 0.8357 (tp) cc_final: 0.8066 (tp) REVERT: E 863 ASN cc_start: 0.7842 (p0) cc_final: 0.7044 (p0) REVERT: E 933 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6626 (pp) REVERT: F 427 GLU cc_start: 0.7657 (tt0) cc_final: 0.7371 (tm-30) REVERT: F 428 MET cc_start: 0.6751 (tpt) cc_final: 0.5611 (tpt) REVERT: F 463 MET cc_start: 0.6680 (tpp) cc_final: 0.6122 (tpp) REVERT: F 498 ARG cc_start: 0.7370 (mmp80) cc_final: 0.7127 (mmp80) REVERT: F 549 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.5224 (mtp) REVERT: F 579 ARG cc_start: 0.6348 (ttp-110) cc_final: 0.4991 (mtt-85) REVERT: F 667 MET cc_start: 0.7253 (tpp) cc_final: 0.6675 (tpp) REVERT: F 778 LYS cc_start: 0.7724 (mmmt) cc_final: 0.6436 (mmmt) REVERT: F 815 GLU cc_start: 0.6638 (mm-30) cc_final: 0.6130 (mm-30) REVERT: F 847 GLU cc_start: 0.7881 (mp0) cc_final: 0.7539 (mp0) REVERT: F 863 ASN cc_start: 0.7089 (p0) cc_final: 0.6773 (p0) REVERT: G 1031 MET cc_start: -0.3254 (tpp) cc_final: -0.3559 (tpp) REVERT: G 1062 LYS cc_start: -0.0209 (tptt) cc_final: -0.0520 (tptt) REVERT: G 1125 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8407 (pp) outliers start: 126 outliers final: 76 residues processed: 734 average time/residue: 0.4890 time to fit residues: 541.5446 Evaluate side-chains 732 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 648 time to evaluate : 3.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1329 LYS Chi-restraints excluded: chain A residue 1376 LYS Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 876 ASP Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 782 GLN Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 858 ARG Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 896 GLN Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 441 ASN Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 639 GLN Chi-restraints excluded: chain D residue 677 SER Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 870 CYS Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 647 ARG Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 692 ILE Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 887 ASP Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 844 THR Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain F residue 1369 THR Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 987 MET Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain G residue 1127 ASP Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 973 MET Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 128 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 383 optimal weight: 40.0000 chunk 318 optimal weight: 0.6980 chunk 177 optimal weight: 9.9990 chunk 31 optimal weight: 0.0370 chunk 126 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN C 499 GLN C 510 HIS ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 GLN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 ASN F 898 HIS ** I1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33050 Z= 0.194 Angle : 0.606 11.990 44611 Z= 0.292 Chirality : 0.041 0.216 5018 Planarity : 0.004 0.065 5713 Dihedral : 6.165 131.345 4369 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.77 % Rotamer: Outliers : 3.48 % Allowed : 24.17 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3965 helix: 0.47 (0.12), residues: 1977 sheet: -0.92 (0.28), residues: 364 loop : -1.51 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 842 HIS 0.004 0.001 HIS E 510 PHE 0.030 0.001 PHE G1042 TYR 0.024 0.001 TYR B 784 ARG 0.007 0.000 ARG D 573 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 654 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 581 GLU cc_start: 0.6969 (mp0) cc_final: 0.6698 (mp0) REVERT: A 614 LYS cc_start: 0.7342 (ttpt) cc_final: 0.6953 (ttpt) REVERT: A 648 ARG cc_start: 0.7708 (mmp-170) cc_final: 0.7446 (mmt180) REVERT: A 883 ASN cc_start: 0.8225 (m-40) cc_final: 0.7661 (t0) REVERT: A 1349 ASP cc_start: 0.6972 (t0) cc_final: 0.6674 (t0) REVERT: B 547 ASP cc_start: 0.7069 (t0) cc_final: 0.6185 (t0) REVERT: B 760 GLU cc_start: 0.6783 (tp30) cc_final: 0.6452 (tp30) REVERT: B 1325 GLU cc_start: 0.6546 (tp30) cc_final: 0.6293 (tp30) REVERT: B 1328 LYS cc_start: 0.7611 (ttpp) cc_final: 0.7346 (ttpp) REVERT: C 410 VAL cc_start: 0.8053 (m) cc_final: 0.7682 (p) REVERT: C 428 MET cc_start: 0.7693 (ptm) cc_final: 0.7415 (ttp) REVERT: C 443 ASN cc_start: 0.6885 (m-40) cc_final: 0.6619 (m-40) REVERT: C 499 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7852 (tp40) REVERT: C 508 LYS cc_start: 0.7978 (tppt) cc_final: 0.7526 (tppt) REVERT: C 557 VAL cc_start: 0.8587 (t) cc_final: 0.8355 (m) REVERT: C 562 ASN cc_start: 0.8013 (t160) cc_final: 0.7711 (t0) REVERT: C 665 ASP cc_start: 0.7754 (m-30) cc_final: 0.7351 (m-30) REVERT: C 725 LEU cc_start: 0.8161 (tp) cc_final: 0.7900 (mt) REVERT: C 782 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: C 803 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8170 (mm) REVERT: C 815 GLU cc_start: 0.6361 (mm-30) cc_final: 0.6047 (mm-30) REVERT: C 879 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6623 (tm-30) REVERT: C 925 MET cc_start: 0.5670 (tmm) cc_final: 0.5363 (tmm) REVERT: D 588 VAL cc_start: 0.7821 (p) cc_final: 0.7586 (m) REVERT: D 589 LYS cc_start: 0.8457 (mmmm) cc_final: 0.7664 (mmmm) REVERT: D 593 LYS cc_start: 0.8336 (mmmt) cc_final: 0.8001 (mmtp) REVERT: D 601 LYS cc_start: 0.8169 (tptt) cc_final: 0.7859 (tptt) REVERT: D 616 PHE cc_start: 0.6879 (t80) cc_final: 0.6584 (t80) REVERT: D 643 PRO cc_start: 0.8639 (Cg_endo) cc_final: 0.8325 (Cg_exo) REVERT: D 666 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7589 (t80) REVERT: D 698 ASP cc_start: 0.7617 (p0) cc_final: 0.7219 (p0) REVERT: D 760 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7026 (tm-30) REVERT: D 778 LYS cc_start: 0.7980 (tptm) cc_final: 0.7760 (tppt) REVERT: D 792 TYR cc_start: 0.7461 (t80) cc_final: 0.7151 (t80) REVERT: E 647 ARG cc_start: 0.5844 (OUTLIER) cc_final: 0.5382 (ptt-90) REVERT: E 708 ASP cc_start: 0.6606 (m-30) cc_final: 0.6308 (m-30) REVERT: E 757 GLU cc_start: 0.7154 (pm20) cc_final: 0.6668 (pm20) REVERT: E 764 GLU cc_start: 0.6791 (pp20) cc_final: 0.6360 (pp20) REVERT: E 812 ARG cc_start: 0.6266 (ttp-110) cc_final: 0.6034 (mtp-110) REVERT: E 824 GLU cc_start: 0.6996 (tp30) cc_final: 0.6558 (tp30) REVERT: E 827 LYS cc_start: 0.8049 (ttmt) cc_final: 0.7361 (ttmm) REVERT: E 856 LEU cc_start: 0.8291 (tp) cc_final: 0.7991 (tp) REVERT: E 863 ASN cc_start: 0.7631 (p0) cc_final: 0.6759 (p0) REVERT: E 933 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6634 (pp) REVERT: F 427 GLU cc_start: 0.7614 (tt0) cc_final: 0.7366 (tm-30) REVERT: F 428 MET cc_start: 0.6688 (tpt) cc_final: 0.5605 (tpt) REVERT: F 463 MET cc_start: 0.6669 (tpp) cc_final: 0.6089 (tpp) REVERT: F 549 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.5193 (mtp) REVERT: F 579 ARG cc_start: 0.6361 (ttp-110) cc_final: 0.5027 (mtt90) REVERT: F 667 MET cc_start: 0.7265 (tpp) cc_final: 0.6654 (tpp) REVERT: F 815 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6244 (mm-30) REVERT: F 847 GLU cc_start: 0.7853 (mp0) cc_final: 0.7511 (mp0) REVERT: F 863 ASN cc_start: 0.7091 (p0) cc_final: 0.6782 (p0) REVERT: G 1031 MET cc_start: -0.3297 (tpp) cc_final: -0.3726 (tpp) REVERT: G 1062 LYS cc_start: -0.0250 (tptt) cc_final: -0.0573 (tptt) REVERT: G 1125 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8446 (pp) outliers start: 126 outliers final: 87 residues processed: 733 average time/residue: 0.5010 time to fit residues: 554.3081 Evaluate side-chains 728 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 634 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1329 LYS Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 876 ASP Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 482 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain C residue 782 GLN Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 441 ASN Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 642 PHE Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 666 PHE Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 870 CYS Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 647 ARG Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 692 ILE Chi-restraints excluded: chain E residue 699 GLN Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 887 ASP Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 767 ILE Chi-restraints excluded: chain F residue 844 THR Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain F residue 1369 THR Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 987 MET Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain G residue 1127 ASP Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 973 MET Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1026 ILE Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 369 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 218 optimal weight: 0.5980 chunk 279 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 322 optimal weight: 0.0000 chunk 213 optimal weight: 0.2980 chunk 381 optimal weight: 40.0000 chunk 238 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 GLN C 896 GLN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 ASN F 898 HIS ** I1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33050 Z= 0.229 Angle : 0.623 12.023 44611 Z= 0.301 Chirality : 0.042 0.216 5018 Planarity : 0.004 0.061 5713 Dihedral : 6.128 131.610 4369 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.18 % Favored : 93.80 % Rotamer: Outliers : 3.45 % Allowed : 24.72 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3965 helix: 0.45 (0.12), residues: 1978 sheet: -0.89 (0.28), residues: 364 loop : -1.45 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 842 HIS 0.004 0.001 HIS E 510 PHE 0.026 0.001 PHE G1042 TYR 0.017 0.001 TYR D 756 ARG 0.007 0.000 ARG E 907 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 650 time to evaluate : 3.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 GLU cc_start: 0.6960 (mp0) cc_final: 0.6694 (mp0) REVERT: A 614 LYS cc_start: 0.7374 (ttpt) cc_final: 0.6950 (ttpp) REVERT: A 648 ARG cc_start: 0.7711 (mmp-170) cc_final: 0.7322 (mmt180) REVERT: A 733 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6569 (tm-30) REVERT: A 883 ASN cc_start: 0.8245 (m-40) cc_final: 0.7647 (t0) REVERT: A 912 ASN cc_start: 0.7598 (m-40) cc_final: 0.7219 (t0) REVERT: A 1349 ASP cc_start: 0.7051 (t0) cc_final: 0.6698 (t0) REVERT: B 547 ASP cc_start: 0.7125 (t0) cc_final: 0.6225 (t0) REVERT: B 760 GLU cc_start: 0.6806 (tp30) cc_final: 0.6499 (tp30) REVERT: B 1325 GLU cc_start: 0.6530 (tp30) cc_final: 0.6165 (tp30) REVERT: C 410 VAL cc_start: 0.8108 (m) cc_final: 0.7655 (p) REVERT: C 428 MET cc_start: 0.7670 (ptm) cc_final: 0.7368 (ttp) REVERT: C 443 ASN cc_start: 0.6869 (m-40) cc_final: 0.6616 (m-40) REVERT: C 499 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7836 (tp40) REVERT: C 505 GLU cc_start: 0.6605 (tp30) cc_final: 0.6273 (tp30) REVERT: C 508 LYS cc_start: 0.8000 (tppt) cc_final: 0.7587 (tppt) REVERT: C 557 VAL cc_start: 0.8568 (t) cc_final: 0.8348 (m) REVERT: C 562 ASN cc_start: 0.8014 (t160) cc_final: 0.7694 (t0) REVERT: C 613 LYS cc_start: 0.7897 (tppt) cc_final: 0.7519 (tppt) REVERT: C 665 ASP cc_start: 0.7749 (m-30) cc_final: 0.7356 (m-30) REVERT: C 725 LEU cc_start: 0.8145 (tp) cc_final: 0.7869 (mt) REVERT: C 803 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8179 (mm) REVERT: C 815 GLU cc_start: 0.6386 (mm-30) cc_final: 0.6107 (mm-30) REVERT: C 879 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6630 (tm-30) REVERT: C 925 MET cc_start: 0.5729 (tmm) cc_final: 0.5419 (tmm) REVERT: D 501 ARG cc_start: 0.6832 (mmm160) cc_final: 0.6051 (mmm160) REVERT: D 554 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.6043 (mp10) REVERT: D 588 VAL cc_start: 0.7831 (p) cc_final: 0.7569 (m) REVERT: D 593 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7825 (mmmt) REVERT: D 601 LYS cc_start: 0.8277 (tptt) cc_final: 0.7960 (tptp) REVERT: D 602 TRP cc_start: 0.8403 (m-10) cc_final: 0.8043 (m-10) REVERT: D 606 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7477 (mm) REVERT: D 616 PHE cc_start: 0.6913 (t80) cc_final: 0.6592 (t80) REVERT: D 643 PRO cc_start: 0.8601 (Cg_endo) cc_final: 0.8212 (Cg_exo) REVERT: D 660 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7135 (mmtm) REVERT: D 666 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7457 (t80) REVERT: D 698 ASP cc_start: 0.7637 (p0) cc_final: 0.7239 (p0) REVERT: D 760 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7086 (tm-30) REVERT: D 778 LYS cc_start: 0.7991 (tptm) cc_final: 0.7773 (tppt) REVERT: D 792 TYR cc_start: 0.7483 (t80) cc_final: 0.7153 (t80) REVERT: E 647 ARG cc_start: 0.5847 (OUTLIER) cc_final: 0.5060 (ptt-90) REVERT: E 708 ASP cc_start: 0.6599 (m-30) cc_final: 0.6306 (m-30) REVERT: E 764 GLU cc_start: 0.6800 (pp20) cc_final: 0.6384 (pp20) REVERT: E 824 GLU cc_start: 0.7021 (tp30) cc_final: 0.6614 (tp30) REVERT: E 827 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7371 (ttmm) REVERT: E 856 LEU cc_start: 0.8272 (tp) cc_final: 0.8006 (tp) REVERT: E 863 ASN cc_start: 0.7635 (p0) cc_final: 0.6384 (p0) REVERT: E 933 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6648 (pp) REVERT: F 427 GLU cc_start: 0.7610 (tt0) cc_final: 0.7376 (tm-30) REVERT: F 428 MET cc_start: 0.6731 (tpt) cc_final: 0.5615 (tpt) REVERT: F 463 MET cc_start: 0.6670 (tpp) cc_final: 0.6068 (tpp) REVERT: F 549 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.5178 (mtp) REVERT: F 572 ARG cc_start: 0.7208 (mtm-85) cc_final: 0.6859 (mtt90) REVERT: F 579 ARG cc_start: 0.6434 (ttp-110) cc_final: 0.5076 (mtt90) REVERT: F 667 MET cc_start: 0.7212 (tpp) cc_final: 0.6587 (tpp) REVERT: F 815 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6261 (mm-30) REVERT: F 847 GLU cc_start: 0.7877 (mp0) cc_final: 0.7521 (mp0) REVERT: F 863 ASN cc_start: 0.7141 (p0) cc_final: 0.6823 (p0) REVERT: G 1125 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8455 (pp) REVERT: I 1031 MET cc_start: 0.3211 (tpp) cc_final: 0.2127 (tpp) outliers start: 125 outliers final: 95 residues processed: 718 average time/residue: 0.4972 time to fit residues: 541.2593 Evaluate side-chains 741 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 637 time to evaluate : 3.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1329 LYS Chi-restraints excluded: chain A residue 1334 CYS Chi-restraints excluded: chain A residue 1374 ILE Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 876 ASP Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 794 GLU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 441 ASN Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 642 PHE Chi-restraints excluded: chain D residue 660 LYS Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 666 PHE Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 870 CYS Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 647 ARG Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 692 ILE Chi-restraints excluded: chain E residue 699 GLN Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 887 ASP Chi-restraints excluded: chain E residue 925 MET Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 767 ILE Chi-restraints excluded: chain F residue 844 THR Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 897 LEU Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain F residue 1369 THR Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 987 MET Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain G residue 1127 ASP Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 973 MET Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1026 ILE Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 30.0000 chunk 152 optimal weight: 3.9990 chunk 227 optimal weight: 0.2980 chunk 114 optimal weight: 0.0040 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 242 optimal weight: 50.0000 chunk 260 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 300 optimal weight: 5.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 GLN E 511 GLN E 727 ASN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 ASN F 898 HIS ** G1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33050 Z= 0.178 Angle : 0.610 12.955 44611 Z= 0.293 Chirality : 0.041 0.203 5018 Planarity : 0.004 0.057 5713 Dihedral : 5.959 129.176 4369 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.22 % Rotamer: Outliers : 3.14 % Allowed : 25.27 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3965 helix: 0.59 (0.12), residues: 1973 sheet: -0.86 (0.28), residues: 364 loop : -1.36 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 603 HIS 0.011 0.001 HIS H1009 PHE 0.023 0.001 PHE G1042 TYR 0.015 0.001 TYR D 756 ARG 0.008 0.000 ARG E 828 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 660 time to evaluate : 4.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 614 LYS cc_start: 0.7372 (ttpt) cc_final: 0.6903 (ttpp) REVERT: A 647 TYR cc_start: 0.8256 (m-80) cc_final: 0.7842 (m-80) REVERT: A 648 ARG cc_start: 0.7700 (mmp-170) cc_final: 0.7282 (mmt180) REVERT: A 883 ASN cc_start: 0.8272 (m-40) cc_final: 0.7674 (t0) REVERT: B 547 ASP cc_start: 0.7135 (t0) cc_final: 0.6201 (t0) REVERT: B 784 TYR cc_start: 0.8417 (m-10) cc_final: 0.8184 (m-10) REVERT: B 1325 GLU cc_start: 0.6475 (tp30) cc_final: 0.6083 (tp30) REVERT: C 410 VAL cc_start: 0.8063 (m) cc_final: 0.7628 (p) REVERT: C 428 MET cc_start: 0.7589 (ptm) cc_final: 0.7363 (ttp) REVERT: C 489 LEU cc_start: 0.7426 (pp) cc_final: 0.7155 (pp) REVERT: C 499 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7785 (tp40) REVERT: C 508 LYS cc_start: 0.7810 (tppt) cc_final: 0.7300 (tppt) REVERT: C 557 VAL cc_start: 0.8502 (t) cc_final: 0.8288 (m) REVERT: C 562 ASN cc_start: 0.8003 (t160) cc_final: 0.7681 (t0) REVERT: C 613 LYS cc_start: 0.7846 (tppt) cc_final: 0.7557 (tppt) REVERT: C 665 ASP cc_start: 0.7748 (m-30) cc_final: 0.7316 (m-30) REVERT: C 725 LEU cc_start: 0.8167 (tp) cc_final: 0.7881 (mt) REVERT: C 803 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8144 (mm) REVERT: C 815 GLU cc_start: 0.6342 (mm-30) cc_final: 0.6055 (mm-30) REVERT: C 879 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6578 (tm-30) REVERT: C 925 MET cc_start: 0.5726 (tmm) cc_final: 0.5496 (tmm) REVERT: D 421 TYR cc_start: 0.7952 (m-10) cc_final: 0.7717 (m-80) REVERT: D 501 ARG cc_start: 0.6814 (mmm160) cc_final: 0.6041 (mmm160) REVERT: D 554 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6064 (mp10) REVERT: D 588 VAL cc_start: 0.7792 (p) cc_final: 0.7587 (m) REVERT: D 593 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7979 (mmtp) REVERT: D 602 TRP cc_start: 0.8415 (m-10) cc_final: 0.7970 (m-10) REVERT: D 616 PHE cc_start: 0.6909 (t80) cc_final: 0.6603 (t80) REVERT: D 698 ASP cc_start: 0.7656 (p0) cc_final: 0.7232 (p0) REVERT: D 760 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7102 (tm-30) REVERT: D 778 LYS cc_start: 0.8012 (tptm) cc_final: 0.7762 (tppt) REVERT: D 792 TYR cc_start: 0.7493 (t80) cc_final: 0.7178 (t80) REVERT: D 797 ASN cc_start: 0.7878 (t0) cc_final: 0.7675 (t0) REVERT: E 647 ARG cc_start: 0.5936 (OUTLIER) cc_final: 0.5110 (ptt-90) REVERT: E 708 ASP cc_start: 0.6616 (m-30) cc_final: 0.6313 (m-30) REVERT: E 757 GLU cc_start: 0.7157 (pm20) cc_final: 0.6669 (pm20) REVERT: E 764 GLU cc_start: 0.6793 (pp20) cc_final: 0.6342 (pp20) REVERT: E 824 GLU cc_start: 0.7173 (tp30) cc_final: 0.6610 (tp30) REVERT: E 827 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7330 (ttmm) REVERT: E 856 LEU cc_start: 0.8276 (tp) cc_final: 0.8036 (tp) REVERT: E 858 ARG cc_start: 0.7379 (ttp-110) cc_final: 0.6917 (ttp-110) REVERT: E 863 ASN cc_start: 0.7603 (p0) cc_final: 0.6342 (p0) REVERT: E 873 GLU cc_start: 0.6601 (mp0) cc_final: 0.6085 (mp0) REVERT: E 933 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6627 (pp) REVERT: F 427 GLU cc_start: 0.7583 (tt0) cc_final: 0.7119 (tm-30) REVERT: F 428 MET cc_start: 0.6826 (tpt) cc_final: 0.6034 (tpt) REVERT: F 463 MET cc_start: 0.6656 (tpp) cc_final: 0.6401 (tpp) REVERT: F 549 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.5189 (mtp) REVERT: F 579 ARG cc_start: 0.6401 (ttp-110) cc_final: 0.5048 (mtt90) REVERT: F 667 MET cc_start: 0.7240 (tpp) cc_final: 0.6601 (tpp) REVERT: F 815 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6278 (mm-30) REVERT: F 847 GLU cc_start: 0.7875 (mp0) cc_final: 0.7526 (mp0) REVERT: F 863 ASN cc_start: 0.7113 (p0) cc_final: 0.6775 (p0) REVERT: G 1031 MET cc_start: -0.3309 (tpp) cc_final: -0.3784 (tpp) REVERT: G 1125 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8428 (pp) outliers start: 114 outliers final: 86 residues processed: 720 average time/residue: 0.5211 time to fit residues: 567.5643 Evaluate side-chains 735 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 643 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1329 LYS Chi-restraints excluded: chain A residue 1334 CYS Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 876 ASP Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 794 GLU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 441 ASN Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 642 PHE Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 870 CYS Chi-restraints excluded: chain D residue 927 LYS Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 647 ARG Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 699 GLN Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 887 ASP Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 844 THR Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 897 LEU Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain F residue 1369 THR Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1116 ARG Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 973 MET Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1026 ILE Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 347 optimal weight: 50.0000 chunk 365 optimal weight: 1.9990 chunk 333 optimal weight: 6.9990 chunk 355 optimal weight: 20.0000 chunk 214 optimal weight: 2.9990 chunk 154 optimal weight: 0.4980 chunk 279 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 321 optimal weight: 0.6980 chunk 336 optimal weight: 0.8980 chunk 354 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 GLN ** D 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 799 GLN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 ASN F 898 HIS ** G1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33050 Z= 0.212 Angle : 0.639 22.171 44611 Z= 0.305 Chirality : 0.042 0.197 5018 Planarity : 0.004 0.056 5713 Dihedral : 5.906 129.650 4369 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.10 % Rotamer: Outliers : 3.20 % Allowed : 25.66 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3965 helix: 0.57 (0.12), residues: 1979 sheet: -0.82 (0.28), residues: 364 loop : -1.40 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 842 HIS 0.004 0.001 HIS E 510 PHE 0.023 0.001 PHE G1042 TYR 0.016 0.001 TYR D 756 ARG 0.008 0.000 ARG B 828 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 659 time to evaluate : 3.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 LYS cc_start: 0.7356 (ttpt) cc_final: 0.6906 (ttpp) REVERT: A 647 TYR cc_start: 0.8265 (m-80) cc_final: 0.7869 (m-80) REVERT: A 648 ARG cc_start: 0.7731 (mmp-170) cc_final: 0.7298 (mmt180) REVERT: A 733 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6507 (tm-30) REVERT: A 883 ASN cc_start: 0.8277 (m-40) cc_final: 0.7659 (t0) REVERT: B 508 LYS cc_start: 0.7834 (tttt) cc_final: 0.7536 (tptt) REVERT: B 547 ASP cc_start: 0.7148 (t0) cc_final: 0.6249 (t0) REVERT: B 760 GLU cc_start: 0.6742 (tp30) cc_final: 0.6312 (tm-30) REVERT: B 876 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7099 (p0) REVERT: B 879 GLU cc_start: 0.7572 (tp30) cc_final: 0.7355 (tp30) REVERT: B 1325 GLU cc_start: 0.6513 (tp30) cc_final: 0.6102 (tp30) REVERT: C 410 VAL cc_start: 0.8089 (m) cc_final: 0.7657 (p) REVERT: C 428 MET cc_start: 0.7597 (ptm) cc_final: 0.7380 (ttp) REVERT: C 489 LEU cc_start: 0.7468 (pp) cc_final: 0.7181 (pp) REVERT: C 499 GLN cc_start: 0.8167 (tp-100) cc_final: 0.7867 (tp40) REVERT: C 508 LYS cc_start: 0.7778 (tppt) cc_final: 0.7279 (tppt) REVERT: C 562 ASN cc_start: 0.8003 (t160) cc_final: 0.7673 (t0) REVERT: C 613 LYS cc_start: 0.7827 (tppt) cc_final: 0.7545 (tppt) REVERT: C 665 ASP cc_start: 0.7669 (m-30) cc_final: 0.7300 (m-30) REVERT: C 725 LEU cc_start: 0.8103 (tp) cc_final: 0.7890 (mt) REVERT: C 803 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8176 (mm) REVERT: C 815 GLU cc_start: 0.6362 (mm-30) cc_final: 0.6099 (mm-30) REVERT: C 879 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6558 (tm-30) REVERT: C 925 MET cc_start: 0.5769 (tmm) cc_final: 0.5561 (tmm) REVERT: D 421 TYR cc_start: 0.7956 (m-10) cc_final: 0.7707 (m-10) REVERT: D 501 ARG cc_start: 0.6833 (mmm160) cc_final: 0.6064 (mmm160) REVERT: D 554 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6103 (mp10) REVERT: D 588 VAL cc_start: 0.7802 (p) cc_final: 0.7583 (m) REVERT: D 589 LYS cc_start: 0.8510 (mmmm) cc_final: 0.8051 (mmmm) REVERT: D 593 LYS cc_start: 0.8353 (mmmt) cc_final: 0.7774 (mmmt) REVERT: D 635 LEU cc_start: 0.8438 (mt) cc_final: 0.8112 (mm) REVERT: D 638 ILE cc_start: 0.8691 (mt) cc_final: 0.8477 (mt) REVERT: D 698 ASP cc_start: 0.7669 (p0) cc_final: 0.7252 (p0) REVERT: D 760 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7108 (tm-30) REVERT: D 778 LYS cc_start: 0.8011 (tptm) cc_final: 0.7619 (tptm) REVERT: D 792 TYR cc_start: 0.7503 (t80) cc_final: 0.7204 (t80) REVERT: D 797 ASN cc_start: 0.7886 (t0) cc_final: 0.7655 (t0) REVERT: D 824 GLU cc_start: 0.6411 (tm-30) cc_final: 0.6070 (tm-30) REVERT: E 647 ARG cc_start: 0.5951 (OUTLIER) cc_final: 0.5199 (ptt-90) REVERT: E 708 ASP cc_start: 0.6609 (m-30) cc_final: 0.6299 (m-30) REVERT: E 757 GLU cc_start: 0.7155 (pm20) cc_final: 0.6679 (pm20) REVERT: E 764 GLU cc_start: 0.6796 (pp20) cc_final: 0.6515 (pp20) REVERT: E 824 GLU cc_start: 0.7202 (tp30) cc_final: 0.6250 (tp30) REVERT: E 827 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7289 (ttmm) REVERT: E 856 LEU cc_start: 0.8303 (tp) cc_final: 0.8047 (tp) REVERT: E 858 ARG cc_start: 0.7365 (ttp-110) cc_final: 0.5886 (tpp80) REVERT: E 873 GLU cc_start: 0.6570 (mp0) cc_final: 0.6076 (mp0) REVERT: E 933 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6641 (pp) REVERT: F 427 GLU cc_start: 0.7650 (tt0) cc_final: 0.7102 (tm-30) REVERT: F 428 MET cc_start: 0.6907 (tpt) cc_final: 0.6076 (tpt) REVERT: F 463 MET cc_start: 0.6659 (tpp) cc_final: 0.6402 (tpp) REVERT: F 549 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.5209 (mtp) REVERT: F 579 ARG cc_start: 0.6493 (ttp-110) cc_final: 0.5151 (mtt90) REVERT: F 667 MET cc_start: 0.7267 (tpp) cc_final: 0.6604 (tpp) REVERT: F 815 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6275 (mm-30) REVERT: F 847 GLU cc_start: 0.7886 (mp0) cc_final: 0.7544 (mp0) REVERT: F 863 ASN cc_start: 0.7180 (p0) cc_final: 0.6861 (p0) REVERT: G 973 MET cc_start: 0.6378 (tpt) cc_final: 0.6112 (tpt) REVERT: G 1062 LYS cc_start: -0.1028 (tptt) cc_final: -0.1539 (tptt) REVERT: G 1125 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8424 (pp) outliers start: 116 outliers final: 89 residues processed: 725 average time/residue: 0.4961 time to fit residues: 543.7119 Evaluate side-chains 750 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 654 time to evaluate : 4.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1329 LYS Chi-restraints excluded: chain A residue 1334 CYS Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 876 ASP Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 794 GLU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 441 ASN Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 642 PHE Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 870 CYS Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 638 ILE Chi-restraints excluded: chain E residue 647 ARG Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 699 GLN Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 887 ASP Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 844 THR Chi-restraints excluded: chain F residue 865 LYS Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 897 LEU Chi-restraints excluded: chain F residue 933 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain F residue 1369 THR Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 973 MET Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1010 LEU Chi-restraints excluded: chain I residue 1026 ILE Chi-restraints excluded: chain I residue 1070 LEU Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 233 optimal weight: 9.9990 chunk 376 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 178 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 394 optimal weight: 30.0000 chunk 363 optimal weight: 50.0000 chunk 314 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 192 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 GLN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 ASN F 898 HIS ** H1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 33050 Z= 0.311 Angle : 0.669 21.078 44611 Z= 0.323 Chirality : 0.044 0.194 5018 Planarity : 0.005 0.058 5713 Dihedral : 5.981 133.205 4366 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.63 % Favored : 93.34 % Rotamer: Outliers : 2.95 % Allowed : 26.01 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3965 helix: 0.43 (0.12), residues: 1976 sheet: -0.84 (0.28), residues: 365 loop : -1.39 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C1358 HIS 0.004 0.001 HIS A1351 PHE 0.021 0.001 PHE G1042 TYR 0.019 0.001 TYR D 756 ARG 0.009 0.000 ARG E 858 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7930 Ramachandran restraints generated. 3965 Oldfield, 0 Emsley, 3965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 664 time to evaluate : 3.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 GLU cc_start: 0.7065 (mp0) cc_final: 0.6811 (mt-10) REVERT: A 614 LYS cc_start: 0.7248 (ttpt) cc_final: 0.6799 (ttpp) REVERT: A 638 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8304 (p) REVERT: A 648 ARG cc_start: 0.7837 (mmp-170) cc_final: 0.7423 (mmt180) REVERT: A 874 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6882 (mt-10) REVERT: A 878 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7615 (mm) REVERT: A 883 ASN cc_start: 0.8296 (m-40) cc_final: 0.7687 (t0) REVERT: A 912 ASN cc_start: 0.7539 (m-40) cc_final: 0.7200 (t0) REVERT: B 463 MET cc_start: 0.7882 (tpp) cc_final: 0.7549 (tpp) REVERT: B 547 ASP cc_start: 0.7211 (t0) cc_final: 0.6306 (t0) REVERT: B 760 GLU cc_start: 0.6757 (tp30) cc_final: 0.6334 (tm-30) REVERT: B 876 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7118 (p0) REVERT: C 428 MET cc_start: 0.7695 (ptm) cc_final: 0.7406 (ttp) REVERT: C 435 TYR cc_start: 0.8068 (m-80) cc_final: 0.7823 (m-10) REVERT: C 499 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7912 (tp40) REVERT: C 505 GLU cc_start: 0.6697 (tp30) cc_final: 0.6192 (tp30) REVERT: C 508 LYS cc_start: 0.7894 (tppt) cc_final: 0.7475 (tppt) REVERT: C 562 ASN cc_start: 0.8012 (t160) cc_final: 0.7686 (t0) REVERT: C 613 LYS cc_start: 0.7811 (tppt) cc_final: 0.7548 (tppt) REVERT: C 665 ASP cc_start: 0.7677 (m-30) cc_final: 0.7240 (m-30) REVERT: C 725 LEU cc_start: 0.8106 (tp) cc_final: 0.7886 (mt) REVERT: C 803 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8248 (mm) REVERT: C 815 GLU cc_start: 0.6402 (mm-30) cc_final: 0.6134 (mm-30) REVERT: C 879 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6585 (tm-30) REVERT: C 925 MET cc_start: 0.5760 (tmm) cc_final: 0.5543 (tmm) REVERT: C 1358 TRP cc_start: 0.8198 (t-100) cc_final: 0.7577 (t-100) REVERT: D 421 TYR cc_start: 0.7949 (m-10) cc_final: 0.7696 (m-10) REVERT: D 501 ARG cc_start: 0.6843 (mmm160) cc_final: 0.6048 (mmm160) REVERT: D 554 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6094 (mp10) REVERT: D 588 VAL cc_start: 0.7992 (p) cc_final: 0.7728 (m) REVERT: D 589 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8119 (mmmm) REVERT: D 593 LYS cc_start: 0.8345 (mmmt) cc_final: 0.7785 (mmmt) REVERT: D 594 ILE cc_start: 0.8287 (mt) cc_final: 0.8057 (tt) REVERT: D 616 PHE cc_start: 0.6908 (t80) cc_final: 0.6638 (t80) REVERT: D 632 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6492 (tm-30) REVERT: D 698 ASP cc_start: 0.7691 (p0) cc_final: 0.7287 (p0) REVERT: D 760 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7142 (tm-30) REVERT: D 792 TYR cc_start: 0.7512 (t80) cc_final: 0.7191 (t80) REVERT: D 824 GLU cc_start: 0.6432 (tm-30) cc_final: 0.6101 (tm-30) REVERT: E 647 ARG cc_start: 0.5987 (OUTLIER) cc_final: 0.5249 (ptt-90) REVERT: E 708 ASP cc_start: 0.6574 (m-30) cc_final: 0.6286 (m-30) REVERT: E 757 GLU cc_start: 0.7155 (pm20) cc_final: 0.6681 (pm20) REVERT: E 764 GLU cc_start: 0.6805 (pp20) cc_final: 0.6476 (pp20) REVERT: E 824 GLU cc_start: 0.7195 (tp30) cc_final: 0.6663 (tp30) REVERT: E 827 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7364 (ttmm) REVERT: E 856 LEU cc_start: 0.8306 (tp) cc_final: 0.8061 (tp) REVERT: E 858 ARG cc_start: 0.7410 (ttp-110) cc_final: 0.6778 (ttm110) REVERT: E 873 GLU cc_start: 0.6626 (mp0) cc_final: 0.6208 (mp0) REVERT: E 933 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6689 (pp) REVERT: F 427 GLU cc_start: 0.7690 (tt0) cc_final: 0.7407 (tm-30) REVERT: F 428 MET cc_start: 0.7006 (tpt) cc_final: 0.6261 (tpt) REVERT: F 463 MET cc_start: 0.6662 (tpp) cc_final: 0.6415 (tpp) REVERT: F 549 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.5266 (mtp) REVERT: F 579 ARG cc_start: 0.6623 (ttp-110) cc_final: 0.5339 (mtt90) REVERT: F 667 MET cc_start: 0.7328 (tpp) cc_final: 0.6639 (tpp) REVERT: F 754 ARG cc_start: 0.6408 (tmt170) cc_final: 0.6009 (tmt170) REVERT: F 815 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6209 (mm-30) REVERT: F 847 GLU cc_start: 0.7913 (mp0) cc_final: 0.7581 (mp0) REVERT: F 863 ASN cc_start: 0.7302 (p0) cc_final: 0.6980 (p0) REVERT: G 1051 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8054 (pp20) REVERT: G 1062 LYS cc_start: -0.1013 (tptt) cc_final: -0.1288 (tptt) REVERT: G 1125 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8474 (pp) outliers start: 107 outliers final: 89 residues processed: 731 average time/residue: 0.5061 time to fit residues: 559.9969 Evaluate side-chains 755 residues out of total 3626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 657 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 894 ASN Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 1321 LEU Chi-restraints excluded: chain A residue 1329 LYS Chi-restraints excluded: chain A residue 1334 CYS Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 876 ASP Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 926 LYS Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 511 GLN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 587 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 LYS Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 794 GLU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 918 THR Chi-restraints excluded: chain D residue 441 ASN Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 587 ASP Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 769 LYS Chi-restraints excluded: chain D residue 832 VAL Chi-restraints excluded: chain D residue 845 ILE Chi-restraints excluded: chain D residue 870 CYS Chi-restraints excluded: chain D residue 927 LYS Chi-restraints excluded: chain D residue 936 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 647 ARG Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 761 SER Chi-restraints excluded: chain E residue 785 VAL Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 887 ASP Chi-restraints excluded: chain E residue 933 LEU Chi-restraints excluded: chain E residue 936 LEU Chi-restraints excluded: chain E residue 1358 TRP Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 549 MET Chi-restraints excluded: chain F residue 630 CYS Chi-restraints excluded: chain F residue 731 TYR Chi-restraints excluded: chain F residue 767 ILE Chi-restraints excluded: chain F residue 844 THR Chi-restraints excluded: chain F residue 865 LYS Chi-restraints excluded: chain F residue 871 LEU Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 897 LEU Chi-restraints excluded: chain F residue 1321 ILE Chi-restraints excluded: chain F residue 1369 THR Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 1044 MET Chi-restraints excluded: chain G residue 1125 LEU Chi-restraints excluded: chain H residue 1044 MET Chi-restraints excluded: chain I residue 345 THR Chi-restraints excluded: chain I residue 973 MET Chi-restraints excluded: chain I residue 987 MET Chi-restraints excluded: chain I residue 1010 LEU Chi-restraints excluded: chain I residue 1026 ILE Chi-restraints excluded: chain I residue 1070 LEU Chi-restraints excluded: chain I residue 1090 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 249 optimal weight: 0.0470 chunk 334 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 323 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.0170 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 GLN ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 ASN F 898 HIS ** H1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 969 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.171864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128621 restraints weight = 49559.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132258 restraints weight = 25139.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134478 restraints weight = 15794.651| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33050 Z= 0.202 Angle : 0.647 21.555 44611 Z= 0.310 Chirality : 0.042 0.188 5018 Planarity : 0.004 0.056 5713 Dihedral : 5.806 130.380 4366 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.73 % Favored : 94.25 % Rotamer: Outliers : 2.79 % Allowed : 26.51 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3965 helix: 0.55 (0.12), residues: 1982 sheet: -0.78 (0.28), residues: 364 loop : -1.36 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 842 HIS 0.004 0.001 HIS E 510 PHE 0.020 0.001 PHE G1042 TYR 0.016 0.001 TYR D 756 ARG 0.008 0.000 ARG B 828 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8732.63 seconds wall clock time: 156 minutes 46.66 seconds (9406.66 seconds total)