Starting phenix.real_space_refine on Wed Mar 20 17:11:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqj_26696/03_2024/7uqj_26696_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqj_26696/03_2024/7uqj_26696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqj_26696/03_2024/7uqj_26696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqj_26696/03_2024/7uqj_26696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqj_26696/03_2024/7uqj_26696_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqj_26696/03_2024/7uqj_26696_updated.pdb" } resolution = 3.0 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= 0.031 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: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 4 5.21 5 S 107 5.16 5 C 17881 2.51 5 N 4741 2.21 5 O 5233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 475": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A ARG 640": "NH1" <-> "NH2" Residue "A GLU 690": "OE1" <-> "OE2" Residue "A GLU 732": "OE1" <-> "OE2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 809": "OE1" <-> "OE2" Residue "A ARG 812": "NH1" <-> "NH2" Residue "A GLU 824": "OE1" <-> "OE2" Residue "A ARG 828": "NH1" <-> "NH2" Residue "A GLU 864": "OE1" <-> "OE2" Residue "A GLU 873": "OE1" <-> "OE2" Residue "A ARG 907": "NH1" <-> "NH2" Residue "A ARG 929": "NH1" <-> "NH2" Residue "A GLU 935": "OE1" <-> "OE2" Residue "A GLU 1347": "OE1" <-> "OE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B GLU 690": "OE1" <-> "OE2" Residue "B ARG 720": "NH1" <-> "NH2" Residue "B GLU 733": "OE1" <-> "OE2" Residue "B GLU 760": "OE1" <-> "OE2" Residue "B GLU 764": "OE1" <-> "OE2" Residue "B GLU 809": "OE1" <-> "OE2" Residue "B ARG 812": "NH1" <-> "NH2" Residue "B GLU 815": "OE1" <-> "OE2" Residue "B GLU 824": "OE1" <-> "OE2" Residue "B ARG 828": "NH1" <-> "NH2" Residue "B GLU 847": "OE1" <-> "OE2" Residue "B ARG 928": "NH1" <-> "NH2" Residue "B GLU 935": "OE1" <-> "OE2" Residue "B GLU 1325": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C GLU 505": "OE1" <-> "OE2" Residue "C ARG 552": "NH1" <-> "NH2" Residue "C GLU 690": "OE1" <-> "OE2" Residue "C GLU 732": "OE1" <-> "OE2" Residue "C GLU 764": "OE1" <-> "OE2" Residue "C ARG 812": "NH1" <-> "NH2" Residue "C GLU 824": "OE1" <-> "OE2" Residue "C GLU 914": "OE1" <-> "OE2" Residue "C ARG 928": "NH1" <-> "NH2" Residue "C GLU 1336": "OE1" <-> "OE2" Residue "C GLU 1347": "OE1" <-> "OE2" Residue "D TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 475": "OE1" <-> "OE2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D GLU 505": "OE1" <-> "OE2" Residue "D GLU 532": "OE1" <-> "OE2" Residue "D ARG 552": "NH1" <-> "NH2" Residue "D GLU 580": "OE1" <-> "OE2" Residue "D ARG 720": "NH1" <-> "NH2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "D GLU 764": "OE1" <-> "OE2" Residue "D ARG 812": "NH1" <-> "NH2" Residue "D ARG 929": "NH1" <-> "NH2" Residue "D GLU 935": "OE1" <-> "OE2" Residue "D GLU 1319": "OE1" <-> "OE2" Residue "D GLU 1372": "OE1" <-> "OE2" Residue "E ARG 448": "NH1" <-> "NH2" Residue "E GLU 475": "OE1" <-> "OE2" Residue "E ARG 483": "NH1" <-> "NH2" Residue "E ARG 498": "NH1" <-> "NH2" Residue "E GLU 505": "OE1" <-> "OE2" Residue "E GLU 506": "OE1" <-> "OE2" Residue "E ARG 552": "NH1" <-> "NH2" Residue "E ARG 812": "NH1" <-> "NH2" Residue "E GLU 815": "OE1" <-> "OE2" Residue "E ARG 828": "NH1" <-> "NH2" Residue "E GLU 879": "OE1" <-> "OE2" Residue "E PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 903": "OE1" <-> "OE2" Residue "E GLU 914": "OE1" <-> "OE2" Residue "E ARG 928": "NH1" <-> "NH2" Residue "E GLU 935": "OE1" <-> "OE2" Residue "E GLU 1347": "OE1" <-> "OE2" Residue "F GLU 437": "OE1" <-> "OE2" Residue "F ARG 476": "NH1" <-> "NH2" Residue "F ARG 483": "NH1" <-> "NH2" Residue "F GLU 495": "OE1" <-> "OE2" Residue "F ARG 498": "NH1" <-> "NH2" Residue "F GLU 505": "OE1" <-> "OE2" Residue "F GLU 506": "OE1" <-> "OE2" Residue "F GLU 519": "OE1" <-> "OE2" Residue "F ARG 552": "NH1" <-> "NH2" Residue "F ARG 573": "NH1" <-> "NH2" Residue "F ARG 576": "NH1" <-> "NH2" Residue "F PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 732": "OE1" <-> "OE2" Residue "F GLU 757": "OE1" <-> "OE2" Residue "F GLU 809": "OE1" <-> "OE2" Residue "F ARG 812": "NH1" <-> "NH2" Residue "F ARG 828": "NH1" <-> "NH2" Residue "F GLU 847": "OE1" <-> "OE2" Residue "F ARG 929": "NH1" <-> "NH2" Residue "F GLU 935": "OE1" <-> "OE2" Residue "F GLU 1319": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27983 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4646 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 33, 'TRANS': 551} Chain breaks: 2 Chain: "B" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4573 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 541} Chain breaks: 2 Chain: "C" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4622 Classifications: {'peptide': 581} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 547} Chain breaks: 2 Chain: "D" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4622 Classifications: {'peptide': 581} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 547} Chain breaks: 2 Chain: "E" Number of atoms: 4598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4598 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 545} Chain breaks: 2 Chain: "F" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4628 Classifications: {'peptide': 581} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 548} Chain breaks: 2 Chain: "G" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 108 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.63, per 1000 atoms: 0.52 Number of scatterers: 27983 At special positions: 0 Unit cell: (125.856, 150.696, 158.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 107 16.00 P 17 15.00 Mg 4 11.99 O 5233 8.00 N 4741 7.00 C 17881 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: 10.96 Conformation dependent library (CDL) restraints added in 5.4 seconds 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 12 sheets defined 45.0% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.93 Creating SS restraints... Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 419 through 426 Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 436 through 439 No H-bonds generated for 'chain 'A' and resid 436 through 439' Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 495 through 509 Processing helix chain 'A' and resid 520 through 523 No H-bonds generated for 'chain 'A' and resid 520 through 523' Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 588 through 597 Processing helix chain 'A' and resid 608 through 618 Processing helix chain 'A' and resid 623 through 641 Processing helix chain 'A' and resid 643 through 646 Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 692 through 711 removed outlier: 3.823A pdb=" N LEU A 696 " --> pdb=" O LYS A 693 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA A 697 " --> pdb=" O PRO A 694 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASP A 698 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASP A 708 " --> pdb=" O ASN A 705 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR A 709 " --> pdb=" O LYS A 706 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 711 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 719 No H-bonds generated for 'chain 'A' and resid 716 through 719' Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 758 through 766 removed outlier: 3.952A pdb=" N GLN A 766 " --> pdb=" O MET A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 792 removed outlier: 3.609A pdb=" N ALA A 787 " --> pdb=" O GLN A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 806 No H-bonds generated for 'chain 'A' and resid 803 through 806' Processing helix chain 'A' and resid 814 through 827 removed outlier: 3.736A pdb=" N VAL A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 844 removed outlier: 3.906A pdb=" N ASN A 843 " --> pdb=" O ASP A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 858 removed outlier: 3.515A pdb=" N LEU A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 882 Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 910 through 916 Processing helix chain 'A' and resid 1324 through 1337 removed outlier: 4.087A pdb=" N LYS A1328 " --> pdb=" O PRO A1324 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A1333 " --> pdb=" O LYS A1329 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A1336 " --> pdb=" O ALA A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1359 Processing helix chain 'A' and resid 1370 through 1376 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 419 through 429 removed outlier: 3.683A pdb=" N ASP B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 436 through 439 No H-bonds generated for 'chain 'B' and resid 436 through 439' Processing helix chain 'B' and resid 460 through 471 removed outlier: 3.608A pdb=" N ALA B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 509 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 Processing helix chain 'B' and resid 564 through 566 No H-bonds generated for 'chain 'B' and resid 564 through 566' Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 588 through 599 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 removed outlier: 3.547A pdb=" N LYS B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 711 removed outlier: 3.551A pdb=" N LEU B 696 " --> pdb=" O LYS B 693 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA B 697 " --> pdb=" O PRO B 694 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP B 698 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 707 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET B 710 " --> pdb=" O LEU B 707 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B 711 " --> pdb=" O ASP B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 730 Processing helix chain 'B' and resid 759 through 766 removed outlier: 4.104A pdb=" N GLN B 766 " --> pdb=" O MET B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 792 removed outlier: 3.849A pdb=" N ALA B 787 " --> pdb=" O GLN B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 806 No H-bonds generated for 'chain 'B' and resid 803 through 806' Processing helix chain 'B' and resid 814 through 827 Processing helix chain 'B' and resid 838 through 844 removed outlier: 3.759A pdb=" N ASN B 843 " --> pdb=" O ASP B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 859 removed outlier: 3.893A pdb=" N VAL B 852 " --> pdb=" O ASN B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 881 No H-bonds generated for 'chain 'B' and resid 878 through 881' Processing helix chain 'B' and resid 884 through 886 No H-bonds generated for 'chain 'B' and resid 884 through 886' Processing helix chain 'B' and resid 902 through 916 removed outlier: 4.293A pdb=" N ASN B 911 " --> pdb=" O ARG B 907 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B 912 " --> pdb=" O TYR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 1326 through 1337 Processing helix chain 'B' and resid 1343 through 1359 removed outlier: 3.576A pdb=" N VAL B1349 " --> pdb=" O GLN B1345 " (cutoff:3.500A) 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 426 removed outlier: 3.585A pdb=" N ASP C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 434 No H-bonds generated for 'chain 'C' and resid 431 through 434' Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 460 through 470 Processing helix chain 'C' and resid 496 through 509 Processing helix chain 'C' and resid 520 through 522 No H-bonds generated for 'chain 'C' and resid 520 through 522' Processing helix chain 'C' and resid 533 through 546 removed outlier: 3.886A pdb=" N VAL C 539 " --> pdb=" O HIS C 535 " (cutoff:3.500A) 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 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 removed outlier: 3.604A pdb=" N TYR C 646 " --> pdb=" O PRO C 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 643 through 646' Processing helix chain 'C' and resid 663 through 670 Processing helix chain 'C' and resid 693 through 711 removed outlier: 5.271A pdb=" N ASP C 698 " --> pdb=" O PRO C 694 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLN C 699 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN C 702 " --> pdb=" O ASP C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 759 through 766 removed outlier: 4.106A 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 816 through 827 Processing helix chain 'C' and resid 838 through 844 removed outlier: 3.959A pdb=" N ASN C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 858 Processing helix chain 'C' and resid 878 through 881 No H-bonds generated for 'chain 'C' and resid 878 through 881' Processing helix chain 'C' and resid 884 through 886 No H-bonds generated for 'chain 'C' and resid 884 through 886' Processing helix chain 'C' and resid 902 through 916 removed outlier: 3.886A pdb=" N ASN C 911 " --> pdb=" O ARG C 907 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU C 912 " --> pdb=" O TYR C 908 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 1324 through 1337 Processing helix chain 'C' and resid 1343 through 1359 Processing helix chain 'C' and resid 1367 through 1377 removed outlier: 3.643A pdb=" N ASP C1371 " --> pdb=" O THR C1367 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 419 through 429 removed outlier: 3.597A pdb=" N GLU D 427 " --> pdb=" O ASP D 423 " (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 471 Processing helix chain 'D' and resid 495 through 509 Processing helix chain 'D' and resid 520 through 523 No H-bonds generated for 'chain 'D' and resid 520 through 523' Processing helix chain 'D' and resid 533 through 546 Processing helix chain 'D' and resid 564 through 566 No H-bonds generated for 'chain 'D' and resid 564 through 566' Processing helix chain 'D' and resid 588 through 598 Processing helix chain 'D' and resid 608 through 616 Processing helix chain 'D' and resid 623 through 641 Processing helix chain 'D' and resid 643 through 647 Processing helix chain 'D' and resid 663 through 672 Processing helix chain 'D' and resid 676 through 678 No H-bonds generated for 'chain 'D' and resid 676 through 678' Processing helix chain 'D' and resid 692 through 711 removed outlier: 3.542A pdb=" N LEU D 696 " --> pdb=" O LYS D 693 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA D 697 " --> pdb=" O PRO D 694 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ASP D 698 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN D 699 " --> pdb=" O LEU D 696 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN D 701 " --> pdb=" O ASP D 698 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 711 " --> pdb=" O ASP D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 729 No H-bonds generated for 'chain 'D' and resid 726 through 729' Processing helix chain 'D' and resid 760 through 765 removed outlier: 3.765A pdb=" N SER D 765 " --> pdb=" O SER D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 792 removed outlier: 3.556A pdb=" N ALA D 787 " --> pdb=" O GLN D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 806 No H-bonds generated for 'chain 'D' and resid 803 through 806' Processing helix chain 'D' and resid 814 through 827 Processing helix chain 'D' and resid 838 through 844 removed outlier: 4.492A 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 880 No H-bonds generated for 'chain 'D' and resid 877 through 880' Processing helix chain 'D' and resid 902 through 916 removed outlier: 3.857A pdb=" N ASN D 911 " --> pdb=" O ARG D 907 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D 912 " --> pdb=" O TYR D 908 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 914 " --> pdb=" O SER D 910 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 915 " --> pdb=" O ASN D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 1324 through 1337 Processing helix chain 'D' and resid 1343 through 1359 Processing helix chain 'D' and resid 1367 through 1376 Processing helix chain 'E' and resid 419 through 434 Proline residue: E 432 - end of helix Processing helix chain 'E' and resid 438 through 441 No H-bonds generated for 'chain 'E' and resid 438 through 441' Processing helix chain 'E' and resid 460 through 472 removed outlier: 3.879A pdb=" N SER E 472 " --> pdb=" O ALA E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 509 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 533 through 547 Processing helix chain 'E' and resid 588 through 598 Processing helix chain 'E' and resid 608 through 616 Processing helix chain 'E' and resid 623 through 641 Processing helix chain 'E' and resid 656 through 658 No H-bonds generated for 'chain 'E' and resid 656 through 658' Processing helix chain 'E' and resid 663 through 671 removed outlier: 3.765A pdb=" N LYS E 671 " --> pdb=" O MET E 667 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 678 No H-bonds generated for 'chain 'E' and resid 676 through 678' Processing helix chain 'E' and resid 692 through 706 removed outlier: 3.828A pdb=" N LEU E 696 " --> pdb=" O LYS E 693 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA E 697 " --> pdb=" O PRO E 694 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP E 698 " --> pdb=" O LEU E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 716 No H-bonds generated for 'chain 'E' and resid 713 through 716' Processing helix chain 'E' and resid 724 through 730 Processing helix chain 'E' and resid 759 through 764 Processing helix chain 'E' and resid 782 through 792 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 825 Processing helix chain 'E' and resid 838 through 844 removed outlier: 3.979A pdb=" N ASN E 843 " --> pdb=" O ASP E 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 847 through 857 Processing helix chain 'E' and resid 878 through 881 No H-bonds generated for 'chain 'E' and resid 878 through 881' Processing helix chain 'E' and resid 884 through 887 removed outlier: 4.065A pdb=" N ASP E 887 " --> pdb=" O ILE E 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 884 through 887' Processing helix chain 'E' and resid 902 through 911 removed outlier: 4.051A pdb=" N ASN E 911 " --> pdb=" O ARG E 907 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 916 No H-bonds generated for 'chain 'E' and resid 913 through 916' Processing helix chain 'E' and resid 1329 through 1337 removed outlier: 3.762A pdb=" N CYS E1333 " --> pdb=" O LYS E1329 " (cutoff:3.500A) Processing helix chain 'E' and resid 1343 through 1359 Processing helix chain 'E' and resid 1367 through 1376 removed outlier: 3.882A pdb=" N GLU E1372 " --> pdb=" O GLY E1368 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 428 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 469 removed outlier: 3.659A pdb=" N ALA F 464 " --> pdb=" O LYS F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 509 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 533 through 548 removed outlier: 3.823A pdb=" N ALA F 544 " --> pdb=" O SER F 540 " (cutoff:3.500A) 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 569 through 572 Processing helix chain 'F' and resid 588 through 599 Processing helix chain 'F' and resid 608 through 616 Processing helix chain 'F' and resid 623 through 641 Processing helix chain 'F' and resid 663 through 671 removed outlier: 3.811A pdb=" N LYS F 671 " --> pdb=" O MET F 667 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 711 Processing helix chain 'F' and resid 724 through 730 removed outlier: 3.724A pdb=" N ILE F 729 " --> pdb=" O LEU F 725 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP F 730 " --> pdb=" O GLN F 726 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 763 Processing helix chain 'F' and resid 782 through 792 removed outlier: 3.654A 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: 3.824A 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 878 through 881 No H-bonds generated for 'chain 'F' and resid 878 through 881' Processing helix chain 'F' and resid 884 through 886 No H-bonds generated for 'chain 'F' and resid 884 through 886' Processing helix chain 'F' and resid 902 through 916 removed outlier: 4.183A pdb=" N ASN F 911 " --> pdb=" O ARG F 907 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU F 912 " --> pdb=" O TYR F 908 " (cutoff:3.500A) Processing helix chain 'F' and resid 1324 through 1337 Processing helix chain 'F' and resid 1343 through 1359 removed outlier: 3.510A pdb=" N VAL F1349 " --> pdb=" O GLN F1345 " (cutoff:3.500A) Processing helix chain 'F' and resid 1368 through 1376 removed outlier: 3.556A pdb=" N GLU F1372 " --> pdb=" O GLY F1368 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 579 through 582 removed outlier: 3.663A pdb=" N ARG A 579 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL A 450 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL A 557 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE A 452 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLY A 559 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N SER A 513 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE A 558 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE A 515 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA A 560 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 517 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR A 479 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE A 516 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE A 481 " --> pdb=" O PHE A 516 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 894 through 897 removed outlier: 7.459A pdb=" N PHE A 895 " --> pdb=" O ARG A 771 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU A 773 " --> pdb=" O PHE A 895 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU A 897 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASN A 775 " --> pdb=" O LEU A 897 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N LEU A 772 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU A 868 " --> pdb=" O LEU A 772 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE A 774 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS A 870 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N GLY A 776 " --> pdb=" O CYS A 870 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 872 " --> pdb=" O GLY A 776 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER A 831 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU A 869 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 833 " --> pdb=" O LEU A 869 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 871 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE A 835 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N GLU A 873 " --> pdb=" O ILE A 835 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASN A 797 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE A 834 " --> pdb=" O ASN A 797 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN A 799 " --> pdb=" O PHE A 834 " (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: 8.367A pdb=" N VAL B 450 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 557 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE B 452 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY B 559 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLY B 454 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR B 561 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER B 513 " --> pdb=" O ILE B 556 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE B 558 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE B 515 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA B 560 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE B 517 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR B 479 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE B 516 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 6.548A 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: 7.797A pdb=" N PHE B 895 " --> pdb=" O ARG B 771 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU B 773 " --> pdb=" O PHE B 895 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B 897 " --> pdb=" O LEU B 773 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASN B 775 " --> pdb=" O LEU B 897 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N LEU B 772 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU B 868 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE B 774 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS B 870 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N GLY B 776 " --> pdb=" O CYS B 870 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER B 831 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU B 869 " --> pdb=" O SER B 831 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL B 833 " --> pdb=" O LEU B 869 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU B 871 " --> pdb=" O VAL B 833 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 835 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASN B 797 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE B 834 " --> pdb=" O ASN B 797 " (cutoff:3.500A) removed outlier: 6.507A 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: 8.366A pdb=" N VAL C 450 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL C 557 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE C 452 " --> pdb=" O VAL C 557 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY C 559 " --> pdb=" O PHE C 452 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N GLY C 454 " --> pdb=" O GLY C 559 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR C 561 " --> pdb=" O GLY C 454 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR C 479 " --> pdb=" O ILE C 514 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE C 516 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE C 481 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASP C 518 " --> pdb=" O PHE C 481 " (cutoff:3.500A) removed outlier: 6.488A 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: 7.626A pdb=" N PHE C 895 " --> pdb=" O ARG C 771 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU C 773 " --> pdb=" O PHE C 895 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU C 897 " --> pdb=" O LEU C 773 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN C 775 " --> pdb=" O LEU C 897 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU C 772 " --> pdb=" O ILE C 866 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU C 868 " --> pdb=" O LEU C 772 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE C 774 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS C 870 " --> pdb=" O ILE C 774 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLY C 776 " --> pdb=" O CYS C 870 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA C 872 " --> pdb=" O GLY C 776 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER C 831 " --> pdb=" O LEU C 867 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU C 869 " --> pdb=" O SER C 831 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL C 833 " --> pdb=" O LEU C 869 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU C 871 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE C 835 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N GLU C 873 " --> pdb=" O ILE C 835 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASN C 797 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE C 834 " --> pdb=" O ASN C 797 " (cutoff:3.500A) removed outlier: 6.381A 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 583 removed outlier: 8.227A pdb=" N VAL D 450 " --> pdb=" O VAL D 555 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D 557 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N PHE D 452 " --> pdb=" O VAL D 557 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY D 559 " --> pdb=" O PHE D 452 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLY D 454 " --> pdb=" O GLY D 559 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR D 561 " --> pdb=" O GLY D 454 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER D 513 " --> pdb=" O ILE D 556 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ILE D 558 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE D 515 " --> pdb=" O ILE D 558 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ALA D 560 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE D 517 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR D 479 " --> pdb=" O ILE D 514 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE D 516 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE D 481 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP D 518 " --> pdb=" O PHE D 481 " (cutoff:3.500A) removed outlier: 6.630A 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 896 removed outlier: 7.884A pdb=" N PHE D 895 " --> pdb=" O ARG D 771 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU D 773 " --> pdb=" O PHE D 895 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU D 772 " --> pdb=" O ILE D 866 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU D 868 " --> pdb=" O LEU D 772 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE D 774 " --> pdb=" O LEU D 868 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N CYS D 870 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER D 831 " --> pdb=" O LEU D 867 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU D 869 " --> pdb=" O SER D 831 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL D 833 " --> pdb=" O LEU D 869 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU D 871 " --> pdb=" O VAL D 833 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE D 835 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN D 797 " --> pdb=" O VAL D 832 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE D 834 " --> pdb=" O ASN D 797 " (cutoff:3.500A) removed outlier: 6.340A 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: 8.216A pdb=" N VAL E 450 " --> pdb=" O VAL E 555 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL E 557 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE E 452 " --> pdb=" O VAL E 557 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY E 559 " --> pdb=" O PHE E 452 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLY E 454 " --> pdb=" O GLY E 559 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER E 513 " --> pdb=" O ILE E 556 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE E 558 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE E 515 " --> pdb=" O ILE E 558 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA E 560 " --> pdb=" O ILE E 515 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE E 517 " --> pdb=" O ALA E 560 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR E 479 " --> pdb=" O ILE E 514 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE E 516 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE E 481 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASP E 518 " --> pdb=" O PHE E 481 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG E 483 " --> pdb=" O ASP E 518 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 894 through 897 removed outlier: 7.347A pdb=" N PHE E 895 " --> pdb=" O ARG E 771 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU E 773 " --> pdb=" O PHE E 895 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU E 897 " --> pdb=" O LEU E 773 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASN E 775 " --> pdb=" O LEU E 897 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU E 772 " --> pdb=" O ILE E 866 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU E 868 " --> pdb=" O LEU E 772 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE E 774 " --> pdb=" O LEU E 868 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS E 870 " --> pdb=" O ILE E 774 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLY E 776 " --> pdb=" O CYS E 870 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA E 872 " --> pdb=" O GLY E 776 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER E 831 " --> pdb=" O LEU E 867 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU E 869 " --> pdb=" O SER E 831 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL E 833 " --> pdb=" O LEU E 869 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU E 871 " --> pdb=" O VAL E 833 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE E 835 " --> pdb=" O LEU E 871 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLU E 873 " --> pdb=" O ILE E 835 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN E 797 " --> pdb=" O VAL E 832 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE E 834 " --> pdb=" O ASN E 797 " (cutoff:3.500A) removed outlier: 6.162A 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 479 through 484 removed outlier: 3.574A pdb=" N GLY F 454 " --> pdb=" O THR F 561 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU F 451 " --> pdb=" O ASP F 578 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU F 580 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N HIS F 453 " --> pdb=" O GLU F 580 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR F 582 " --> pdb=" O HIS F 453 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 894 through 897 removed outlier: 7.400A pdb=" N PHE F 895 " --> pdb=" O ARG F 771 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU F 773 " --> pdb=" O PHE F 895 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU F 897 " --> pdb=" O LEU F 773 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN F 775 " --> pdb=" O LEU F 897 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU F 772 " --> pdb=" O ILE F 866 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU F 868 " --> pdb=" O LEU F 772 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE F 774 " --> pdb=" O LEU F 868 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N CYS F 870 " --> pdb=" O ILE F 774 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY F 776 " --> pdb=" O CYS F 870 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA F 872 " --> pdb=" O GLY F 776 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER F 831 " --> pdb=" O LEU F 867 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU F 869 " --> pdb=" O SER F 831 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL F 833 " --> pdb=" O LEU F 869 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU F 871 " --> pdb=" O VAL F 833 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE F 835 " --> pdb=" O LEU F 871 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU F 873 " --> pdb=" O ILE F 835 " (cutoff:3.500A) 889 hydrogen bonds defined for protein. 2514 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: 8.66 Time building geometry restraints manager: 11.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.31: 4679 1.31 - 1.47: 10681 1.47 - 1.63: 12990 1.63 - 1.79: 117 1.79 - 1.95: 56 Bond restraints: 28523 Sorted by residual: bond pdb=" C LEU C 860 " pdb=" O LEU C 860 " ideal model delta sigma weight residual 1.234 1.151 0.084 1.33e-02 5.65e+03 3.95e+01 bond pdb=" C LEU A 912 " pdb=" O LEU A 912 " ideal model delta sigma weight residual 1.237 1.171 0.065 1.16e-02 7.43e+03 3.17e+01 bond pdb=" C GLN C 861 " pdb=" O GLN C 861 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.22e-02 6.72e+03 2.67e+01 bond pdb=" C SER C 859 " pdb=" O SER C 859 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.29e-02 6.01e+03 1.89e+01 bond pdb=" C CYS C 768 " pdb=" N LYS C 769 " ideal model delta sigma weight residual 1.332 1.299 0.033 8.60e-03 1.35e+04 1.43e+01 ... (remaining 28518 not shown) Histogram of bond angle deviations from ideal: 97.66 - 105.37: 711 105.37 - 113.08: 15503 113.08 - 120.79: 13699 120.79 - 128.50: 8506 128.50 - 136.21: 166 Bond angle restraints: 38585 Sorted by residual: angle pdb=" C SER D 831 " pdb=" N VAL D 832 " pdb=" CA VAL D 832 " ideal model delta sigma weight residual 122.99 112.28 10.71 1.39e+00 5.18e-01 5.93e+01 angle pdb=" CA GLN C 861 " pdb=" C GLN C 861 " pdb=" O GLN C 861 " ideal model delta sigma weight residual 120.92 112.77 8.15 1.15e+00 7.56e-01 5.03e+01 angle pdb=" N HIS C 510 " pdb=" CA HIS C 510 " pdb=" C HIS C 510 " ideal model delta sigma weight residual 109.96 100.37 9.59 1.49e+00 4.50e-01 4.14e+01 angle pdb=" CA GLN C 861 " pdb=" C GLN C 861 " pdb=" N SER C 862 " ideal model delta sigma weight residual 115.86 123.41 -7.55 1.24e+00 6.50e-01 3.70e+01 angle pdb=" N PRO B 512 " pdb=" CA PRO B 512 " pdb=" C PRO B 512 " ideal model delta sigma weight residual 110.74 101.04 9.70 1.66e+00 3.63e-01 3.41e+01 ... (remaining 38580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.18: 16946 32.18 - 64.36: 621 64.36 - 96.54: 74 96.54 - 128.72: 5 128.72 - 160.90: 4 Dihedral angle restraints: 17650 sinusoidal: 7408 harmonic: 10242 Sorted by residual: dihedral pdb=" C5' ADP A1401 " pdb=" O5' ADP A1401 " pdb=" PA ADP A1401 " pdb=" O2A ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 100.91 -160.90 1 2.00e+01 2.50e-03 4.67e+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 71.45 -131.45 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O1B ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PB ADP A1401 " pdb=" PA ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 65.20 -125.20 1 2.00e+01 2.50e-03 3.78e+01 ... (remaining 17647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3557 0.076 - 0.152: 749 0.152 - 0.228: 74 0.228 - 0.304: 17 0.304 - 0.380: 6 Chirality restraints: 4403 Sorted by residual: chirality pdb=" CA THR E 813 " pdb=" N THR E 813 " pdb=" C THR E 813 " pdb=" CB THR E 813 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE D 845 " pdb=" CA ILE D 845 " pdb=" CG1 ILE D 845 " pdb=" CG2 ILE D 845 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA ILE F 488 " pdb=" N ILE F 488 " pdb=" C ILE F 488 " pdb=" CB ILE F 488 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 4400 not shown) Planarity restraints: 4918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS D 510 " -0.016 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C HIS D 510 " 0.058 2.00e-02 2.50e+03 pdb=" O HIS D 510 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN D 511 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 505 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C GLU D 505 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU D 505 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU D 506 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 933 " -0.050 5.00e-02 4.00e+02 7.55e-02 9.11e+00 pdb=" N PRO E 934 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO E 934 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 934 " -0.041 5.00e-02 4.00e+02 ... (remaining 4915 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 235 2.58 - 3.16: 21993 3.16 - 3.74: 44257 3.74 - 4.32: 63926 4.32 - 4.90: 102303 Nonbonded interactions: 232714 Sorted by model distance: nonbonded pdb=" O3G AGS D1401 " pdb="MG MG D1402 " model vdw 2.001 2.170 nonbonded pdb=" O2G AGS E1401 " pdb="MG MG E1402 " model vdw 2.025 2.170 nonbonded pdb=" OG1 THR E 461 " pdb="MG MG E1402 " model vdw 2.033 2.170 nonbonded pdb=" OG1 THR D 461 " pdb="MG MG D1402 " model vdw 2.058 2.170 nonbonded pdb=" O1B AGS C1401 " pdb="MG MG C1402 " model vdw 2.081 2.170 ... (remaining 232709 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 407 through 735 or resid 756 through 1378)) selection = (chain 'B' and (resid 407 through 939 or resid 1319 through 1378)) selection = (chain 'C' and (resid 407 through 939 or resid 1319 through 1378)) selection = (chain 'D' and (resid 407 through 939 or resid 1319 through 1378)) selection = (chain 'E' and (resid 407 through 735 or resid 756 through 939 or resid 1319 thr \ ough 1378)) selection = (chain 'F' and (resid 407 through 735 or resid 756 through 939 or resid 1319 thr \ ough 1378)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 14.260 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 74.780 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.120 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:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 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 : 0.010 0.126 28523 Z= 0.675 Angle : 1.075 12.292 38585 Z= 0.629 Chirality : 0.064 0.380 4403 Planarity : 0.008 0.075 4918 Dihedral : 17.027 160.904 10962 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.18 % Favored : 94.71 % Rotamer: Outliers : 1.08 % Allowed : 10.23 % Favored : 88.68 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.55 % 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: -3.16 (0.12), residues: 3457 helix: -2.35 (0.10), residues: 1709 sheet: -1.09 (0.26), residues: 361 loop : -1.79 (0.15), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 841 HIS 0.010 0.003 HIS A1350 PHE 0.031 0.003 PHE D1341 TYR 0.019 0.003 TYR C 784 ARG 0.018 0.001 ARG D 573 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 813 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 715 ASP cc_start: 0.6418 (OUTLIER) cc_final: 0.6213 (m-30) REVERT: A 792 TYR cc_start: 0.6952 (t80) cc_final: 0.6276 (t80) REVERT: B 728 PHE cc_start: 0.8387 (m-10) cc_final: 0.8187 (m-80) REVERT: B 757 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6116 (mp0) REVERT: B 873 GLU cc_start: 0.5808 (tt0) cc_final: 0.5537 (tt0) REVERT: B 1336 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6385 (tm-30) REVERT: C 541 THR cc_start: 0.5951 (m) cc_final: 0.4895 (p) REVERT: C 578 ASP cc_start: 0.5805 (OUTLIER) cc_final: 0.5383 (m-30) REVERT: C 731 TYR cc_start: 0.7544 (m-80) cc_final: 0.6915 (m-80) REVERT: C 1329 LYS cc_start: 0.7843 (tttt) cc_final: 0.7579 (tttt) REVERT: D 757 GLU cc_start: 0.5180 (mm-30) cc_final: 0.4242 (mm-30) REVERT: F 505 GLU cc_start: 0.6495 (tp30) cc_final: 0.6273 (tp30) REVERT: F 782 GLN cc_start: 0.7187 (mp10) cc_final: 0.6931 (mp10) REVERT: F 936 LEU cc_start: 0.8019 (mt) cc_final: 0.7425 (mt) outliers start: 34 outliers final: 17 residues processed: 838 average time/residue: 1.3222 time to fit residues: 1294.4983 Evaluate side-chains 654 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 635 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 715 ASP Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 1377 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain E residue 844 THR Chi-restraints excluded: chain E residue 847 GLU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 863 ASN Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 293 optimal weight: 2.9990 chunk 263 optimal weight: 0.7980 chunk 145 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 177 optimal weight: 0.3980 chunk 140 optimal weight: 5.9990 chunk 271 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 315 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 GLN A 533 GLN A 609 ASN A 639 GLN A 780 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN A 874 ASN A 898 HIS A 904 ASN A1345 GLN B 441 ASN B 511 GLN B 533 GLN B 535 HIS B 562 ASN B 644 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 ASN B 829 GLN B1345 GLN C 443 ASN C 531 GLN C 562 ASN C 712 ASN C 800 ASN C 861 GLN C 874 ASN C 893 ASN C 896 GLN C1345 GLN C1350 HIS D 511 GLN D 535 HIS D 562 ASN D 596 GLN D 686 GLN D 699 GLN D 702 ASN D 775 ASN D 797 ASN D 896 GLN D1340 ASN D1345 GLN E 531 GLN E 535 HIS ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 699 GLN E 721 ASN E 726 GLN E 727 ASN E 782 GLN E 848 ASN E1340 ASN E1345 GLN F 420 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 GLN ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 702 ASN F 721 ASN F 775 ASN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 797 ASN F 799 GLN F 820 GLN F 861 GLN F 863 ASN F 893 ASN F 896 GLN F 937 GLN F1326 GLN G 20 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 28523 Z= 0.337 Angle : 0.756 16.561 38585 Z= 0.375 Chirality : 0.046 0.329 4403 Planarity : 0.006 0.075 4918 Dihedral : 9.835 175.716 3865 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 4.05 % Allowed : 18.84 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -1.56 (0.13), residues: 3457 helix: -0.81 (0.12), residues: 1694 sheet: -0.65 (0.26), residues: 383 loop : -1.24 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 841 HIS 0.008 0.002 HIS E1350 PHE 0.039 0.002 PHE D 822 TYR 0.035 0.002 TYR E 421 ARG 0.012 0.001 ARG A 907 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 807 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7343 (mt0) REVERT: A 481 PHE cc_start: 0.7782 (m-80) cc_final: 0.7541 (m-80) REVERT: A 549 MET cc_start: 0.4119 (mmt) cc_final: 0.2032 (mmt) REVERT: A 724 LEU cc_start: 0.7817 (mt) cc_final: 0.7574 (mp) REVERT: A 728 PHE cc_start: 0.8344 (m-10) cc_final: 0.8099 (m-80) REVERT: A 1319 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6790 (mt-10) REVERT: A 1365 ASP cc_start: 0.6917 (p0) cc_final: 0.6703 (p0) REVERT: B 431 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7566 (tp) REVERT: B 547 ASP cc_start: 0.6750 (t0) cc_final: 0.6512 (t70) REVERT: B 627 ARG cc_start: 0.7615 (ttt180) cc_final: 0.7276 (ttt180) REVERT: B 632 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6584 (tm-30) REVERT: B 757 GLU cc_start: 0.6607 (mm-30) cc_final: 0.5073 (mm-30) REVERT: B 873 GLU cc_start: 0.6484 (tt0) cc_final: 0.6273 (tt0) REVERT: C 612 ASP cc_start: 0.6845 (m-30) cc_final: 0.6619 (m-30) REVERT: C 731 TYR cc_start: 0.7510 (m-80) cc_final: 0.7181 (m-80) REVERT: C 802 ASP cc_start: 0.7262 (p0) cc_final: 0.6974 (p0) REVERT: E 421 TYR cc_start: 0.7018 (m-80) cc_final: 0.6510 (m-80) REVERT: E 477 LYS cc_start: 0.6917 (mmmt) cc_final: 0.6632 (mptp) REVERT: E 845 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6798 (tp) REVERT: F 450 VAL cc_start: 0.7514 (OUTLIER) cc_final: 0.7273 (t) REVERT: F 516 PHE cc_start: 0.6714 (t80) cc_final: 0.5416 (t80) REVERT: F 546 MET cc_start: 0.6968 (mmm) cc_final: 0.6652 (mmm) REVERT: F 731 TYR cc_start: 0.6261 (m-10) cc_final: 0.5967 (m-10) REVERT: F 885 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6348 (mp) REVERT: F 1361 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7093 (ttmt) outliers start: 127 outliers final: 38 residues processed: 867 average time/residue: 1.3363 time to fit residues: 1350.7912 Evaluate side-chains 744 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 700 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 893 ASN Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 811 SER Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 1365 ASP Chi-restraints excluded: chain D residue 440 GLN Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain D residue 797 ASN Chi-restraints excluded: chain D residue 898 HIS Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain E residue 561 THR Chi-restraints excluded: chain E residue 597 ILE Chi-restraints excluded: chain E residue 607 SER Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 885 LEU Chi-restraints excluded: chain F residue 898 HIS Chi-restraints excluded: chain F residue 1351 SER Chi-restraints excluded: chain F residue 1361 LYS Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 175 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 chunk 214 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 315 optimal weight: 0.0970 chunk 341 optimal weight: 1.9990 chunk 281 optimal weight: 6.9990 chunk 313 optimal weight: 0.6980 chunk 107 optimal weight: 0.0770 chunk 253 optimal weight: 1.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 GLN A 780 ASN A 799 GLN A 800 ASN A1340 ASN B 511 GLN B 686 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 ASN C 791 ASN C1326 GLN D 531 GLN D 797 ASN D 799 GLN D1350 HIS E 554 GLN E 639 GLN E 799 GLN E 896 GLN E1350 HIS F 511 GLN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 GLN F 837 ASN F1326 GLN F1345 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28523 Z= 0.227 Angle : 0.613 12.379 38585 Z= 0.305 Chirality : 0.042 0.235 4403 Planarity : 0.005 0.045 4918 Dihedral : 9.273 179.710 3841 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 4.08 % Allowed : 23.81 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.83 (0.14), residues: 3457 helix: -0.13 (0.12), residues: 1730 sheet: -0.38 (0.27), residues: 369 loop : -0.99 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 841 HIS 0.007 0.001 HIS E1350 PHE 0.033 0.002 PHE F 895 TYR 0.012 0.001 TYR F 435 ARG 0.009 0.001 ARG F 465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 773 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7520 (mt0) REVERT: A 463 MET cc_start: 0.7633 (tpp) cc_final: 0.7262 (tpp) REVERT: A 549 MET cc_start: 0.4133 (mmt) cc_final: 0.2621 (mmt) REVERT: A 600 ARG cc_start: 0.7183 (ttp-170) cc_final: 0.6833 (ptt180) REVERT: A 724 LEU cc_start: 0.7853 (mt) cc_final: 0.7609 (mp) REVERT: A 807 VAL cc_start: 0.7780 (m) cc_final: 0.7561 (t) REVERT: A 907 ARG cc_start: 0.7177 (ttp80) cc_final: 0.6882 (mtp-110) REVERT: A 1319 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7020 (mt-10) REVERT: A 1365 ASP cc_start: 0.6887 (p0) cc_final: 0.6674 (p0) REVERT: B 431 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7788 (mp) REVERT: B 627 ARG cc_start: 0.7594 (ttt180) cc_final: 0.7340 (ttt180) REVERT: B 757 GLU cc_start: 0.6444 (mm-30) cc_final: 0.4937 (mm-30) REVERT: C 431 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7237 (mm) REVERT: C 463 MET cc_start: 0.8335 (tpp) cc_final: 0.8021 (tpp) REVERT: C 502 LEU cc_start: 0.8373 (tm) cc_final: 0.8083 (tp) REVERT: C 612 ASP cc_start: 0.6837 (m-30) cc_final: 0.6633 (m-30) REVERT: C 762 MET cc_start: 0.7921 (mmm) cc_final: 0.7623 (mmt) REVERT: C 802 ASP cc_start: 0.7579 (p0) cc_final: 0.7314 (p0) REVERT: C 811 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8548 (p) REVERT: C 823 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6768 (mmt) REVERT: C 864 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6620 (mm-30) REVERT: D 437 GLU cc_start: 0.6723 (pm20) cc_final: 0.6442 (mp0) REVERT: D 463 MET cc_start: 0.8018 (tpp) cc_final: 0.7695 (tpp) REVERT: D 499 GLN cc_start: 0.7012 (mm110) cc_final: 0.6806 (mm-40) REVERT: D 531 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.6943 (mp-120) REVERT: D 728 PHE cc_start: 0.6001 (m-10) cc_final: 0.5735 (m-80) REVERT: E 477 LYS cc_start: 0.7430 (mmmt) cc_final: 0.7207 (mptp) REVERT: E 651 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6470 (ptmt) REVERT: E 795 GLU cc_start: 0.6227 (pm20) cc_final: 0.6024 (pm20) REVERT: E 1356 ILE cc_start: 0.7932 (mp) cc_final: 0.7693 (mt) REVERT: F 501 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6853 (ttp80) REVERT: F 502 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7593 (tp) REVERT: F 516 PHE cc_start: 0.6738 (t80) cc_final: 0.6417 (t80) REVERT: F 518 ASP cc_start: 0.6890 (m-30) cc_final: 0.6445 (m-30) REVERT: F 558 ILE cc_start: 0.6618 (mp) cc_final: 0.6352 (mt) REVERT: F 665 ASP cc_start: 0.5443 (t70) cc_final: 0.4552 (t0) REVERT: F 712 ASN cc_start: 0.7141 (t0) cc_final: 0.6912 (t0) REVERT: F 713 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6708 (tt) REVERT: F 767 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7369 (mt) REVERT: F 938 LYS cc_start: 0.7711 (ttmm) cc_final: 0.7190 (ttmm) outliers start: 128 outliers final: 37 residues processed: 832 average time/residue: 1.4033 time to fit residues: 1354.8791 Evaluate side-chains 766 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 718 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 893 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 1348 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 811 SER Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 898 HIS Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 480 PHE Chi-restraints excluded: chain F residue 482 MET Chi-restraints excluded: chain F residue 501 ARG Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 688 LEU Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 713 ILE Chi-restraints excluded: chain F residue 767 ILE Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 898 HIS Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 311 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 316 optimal weight: 0.5980 chunk 335 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 300 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 780 ASN A 863 ASN B 511 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN B1326 GLN C 554 GLN C 727 ASN ** C1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 ASN D 721 ASN ** D 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN E 596 GLN E 639 GLN ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1345 GLN F 726 GLN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 837 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 28523 Z= 0.349 Angle : 0.704 23.790 38585 Z= 0.350 Chirality : 0.047 0.315 4403 Planarity : 0.005 0.077 4918 Dihedral : 9.222 172.312 3837 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 5.20 % Allowed : 23.97 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.66 (0.14), residues: 3457 helix: -0.01 (0.12), residues: 1733 sheet: -0.29 (0.26), residues: 388 loop : -0.88 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 841 HIS 0.006 0.001 HIS D1337 PHE 0.051 0.002 PHE F 728 TYR 0.017 0.002 TYR E 792 ARG 0.013 0.001 ARG F 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 858 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ASP cc_start: 0.7261 (t70) cc_final: 0.6929 (t0) REVERT: A 415 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7983 (mm) REVERT: A 424 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: A 437 GLU cc_start: 0.7785 (pm20) cc_final: 0.7422 (pm20) REVERT: A 463 MET cc_start: 0.7826 (tpp) cc_final: 0.7510 (tpp) REVERT: A 500 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8326 (mt) REVERT: A 549 MET cc_start: 0.4143 (mmt) cc_final: 0.2668 (mmt) REVERT: A 600 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.7035 (ptt180) REVERT: A 690 GLU cc_start: 0.6416 (tp30) cc_final: 0.6107 (tp30) REVERT: A 762 MET cc_start: 0.7979 (mmm) cc_final: 0.7655 (mmm) REVERT: A 807 VAL cc_start: 0.7913 (m) cc_final: 0.7694 (t) REVERT: A 907 ARG cc_start: 0.7169 (ttp80) cc_final: 0.6728 (mtp180) REVERT: A 1365 ASP cc_start: 0.6882 (p0) cc_final: 0.6620 (p0) REVERT: B 431 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8096 (mp) REVERT: B 433 LEU cc_start: 0.7855 (mt) cc_final: 0.7339 (mt) REVERT: B 482 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6590 (ttp) REVERT: B 616 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.7172 (t80) REVERT: B 627 ARG cc_start: 0.7553 (ttt180) cc_final: 0.7264 (ttt180) REVERT: B 803 LEU cc_start: 0.8448 (mm) cc_final: 0.8181 (mp) REVERT: B 1336 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6800 (tm-30) REVERT: C 431 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7717 (mm) REVERT: C 462 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8266 (tp) REVERT: C 463 MET cc_start: 0.8229 (tpp) cc_final: 0.8002 (tpp) REVERT: C 502 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8197 (tp) REVERT: C 708 ASP cc_start: 0.6905 (p0) cc_final: 0.6658 (p0) REVERT: C 823 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6797 (mmt) REVERT: D 409 ASN cc_start: 0.7957 (p0) cc_final: 0.7654 (p0) REVERT: D 437 GLU cc_start: 0.7248 (pm20) cc_final: 0.6976 (pm20) REVERT: D 442 PHE cc_start: 0.8041 (m-80) cc_final: 0.7833 (m-80) REVERT: D 823 MET cc_start: 0.6637 (tpp) cc_final: 0.6430 (mpp) REVERT: D 1329 LYS cc_start: 0.7069 (tptp) cc_final: 0.6732 (tptp) REVERT: E 408 MET cc_start: 0.4505 (mmm) cc_final: 0.4214 (tmm) REVERT: E 424 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7378 (mt0) REVERT: E 432 PRO cc_start: 0.7731 (Cg_endo) cc_final: 0.7507 (Cg_exo) REVERT: E 477 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7944 (mptp) REVERT: E 502 LEU cc_start: 0.8007 (mm) cc_final: 0.7736 (mp) REVERT: E 518 ASP cc_start: 0.7374 (t0) cc_final: 0.6631 (t70) REVERT: E 532 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6863 (mm-30) REVERT: E 1336 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6346 (tm-30) REVERT: E 1356 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8022 (mt) REVERT: E 1365 ASP cc_start: 0.7239 (t0) cc_final: 0.7011 (t70) REVERT: F 424 GLN cc_start: 0.7421 (tt0) cc_final: 0.7200 (tt0) REVERT: F 470 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7688 (m) REVERT: F 502 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7784 (tt) REVERT: F 516 PHE cc_start: 0.7586 (t80) cc_final: 0.7357 (t80) REVERT: F 519 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6569 (mm-30) REVERT: F 665 ASP cc_start: 0.6047 (t70) cc_final: 0.5455 (t0) REVERT: F 707 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8264 (tp) REVERT: F 913 ILE cc_start: 0.8179 (pp) cc_final: 0.7936 (mt) REVERT: F 1336 GLU cc_start: 0.6412 (tm-30) cc_final: 0.6168 (tm-30) outliers start: 163 outliers final: 50 residues processed: 938 average time/residue: 1.3901 time to fit residues: 1518.3990 Evaluate side-chains 878 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 812 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 893 ASN Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 482 MET Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 616 PHE Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 1348 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 1377 LEU Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 884 ILE Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 424 GLN Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 758 PHE Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 1342 THR Chi-restraints excluded: chain E residue 1356 ILE Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 657 SER Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 725 LEU Chi-restraints excluded: chain F residue 906 THR Chi-restraints excluded: chain F residue 1349 VAL Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 279 optimal weight: 0.9980 chunk 190 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 249 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 286 optimal weight: 0.7980 chunk 231 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 301 optimal weight: 0.8980 chunk 84 optimal weight: 0.0270 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 GLN A 820 GLN B 443 ASN B 511 GLN C 554 GLN C1326 GLN D 420 ASN D 562 ASN D 775 ASN D 799 GLN ** D 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 GLN E 531 GLN ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 775 ASN F 441 ASN F 511 GLN F 699 GLN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 843 ASN F1340 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.7049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28523 Z= 0.232 Angle : 0.595 13.040 38585 Z= 0.291 Chirality : 0.042 0.234 4403 Planarity : 0.004 0.062 4918 Dihedral : 8.917 171.026 3835 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 4.14 % Allowed : 27.73 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.27 (0.15), residues: 3457 helix: 0.37 (0.13), residues: 1750 sheet: -0.30 (0.27), residues: 388 loop : -0.72 (0.18), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 841 HIS 0.003 0.001 HIS C1350 PHE 0.030 0.002 PHE E 592 TYR 0.016 0.001 TYR E 792 ARG 0.010 0.001 ARG B 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 838 time to evaluate : 3.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ASP cc_start: 0.7268 (t70) cc_final: 0.6857 (t0) REVERT: A 424 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: A 463 MET cc_start: 0.7800 (tpp) cc_final: 0.7491 (tpp) REVERT: A 500 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8343 (mt) REVERT: A 549 MET cc_start: 0.4106 (mmt) cc_final: 0.2664 (mmt) REVERT: A 600 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.7015 (ptt180) REVERT: A 690 GLU cc_start: 0.6345 (tp30) cc_final: 0.6095 (tp30) REVERT: A 807 VAL cc_start: 0.7897 (m) cc_final: 0.7645 (t) REVERT: A 813 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8269 (t) REVERT: A 820 GLN cc_start: 0.7166 (mt0) cc_final: 0.6950 (mt0) REVERT: A 824 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: A 1365 ASP cc_start: 0.6800 (p0) cc_final: 0.6560 (p0) REVERT: B 431 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7914 (tp) REVERT: B 616 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.7194 (t80) REVERT: B 627 ARG cc_start: 0.7486 (ttt180) cc_final: 0.7233 (ttt180) REVERT: B 858 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.6856 (ttp80) REVERT: B 1336 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6867 (tm-30) REVERT: C 419 ASP cc_start: 0.7285 (m-30) cc_final: 0.7068 (m-30) REVERT: C 462 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8270 (tp) REVERT: C 463 MET cc_start: 0.8202 (tpp) cc_final: 0.7972 (tpp) REVERT: C 502 LEU cc_start: 0.8379 (tm) cc_final: 0.8082 (tp) REVERT: C 708 ASP cc_start: 0.6942 (p0) cc_final: 0.6736 (p0) REVERT: C 823 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6803 (mmt) REVERT: D 442 PHE cc_start: 0.8139 (m-80) cc_final: 0.7883 (m-80) REVERT: D 1329 LYS cc_start: 0.7008 (tptp) cc_final: 0.6659 (tptp) REVERT: E 408 MET cc_start: 0.4604 (mmm) cc_final: 0.4312 (tmm) REVERT: E 425 LEU cc_start: 0.8312 (tt) cc_final: 0.8051 (tp) REVERT: E 440 GLN cc_start: 0.7275 (mm-40) cc_final: 0.7053 (mm-40) REVERT: E 460 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7899 (mtpm) REVERT: E 477 LYS cc_start: 0.8269 (mmmt) cc_final: 0.8057 (mptp) REVERT: E 502 LEU cc_start: 0.8047 (mm) cc_final: 0.7775 (OUTLIER) REVERT: E 532 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6821 (mm-30) REVERT: E 840 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7871 (mt) REVERT: E 1336 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6381 (tm-30) REVERT: E 1365 ASP cc_start: 0.7368 (t0) cc_final: 0.7104 (t0) REVERT: F 502 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7853 (tt) REVERT: F 519 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6557 (mm-30) REVERT: F 527 ARG cc_start: 0.8402 (mtm180) cc_final: 0.8168 (mtm180) REVERT: F 665 ASP cc_start: 0.6190 (t70) cc_final: 0.5811 (t70) REVERT: F 707 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8250 (tp) REVERT: F 767 ILE cc_start: 0.8110 (pt) cc_final: 0.7694 (mt) REVERT: F 913 ILE cc_start: 0.8281 (pp) cc_final: 0.8013 (mt) REVERT: F 938 LYS cc_start: 0.7638 (ttmm) cc_final: 0.7182 (ttmm) REVERT: F 1336 GLU cc_start: 0.6554 (tm-30) cc_final: 0.6296 (tm-30) outliers start: 130 outliers final: 49 residues processed: 901 average time/residue: 1.4590 time to fit residues: 1512.9929 Evaluate side-chains 869 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 807 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 893 ASN Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 616 PHE Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 858 ARG Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 1348 ASP Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 549 MET Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 831 SER Chi-restraints excluded: chain E residue 840 ILE Chi-restraints excluded: chain E residue 1327 ILE Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 919 LYS Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 112 optimal weight: 0.7980 chunk 302 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 335 optimal weight: 0.7980 chunk 278 optimal weight: 0.0570 chunk 155 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 111 optimal weight: 0.4980 chunk 176 optimal weight: 0.2980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN A 554 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 ASN D 721 ASN ** D 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 GLN ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 596 GLN ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 ASN ** F 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 ASN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.7308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28523 Z= 0.204 Angle : 0.577 12.152 38585 Z= 0.283 Chirality : 0.041 0.173 4403 Planarity : 0.004 0.056 4918 Dihedral : 8.748 168.269 3835 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 3.73 % Allowed : 29.36 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: -0.03 (0.15), residues: 3457 helix: 0.62 (0.13), residues: 1726 sheet: -0.22 (0.26), residues: 403 loop : -0.67 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 841 HIS 0.003 0.001 HIS C1350 PHE 0.025 0.001 PHE A 642 TYR 0.018 0.001 TYR E 792 ARG 0.009 0.001 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 824 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 ASP cc_start: 0.7284 (t70) cc_final: 0.7002 (t0) REVERT: A 424 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: A 437 GLU cc_start: 0.7879 (pm20) cc_final: 0.7354 (pm20) REVERT: A 463 MET cc_start: 0.7791 (tpp) cc_final: 0.7473 (tpp) REVERT: A 495 GLU cc_start: 0.6889 (tp30) cc_final: 0.6299 (tp30) REVERT: A 500 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8334 (mt) REVERT: A 549 MET cc_start: 0.4113 (mmt) cc_final: 0.2867 (mmt) REVERT: A 600 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6991 (ptp-170) REVERT: A 667 MET cc_start: 0.7011 (mmp) cc_final: 0.6794 (mmm) REVERT: A 690 GLU cc_start: 0.6385 (tp30) cc_final: 0.6145 (tp30) REVERT: A 762 MET cc_start: 0.8133 (mmm) cc_final: 0.7892 (mmt) REVERT: A 807 VAL cc_start: 0.7874 (m) cc_final: 0.7633 (t) REVERT: A 820 GLN cc_start: 0.7089 (mt0) cc_final: 0.6869 (mt0) REVERT: A 824 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: A 1319 GLU cc_start: 0.8063 (mt-10) cc_final: 0.6030 (tt0) REVERT: A 1336 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6851 (tm-30) REVERT: A 1365 ASP cc_start: 0.6754 (p0) cc_final: 0.6532 (p0) REVERT: B 1336 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6867 (tm-30) REVERT: C 419 ASP cc_start: 0.7282 (m-30) cc_final: 0.7061 (m-30) REVERT: C 462 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8274 (tp) REVERT: C 502 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8045 (tp) REVERT: C 650 ASP cc_start: 0.7298 (p0) cc_final: 0.6526 (p0) REVERT: C 708 ASP cc_start: 0.6879 (p0) cc_final: 0.6657 (p0) REVERT: C 879 GLU cc_start: 0.7420 (tp30) cc_final: 0.7171 (tp30) REVERT: D 762 MET cc_start: 0.7687 (mmm) cc_final: 0.7177 (mmm) REVERT: D 1329 LYS cc_start: 0.7050 (tptp) cc_final: 0.6682 (tptp) REVERT: E 408 MET cc_start: 0.4656 (mmm) cc_final: 0.4367 (tmm) REVERT: E 440 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6984 (mm-40) REVERT: E 460 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8116 (mtpt) REVERT: E 502 LEU cc_start: 0.8033 (mm) cc_final: 0.7576 (OUTLIER) REVERT: E 505 GLU cc_start: 0.6367 (mt-10) cc_final: 0.6159 (mp0) REVERT: E 532 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6842 (mm-30) REVERT: E 538 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8122 (mt) REVERT: E 840 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7966 (mt) REVERT: E 1336 GLU cc_start: 0.6814 (tm-30) cc_final: 0.6410 (tm-30) REVERT: F 470 SER cc_start: 0.8109 (OUTLIER) cc_final: 0.7843 (m) REVERT: F 502 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7862 (tt) REVERT: F 519 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6532 (mm-30) REVERT: F 568 ASP cc_start: 0.6982 (t0) cc_final: 0.6766 (p0) REVERT: F 632 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6866 (mm-30) REVERT: F 665 ASP cc_start: 0.6225 (t70) cc_final: 0.5915 (t70) REVERT: F 707 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8244 (tp) REVERT: F 767 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7660 (mt) REVERT: F 913 ILE cc_start: 0.8386 (pp) cc_final: 0.8078 (mt) REVERT: F 1336 GLU cc_start: 0.6610 (tm-30) cc_final: 0.6389 (tm-30) outliers start: 117 outliers final: 55 residues processed: 874 average time/residue: 1.4876 time to fit residues: 1492.9247 Evaluate side-chains 856 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 789 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 893 ASN Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain B residue 1348 ASP Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 847 GLU Chi-restraints excluded: chain D residue 898 HIS Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 673 ILE Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 840 ILE Chi-restraints excluded: chain E residue 1342 THR Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 767 ILE Chi-restraints excluded: chain F residue 880 VAL Chi-restraints excluded: chain F residue 919 LYS Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 323 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 191 optimal weight: 0.0010 chunk 245 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 282 optimal weight: 0.0270 chunk 187 optimal weight: 3.9990 chunk 334 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 203 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 overall best weight: 0.7248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN A 554 GLN ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 911 ASN D 562 ASN ** D 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 911 ASN E 424 GLN E 531 GLN E 644 GLN F 441 ASN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.7641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28523 Z= 0.250 Angle : 0.606 12.731 38585 Z= 0.295 Chirality : 0.043 0.180 4403 Planarity : 0.004 0.055 4918 Dihedral : 8.776 167.208 3835 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 3.86 % Allowed : 30.03 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 0.05 (0.15), residues: 3457 helix: 0.61 (0.13), residues: 1754 sheet: -0.12 (0.26), residues: 402 loop : -0.56 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 841 HIS 0.004 0.001 HIS C1350 PHE 0.028 0.002 PHE A 642 TYR 0.017 0.001 TYR E 792 ARG 0.010 0.001 ARG B 907 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 828 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ASP cc_start: 0.7303 (t70) cc_final: 0.7047 (t0) REVERT: A 418 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6829 (pp) REVERT: A 424 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7786 (mt0) REVERT: A 437 GLU cc_start: 0.7948 (pm20) cc_final: 0.7439 (pm20) REVERT: A 463 MET cc_start: 0.7777 (tpp) cc_final: 0.7495 (tpp) REVERT: A 495 GLU cc_start: 0.6892 (tp30) cc_final: 0.6306 (tp30) REVERT: A 500 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 549 MET cc_start: 0.4027 (mmt) cc_final: 0.2630 (mmt) REVERT: A 592 PHE cc_start: 0.8567 (t80) cc_final: 0.8286 (t80) REVERT: A 600 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.7012 (ptp-170) REVERT: A 690 GLU cc_start: 0.6491 (tp30) cc_final: 0.6278 (tp30) REVERT: A 807 VAL cc_start: 0.7886 (m) cc_final: 0.7658 (t) REVERT: A 820 GLN cc_start: 0.7121 (mt0) cc_final: 0.6886 (mt0) REVERT: A 824 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: A 1319 GLU cc_start: 0.8070 (mt-10) cc_final: 0.6413 (tt0) REVERT: A 1365 ASP cc_start: 0.6666 (p0) cc_final: 0.6461 (p0) REVERT: B 598 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7366 (mp10) REVERT: C 419 ASP cc_start: 0.7255 (m-30) cc_final: 0.7047 (m-30) REVERT: C 462 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8252 (tp) REVERT: C 502 LEU cc_start: 0.8328 (tm) cc_final: 0.8038 (tp) REVERT: C 627 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6877 (ttp-110) REVERT: D 421 TYR cc_start: 0.8208 (m-10) cc_final: 0.8000 (m-10) REVERT: D 439 TYR cc_start: 0.7921 (m-80) cc_final: 0.7693 (m-80) REVERT: D 757 GLU cc_start: 0.5655 (mm-30) cc_final: 0.4636 (tp30) REVERT: D 762 MET cc_start: 0.7760 (mmm) cc_final: 0.7318 (mmm) REVERT: D 907 ARG cc_start: 0.7192 (ttp80) cc_final: 0.6937 (mtp-110) REVERT: D 1329 LYS cc_start: 0.7126 (tptp) cc_final: 0.6778 (tptp) REVERT: E 408 MET cc_start: 0.5022 (mmm) cc_final: 0.4702 (tmm) REVERT: E 460 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7961 (mtpm) REVERT: E 477 LYS cc_start: 0.8462 (mptt) cc_final: 0.8242 (mptt) REVERT: E 502 LEU cc_start: 0.8077 (mm) cc_final: 0.7822 (OUTLIER) REVERT: E 519 GLU cc_start: 0.6467 (mp0) cc_final: 0.6175 (mp0) REVERT: E 532 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6870 (mm-30) REVERT: E 847 GLU cc_start: 0.6444 (tm-30) cc_final: 0.6199 (tm-30) REVERT: E 935 GLU cc_start: 0.6472 (mm-30) cc_final: 0.6247 (mm-30) REVERT: E 1336 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6556 (tm-30) REVERT: F 423 ASP cc_start: 0.7499 (m-30) cc_final: 0.7261 (m-30) REVERT: F 426 LYS cc_start: 0.8267 (tppp) cc_final: 0.7803 (ttpp) REVERT: F 470 SER cc_start: 0.8192 (OUTLIER) cc_final: 0.7974 (m) REVERT: F 484 LYS cc_start: 0.7364 (mtmm) cc_final: 0.7023 (mtmm) REVERT: F 501 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7511 (ttm110) REVERT: F 502 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7887 (mm) REVERT: F 518 ASP cc_start: 0.7213 (m-30) cc_final: 0.6590 (m-30) REVERT: F 519 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6579 (mm-30) REVERT: F 527 ARG cc_start: 0.8521 (mtm180) cc_final: 0.8312 (mtm180) REVERT: F 568 ASP cc_start: 0.7056 (t0) cc_final: 0.6825 (p0) REVERT: F 632 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6881 (mm-30) REVERT: F 665 ASP cc_start: 0.6466 (t70) cc_final: 0.6262 (t70) REVERT: F 767 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7686 (mt) REVERT: F 913 ILE cc_start: 0.8522 (pp) cc_final: 0.8177 (mt) REVERT: F 938 LYS cc_start: 0.7690 (ttmm) cc_final: 0.7149 (ttmm) outliers start: 121 outliers final: 69 residues processed: 890 average time/residue: 1.5132 time to fit residues: 1542.8145 Evaluate side-chains 877 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 797 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 893 ASN Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain B residue 1348 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 1377 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 841 TRP Chi-restraints excluded: chain D residue 847 GLU Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 758 PHE Chi-restraints excluded: chain E residue 802 ASP Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 831 SER Chi-restraints excluded: chain E residue 1327 ILE Chi-restraints excluded: chain E residue 1334 LEU Chi-restraints excluded: chain E residue 1342 THR Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 725 LEU Chi-restraints excluded: chain F residue 767 ILE Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 880 VAL Chi-restraints excluded: chain F residue 919 LYS Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 206 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 199 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 262 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN A 554 GLN B 848 ASN ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 GLN ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN F 441 ASN ** F 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.7988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28523 Z= 0.267 Angle : 0.616 13.334 38585 Z= 0.301 Chirality : 0.043 0.174 4403 Planarity : 0.005 0.060 4918 Dihedral : 8.852 167.845 3835 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 3.86 % Allowed : 30.28 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 0.08 (0.15), residues: 3457 helix: 0.61 (0.13), residues: 1756 sheet: -0.06 (0.26), residues: 402 loop : -0.52 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 841 HIS 0.004 0.001 HIS C1350 PHE 0.025 0.002 PHE E 592 TYR 0.018 0.002 TYR E 792 ARG 0.012 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 823 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ASP cc_start: 0.7321 (t70) cc_final: 0.7067 (t0) REVERT: A 424 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: A 437 GLU cc_start: 0.8000 (pm20) cc_final: 0.7504 (pm20) REVERT: A 463 MET cc_start: 0.7765 (tpp) cc_final: 0.7554 (tpp) REVERT: A 477 LYS cc_start: 0.7976 (mppt) cc_final: 0.7766 (mppt) REVERT: A 500 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8362 (mt) REVERT: A 549 MET cc_start: 0.3888 (mmt) cc_final: 0.2023 (mmt) REVERT: A 597 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8188 (mp) REVERT: A 600 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.7028 (ptp-170) REVERT: A 690 GLU cc_start: 0.6549 (tp30) cc_final: 0.6338 (tp30) REVERT: A 729 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8079 (mp) REVERT: A 820 GLN cc_start: 0.7122 (mt0) cc_final: 0.6893 (mt0) REVERT: A 824 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: A 1319 GLU cc_start: 0.8093 (mt-10) cc_final: 0.6289 (tt0) REVERT: B 627 ARG cc_start: 0.7400 (ttt180) cc_final: 0.7183 (ttp-170) REVERT: B 868 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8138 (tp) REVERT: C 502 LEU cc_start: 0.8273 (tm) cc_final: 0.7975 (tp) REVERT: C 627 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6867 (ttp-110) REVERT: C 879 GLU cc_start: 0.7365 (tp30) cc_final: 0.7114 (tp30) REVERT: C 1361 LYS cc_start: 0.7708 (ttpp) cc_final: 0.7365 (ttpp) REVERT: D 427 GLU cc_start: 0.7615 (pp20) cc_final: 0.7298 (pp20) REVERT: D 437 GLU cc_start: 0.7568 (pm20) cc_final: 0.7063 (pm20) REVERT: D 440 GLN cc_start: 0.6998 (mt0) cc_final: 0.6728 (mt0) REVERT: D 589 LYS cc_start: 0.7392 (ttmm) cc_final: 0.7140 (mtpp) REVERT: D 757 GLU cc_start: 0.5473 (mm-30) cc_final: 0.4980 (mm-30) REVERT: D 762 MET cc_start: 0.7820 (mmm) cc_final: 0.7388 (mmm) REVERT: D 907 ARG cc_start: 0.7212 (ttp80) cc_final: 0.6962 (mtp-110) REVERT: D 1329 LYS cc_start: 0.7145 (tptp) cc_final: 0.6785 (tptp) REVERT: E 408 MET cc_start: 0.5197 (mmm) cc_final: 0.4915 (tmm) REVERT: E 424 GLN cc_start: 0.7797 (mt0) cc_final: 0.7565 (mt0) REVERT: E 460 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8001 (mtpm) REVERT: E 477 LYS cc_start: 0.8479 (mptt) cc_final: 0.8242 (mptt) REVERT: E 502 LEU cc_start: 0.8081 (mm) cc_final: 0.7799 (mp) REVERT: E 519 GLU cc_start: 0.6503 (mp0) cc_final: 0.6208 (mp0) REVERT: E 847 GLU cc_start: 0.6375 (tm-30) cc_final: 0.6148 (tm-30) REVERT: E 1367 THR cc_start: 0.8115 (m) cc_final: 0.7433 (m) REVERT: F 426 LYS cc_start: 0.8257 (tppp) cc_final: 0.7805 (ttpp) REVERT: F 484 LYS cc_start: 0.7397 (mtmm) cc_final: 0.7121 (mtmm) REVERT: F 502 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7871 (mm) REVERT: F 516 PHE cc_start: 0.7637 (t80) cc_final: 0.7192 (t80) REVERT: F 518 ASP cc_start: 0.7227 (m-30) cc_final: 0.6619 (m-30) REVERT: F 519 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6596 (mm-30) REVERT: F 767 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7765 (mt) REVERT: F 894 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7973 (mp) REVERT: F 938 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7329 (ttmm) outliers start: 121 outliers final: 66 residues processed: 882 average time/residue: 1.5436 time to fit residues: 1558.3304 Evaluate side-chains 886 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 808 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 893 ASN Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 483 ARG Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain B residue 1348 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 1377 LEU Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 509 LYS Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 673 ILE Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 802 ASP Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 831 SER Chi-restraints excluded: chain E residue 1334 LEU Chi-restraints excluded: chain E residue 1342 THR Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 661 VAL Chi-restraints excluded: chain F residue 710 MET Chi-restraints excluded: chain F residue 725 LEU Chi-restraints excluded: chain F residue 767 ILE Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 847 GLU Chi-restraints excluded: chain F residue 880 VAL Chi-restraints excluded: chain F residue 894 ILE Chi-restraints excluded: chain F residue 919 LYS Chi-restraints excluded: chain F residue 923 ILE Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 304 optimal weight: 0.7980 chunk 320 optimal weight: 0.8980 chunk 292 optimal weight: 0.2980 chunk 311 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 244 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 281 optimal weight: 0.1980 chunk 294 optimal weight: 8.9990 chunk 310 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN A 554 GLN A 598 GLN B 562 ASN B 848 ASN D 420 ASN ** D 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN F 441 ASN F 699 GLN ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 911 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.8113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28523 Z= 0.220 Angle : 0.617 12.371 38585 Z= 0.302 Chirality : 0.042 0.209 4403 Planarity : 0.005 0.092 4918 Dihedral : 8.791 166.473 3835 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 3.00 % Allowed : 31.65 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 0.20 (0.15), residues: 3457 helix: 0.70 (0.13), residues: 1759 sheet: -0.03 (0.26), residues: 400 loop : -0.45 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 841 HIS 0.003 0.001 HIS C1350 PHE 0.031 0.002 PHE E 592 TYR 0.025 0.001 TYR E 792 ARG 0.016 0.001 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 811 time to evaluate : 3.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ASP cc_start: 0.7301 (t70) cc_final: 0.7079 (t0) REVERT: A 421 TYR cc_start: 0.7847 (m-10) cc_final: 0.7613 (m-10) REVERT: A 424 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7805 (mt0) REVERT: A 437 GLU cc_start: 0.8021 (pm20) cc_final: 0.7585 (pm20) REVERT: A 463 MET cc_start: 0.7768 (tpp) cc_final: 0.7562 (tpp) REVERT: A 467 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8078 (tp) REVERT: A 500 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8344 (mt) REVERT: A 502 LEU cc_start: 0.8996 (mt) cc_final: 0.8762 (mp) REVERT: A 549 MET cc_start: 0.3774 (mmt) cc_final: 0.1064 (mmt) REVERT: A 729 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 820 GLN cc_start: 0.7095 (mt0) cc_final: 0.6848 (mt0) REVERT: A 824 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: A 1319 GLU cc_start: 0.8071 (mt-10) cc_final: 0.6331 (tt0) REVERT: B 627 ARG cc_start: 0.7385 (ttt180) cc_final: 0.7089 (ttt180) REVERT: B 632 GLU cc_start: 0.6402 (mm-30) cc_final: 0.6198 (mm-30) REVERT: B 868 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8100 (tp) REVERT: C 502 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7911 (tp) REVERT: C 627 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6874 (ttp-110) REVERT: C 812 ARG cc_start: 0.7244 (mtp-110) cc_final: 0.7010 (mtp-110) REVERT: C 1361 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7489 (ttpt) REVERT: D 427 GLU cc_start: 0.7534 (pp20) cc_final: 0.7228 (pp20) REVERT: D 428 MET cc_start: 0.7725 (ttm) cc_final: 0.7510 (mtm) REVERT: D 437 GLU cc_start: 0.7558 (pm20) cc_final: 0.7024 (pm20) REVERT: D 440 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6717 (mt0) REVERT: D 589 LYS cc_start: 0.7387 (ttmm) cc_final: 0.7183 (mtpp) REVERT: D 757 GLU cc_start: 0.5574 (mm-30) cc_final: 0.4993 (mm-30) REVERT: D 762 MET cc_start: 0.7819 (mmm) cc_final: 0.7383 (mmm) REVERT: D 907 ARG cc_start: 0.7176 (ttp80) cc_final: 0.6942 (mtp-110) REVERT: D 1329 LYS cc_start: 0.7127 (tptp) cc_final: 0.6768 (tptp) REVERT: E 408 MET cc_start: 0.5243 (mmm) cc_final: 0.4976 (tmm) REVERT: E 460 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8039 (mtpt) REVERT: E 477 LYS cc_start: 0.8459 (mptt) cc_final: 0.8236 (mptt) REVERT: E 502 LEU cc_start: 0.8022 (mm) cc_final: 0.7770 (mp) REVERT: E 519 GLU cc_start: 0.6495 (mp0) cc_final: 0.6150 (mp0) REVERT: E 589 LYS cc_start: 0.7697 (ptpp) cc_final: 0.7441 (mtmm) REVERT: E 730 ASP cc_start: 0.7095 (m-30) cc_final: 0.6833 (m-30) REVERT: E 757 GLU cc_start: 0.6199 (mm-30) cc_final: 0.5476 (tp30) REVERT: E 832 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8407 (p) REVERT: E 847 GLU cc_start: 0.6354 (tm-30) cc_final: 0.6140 (tm-30) REVERT: F 426 LYS cc_start: 0.8244 (tppp) cc_final: 0.7816 (ttpp) REVERT: F 484 LYS cc_start: 0.7399 (mtmm) cc_final: 0.7110 (mtmm) REVERT: F 502 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7840 (mm) REVERT: F 516 PHE cc_start: 0.7642 (t80) cc_final: 0.7181 (t80) REVERT: F 518 ASP cc_start: 0.7182 (m-30) cc_final: 0.6588 (m-30) REVERT: F 519 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6644 (mm-30) REVERT: F 632 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6862 (mm-30) REVERT: F 767 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7763 (mt) REVERT: F 913 ILE cc_start: 0.8559 (pp) cc_final: 0.8249 (mt) REVERT: F 938 LYS cc_start: 0.7711 (ttmm) cc_final: 0.7264 (ttmm) REVERT: F 1321 ILE cc_start: 0.8221 (mp) cc_final: 0.7888 (mp) outliers start: 94 outliers final: 59 residues processed: 857 average time/residue: 1.5673 time to fit residues: 1544.3139 Evaluate side-chains 866 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 794 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 893 ASN Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 483 ARG Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 839 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain C residue 627 ARG Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain D residue 440 GLN Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 670 LEU Chi-restraints excluded: chain E residue 673 ILE Chi-restraints excluded: chain E residue 710 MET Chi-restraints excluded: chain E residue 802 ASP Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 832 VAL Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain E residue 1327 ILE Chi-restraints excluded: chain E residue 1329 LYS Chi-restraints excluded: chain E residue 1334 LEU Chi-restraints excluded: chain E residue 1342 THR Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 767 ILE Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 815 GLU Chi-restraints excluded: chain F residue 919 LYS Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 204 optimal weight: 0.5980 chunk 329 optimal weight: 0.5980 chunk 201 optimal weight: 0.0770 chunk 156 optimal weight: 1.9990 chunk 229 optimal weight: 0.5980 chunk 345 optimal weight: 0.9980 chunk 318 optimal weight: 0.8980 chunk 275 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN A 554 GLN B 562 ASN B 848 ASN D 554 GLN ** D 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN E1326 GLN F 441 ASN ** F 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 ASN F 911 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.8232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28523 Z= 0.204 Angle : 0.613 11.833 38585 Z= 0.300 Chirality : 0.042 0.196 4403 Planarity : 0.005 0.087 4918 Dihedral : 8.709 164.469 3835 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.81 % Rotamer: Outliers : 2.45 % Allowed : 32.16 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 0.29 (0.15), residues: 3457 helix: 0.79 (0.13), residues: 1736 sheet: 0.02 (0.26), residues: 399 loop : -0.41 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 841 HIS 0.003 0.001 HIS C1350 PHE 0.027 0.001 PHE E 592 TYR 0.024 0.001 TYR E 792 ARG 0.019 0.001 ARG F 501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 805 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7895 (m-10) cc_final: 0.7658 (m-10) REVERT: A 424 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: A 437 GLU cc_start: 0.8035 (pm20) cc_final: 0.7635 (pm20) REVERT: A 463 MET cc_start: 0.7741 (tpp) cc_final: 0.7526 (tpp) REVERT: A 467 LEU cc_start: 0.8291 (tt) cc_final: 0.8062 (tp) REVERT: A 502 LEU cc_start: 0.8975 (mt) cc_final: 0.8747 (mp) REVERT: A 549 MET cc_start: 0.3718 (mmt) cc_final: 0.1158 (mmt) REVERT: A 597 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8062 (mp) REVERT: A 726 GLN cc_start: 0.7857 (tp40) cc_final: 0.7654 (mm-40) REVERT: A 729 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8098 (mp) REVERT: A 820 GLN cc_start: 0.7078 (mt0) cc_final: 0.6831 (mt0) REVERT: A 824 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: A 1319 GLU cc_start: 0.8056 (mt-10) cc_final: 0.6420 (mt-10) REVERT: B 627 ARG cc_start: 0.7321 (ttt180) cc_final: 0.7005 (ttt180) REVERT: B 868 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8094 (tp) REVERT: C 462 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8257 (tp) REVERT: C 502 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7931 (tp) REVERT: C 509 LYS cc_start: 0.7952 (ttpp) cc_final: 0.7747 (ttmt) REVERT: C 1361 LYS cc_start: 0.7740 (ttpp) cc_final: 0.7505 (ttpt) REVERT: D 440 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6733 (mt0) REVERT: D 589 LYS cc_start: 0.7390 (ttmm) cc_final: 0.7187 (mtpp) REVERT: D 757 GLU cc_start: 0.5554 (mm-30) cc_final: 0.4726 (tp30) REVERT: D 762 MET cc_start: 0.7805 (mmm) cc_final: 0.7380 (mmm) REVERT: D 907 ARG cc_start: 0.7154 (ttp80) cc_final: 0.6936 (mtp-110) REVERT: D 1329 LYS cc_start: 0.7156 (tptp) cc_final: 0.6805 (tptp) REVERT: D 1362 SER cc_start: 0.7910 (m) cc_final: 0.7568 (p) REVERT: E 408 MET cc_start: 0.5246 (mmm) cc_final: 0.4972 (tmm) REVERT: E 460 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8028 (mtpt) REVERT: E 502 LEU cc_start: 0.8001 (mm) cc_final: 0.7775 (mp) REVERT: E 519 GLU cc_start: 0.6478 (mp0) cc_final: 0.6152 (mp0) REVERT: E 589 LYS cc_start: 0.7678 (ptpp) cc_final: 0.7437 (mtmm) REVERT: E 730 ASP cc_start: 0.7088 (m-30) cc_final: 0.6887 (m-30) REVERT: E 757 GLU cc_start: 0.6076 (mm-30) cc_final: 0.5535 (tp30) REVERT: E 824 GLU cc_start: 0.6561 (mp0) cc_final: 0.6248 (mp0) REVERT: E 847 GLU cc_start: 0.6335 (tm-30) cc_final: 0.6119 (tm-30) REVERT: F 426 LYS cc_start: 0.8293 (tppp) cc_final: 0.7813 (ttpp) REVERT: F 467 LEU cc_start: 0.8125 (tt) cc_final: 0.7917 (pp) REVERT: F 484 LYS cc_start: 0.7394 (mtmm) cc_final: 0.7122 (mtmm) REVERT: F 502 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7805 (mm) REVERT: F 516 PHE cc_start: 0.7632 (t80) cc_final: 0.7171 (t80) REVERT: F 518 ASP cc_start: 0.7160 (m-30) cc_final: 0.6531 (m-30) REVERT: F 519 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6638 (mm-30) REVERT: F 655 ASP cc_start: 0.7391 (t0) cc_final: 0.7165 (t70) REVERT: F 767 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7770 (mt) REVERT: F 913 ILE cc_start: 0.8579 (pp) cc_final: 0.8255 (mt) REVERT: F 938 LYS cc_start: 0.7666 (ttmm) cc_final: 0.7234 (ttmm) REVERT: F 1321 ILE cc_start: 0.8050 (mp) cc_final: 0.7835 (mp) REVERT: F 1361 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7702 (ttpp) outliers start: 77 outliers final: 52 residues processed: 843 average time/residue: 1.5354 time to fit residues: 1479.0898 Evaluate side-chains 852 residues out of total 3137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 789 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 893 ASN Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 839 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain D residue 440 GLN Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 913 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 628 SER Chi-restraints excluded: chain E residue 670 LEU Chi-restraints excluded: chain E residue 673 ILE Chi-restraints excluded: chain E residue 802 ASP Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain E residue 1327 ILE Chi-restraints excluded: chain E residue 1334 LEU Chi-restraints excluded: chain E residue 1342 THR Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain F residue 767 ILE Chi-restraints excluded: chain F residue 778 LYS Chi-restraints excluded: chain F residue 813 THR Chi-restraints excluded: chain F residue 815 GLU Chi-restraints excluded: chain F residue 919 LYS Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 218 optimal weight: 0.0050 chunk 293 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 275 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN A 554 GLN B 562 ASN B 820 GLN B 848 ASN ** D 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 639 GLN F 441 ASN F 639 GLN ** F 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 GLN F 911 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.114490 restraints weight = 39599.460| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.92 r_work: 0.3314 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.8335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28523 Z= 0.224 Angle : 0.621 11.617 38585 Z= 0.304 Chirality : 0.042 0.174 4403 Planarity : 0.005 0.083 4918 Dihedral : 8.685 162.562 3835 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.11 % Favored : 95.86 % Rotamer: Outliers : 2.49 % Allowed : 32.48 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 0.31 (0.15), residues: 3457 helix: 0.78 (0.13), residues: 1746 sheet: 0.05 (0.26), residues: 401 loop : -0.39 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 841 HIS 0.003 0.001 HIS C1350 PHE 0.027 0.001 PHE E 592 TYR 0.017 0.001 TYR E 435 ARG 0.019 0.001 ARG F 501 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18131.61 seconds wall clock time: 318 minutes 12.07 seconds (19092.07 seconds total)