Starting phenix.real_space_refine on Sat Aug 23 18:08:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io4_35607/08_2025/8io4_35607.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io4_35607/08_2025/8io4_35607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8io4_35607/08_2025/8io4_35607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io4_35607/08_2025/8io4_35607.map" model { file = "/net/cci-nas-00/data/ceres_data/8io4_35607/08_2025/8io4_35607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io4_35607/08_2025/8io4_35607.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 9008 2.51 5 N 2324 2.21 5 O 2336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13736 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3434 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 2.76, per 1000 atoms: 0.20 Number of scatterers: 13736 At special positions: 0 Unit cell: (111.219, 111.219, 118.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2336 8.00 N 2324 7.00 C 9008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 630.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3232 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 65.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 404 through 432 removed outlier: 3.675A pdb=" N ALA A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 450 through 470 Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.874A pdb=" N ILE A 489 " --> pdb=" O HIS A 485 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 505 removed outlier: 3.994A pdb=" N VAL A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 531 removed outlier: 4.191A pdb=" N LEU A 524 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 525 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.870A pdb=" N ALA A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.726A pdb=" N TYR A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 547 through 576 removed outlier: 3.763A pdb=" N PHE A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 593 Processing helix chain 'A' and resid 606 through 623 removed outlier: 4.579A pdb=" N THR A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 687 removed outlier: 3.723A pdb=" N LYS A 638 " --> pdb=" O THR A 634 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 639 " --> pdb=" O ASN A 635 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 709 removed outlier: 4.074A pdb=" N ARG A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 707 " --> pdb=" O HIS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 720 removed outlier: 4.010A pdb=" N VAL A 716 " --> pdb=" O ASP A 712 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 732 removed outlier: 3.547A pdb=" N ALA A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS A 731 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 732 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 746 Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.804A pdb=" N LYS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 845 removed outlier: 3.613A pdb=" N TYR A 845 " --> pdb=" O VAL A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 855 removed outlier: 3.587A pdb=" N SER A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 432 removed outlier: 3.675A pdb=" N ALA C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 450 through 470 Processing helix chain 'C' and resid 485 through 494 removed outlier: 3.874A pdb=" N ILE C 489 " --> pdb=" O HIS C 485 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 491 " --> pdb=" O GLY C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 505 removed outlier: 3.994A pdb=" N VAL C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 531 removed outlier: 4.191A pdb=" N LEU C 524 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 525 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 527 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 538 removed outlier: 3.870A pdb=" N ALA C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 removed outlier: 3.726A pdb=" N TYR C 542 " --> pdb=" O LYS C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 547 through 576 removed outlier: 3.763A pdb=" N PHE C 551 " --> pdb=" O ALA C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 Processing helix chain 'C' and resid 606 through 623 removed outlier: 4.579A pdb=" N THR C 613 " --> pdb=" O ASP C 609 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 687 removed outlier: 3.723A pdb=" N LYS C 638 " --> pdb=" O THR C 634 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE C 639 " --> pdb=" O ASN C 635 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR C 670 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 709 removed outlier: 4.074A pdb=" N ARG C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR C 707 " --> pdb=" O HIS C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 720 removed outlier: 4.010A pdb=" N VAL C 716 " --> pdb=" O ASP C 712 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 720 " --> pdb=" O VAL C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 732 removed outlier: 3.547A pdb=" N ALA C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 728 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS C 729 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS C 731 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU C 732 " --> pdb=" O ILE C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 746 Processing helix chain 'C' and resid 747 through 757 removed outlier: 3.804A pdb=" N LYS C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 845 removed outlier: 3.612A pdb=" N TYR C 845 " --> pdb=" O VAL C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 855 removed outlier: 3.587A pdb=" N SER C 855 " --> pdb=" O HIS C 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 432 removed outlier: 3.680A pdb=" N ALA D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 450 through 470 Processing helix chain 'D' and resid 485 through 494 removed outlier: 3.874A pdb=" N ILE D 489 " --> pdb=" O HIS D 485 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL D 491 " --> pdb=" O GLY D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 505 removed outlier: 3.994A pdb=" N VAL D 503 " --> pdb=" O LEU D 499 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA D 504 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 531 removed outlier: 4.191A pdb=" N LEU D 524 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 525 " --> pdb=" O GLY D 522 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 527 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 538 removed outlier: 3.860A pdb=" N ALA D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 576 removed outlier: 3.587A pdb=" N PHE D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 593 Processing helix chain 'D' and resid 606 through 623 removed outlier: 4.580A pdb=" N THR D 613 " --> pdb=" O ASP D 609 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA D 614 " --> pdb=" O LYS D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 687 removed outlier: 3.719A pdb=" N LYS D 638 " --> pdb=" O THR D 634 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE D 639 " --> pdb=" O ASN D 635 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 709 removed outlier: 4.205A pdb=" N ARG D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 720 removed outlier: 3.903A pdb=" N VAL D 716 " --> pdb=" O ASP D 712 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 720 " --> pdb=" O VAL D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 732 removed outlier: 4.240A pdb=" N ILE D 728 " --> pdb=" O LEU D 724 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS D 729 " --> pdb=" O GLN D 725 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS D 731 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 746 removed outlier: 3.651A pdb=" N ALA D 746 " --> pdb=" O PHE D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 757 removed outlier: 3.862A pdb=" N LYS D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 845 removed outlier: 3.618A pdb=" N TYR D 845 " --> pdb=" O VAL D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 855 removed outlier: 3.569A pdb=" N SER D 855 " --> pdb=" O HIS D 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 432 removed outlier: 3.680A pdb=" N ALA B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 450 through 470 Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.874A pdb=" N ILE B 489 " --> pdb=" O HIS B 485 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 505 removed outlier: 3.994A pdb=" N VAL B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 504 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 531 removed outlier: 4.191A pdb=" N LEU B 524 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 527 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.859A pdb=" N ALA B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 576 removed outlier: 3.587A pdb=" N PHE B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 593 Processing helix chain 'B' and resid 606 through 623 removed outlier: 4.580A pdb=" N THR B 613 " --> pdb=" O ASP B 609 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 687 removed outlier: 3.719A pdb=" N LYS B 638 " --> pdb=" O THR B 634 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 639 " --> pdb=" O ASN B 635 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 709 removed outlier: 4.205A pdb=" N ARG B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 720 removed outlier: 3.903A pdb=" N VAL B 716 " --> pdb=" O ASP B 712 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE B 720 " --> pdb=" O VAL B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 732 removed outlier: 4.239A pdb=" N ILE B 728 " --> pdb=" O LEU B 724 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS B 729 " --> pdb=" O GLN B 725 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS B 731 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 746 removed outlier: 3.649A pdb=" N ALA B 746 " --> pdb=" O PHE B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 757 removed outlier: 3.863A pdb=" N LYS B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 845 removed outlier: 3.618A pdb=" N TYR B 845 " --> pdb=" O VAL B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 855 removed outlier: 3.569A pdb=" N SER B 855 " --> pdb=" O HIS B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 759 through 761 Processing sheet with id=AA2, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.435A pdb=" N ILE A 787 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE A 798 " --> pdb=" O ILE A 787 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 805 through 806 removed outlier: 3.829A pdb=" N GLY A 806 " --> pdb=" O PHE A 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 759 through 761 Processing sheet with id=AA5, first strand: chain 'C' and resid 787 through 790 removed outlier: 6.435A pdb=" N ILE C 787 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE C 798 " --> pdb=" O ILE C 787 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 805 through 806 removed outlier: 3.828A pdb=" N GLY C 806 " --> pdb=" O PHE C 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 759 through 761 Processing sheet with id=AA8, first strand: chain 'D' and resid 787 through 790 removed outlier: 6.443A pdb=" N ILE D 787 " --> pdb=" O ILE D 798 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE D 798 " --> pdb=" O ILE D 787 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 805 through 806 removed outlier: 3.779A pdb=" N GLY D 806 " --> pdb=" O PHE D 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 759 through 761 Processing sheet with id=AB2, first strand: chain 'B' and resid 787 through 790 removed outlier: 6.443A pdb=" N ILE B 787 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B 798 " --> pdb=" O ILE B 787 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 805 through 806 removed outlier: 3.779A pdb=" N GLY B 806 " --> pdb=" O PHE B 860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 742 hydrogen bonds defined for protein. 2112 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: 1.99 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4252 1.34 - 1.46: 2501 1.46 - 1.58: 7239 1.58 - 1.70: 0 1.70 - 1.81: 104 Bond restraints: 14096 Sorted by residual: bond pdb=" C THR C 425 " pdb=" N PRO C 426 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.99e+00 bond pdb=" C THR B 425 " pdb=" N PRO B 426 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.99e+00 bond pdb=" C THR A 425 " pdb=" N PRO A 426 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.99e+00 bond pdb=" C THR D 425 " pdb=" N PRO D 426 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.99e+00 bond pdb=" C GLN A 450 " pdb=" N PRO A 451 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.28e-02 6.10e+03 5.27e+00 ... (remaining 14091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 18236 1.60 - 3.20: 758 3.20 - 4.81: 119 4.81 - 6.41: 28 6.41 - 8.01: 11 Bond angle restraints: 19152 Sorted by residual: angle pdb=" N GLY B 806 " pdb=" CA GLY B 806 " pdb=" C GLY B 806 " ideal model delta sigma weight residual 110.20 114.59 -4.39 1.32e+00 5.74e-01 1.11e+01 angle pdb=" N GLY D 806 " pdb=" CA GLY D 806 " pdb=" C GLY D 806 " ideal model delta sigma weight residual 110.20 114.59 -4.39 1.32e+00 5.74e-01 1.11e+01 angle pdb=" C CYS C 449 " pdb=" N GLN C 450 " pdb=" CA GLN C 450 " ideal model delta sigma weight residual 121.80 129.81 -8.01 2.44e+00 1.68e-01 1.08e+01 angle pdb=" C CYS A 449 " pdb=" N GLN A 450 " pdb=" CA GLN A 450 " ideal model delta sigma weight residual 121.80 129.81 -8.01 2.44e+00 1.68e-01 1.08e+01 angle pdb=" C CYS D 449 " pdb=" N GLN D 450 " pdb=" CA GLN D 450 " ideal model delta sigma weight residual 121.80 129.81 -8.01 2.44e+00 1.68e-01 1.08e+01 ... (remaining 19147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7444 17.93 - 35.86: 646 35.86 - 53.79: 102 53.79 - 71.72: 8 71.72 - 89.64: 8 Dihedral angle restraints: 8208 sinusoidal: 3192 harmonic: 5016 Sorted by residual: dihedral pdb=" CA TYR B 542 " pdb=" C TYR B 542 " pdb=" N SER B 543 " pdb=" CA SER B 543 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TYR D 542 " pdb=" C TYR D 542 " pdb=" N SER D 543 " pdb=" CA SER D 543 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLU C 544 " pdb=" C GLU C 544 " pdb=" N TYR C 545 " pdb=" CA TYR C 545 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 8205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1320 0.031 - 0.062: 539 0.062 - 0.092: 246 0.092 - 0.123: 55 0.123 - 0.154: 16 Chirality restraints: 2176 Sorted by residual: chirality pdb=" CA THR B 425 " pdb=" N THR B 425 " pdb=" C THR B 425 " pdb=" CB THR B 425 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA THR A 425 " pdb=" N THR A 425 " pdb=" C THR A 425 " pdb=" CB THR A 425 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA THR C 425 " pdb=" N THR C 425 " pdb=" C THR C 425 " pdb=" CB THR C 425 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2173 not shown) Planarity restraints: 2376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 412 " -0.012 2.00e-02 2.50e+03 9.84e-03 2.42e+00 pdb=" CG TRP B 412 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP B 412 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 412 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 412 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 412 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 412 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 412 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 412 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 412 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 807 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO B 808 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 808 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 808 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 807 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO D 808 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 808 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 808 " 0.021 5.00e-02 4.00e+02 ... (remaining 2373 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 841 2.73 - 3.28: 14837 3.28 - 3.82: 22598 3.82 - 4.36: 25292 4.36 - 4.90: 43040 Nonbonded interactions: 106608 Sorted by model distance: nonbonded pdb=" OG1 THR D 761 " pdb=" NZ LYS D 832 " model vdw 2.193 3.120 nonbonded pdb=" OG1 THR B 761 " pdb=" NZ LYS B 832 " model vdw 2.193 3.120 nonbonded pdb=" OG1 THR A 761 " pdb=" NZ LYS A 832 " model vdw 2.211 3.120 nonbonded pdb=" OG1 THR C 761 " pdb=" NZ LYS C 832 " model vdw 2.212 3.120 nonbonded pdb=" O HIS C 703 " pdb=" OG SER C 706 " model vdw 2.231 3.040 ... (remaining 106603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.940 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14096 Z= 0.164 Angle : 0.746 8.012 19152 Z= 0.419 Chirality : 0.042 0.154 2176 Planarity : 0.004 0.038 2376 Dihedral : 13.371 89.645 4976 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.52 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.20), residues: 1684 helix: 0.36 (0.16), residues: 1024 sheet: None (None), residues: 0 loop : -2.09 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 685 TYR 0.018 0.001 TYR B 845 PHE 0.025 0.001 PHE A 852 TRP 0.026 0.002 TRP B 412 HIS 0.007 0.001 HIS B 831 Details of bonding type rmsd covalent geometry : bond 0.00296 (14096) covalent geometry : angle 0.74604 (19152) hydrogen bonds : bond 0.15086 ( 742) hydrogen bonds : angle 5.84690 ( 2112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 GLU cc_start: 0.7308 (pp20) cc_final: 0.6781 (pp20) REVERT: A 545 TYR cc_start: 0.5719 (m-10) cc_final: 0.5518 (m-80) REVERT: A 550 LEU cc_start: 0.8585 (mt) cc_final: 0.8315 (mp) REVERT: A 698 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8252 (mm-30) REVERT: A 705 TRP cc_start: 0.7972 (t60) cc_final: 0.7514 (t60) REVERT: C 544 GLU cc_start: 0.7307 (pp20) cc_final: 0.6778 (pp20) REVERT: C 550 LEU cc_start: 0.8579 (mt) cc_final: 0.8314 (mp) REVERT: C 698 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8243 (mm-30) REVERT: C 705 TRP cc_start: 0.7956 (t60) cc_final: 0.7499 (t60) REVERT: D 550 LEU cc_start: 0.8592 (mt) cc_final: 0.8318 (mp) REVERT: D 699 GLU cc_start: 0.7315 (tm-30) cc_final: 0.7024 (tm-30) REVERT: D 845 TYR cc_start: 0.5622 (m-80) cc_final: 0.5406 (m-80) REVERT: B 550 LEU cc_start: 0.8604 (mt) cc_final: 0.8336 (mp) REVERT: B 699 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7032 (tm-30) REVERT: B 845 TYR cc_start: 0.5615 (m-80) cc_final: 0.5397 (m-80) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.1147 time to fit residues: 58.9856 Evaluate side-chains 270 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN C 635 ASN D 635 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 HIS B 635 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.225252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.172158 restraints weight = 21569.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.162032 restraints weight = 23530.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.160700 restraints weight = 20849.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.161164 restraints weight = 14551.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.161108 restraints weight = 12080.748| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14096 Z= 0.198 Angle : 0.702 8.765 19152 Z= 0.356 Chirality : 0.044 0.152 2176 Planarity : 0.005 0.046 2376 Dihedral : 4.590 16.327 1876 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.07 % Favored : 92.52 % Rotamer: Outliers : 2.06 % Allowed : 13.05 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.20), residues: 1684 helix: 0.24 (0.16), residues: 1024 sheet: -0.79 (0.76), residues: 40 loop : -2.25 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 537 TYR 0.014 0.002 TYR B 652 PHE 0.019 0.002 PHE D 701 TRP 0.018 0.002 TRP D 705 HIS 0.010 0.002 HIS B 731 Details of bonding type rmsd covalent geometry : bond 0.00440 (14096) covalent geometry : angle 0.70199 (19152) hydrogen bonds : bond 0.05286 ( 742) hydrogen bonds : angle 5.00507 ( 2112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 298 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 VAL cc_start: 0.8562 (t) cc_final: 0.8264 (p) REVERT: A 545 TYR cc_start: 0.5495 (m-10) cc_final: 0.5214 (m-10) REVERT: A 705 TRP cc_start: 0.8125 (t60) cc_final: 0.7814 (t60) REVERT: C 418 VAL cc_start: 0.8548 (t) cc_final: 0.8255 (p) REVERT: C 705 TRP cc_start: 0.8113 (t60) cc_final: 0.7806 (t60) REVERT: D 418 VAL cc_start: 0.8560 (t) cc_final: 0.8264 (p) REVERT: D 550 LEU cc_start: 0.8700 (mt) cc_final: 0.8459 (mp) REVERT: B 418 VAL cc_start: 0.8554 (t) cc_final: 0.8263 (p) REVERT: B 550 LEU cc_start: 0.8707 (mt) cc_final: 0.8469 (mp) outliers start: 30 outliers final: 26 residues processed: 310 average time/residue: 0.1111 time to fit residues: 48.9017 Evaluate side-chains 299 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 635 ASN Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 169 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 135 optimal weight: 0.0570 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN ** C 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS B 470 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.225984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.171674 restraints weight = 21699.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.161929 restraints weight = 24599.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.159734 restraints weight = 22947.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.158855 restraints weight = 17516.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.159231 restraints weight = 14869.539| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14096 Z= 0.163 Angle : 0.656 8.336 19152 Z= 0.332 Chirality : 0.043 0.147 2176 Planarity : 0.004 0.046 2376 Dihedral : 4.474 16.043 1876 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.89 % Favored : 92.87 % Rotamer: Outliers : 3.71 % Allowed : 13.26 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.20), residues: 1684 helix: 0.29 (0.16), residues: 1032 sheet: -1.36 (0.58), residues: 64 loop : -2.20 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 534 TYR 0.013 0.001 TYR B 652 PHE 0.011 0.001 PHE C 720 TRP 0.017 0.002 TRP C 705 HIS 0.007 0.001 HIS B 731 Details of bonding type rmsd covalent geometry : bond 0.00358 (14096) covalent geometry : angle 0.65595 (19152) hydrogen bonds : bond 0.04937 ( 742) hydrogen bonds : angle 4.81942 ( 2112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 302 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 VAL cc_start: 0.8603 (t) cc_final: 0.8348 (p) REVERT: C 418 VAL cc_start: 0.8587 (t) cc_final: 0.8339 (p) REVERT: C 545 TYR cc_start: 0.5834 (m-10) cc_final: 0.5532 (m-10) REVERT: D 418 VAL cc_start: 0.8582 (t) cc_final: 0.8327 (p) REVERT: D 552 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8039 (tt) REVERT: D 705 TRP cc_start: 0.8257 (t60) cc_final: 0.7913 (t60) REVERT: B 418 VAL cc_start: 0.8589 (t) cc_final: 0.8334 (p) REVERT: B 552 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8016 (tt) REVERT: B 705 TRP cc_start: 0.8254 (t60) cc_final: 0.7921 (t60) outliers start: 54 outliers final: 40 residues processed: 326 average time/residue: 0.1300 time to fit residues: 60.6019 Evaluate side-chains 309 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 267 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 33 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.226927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.169734 restraints weight = 21644.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.156944 restraints weight = 22703.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.155205 restraints weight = 15393.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.155979 restraints weight = 10617.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.155957 restraints weight = 8448.307| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14096 Z= 0.140 Angle : 0.630 7.323 19152 Z= 0.319 Chirality : 0.042 0.146 2176 Planarity : 0.004 0.047 2376 Dihedral : 4.312 15.780 1876 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.60 % Favored : 91.92 % Rotamer: Outliers : 3.43 % Allowed : 15.38 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.20), residues: 1684 helix: 0.48 (0.16), residues: 1032 sheet: -1.34 (0.58), residues: 64 loop : -2.20 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 685 TYR 0.011 0.001 TYR B 652 PHE 0.025 0.002 PHE B 701 TRP 0.015 0.001 TRP A 705 HIS 0.006 0.001 HIS B 731 Details of bonding type rmsd covalent geometry : bond 0.00305 (14096) covalent geometry : angle 0.62961 (19152) hydrogen bonds : bond 0.04663 ( 742) hydrogen bonds : angle 4.72741 ( 2112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 276 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 VAL cc_start: 0.8560 (t) cc_final: 0.8306 (p) REVERT: A 698 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8391 (mm-30) REVERT: A 705 TRP cc_start: 0.8245 (t60) cc_final: 0.7844 (t60) REVERT: C 418 VAL cc_start: 0.8555 (t) cc_final: 0.8303 (p) REVERT: C 545 TYR cc_start: 0.5769 (m-10) cc_final: 0.5363 (m-10) REVERT: C 698 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8393 (mm-30) REVERT: C 705 TRP cc_start: 0.8241 (t60) cc_final: 0.7842 (t60) REVERT: D 418 VAL cc_start: 0.8579 (t) cc_final: 0.8325 (p) REVERT: D 538 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8138 (mmtt) REVERT: D 698 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8360 (mm-30) REVERT: D 705 TRP cc_start: 0.8272 (t60) cc_final: 0.7885 (t60) REVERT: B 418 VAL cc_start: 0.8570 (t) cc_final: 0.8314 (p) REVERT: B 538 LYS cc_start: 0.8341 (mmtt) cc_final: 0.8135 (mmtt) REVERT: B 539 LEU cc_start: 0.8582 (tp) cc_final: 0.8025 (pp) REVERT: B 698 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8353 (mm-30) REVERT: B 705 TRP cc_start: 0.8273 (t60) cc_final: 0.7889 (t60) outliers start: 50 outliers final: 40 residues processed: 298 average time/residue: 0.1216 time to fit residues: 52.9900 Evaluate side-chains 305 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 141 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 140 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN C 573 ASN C 733 ASN D 573 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.223845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.167638 restraints weight = 21713.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.157589 restraints weight = 25144.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.157200 restraints weight = 20030.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.157141 restraints weight = 13411.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.157380 restraints weight = 12135.842| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14096 Z= 0.203 Angle : 0.686 8.698 19152 Z= 0.349 Chirality : 0.044 0.176 2176 Planarity : 0.004 0.042 2376 Dihedral : 4.568 17.681 1876 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.54 % Favored : 91.98 % Rotamer: Outliers : 3.85 % Allowed : 17.31 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.20), residues: 1684 helix: 0.36 (0.16), residues: 1036 sheet: -3.16 (0.46), residues: 40 loop : -1.88 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 537 TYR 0.015 0.002 TYR A 652 PHE 0.023 0.002 PHE A 701 TRP 0.014 0.002 TRP A 568 HIS 0.008 0.001 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00462 (14096) covalent geometry : angle 0.68614 (19152) hydrogen bonds : bond 0.05160 ( 742) hydrogen bonds : angle 4.92169 ( 2112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 279 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 VAL cc_start: 0.8554 (t) cc_final: 0.8352 (p) REVERT: A 705 TRP cc_start: 0.8152 (t60) cc_final: 0.7884 (t60) REVERT: C 418 VAL cc_start: 0.8559 (t) cc_final: 0.8352 (p) REVERT: C 705 TRP cc_start: 0.8123 (t60) cc_final: 0.7865 (t60) REVERT: D 418 VAL cc_start: 0.8548 (t) cc_final: 0.8342 (p) REVERT: D 552 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8013 (tt) REVERT: D 705 TRP cc_start: 0.8237 (t60) cc_final: 0.7937 (t60) REVERT: D 842 LEU cc_start: 0.6944 (mm) cc_final: 0.6551 (pp) REVERT: B 418 VAL cc_start: 0.8566 (t) cc_final: 0.8363 (p) REVERT: B 552 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8040 (tt) REVERT: B 705 TRP cc_start: 0.8232 (t60) cc_final: 0.7920 (t60) REVERT: B 842 LEU cc_start: 0.6948 (mm) cc_final: 0.6554 (pp) outliers start: 56 outliers final: 46 residues processed: 307 average time/residue: 0.1197 time to fit residues: 53.7953 Evaluate side-chains 306 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 573 ASN Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 163 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.222986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.168150 restraints weight = 21715.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.160374 restraints weight = 27434.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.158477 restraints weight = 23718.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.158434 restraints weight = 18902.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.158603 restraints weight = 16414.751| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14096 Z= 0.214 Angle : 0.709 8.754 19152 Z= 0.362 Chirality : 0.044 0.165 2176 Planarity : 0.004 0.038 2376 Dihedral : 4.632 18.576 1876 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.66 % Favored : 91.86 % Rotamer: Outliers : 4.74 % Allowed : 18.82 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.20), residues: 1684 helix: 0.33 (0.16), residues: 1016 sheet: -3.11 (0.47), residues: 40 loop : -1.81 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 685 TYR 0.015 0.002 TYR A 616 PHE 0.026 0.002 PHE B 701 TRP 0.014 0.002 TRP D 705 HIS 0.007 0.001 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00491 (14096) covalent geometry : angle 0.70867 (19152) hydrogen bonds : bond 0.05174 ( 742) hydrogen bonds : angle 4.98101 ( 2112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 287 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8042 (tt) REVERT: C 552 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8037 (tt) REVERT: D 552 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8072 (tt) REVERT: B 552 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8045 (tt) outliers start: 69 outliers final: 48 residues processed: 320 average time/residue: 0.1206 time to fit residues: 56.3842 Evaluate side-chains 317 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 265 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 845 TYR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 845 TYR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 573 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 135 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.226002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.170500 restraints weight = 21715.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.161817 restraints weight = 24294.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.160249 restraints weight = 17392.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.160236 restraints weight = 12877.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.160012 restraints weight = 10258.157| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14096 Z= 0.147 Angle : 0.682 10.487 19152 Z= 0.340 Chirality : 0.043 0.165 2176 Planarity : 0.004 0.039 2376 Dihedral : 4.416 18.012 1876 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.01 % Favored : 92.52 % Rotamer: Outliers : 4.46 % Allowed : 20.40 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.20), residues: 1684 helix: 0.46 (0.16), residues: 1008 sheet: -3.06 (0.47), residues: 40 loop : -1.79 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 685 TYR 0.012 0.001 TYR B 616 PHE 0.025 0.001 PHE A 701 TRP 0.017 0.002 TRP D 705 HIS 0.006 0.001 HIS C 731 Details of bonding type rmsd covalent geometry : bond 0.00329 (14096) covalent geometry : angle 0.68242 (19152) hydrogen bonds : bond 0.04743 ( 742) hydrogen bonds : angle 4.84303 ( 2112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 274 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 842 LEU cc_start: 0.7054 (mm) cc_final: 0.6719 (pp) REVERT: C 550 LEU cc_start: 0.8825 (mt) cc_final: 0.8508 (mp) REVERT: C 842 LEU cc_start: 0.7045 (mm) cc_final: 0.6711 (pp) REVERT: D 552 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8016 (tt) REVERT: D 698 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8209 (mm-30) REVERT: D 705 TRP cc_start: 0.8215 (t60) cc_final: 0.7935 (t60) REVERT: B 532 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9017 (tt) REVERT: B 705 TRP cc_start: 0.8190 (t60) cc_final: 0.7936 (t60) outliers start: 65 outliers final: 48 residues processed: 300 average time/residue: 0.1227 time to fit residues: 53.2865 Evaluate side-chains 303 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 253 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 845 TYR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 845 TYR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 635 ASN Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 31 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS B 635 ASN ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.224968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.169233 restraints weight = 21589.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.159237 restraints weight = 25228.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.159286 restraints weight = 21431.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.159084 restraints weight = 13342.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.158839 restraints weight = 11938.879| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14096 Z= 0.163 Angle : 0.716 10.928 19152 Z= 0.359 Chirality : 0.044 0.214 2176 Planarity : 0.004 0.038 2376 Dihedral : 4.430 18.049 1876 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.19 % Favored : 92.34 % Rotamer: Outliers : 4.12 % Allowed : 21.63 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.20), residues: 1684 helix: 0.41 (0.16), residues: 1016 sheet: -2.95 (0.49), residues: 40 loop : -1.97 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 685 TYR 0.015 0.002 TYR D 673 PHE 0.026 0.002 PHE D 701 TRP 0.023 0.002 TRP B 412 HIS 0.008 0.001 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00370 (14096) covalent geometry : angle 0.71575 (19152) hydrogen bonds : bond 0.04782 ( 742) hydrogen bonds : angle 4.90088 ( 2112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 550 LEU cc_start: 0.8829 (mt) cc_final: 0.8504 (mp) REVERT: D 532 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9056 (tt) REVERT: D 552 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8043 (tt) REVERT: B 532 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9043 (tt) REVERT: B 552 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8038 (tt) outliers start: 60 outliers final: 52 residues processed: 296 average time/residue: 0.1130 time to fit residues: 48.4930 Evaluate side-chains 312 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 256 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 845 TYR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 845 TYR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 635 ASN Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 151 optimal weight: 0.9980 chunk 52 optimal weight: 0.0370 chunk 41 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 111 optimal weight: 0.0010 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 overall best weight: 0.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN A 635 ASN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN D 629 ASN D 635 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.226981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.172486 restraints weight = 21884.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.162509 restraints weight = 24348.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.160467 restraints weight = 18804.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.160957 restraints weight = 14353.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.161800 restraints weight = 11313.159| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14096 Z= 0.141 Angle : 0.718 11.385 19152 Z= 0.357 Chirality : 0.044 0.268 2176 Planarity : 0.004 0.037 2376 Dihedral : 4.285 17.623 1876 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.71 % Favored : 92.76 % Rotamer: Outliers : 3.43 % Allowed : 22.46 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.20), residues: 1684 helix: 0.46 (0.16), residues: 1008 sheet: -2.80 (0.54), residues: 40 loop : -1.81 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 685 TYR 0.016 0.001 TYR B 673 PHE 0.014 0.001 PHE B 656 TRP 0.026 0.002 TRP D 412 HIS 0.008 0.001 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00311 (14096) covalent geometry : angle 0.71797 (19152) hydrogen bonds : bond 0.04599 ( 742) hydrogen bonds : angle 4.88707 ( 2112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 267 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 TRP cc_start: 0.8135 (t60) cc_final: 0.7656 (t60) REVERT: C 550 LEU cc_start: 0.8829 (mt) cc_final: 0.8517 (mp) REVERT: C 705 TRP cc_start: 0.8100 (t60) cc_final: 0.7631 (t60) REVERT: D 532 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9009 (tt) REVERT: D 550 LEU cc_start: 0.8660 (mt) cc_final: 0.8303 (mp) REVERT: B 532 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9005 (tt) REVERT: B 550 LEU cc_start: 0.8686 (mt) cc_final: 0.8331 (mp) outliers start: 50 outliers final: 38 residues processed: 289 average time/residue: 0.1072 time to fit residues: 45.0806 Evaluate side-chains 301 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 845 TYR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 845 TYR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 635 ASN Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 733 ASN D 635 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.217064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.167349 restraints weight = 24274.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.162050 restraints weight = 36002.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.160547 restraints weight = 27374.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.159770 restraints weight = 23838.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.160008 restraints weight = 20670.626| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14096 Z= 0.168 Angle : 0.751 11.840 19152 Z= 0.376 Chirality : 0.046 0.374 2176 Planarity : 0.004 0.036 2376 Dihedral : 4.359 17.386 1876 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.89 % Favored : 92.58 % Rotamer: Outliers : 3.37 % Allowed : 22.53 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.20), residues: 1684 helix: 0.38 (0.16), residues: 1016 sheet: -2.76 (0.58), residues: 40 loop : -1.78 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 685 TYR 0.015 0.001 TYR B 673 PHE 0.026 0.002 PHE B 701 TRP 0.030 0.002 TRP C 412 HIS 0.007 0.001 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00382 (14096) covalent geometry : angle 0.75080 (19152) hydrogen bonds : bond 0.04803 ( 742) hydrogen bonds : angle 4.91244 ( 2112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 TYR cc_start: 0.6535 (m-80) cc_final: 0.6287 (m-80) REVERT: C 550 LEU cc_start: 0.8783 (mt) cc_final: 0.8503 (mp) REVERT: C 552 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7865 (tt) REVERT: D 532 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8852 (tt) REVERT: D 550 LEU cc_start: 0.8649 (mt) cc_final: 0.8300 (mp) REVERT: B 532 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8857 (tt) REVERT: B 550 LEU cc_start: 0.8647 (mt) cc_final: 0.8298 (mp) REVERT: B 552 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7920 (tt) outliers start: 49 outliers final: 41 residues processed: 283 average time/residue: 0.1019 time to fit residues: 41.8436 Evaluate side-chains 302 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 257 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 566 CYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 566 CYS Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 635 ASN Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 826 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 122 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 160 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN ** D 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.217796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.143413 restraints weight = 23573.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141865 restraints weight = 12325.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.141553 restraints weight = 8122.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.142518 restraints weight = 7400.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.142474 restraints weight = 6723.283| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14096 Z= 0.154 Angle : 0.751 12.204 19152 Z= 0.373 Chirality : 0.046 0.458 2176 Planarity : 0.004 0.036 2376 Dihedral : 4.308 17.346 1876 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.95 % Favored : 92.40 % Rotamer: Outliers : 2.82 % Allowed : 23.01 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.20), residues: 1684 helix: 0.31 (0.16), residues: 1024 sheet: -2.76 (0.59), residues: 40 loop : -1.69 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 685 TYR 0.015 0.001 TYR B 673 PHE 0.029 0.001 PHE C 701 TRP 0.024 0.002 TRP C 412 HIS 0.007 0.001 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00346 (14096) covalent geometry : angle 0.75101 (19152) hydrogen bonds : bond 0.04695 ( 742) hydrogen bonds : angle 4.93615 ( 2112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2752.60 seconds wall clock time: 48 minutes 18.04 seconds (2898.04 seconds total)