Starting phenix.real_space_refine on Tue Nov 18 21:17:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbw_7852/11_2025/6dbw_7852_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbw_7852/11_2025/6dbw_7852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dbw_7852/11_2025/6dbw_7852_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbw_7852/11_2025/6dbw_7852_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dbw_7852/11_2025/6dbw_7852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbw_7852/11_2025/6dbw_7852.map" } resolution = 4.7 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= 0.006 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 2 6.06 5 P 100 5.49 5 S 112 5.16 5 C 10625 2.51 5 N 3103 2.21 5 O 3472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17418 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4954 Classifications: {'peptide': 614} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 589} Chain breaks: 1 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "C" Number of atoms: 4980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 615, 4964 Classifications: {'peptide': 615} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 590} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 615, 4964 Classifications: {'peptide': 615} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 590} Chain breaks: 1 bond proxies already assigned to first conformer: 5041 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1023 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1027 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2626 SG CYS A 749 34.112 54.919 58.922 1.00153.23 S ATOM 2647 SG CYS A 752 31.066 53.976 56.338 1.00173.11 S ATOM 10304 SG CYS C 749 105.397 97.007 63.081 1.00105.27 S Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" P DA E 39 " occ=0.63 ... (19 atoms not shown) pdb=" C4 DA E 39 " occ=0.63 residue: pdb=" P DA E 40 " occ=0.74 ... (19 atoms not shown) pdb=" C4 DA E 40 " occ=0.74 residue: pdb=" P DA E 41 " occ=0.57 ... (19 atoms not shown) pdb=" C4 DA E 41 " occ=0.57 residue: pdb=" P DA E 42 " occ=0.60 ... (19 atoms not shown) pdb=" C4 DA E 42 " occ=0.60 residue: pdb=" P DC E 44 " occ=0.45 ... (17 atoms not shown) pdb=" C6 DC E 44 " occ=0.45 residue: pdb=" P DG F 7 " occ=0.62 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.62 residue: pdb=" P DG F 8 " occ=0.55 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.55 residue: pdb=" P DT F 9 " occ=0.63 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.63 residue: pdb=" P DT F 10 " occ=0.59 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.59 residue: pdb=" P DT F 11 " occ=0.63 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.63 residue: pdb=" P DT F 12 " occ=0.64 ... (18 atoms not shown) pdb=" C6 DT F 12 " occ=0.64 residue: pdb=" P DT F 13 " occ=0.67 ... (18 atoms not shown) pdb=" C6 DT F 13 " occ=0.67 residue: pdb=" P DG F 14 " occ=0.49 ... (20 atoms not shown) pdb=" C4 DG F 14 " occ=0.49 Time building chain proxies: 5.31, per 1000 atoms: 0.30 Number of scatterers: 17418 At special positions: 0 Unit cell: (131.44, 153.7, 149.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 4 19.99 S 112 16.00 P 100 15.00 O 3472 8.00 N 3103 7.00 C 10625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 882.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 752 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " Number of angles added : 2 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 18 sheets defined 38.0% alpha, 22.5% beta 38 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 419 through 442 removed outlier: 5.523A pdb=" N ASP A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 461 removed outlier: 3.951A pdb=" N GLY A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.586A pdb=" N ALA A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 493 removed outlier: 3.518A pdb=" N CYS A 486 " --> pdb=" O HIS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 518 through 526 removed outlier: 3.795A pdb=" N LEU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 601 removed outlier: 5.059A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 705 removed outlier: 3.731A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 757 through 762 removed outlier: 4.189A pdb=" N GLN A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 799 Processing helix chain 'A' and resid 814 through 835 removed outlier: 3.598A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 862 removed outlier: 3.631A pdb=" N LYS A 862 " --> pdb=" O GLN A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 889 removed outlier: 3.735A pdb=" N VAL A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 892 No H-bonds generated for 'chain 'A' and resid 890 through 892' Processing helix chain 'A' and resid 895 through 912 Processing helix chain 'A' and resid 912 through 917 Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 930 removed outlier: 4.214A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 955 through 964 Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.732A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1016 removed outlier: 4.000A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A1011 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A1016 " --> pdb=" O HIS A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1027 Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 414 through 418 Processing helix chain 'C' and resid 419 through 442 removed outlier: 5.955A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 461 removed outlier: 3.630A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 482 through 493 removed outlier: 3.537A pdb=" N CYS C 486 " --> pdb=" O HIS C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 530 removed outlier: 3.915A pdb=" N LEU C 522 " --> pdb=" O PRO C 518 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 529 " --> pdb=" O ALA C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 589 through 600 Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.812A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix removed outlier: 3.802A pdb=" N MET C 705 " --> pdb=" O ARG C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 755 through 762 removed outlier: 3.682A pdb=" N ALA C 759 " --> pdb=" O THR C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 814 through 835 removed outlier: 4.202A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 890 removed outlier: 3.755A pdb=" N GLU C 890 " --> pdb=" O GLU C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 910 Processing helix chain 'C' and resid 911 through 917 removed outlier: 3.698A pdb=" N TRP C 915 " --> pdb=" O MET C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 955 through 964 removed outlier: 3.548A pdb=" N HIS C 959 " --> pdb=" O THR C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 981 through 998 removed outlier: 4.214A pdb=" N SER C 985 " --> pdb=" O GLU C 981 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1016 removed outlier: 4.374A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS C1011 " --> pdb=" O GLU C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 removed outlier: 4.914A pdb=" N PHE C1024 " --> pdb=" O TYR C1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 537 through 539 removed outlier: 4.101A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 721 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A 727 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS A 619 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 539 removed outlier: 4.101A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 721 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A 727 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS A 619 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 651 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR A 661 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 5.790A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 318 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8 removed outlier: 7.508A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.766A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 113 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ARG B 123 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL B 111 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLU B 125 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU B 109 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS B 127 " --> pdb=" O TYR B 107 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TYR B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.676A pdb=" N GLU B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA9, first strand: chain 'B' and resid 210 through 211 Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB2, first strand: chain 'C' and resid 537 through 539 removed outlier: 3.755A pdb=" N GLU C 537 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N PHE C 611 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 11.335A pdb=" N PHE C 724 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N VAL C 613 " --> pdb=" O PHE C 724 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N GLY C 726 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 10.780A pdb=" N VAL C 615 " --> pdb=" O GLY C 726 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N GLY C 728 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU C 617 " --> pdb=" O GLY C 728 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C 641 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 639 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 537 through 539 removed outlier: 3.755A pdb=" N GLU C 537 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N PHE C 611 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 11.335A pdb=" N PHE C 724 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N VAL C 613 " --> pdb=" O PHE C 724 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N GLY C 726 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 10.780A pdb=" N VAL C 615 " --> pdb=" O GLY C 726 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N GLY C 728 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU C 617 " --> pdb=" O GLY C 728 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C 641 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 639 " --> pdb=" O MET C 622 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 24 removed outlier: 5.460A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY D 320 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 330 " --> pdb=" O PHE D 318 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE D 318 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 78 removed outlier: 5.590A pdb=" N TYR D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS D 127 " --> pdb=" O TYR D 107 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU D 109 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU D 125 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL D 111 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ARG D 123 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER D 113 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 138 through 147 removed outlier: 4.735A pdb=" N HIS D 140 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY D 157 " --> pdb=" O HIS D 140 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 142 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 155 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 144 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS D 153 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN D 146 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR D 151 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 147 removed outlier: 4.735A pdb=" N HIS D 140 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY D 157 " --> pdb=" O HIS D 140 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 142 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 155 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 144 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS D 153 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN D 146 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR D 151 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY D 157 " --> pdb=" O GLN D 181 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLN D 181 " --> pdb=" O GLY D 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 209 through 212 removed outlier: 4.072A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 263 through 265 690 hydrogen bonds defined for protein. 1937 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 1 1.18 - 1.34: 5473 1.34 - 1.50: 5439 1.50 - 1.66: 6911 1.66 - 1.82: 168 Bond restraints: 17992 Sorted by residual: bond pdb=" CD GLN A 517 " pdb=" NE2 GLN A 517 " ideal model delta sigma weight residual 1.328 1.584 -0.256 2.10e-02 2.27e+03 1.49e+02 bond pdb=" CD GLN A 517 " pdb=" OE1 GLN A 517 " ideal model delta sigma weight residual 1.231 1.022 0.209 1.90e-02 2.77e+03 1.21e+02 bond pdb=" CG HIS C 414 " pdb=" ND1 HIS C 414 " ideal model delta sigma weight residual 1.378 1.285 0.093 1.10e-02 8.26e+03 7.11e+01 bond pdb=" CG HIS C1012 " pdb=" CD2 HIS C1012 " ideal model delta sigma weight residual 1.354 1.444 -0.090 1.10e-02 8.26e+03 6.67e+01 bond pdb=" CA HIS C1012 " pdb=" C HIS C1012 " ideal model delta sigma weight residual 1.524 1.427 0.097 1.32e-02 5.74e+03 5.42e+01 ... (remaining 17987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.76: 24697 11.76 - 23.52: 15 23.52 - 35.28: 7 35.28 - 47.04: 6 47.04 - 58.79: 1 Bond angle restraints: 24726 Sorted by residual: angle pdb=" CB HIS C1012 " pdb=" CG HIS C1012 " pdb=" CD2 HIS C1012 " ideal model delta sigma weight residual 131.20 90.48 40.72 1.30e+00 5.92e-01 9.81e+02 angle pdb=" CB HIS C1012 " pdb=" CG HIS C1012 " pdb=" ND1 HIS C1012 " ideal model delta sigma weight residual 122.70 168.72 -46.02 1.50e+00 4.44e-01 9.41e+02 angle pdb=" CB HIS D 237 " pdb=" CG HIS D 237 " pdb=" CD2 HIS D 237 " ideal model delta sigma weight residual 131.20 91.76 39.44 1.30e+00 5.92e-01 9.21e+02 angle pdb=" CB HIS C 959 " pdb=" CG HIS C 959 " pdb=" CD2 HIS C 959 " ideal model delta sigma weight residual 131.20 92.73 38.47 1.30e+00 5.92e-01 8.76e+02 angle pdb=" CG GLN A 517 " pdb=" CD GLN A 517 " pdb=" OE1 GLN A 517 " ideal model delta sigma weight residual 120.80 179.59 -58.79 2.00e+00 2.50e-01 8.64e+02 ... (remaining 24721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 9900 36.00 - 72.00: 694 72.00 - 107.99: 30 107.99 - 143.99: 1 143.99 - 179.99: 4 Dihedral angle restraints: 10629 sinusoidal: 5044 harmonic: 5585 Sorted by residual: dihedral pdb=" C HIS C 959 " pdb=" N HIS C 959 " pdb=" CA HIS C 959 " pdb=" CB HIS C 959 " ideal model delta harmonic sigma weight residual -122.60 -87.83 -34.77 0 2.50e+00 1.60e-01 1.93e+02 dihedral pdb=" CD BARG C 850 " pdb=" NE BARG C 850 " pdb=" CZ BARG C 850 " pdb=" NH1BARG C 850 " ideal model delta sinusoidal sigma weight residual 0.00 179.99 -179.99 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" N HIS D 237 " pdb=" C HIS D 237 " pdb=" CA HIS D 237 " pdb=" CB HIS D 237 " ideal model delta harmonic sigma weight residual 122.80 155.39 -32.59 0 2.50e+00 1.60e-01 1.70e+02 ... (remaining 10626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.272: 2684 0.272 - 0.543: 7 0.543 - 0.815: 0 0.815 - 1.086: 1 1.086 - 1.358: 2 Chirality restraints: 2694 Sorted by residual: chirality pdb=" CA HIS D 237 " pdb=" N HIS D 237 " pdb=" C HIS D 237 " pdb=" CB HIS D 237 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.61e+01 chirality pdb=" CA HIS A1028 " pdb=" N HIS A1028 " pdb=" C HIS A1028 " pdb=" CB HIS A1028 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.68e+01 chirality pdb=" CA HIS C 414 " pdb=" N HIS C 414 " pdb=" C HIS C 414 " pdb=" CB HIS C 414 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.88e+01 ... (remaining 2691 not shown) Planarity restraints: 2854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 414 " -0.078 2.00e-02 2.50e+03 1.99e-01 5.94e+02 pdb=" CG HIS C 414 " 0.307 2.00e-02 2.50e+03 pdb=" ND1 HIS C 414 " -0.281 2.00e-02 2.50e+03 pdb=" CD2 HIS C 414 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS C 414 " 0.205 2.00e-02 2.50e+03 pdb=" NE2 HIS C 414 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 959 " 0.094 2.00e-02 2.50e+03 1.36e-01 2.78e+02 pdb=" CG HIS C 959 " -0.185 2.00e-02 2.50e+03 pdb=" ND1 HIS C 959 " 0.165 2.00e-02 2.50e+03 pdb=" CD2 HIS C 959 " -0.085 2.00e-02 2.50e+03 pdb=" CE1 HIS C 959 " -0.124 2.00e-02 2.50e+03 pdb=" NE2 HIS C 959 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 414 " -0.075 2.00e-02 2.50e+03 1.47e-01 2.17e+02 pdb=" C HIS C 414 " 0.255 2.00e-02 2.50e+03 pdb=" O HIS C 414 " -0.105 2.00e-02 2.50e+03 pdb=" N LEU C 415 " -0.075 2.00e-02 2.50e+03 ... (remaining 2851 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 183 2.41 - 3.04: 11593 3.04 - 3.66: 29455 3.66 - 4.28: 40786 4.28 - 4.90: 61906 Nonbonded interactions: 143923 Sorted by model distance: nonbonded pdb=" NZ LYS D 86 " pdb=" OE2 GLU D 125 " model vdw 1.792 3.120 nonbonded pdb=" NZ LYS C 435 " pdb=" OE2 GLU C 439 " model vdw 1.815 3.120 nonbonded pdb=" NZ LYS A 638 " pdb=" OD2 ASP A 683 " model vdw 1.846 3.120 nonbonded pdb=" NH1 ARG D 159 " pdb=" OG SER D 205 " model vdw 1.866 3.120 nonbonded pdb=" NH2 ARG A 641 " pdb=" O ASN A 983 " model vdw 1.913 3.120 ... (remaining 143918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 408 through 512 or resid 514 through 626 or resid 636 thro \ ugh 849 or resid 851 through 1103)) selection = (chain 'C' and (resid 408 through 512 or resid 514 through 626 or resid 636 thro \ ugh 849 or resid 851 through 1029 or resid 1101 through 1103)) } ncs_group { reference = chain 'B' 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=0.00 max=1.00 mean=0.99 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.220 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.008 0.595 17999 Z= 0.360 Angle : 1.281 58.794 24728 Z= 0.844 Chirality : 0.062 1.358 2694 Planarity : 0.008 0.199 2854 Dihedral : 20.938 179.991 7035 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 30.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.60 % Favored : 91.35 % Rotamer: Outliers : 0.29 % Allowed : 28.73 % Favored : 70.97 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.15), residues: 1921 helix: -2.57 (0.15), residues: 646 sheet: -2.59 (0.24), residues: 327 loop : -2.88 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG A 878 TYR 0.025 0.003 TYR B 277 PHE 0.026 0.002 PHE B 156 TRP 0.026 0.002 TRP A 978 HIS 0.323 0.013 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00585 (17992) covalent geometry : angle 1.27660 (24726) hydrogen bonds : bond 0.15057 ( 746) hydrogen bonds : angle 7.15452 ( 2107) metal coordination : bond 0.27130 ( 7) metal coordination : angle 11.80133 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 362 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LEU cc_start: 0.9131 (mt) cc_final: 0.8867 (pp) REVERT: A 522 LEU cc_start: 0.9609 (mt) cc_final: 0.9406 (mt) REVERT: A 681 PHE cc_start: 0.8754 (m-10) cc_final: 0.8532 (m-80) REVERT: A 710 ILE cc_start: 0.8789 (mt) cc_final: 0.8367 (mp) REVERT: A 731 GLU cc_start: 0.9300 (tp30) cc_final: 0.9041 (tm-30) REVERT: A 732 LYS cc_start: 0.9394 (ttpt) cc_final: 0.9178 (tmtt) REVERT: A 733 MET cc_start: 0.9202 (ttm) cc_final: 0.8877 (tmm) REVERT: A 738 GLU cc_start: 0.9316 (tp30) cc_final: 0.8934 (tm-30) REVERT: A 802 SER cc_start: 0.8871 (p) cc_final: 0.8603 (t) REVERT: A 820 ILE cc_start: 0.9642 (mt) cc_final: 0.9194 (tt) REVERT: A 828 LYS cc_start: 0.9541 (tttt) cc_final: 0.9024 (tptm) REVERT: A 911 MET cc_start: 0.8685 (ptm) cc_final: 0.8340 (ptm) REVERT: A 945 MET cc_start: 0.9163 (mtp) cc_final: 0.8729 (tpp) REVERT: A 995 LYS cc_start: 0.9006 (mttp) cc_final: 0.8532 (mtpp) REVERT: A 1005 GLU cc_start: 0.9577 (pt0) cc_final: 0.9036 (pt0) REVERT: A 1025 MET cc_start: 0.9011 (tpp) cc_final: 0.8774 (tpp) REVERT: B 22 LEU cc_start: 0.8709 (mt) cc_final: 0.8335 (tp) REVERT: B 23 ASP cc_start: 0.9058 (t0) cc_final: 0.8837 (t0) REVERT: B 56 LYS cc_start: 0.9033 (mptp) cc_final: 0.8703 (mmtt) REVERT: B 84 ASP cc_start: 0.9344 (m-30) cc_final: 0.8898 (t70) REVERT: B 126 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8189 (tm-30) REVERT: B 129 LEU cc_start: 0.8928 (mt) cc_final: 0.8651 (pt) REVERT: B 197 LEU cc_start: 0.8955 (mt) cc_final: 0.8670 (tp) REVERT: B 227 ASP cc_start: 0.9388 (m-30) cc_final: 0.9077 (t0) REVERT: B 280 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9188 (tp30) REVERT: B 285 MET cc_start: 0.8293 (mmt) cc_final: 0.7728 (tpp) REVERT: C 454 PHE cc_start: 0.7521 (t80) cc_final: 0.7182 (t80) REVERT: C 503 MET cc_start: 0.8880 (ttp) cc_final: 0.8494 (ptm) REVERT: C 527 LYS cc_start: 0.9517 (mttt) cc_final: 0.9197 (tptp) REVERT: C 560 TRP cc_start: 0.8638 (t60) cc_final: 0.8436 (t-100) REVERT: C 566 ASP cc_start: 0.9230 (m-30) cc_final: 0.8223 (t0) REVERT: C 594 MET cc_start: 0.9161 (mmm) cc_final: 0.8534 (mmm) REVERT: C 598 ARG cc_start: 0.9628 (mmt-90) cc_final: 0.9410 (mmp80) REVERT: C 616 LYS cc_start: 0.9226 (ptmt) cc_final: 0.9021 (ptmt) REVERT: C 642 PHE cc_start: 0.8370 (t80) cc_final: 0.8164 (t80) REVERT: C 748 ILE cc_start: 0.9019 (pt) cc_final: 0.8808 (pt) REVERT: C 763 MET cc_start: 0.8393 (mtt) cc_final: 0.8144 (mtm) REVERT: C 768 ILE cc_start: 0.8263 (mt) cc_final: 0.7917 (mm) REVERT: C 859 LEU cc_start: 0.9112 (mt) cc_final: 0.8788 (pp) REVERT: C 871 MET cc_start: 0.7013 (ttp) cc_final: 0.6483 (ttm) REVERT: C 875 TYR cc_start: 0.8729 (t80) cc_final: 0.8341 (t80) REVERT: C 997 ASN cc_start: 0.8859 (m110) cc_final: 0.7979 (t0) REVERT: C 1007 GLU cc_start: 0.9234 (tt0) cc_final: 0.8564 (tp30) REVERT: D 65 ASN cc_start: 0.9394 (p0) cc_final: 0.9113 (p0) REVERT: D 84 ASP cc_start: 0.9276 (m-30) cc_final: 0.8607 (p0) REVERT: D 285 MET cc_start: 0.7524 (mmm) cc_final: 0.7059 (tpt) outliers start: 2 outliers final: 1 residues processed: 364 average time/residue: 0.1676 time to fit residues: 87.2865 Evaluate side-chains 228 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 ASN A 983 ASN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 HIS ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS C 520 HIS C 687 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN C 831 GLN D 99 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.062910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.041820 restraints weight = 215340.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.043876 restraints weight = 98061.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.045229 restraints weight = 60042.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.046130 restraints weight = 43258.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.046726 restraints weight = 34373.265| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 17999 Z= 0.269 Angle : 0.830 10.630 24728 Z= 0.444 Chirality : 0.047 0.182 2694 Planarity : 0.007 0.095 2854 Dihedral : 22.415 178.855 3229 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.24 % Allowed : 4.84 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.17), residues: 1921 helix: -1.45 (0.18), residues: 665 sheet: -2.07 (0.26), residues: 328 loop : -2.35 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 878 TYR 0.022 0.003 TYR A 729 PHE 0.022 0.003 PHE C 644 TRP 0.018 0.002 TRP C 915 HIS 0.028 0.003 HIS C 959 Details of bonding type rmsd covalent geometry : bond 0.00568 (17992) covalent geometry : angle 0.82847 (24726) hydrogen bonds : bond 0.06087 ( 746) hydrogen bonds : angle 5.81353 ( 2107) metal coordination : bond 0.03402 ( 7) metal coordination : angle 4.90742 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 LEU cc_start: 0.7990 (tp) cc_final: 0.7652 (tp) REVERT: A 503 MET cc_start: 0.9166 (ppp) cc_final: 0.8947 (ppp) REVERT: A 572 ILE cc_start: 0.8935 (tp) cc_final: 0.8728 (tp) REVERT: A 594 MET cc_start: 0.9504 (mmm) cc_final: 0.9277 (mmt) REVERT: A 624 ASP cc_start: 0.7446 (m-30) cc_final: 0.7236 (t0) REVERT: A 647 MET cc_start: 0.8923 (mmm) cc_final: 0.8494 (mmm) REVERT: A 731 GLU cc_start: 0.8916 (tp30) cc_final: 0.8309 (tm-30) REVERT: A 733 MET cc_start: 0.9649 (ttm) cc_final: 0.8804 (tmm) REVERT: A 738 GLU cc_start: 0.8757 (tp30) cc_final: 0.7943 (tm-30) REVERT: A 802 SER cc_start: 0.9101 (p) cc_final: 0.8804 (t) REVERT: A 806 PHE cc_start: 0.9011 (p90) cc_final: 0.7852 (p90) REVERT: A 807 MET cc_start: 0.8644 (tpp) cc_final: 0.8388 (tpp) REVERT: A 828 LYS cc_start: 0.9450 (tttt) cc_final: 0.8919 (tptm) REVERT: A 847 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8570 (mp0) REVERT: A 911 MET cc_start: 0.8529 (ptm) cc_final: 0.8194 (ptm) REVERT: A 995 LYS cc_start: 0.8503 (ttmm) cc_final: 0.7798 (ttmm) REVERT: A 1003 THR cc_start: 0.9335 (p) cc_final: 0.8683 (t) REVERT: A 1024 PHE cc_start: 0.9104 (m-80) cc_final: 0.8884 (m-80) REVERT: B 22 LEU cc_start: 0.9276 (mt) cc_final: 0.8873 (tp) REVERT: B 84 ASP cc_start: 0.9080 (m-30) cc_final: 0.8711 (t70) REVERT: B 126 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7469 (tm-30) REVERT: B 185 ILE cc_start: 0.9609 (tt) cc_final: 0.9359 (mp) REVERT: B 197 LEU cc_start: 0.9028 (mt) cc_final: 0.8815 (tp) REVERT: B 232 ARG cc_start: 0.9370 (pmt-80) cc_final: 0.9116 (ptm160) REVERT: C 495 LEU cc_start: 0.9399 (mm) cc_final: 0.9018 (tp) REVERT: C 522 LEU cc_start: 0.9212 (mt) cc_final: 0.8896 (mt) REVERT: C 526 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8368 (mt-10) REVERT: C 527 LYS cc_start: 0.9691 (mttt) cc_final: 0.9039 (tptp) REVERT: C 594 MET cc_start: 0.9126 (mmm) cc_final: 0.8528 (mmm) REVERT: C 598 ARG cc_start: 0.9592 (mmt-90) cc_final: 0.9314 (mmp80) REVERT: C 606 MET cc_start: 0.8860 (ptt) cc_final: 0.8139 (ppp) REVERT: C 616 LYS cc_start: 0.9493 (ptmt) cc_final: 0.8699 (ptpt) REVERT: C 677 LEU cc_start: 0.9163 (tp) cc_final: 0.8874 (tp) REVERT: C 680 MET cc_start: 0.9230 (pmm) cc_final: 0.8966 (pmm) REVERT: C 700 GLU cc_start: 0.9222 (tt0) cc_final: 0.8705 (tm-30) REVERT: C 733 MET cc_start: 0.9178 (mmt) cc_final: 0.8729 (mmm) REVERT: C 807 MET cc_start: 0.9214 (tmm) cc_final: 0.8812 (tmm) REVERT: C 863 MET cc_start: 0.7388 (mmm) cc_final: 0.7123 (mtp) REVERT: C 871 MET cc_start: 0.7016 (ttp) cc_final: 0.6630 (ttp) REVERT: C 875 TYR cc_start: 0.9267 (t80) cc_final: 0.8867 (t80) REVERT: C 938 PHE cc_start: 0.9390 (t80) cc_final: 0.9044 (t80) REVERT: C 1010 LEU cc_start: 0.9824 (tp) cc_final: 0.9598 (tp) REVERT: C 1025 MET cc_start: 0.8836 (mpp) cc_final: 0.8621 (mpp) REVERT: D 65 ASN cc_start: 0.9589 (p0) cc_final: 0.9375 (p0) REVERT: D 173 ASN cc_start: 0.9476 (m-40) cc_final: 0.9091 (m-40) outliers start: 1 outliers final: 1 residues processed: 283 average time/residue: 0.1734 time to fit residues: 70.7360 Evaluate side-chains 203 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 3 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 chunk 6 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 ASN A 983 ASN B 99 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 GLN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.059775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.038849 restraints weight = 247677.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.040843 restraints weight = 110664.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.042143 restraints weight = 67350.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.043011 restraints weight = 48392.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.043599 restraints weight = 38609.917| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 17999 Z= 0.343 Angle : 0.855 11.135 24728 Z= 0.457 Chirality : 0.046 0.262 2694 Planarity : 0.006 0.064 2854 Dihedral : 22.383 179.818 3229 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 28.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.18 % Allowed : 5.31 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.17), residues: 1921 helix: -1.35 (0.18), residues: 670 sheet: -1.97 (0.26), residues: 354 loop : -2.20 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 991 TYR 0.024 0.003 TYR B 277 PHE 0.028 0.003 PHE A 642 TRP 0.033 0.003 TRP C 915 HIS 0.014 0.002 HIS A 959 Details of bonding type rmsd covalent geometry : bond 0.00711 (17992) covalent geometry : angle 0.85398 (24726) hydrogen bonds : bond 0.06181 ( 746) hydrogen bonds : angle 5.97751 ( 2107) metal coordination : bond 0.01857 ( 7) metal coordination : angle 3.45016 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.9278 (ppp) cc_final: 0.9061 (ppp) REVERT: A 526 GLU cc_start: 0.9058 (pm20) cc_final: 0.8809 (pm20) REVERT: A 667 LYS cc_start: 0.9552 (mtpt) cc_final: 0.9254 (ptpt) REVERT: A 684 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8703 (tm-30) REVERT: A 700 GLU cc_start: 0.9483 (pt0) cc_final: 0.9105 (pt0) REVERT: A 729 TYR cc_start: 0.8320 (m-80) cc_final: 0.7467 (m-80) REVERT: A 731 GLU cc_start: 0.8969 (tp30) cc_final: 0.8650 (tt0) REVERT: A 733 MET cc_start: 0.9431 (ttm) cc_final: 0.8749 (tmm) REVERT: A 738 GLU cc_start: 0.8776 (tp30) cc_final: 0.7965 (tm-30) REVERT: A 802 SER cc_start: 0.9196 (p) cc_final: 0.8849 (m) REVERT: A 806 PHE cc_start: 0.9145 (p90) cc_final: 0.7881 (p90) REVERT: A 807 MET cc_start: 0.8671 (tpp) cc_final: 0.8172 (tpp) REVERT: A 817 HIS cc_start: 0.9371 (m90) cc_final: 0.9113 (m90) REVERT: A 828 LYS cc_start: 0.9499 (tttt) cc_final: 0.8990 (tptm) REVERT: A 831 GLN cc_start: 0.9226 (tt0) cc_final: 0.8962 (tm-30) REVERT: A 847 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8489 (mp0) REVERT: A 911 MET cc_start: 0.8649 (ptm) cc_final: 0.8381 (ptm) REVERT: A 912 LYS cc_start: 0.9778 (pptt) cc_final: 0.9560 (pptt) REVERT: A 945 MET cc_start: 0.8848 (ttt) cc_final: 0.8451 (tpp) REVERT: A 1003 THR cc_start: 0.9292 (p) cc_final: 0.8954 (p) REVERT: A 1024 PHE cc_start: 0.9133 (m-80) cc_final: 0.8886 (m-80) REVERT: B 22 LEU cc_start: 0.9242 (mt) cc_final: 0.8788 (tp) REVERT: B 129 LEU cc_start: 0.8714 (mp) cc_final: 0.8390 (mp) REVERT: B 185 ILE cc_start: 0.9671 (tt) cc_final: 0.9333 (mp) REVERT: B 197 LEU cc_start: 0.9054 (mt) cc_final: 0.8804 (tt) REVERT: C 474 MET cc_start: 0.6485 (tpt) cc_final: 0.6244 (mmm) REVERT: C 522 LEU cc_start: 0.9219 (mt) cc_final: 0.8791 (mt) REVERT: C 530 LEU cc_start: 0.9392 (mt) cc_final: 0.9108 (mt) REVERT: C 594 MET cc_start: 0.9221 (mmm) cc_final: 0.8008 (mmm) REVERT: C 598 ARG cc_start: 0.9646 (mmt-90) cc_final: 0.9219 (mmp-170) REVERT: C 606 MET cc_start: 0.9023 (ptt) cc_final: 0.8641 (ppp) REVERT: C 616 LYS cc_start: 0.9499 (ptmt) cc_final: 0.9071 (ptmt) REVERT: C 680 MET cc_start: 0.9274 (pmm) cc_final: 0.8763 (pmm) REVERT: C 700 GLU cc_start: 0.9360 (tt0) cc_final: 0.8676 (tm-30) REVERT: C 705 MET cc_start: 0.9406 (mmt) cc_final: 0.9008 (mpp) REVERT: C 733 MET cc_start: 0.9355 (mmt) cc_final: 0.9088 (mmp) REVERT: C 737 MET cc_start: 0.9052 (tmm) cc_final: 0.8446 (tmm) REVERT: C 807 MET cc_start: 0.9272 (tmm) cc_final: 0.8928 (tmm) REVERT: C 933 TYR cc_start: 0.8994 (t80) cc_final: 0.8741 (t80) REVERT: C 938 PHE cc_start: 0.9369 (t80) cc_final: 0.9049 (t80) REVERT: C 1007 GLU cc_start: 0.9136 (tt0) cc_final: 0.8818 (tt0) REVERT: C 1010 LEU cc_start: 0.9811 (tp) cc_final: 0.9592 (tp) REVERT: D 65 ASN cc_start: 0.9546 (p0) cc_final: 0.9300 (p0) REVERT: D 173 ASN cc_start: 0.9323 (m-40) cc_final: 0.8914 (m-40) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1539 time to fit residues: 52.2441 Evaluate side-chains 180 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 100 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 165 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS ** D 278 GLN ** 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 = 0.3375 r_free = 0.3375 target = 0.061470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.040688 restraints weight = 203783.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.042616 restraints weight = 97330.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.043916 restraints weight = 61024.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.044778 restraints weight = 44362.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.045368 restraints weight = 35535.274| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 17999 Z= 0.224 Angle : 0.742 11.177 24728 Z= 0.397 Chirality : 0.044 0.187 2694 Planarity : 0.005 0.065 2854 Dihedral : 22.234 179.042 3229 Min Nonbonded Distance : 1.590 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.18 % Allowed : 3.42 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.18), residues: 1921 helix: -0.90 (0.19), residues: 674 sheet: -1.69 (0.27), residues: 327 loop : -2.07 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 778 TYR 0.026 0.003 TYR C 931 PHE 0.020 0.002 PHE A 642 TRP 0.036 0.002 TRP C 915 HIS 0.017 0.002 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00476 (17992) covalent geometry : angle 0.74178 (24726) hydrogen bonds : bond 0.05077 ( 746) hydrogen bonds : angle 5.62085 ( 2107) metal coordination : bond 0.01157 ( 7) metal coordination : angle 3.21944 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 TYR cc_start: 0.8923 (t80) cc_final: 0.8632 (t80) REVERT: A 503 MET cc_start: 0.9207 (ppp) cc_final: 0.8998 (ppp) REVERT: A 526 GLU cc_start: 0.8973 (pm20) cc_final: 0.8756 (pm20) REVERT: A 590 GLU cc_start: 0.9567 (tt0) cc_final: 0.8898 (pp20) REVERT: A 667 LYS cc_start: 0.9540 (mtpt) cc_final: 0.9265 (ptpt) REVERT: A 677 LEU cc_start: 0.9324 (pt) cc_final: 0.9076 (pt) REVERT: A 684 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8486 (tm-30) REVERT: A 729 TYR cc_start: 0.8317 (m-80) cc_final: 0.7698 (m-80) REVERT: A 731 GLU cc_start: 0.8898 (tp30) cc_final: 0.8580 (tm-30) REVERT: A 732 LYS cc_start: 0.9180 (tmtt) cc_final: 0.8938 (tptp) REVERT: A 733 MET cc_start: 0.9331 (ttm) cc_final: 0.8642 (tmm) REVERT: A 737 MET cc_start: 0.7998 (ttm) cc_final: 0.7677 (ttm) REVERT: A 738 GLU cc_start: 0.8802 (tp30) cc_final: 0.7968 (tm-30) REVERT: A 802 SER cc_start: 0.9228 (p) cc_final: 0.8854 (m) REVERT: A 817 HIS cc_start: 0.9296 (m90) cc_final: 0.9058 (m90) REVERT: A 828 LYS cc_start: 0.9441 (tttt) cc_final: 0.8898 (tptp) REVERT: A 847 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8550 (mp0) REVERT: A 863 MET cc_start: 0.7910 (tpt) cc_final: 0.7553 (tpt) REVERT: A 911 MET cc_start: 0.8577 (ptm) cc_final: 0.8353 (ptm) REVERT: A 912 LYS cc_start: 0.9781 (pptt) cc_final: 0.9559 (pptt) REVERT: A 995 LYS cc_start: 0.8508 (ttmm) cc_final: 0.7689 (ttmm) REVERT: A 1003 THR cc_start: 0.9385 (p) cc_final: 0.8935 (t) REVERT: A 1024 PHE cc_start: 0.9101 (m-80) cc_final: 0.8856 (m-80) REVERT: B 129 LEU cc_start: 0.8735 (mp) cc_final: 0.8477 (mp) REVERT: B 197 LEU cc_start: 0.8990 (mt) cc_final: 0.8765 (tt) REVERT: B 219 LEU cc_start: 0.9090 (tp) cc_final: 0.8816 (tp) REVERT: B 253 HIS cc_start: 0.8517 (t-90) cc_final: 0.8274 (t-90) REVERT: C 454 PHE cc_start: 0.7454 (t80) cc_final: 0.6985 (t80) REVERT: C 473 MET cc_start: 0.5278 (ttt) cc_final: 0.4208 (ttt) REVERT: C 522 LEU cc_start: 0.9234 (mt) cc_final: 0.8666 (mp) REVERT: C 526 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8386 (mt-10) REVERT: C 530 LEU cc_start: 0.9370 (mt) cc_final: 0.9143 (mt) REVERT: C 594 MET cc_start: 0.9246 (mmm) cc_final: 0.8223 (mmm) REVERT: C 598 ARG cc_start: 0.9603 (mmt-90) cc_final: 0.9263 (mmp80) REVERT: C 606 MET cc_start: 0.8897 (ptt) cc_final: 0.8122 (ppp) REVERT: C 616 LYS cc_start: 0.9545 (ptmt) cc_final: 0.9027 (ptmt) REVERT: C 680 MET cc_start: 0.9247 (pmm) cc_final: 0.8785 (pmm) REVERT: C 700 GLU cc_start: 0.9272 (tt0) cc_final: 0.8612 (tm-30) REVERT: C 733 MET cc_start: 0.9286 (mmt) cc_final: 0.8962 (mmm) REVERT: C 737 MET cc_start: 0.9156 (tmm) cc_final: 0.8598 (tmm) REVERT: C 807 MET cc_start: 0.9255 (tmm) cc_final: 0.9034 (tmm) REVERT: C 875 TYR cc_start: 0.9401 (t80) cc_final: 0.9145 (t80) REVERT: C 878 ARG cc_start: 0.9204 (mtt90) cc_final: 0.8684 (ptp-110) REVERT: C 911 MET cc_start: 0.8535 (tpt) cc_final: 0.7634 (tpp) REVERT: C 938 PHE cc_start: 0.9347 (t80) cc_final: 0.9073 (t80) REVERT: D 1 MET cc_start: 0.8163 (mtm) cc_final: 0.7650 (mpp) REVERT: D 65 ASN cc_start: 0.9515 (p0) cc_final: 0.9245 (p0) REVERT: D 161 TYR cc_start: 0.8208 (m-10) cc_final: 0.7931 (m-10) REVERT: D 347 GLN cc_start: 0.8931 (tt0) cc_final: 0.8573 (tm-30) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1550 time to fit residues: 55.0375 Evaluate side-chains 183 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 15 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.062524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.041313 restraints weight = 209526.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.043359 restraints weight = 98761.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.044707 restraints weight = 61388.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045602 restraints weight = 44409.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046246 restraints weight = 35540.253| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17999 Z= 0.171 Angle : 0.699 9.314 24728 Z= 0.375 Chirality : 0.043 0.176 2694 Planarity : 0.005 0.064 2854 Dihedral : 22.092 179.763 3229 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.18 % Allowed : 2.42 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.18), residues: 1921 helix: -0.47 (0.19), residues: 661 sheet: -1.43 (0.28), residues: 336 loop : -2.00 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 778 TYR 0.034 0.002 TYR B 107 PHE 0.016 0.002 PHE B 156 TRP 0.025 0.002 TRP C 915 HIS 0.012 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00369 (17992) covalent geometry : angle 0.69835 (24726) hydrogen bonds : bond 0.04778 ( 746) hydrogen bonds : angle 5.34294 ( 2107) metal coordination : bond 0.00734 ( 7) metal coordination : angle 2.91972 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 TYR cc_start: 0.8973 (t80) cc_final: 0.8632 (t80) REVERT: A 503 MET cc_start: 0.9147 (ppp) cc_final: 0.8945 (ppp) REVERT: A 526 GLU cc_start: 0.9003 (pm20) cc_final: 0.8743 (pm20) REVERT: A 578 TYR cc_start: 0.8800 (t80) cc_final: 0.8597 (t80) REVERT: A 667 LYS cc_start: 0.9573 (mtpt) cc_final: 0.9342 (ptpt) REVERT: A 675 ARG cc_start: 0.8593 (mtp180) cc_final: 0.8363 (mtp180) REVERT: A 684 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8157 (tm-30) REVERT: A 731 GLU cc_start: 0.9084 (tp30) cc_final: 0.8490 (tm-30) REVERT: A 732 LYS cc_start: 0.9187 (tmtt) cc_final: 0.8845 (tptp) REVERT: A 733 MET cc_start: 0.9351 (ttm) cc_final: 0.8125 (tmm) REVERT: A 737 MET cc_start: 0.8016 (ttm) cc_final: 0.7133 (ttm) REVERT: A 738 GLU cc_start: 0.8897 (tp30) cc_final: 0.8106 (tm-30) REVERT: A 802 SER cc_start: 0.9260 (p) cc_final: 0.8924 (m) REVERT: A 817 HIS cc_start: 0.9250 (m90) cc_final: 0.9006 (m90) REVERT: A 831 GLN cc_start: 0.9294 (tt0) cc_final: 0.8824 (tm-30) REVERT: A 847 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8573 (mp0) REVERT: A 904 LEU cc_start: 0.9071 (mt) cc_final: 0.8795 (mt) REVERT: A 912 LYS cc_start: 0.9795 (pptt) cc_final: 0.9561 (pptt) REVERT: A 987 ASN cc_start: 0.9387 (p0) cc_final: 0.9164 (p0) REVERT: A 995 LYS cc_start: 0.8400 (ttmm) cc_final: 0.7635 (ttmm) REVERT: A 1006 LEU cc_start: 0.9593 (tp) cc_final: 0.9341 (tp) REVERT: A 1024 PHE cc_start: 0.9102 (m-80) cc_final: 0.8825 (m-80) REVERT: B 197 LEU cc_start: 0.9001 (mt) cc_final: 0.8665 (tt) REVERT: B 219 LEU cc_start: 0.9095 (tp) cc_final: 0.8889 (tp) REVERT: B 253 HIS cc_start: 0.8598 (t-90) cc_final: 0.8362 (t-90) REVERT: C 522 LEU cc_start: 0.9268 (mt) cc_final: 0.8996 (mp) REVERT: C 594 MET cc_start: 0.9262 (mmm) cc_final: 0.8284 (mmm) REVERT: C 598 ARG cc_start: 0.9641 (mmt-90) cc_final: 0.9297 (mmp80) REVERT: C 606 MET cc_start: 0.8884 (ptt) cc_final: 0.8165 (ppp) REVERT: C 616 LYS cc_start: 0.9579 (ptmt) cc_final: 0.9084 (ptmt) REVERT: C 680 MET cc_start: 0.9280 (pmm) cc_final: 0.8784 (pmm) REVERT: C 700 GLU cc_start: 0.9290 (tt0) cc_final: 0.8568 (tm-30) REVERT: C 733 MET cc_start: 0.9369 (mmt) cc_final: 0.9038 (mmp) REVERT: C 737 MET cc_start: 0.9138 (tmm) cc_final: 0.8588 (tmm) REVERT: C 807 MET cc_start: 0.9238 (tmm) cc_final: 0.8930 (tmm) REVERT: C 874 ASN cc_start: 0.8993 (p0) cc_final: 0.8603 (p0) REVERT: C 875 TYR cc_start: 0.9397 (t80) cc_final: 0.9130 (t80) REVERT: C 878 ARG cc_start: 0.9196 (mtt90) cc_final: 0.8662 (ptp-110) REVERT: C 938 PHE cc_start: 0.9323 (t80) cc_final: 0.8983 (t80) REVERT: C 1010 LEU cc_start: 0.9811 (tp) cc_final: 0.9605 (tp) REVERT: C 1013 HIS cc_start: 0.9503 (t-90) cc_final: 0.8817 (t-170) REVERT: C 1026 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8730 (tp30) REVERT: D 1 MET cc_start: 0.7890 (mtm) cc_final: 0.7505 (mpp) REVERT: D 65 ASN cc_start: 0.9509 (p0) cc_final: 0.9253 (p0) REVERT: D 173 ASN cc_start: 0.9323 (m-40) cc_final: 0.8931 (m-40) REVERT: D 347 GLN cc_start: 0.8939 (tt0) cc_final: 0.8584 (tm-30) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1569 time to fit residues: 53.5074 Evaluate side-chains 188 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 83 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 185 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 195 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN B 99 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** 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 = 0.3355 r_free = 0.3355 target = 0.060596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.039663 restraints weight = 240444.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.041646 restraints weight = 110963.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.042994 restraints weight = 68694.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.043900 restraints weight = 49404.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.044520 restraints weight = 39151.484| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 17999 Z= 0.240 Angle : 0.746 10.784 24728 Z= 0.398 Chirality : 0.043 0.215 2694 Planarity : 0.005 0.063 2854 Dihedral : 22.076 179.504 3229 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.24 % Allowed : 2.24 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.18), residues: 1921 helix: -0.47 (0.19), residues: 669 sheet: -1.44 (0.28), residues: 337 loop : -2.01 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 235 TYR 0.023 0.002 TYR B 90 PHE 0.034 0.002 PHE A 826 TRP 0.024 0.002 TRP C 915 HIS 0.013 0.002 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00506 (17992) covalent geometry : angle 0.74591 (24726) hydrogen bonds : bond 0.05159 ( 746) hydrogen bonds : angle 5.43439 ( 2107) metal coordination : bond 0.01127 ( 7) metal coordination : angle 2.87957 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 TYR cc_start: 0.8959 (t80) cc_final: 0.8625 (t80) REVERT: A 503 MET cc_start: 0.9210 (ppp) cc_final: 0.8988 (ppp) REVERT: A 522 LEU cc_start: 0.9758 (mt) cc_final: 0.9542 (mt) REVERT: A 526 GLU cc_start: 0.9024 (pm20) cc_final: 0.8816 (pm20) REVERT: A 590 GLU cc_start: 0.9554 (tt0) cc_final: 0.9099 (pp20) REVERT: A 622 MET cc_start: 0.8961 (mmm) cc_final: 0.8584 (mmt) REVERT: A 667 LYS cc_start: 0.9553 (mtpt) cc_final: 0.9336 (ptpt) REVERT: A 684 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8527 (tm-30) REVERT: A 700 GLU cc_start: 0.9472 (pt0) cc_final: 0.9271 (pt0) REVERT: A 731 GLU cc_start: 0.9083 (tp30) cc_final: 0.8716 (tt0) REVERT: A 733 MET cc_start: 0.9350 (ttm) cc_final: 0.8334 (tmm) REVERT: A 737 MET cc_start: 0.7862 (ttm) cc_final: 0.7282 (ttm) REVERT: A 738 GLU cc_start: 0.8810 (tp30) cc_final: 0.7838 (tm-30) REVERT: A 802 SER cc_start: 0.9176 (p) cc_final: 0.8833 (t) REVERT: A 817 HIS cc_start: 0.9301 (m90) cc_final: 0.9078 (m90) REVERT: A 831 GLN cc_start: 0.9276 (tt0) cc_final: 0.8848 (tm-30) REVERT: A 847 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8569 (mp0) REVERT: A 863 MET cc_start: 0.7700 (tpt) cc_final: 0.7365 (tpt) REVERT: A 912 LYS cc_start: 0.9782 (pptt) cc_final: 0.9516 (pptt) REVERT: A 995 LYS cc_start: 0.8499 (ttmm) cc_final: 0.7706 (ttmm) REVERT: A 1006 LEU cc_start: 0.9604 (tp) cc_final: 0.9312 (tp) REVERT: A 1024 PHE cc_start: 0.9059 (m-80) cc_final: 0.8812 (m-80) REVERT: B 197 LEU cc_start: 0.9074 (mt) cc_final: 0.8834 (tp) REVERT: B 219 LEU cc_start: 0.9100 (tp) cc_final: 0.8787 (tp) REVERT: C 522 LEU cc_start: 0.9328 (mt) cc_final: 0.9042 (mp) REVERT: C 527 LYS cc_start: 0.9541 (mttt) cc_final: 0.9305 (mtmm) REVERT: C 594 MET cc_start: 0.9353 (mmm) cc_final: 0.8475 (mmm) REVERT: C 598 ARG cc_start: 0.9619 (mmt-90) cc_final: 0.9296 (mmp80) REVERT: C 606 MET cc_start: 0.8911 (ptt) cc_final: 0.8436 (ppp) REVERT: C 616 LYS cc_start: 0.9546 (ptmt) cc_final: 0.8677 (ptmt) REVERT: C 680 MET cc_start: 0.9342 (pmm) cc_final: 0.8815 (pmm) REVERT: C 700 GLU cc_start: 0.9352 (tt0) cc_final: 0.8672 (tm-30) REVERT: C 733 MET cc_start: 0.9313 (mmt) cc_final: 0.9025 (mmm) REVERT: C 737 MET cc_start: 0.9183 (tmm) cc_final: 0.8747 (tmm) REVERT: C 878 ARG cc_start: 0.9260 (mtt90) cc_final: 0.8690 (ptp-110) REVERT: C 911 MET cc_start: 0.8626 (tpt) cc_final: 0.8339 (tpp) REVERT: C 938 PHE cc_start: 0.9326 (t80) cc_final: 0.9031 (t80) REVERT: C 1010 LEU cc_start: 0.9804 (tp) cc_final: 0.9599 (tp) REVERT: C 1013 HIS cc_start: 0.9410 (t-90) cc_final: 0.8768 (t-170) REVERT: D 1 MET cc_start: 0.7930 (mtm) cc_final: 0.7628 (mpp) REVERT: D 65 ASN cc_start: 0.9523 (p0) cc_final: 0.9264 (p0) REVERT: D 72 LEU cc_start: 0.9431 (mp) cc_final: 0.9229 (mp) REVERT: D 161 TYR cc_start: 0.8271 (m-10) cc_final: 0.7964 (m-10) REVERT: D 347 GLN cc_start: 0.8869 (tt0) cc_final: 0.8528 (tm-30) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.1527 time to fit residues: 51.7394 Evaluate side-chains 184 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 196 optimal weight: 30.0000 chunk 76 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN B 278 GLN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 ASN ** D 278 GLN ** 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 = 0.3429 r_free = 0.3429 target = 0.063685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.042503 restraints weight = 189509.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.044498 restraints weight = 92577.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045807 restraints weight = 58597.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.046704 restraints weight = 43029.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047304 restraints weight = 34748.103| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17999 Z= 0.141 Angle : 0.688 9.247 24728 Z= 0.365 Chirality : 0.043 0.192 2694 Planarity : 0.005 0.062 2854 Dihedral : 21.965 179.800 3229 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.24 % Allowed : 1.59 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.18), residues: 1921 helix: -0.18 (0.20), residues: 669 sheet: -1.18 (0.28), residues: 334 loop : -1.94 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 523 TYR 0.032 0.002 TYR B 107 PHE 0.026 0.001 PHE A 826 TRP 0.025 0.002 TRP C 560 HIS 0.009 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00306 (17992) covalent geometry : angle 0.68513 (24726) hydrogen bonds : bond 0.04465 ( 746) hydrogen bonds : angle 5.12447 ( 2107) metal coordination : bond 0.01656 ( 7) metal coordination : angle 6.52329 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 CYS cc_start: 0.9451 (m) cc_final: 0.9203 (m) REVERT: A 500 TYR cc_start: 0.8973 (t80) cc_final: 0.8633 (t80) REVERT: A 522 LEU cc_start: 0.9745 (mt) cc_final: 0.9514 (mt) REVERT: A 526 GLU cc_start: 0.9019 (pm20) cc_final: 0.8780 (pm20) REVERT: A 578 TYR cc_start: 0.8776 (t80) cc_final: 0.8557 (t80) REVERT: A 590 GLU cc_start: 0.9571 (tt0) cc_final: 0.9189 (pp20) REVERT: A 622 MET cc_start: 0.8849 (mmm) cc_final: 0.8375 (mmt) REVERT: A 647 MET cc_start: 0.8695 (mmm) cc_final: 0.8430 (mmm) REVERT: A 667 LYS cc_start: 0.9578 (mtpt) cc_final: 0.9333 (ptpt) REVERT: A 684 GLU cc_start: 0.8701 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 731 GLU cc_start: 0.9068 (tp30) cc_final: 0.8484 (tm-30) REVERT: A 732 LYS cc_start: 0.9197 (tmtt) cc_final: 0.8809 (tptt) REVERT: A 733 MET cc_start: 0.9304 (ttm) cc_final: 0.7941 (tmm) REVERT: A 736 GLU cc_start: 0.9166 (pp20) cc_final: 0.7737 (pp20) REVERT: A 737 MET cc_start: 0.7696 (ttm) cc_final: 0.7328 (ttm) REVERT: A 738 GLU cc_start: 0.8780 (tp30) cc_final: 0.7768 (tm-30) REVERT: A 802 SER cc_start: 0.9096 (p) cc_final: 0.8730 (m) REVERT: A 817 HIS cc_start: 0.9207 (m90) cc_final: 0.8927 (m90) REVERT: A 831 GLN cc_start: 0.9239 (tt0) cc_final: 0.8737 (tm-30) REVERT: A 847 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8558 (mp0) REVERT: A 859 LEU cc_start: 0.9439 (mt) cc_final: 0.9180 (pp) REVERT: A 863 MET cc_start: 0.7670 (tpt) cc_final: 0.7286 (tpt) REVERT: A 912 LYS cc_start: 0.9789 (pptt) cc_final: 0.9512 (pptt) REVERT: A 987 ASN cc_start: 0.9619 (p0) cc_final: 0.9414 (p0) REVERT: A 995 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8275 (tppt) REVERT: A 1006 LEU cc_start: 0.9581 (tp) cc_final: 0.9325 (tp) REVERT: A 1024 PHE cc_start: 0.9053 (m-80) cc_final: 0.8826 (m-80) REVERT: B 197 LEU cc_start: 0.8984 (mt) cc_final: 0.8724 (tp) REVERT: B 219 LEU cc_start: 0.9060 (tp) cc_final: 0.8835 (tp) REVERT: B 253 HIS cc_start: 0.8603 (t-90) cc_final: 0.8374 (t-90) REVERT: B 285 MET cc_start: 0.7832 (tpp) cc_final: 0.7581 (tpp) REVERT: C 454 PHE cc_start: 0.7472 (t80) cc_final: 0.7156 (t80) REVERT: C 594 MET cc_start: 0.9313 (mmm) cc_final: 0.8481 (mmm) REVERT: C 598 ARG cc_start: 0.9594 (mmt-90) cc_final: 0.9336 (mmp80) REVERT: C 606 MET cc_start: 0.8798 (ptt) cc_final: 0.8071 (ppp) REVERT: C 616 LYS cc_start: 0.9585 (ptmt) cc_final: 0.8699 (ptmt) REVERT: C 680 MET cc_start: 0.9309 (pmm) cc_final: 0.8800 (pmm) REVERT: C 700 GLU cc_start: 0.9309 (tt0) cc_final: 0.8522 (tm-30) REVERT: C 733 MET cc_start: 0.9369 (mmt) cc_final: 0.9067 (mmp) REVERT: C 737 MET cc_start: 0.9113 (tmm) cc_final: 0.8905 (tmm) REVERT: C 874 ASN cc_start: 0.8973 (p0) cc_final: 0.8541 (p0) REVERT: C 875 TYR cc_start: 0.9413 (t80) cc_final: 0.9149 (t80) REVERT: C 878 ARG cc_start: 0.9226 (mtt90) cc_final: 0.8673 (ptp-110) REVERT: C 911 MET cc_start: 0.8705 (tpt) cc_final: 0.8297 (tpp) REVERT: C 938 PHE cc_start: 0.9338 (t80) cc_final: 0.9024 (t80) REVERT: C 1013 HIS cc_start: 0.9363 (t-90) cc_final: 0.8774 (t-170) REVERT: C 1026 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8766 (tp30) REVERT: D 1 MET cc_start: 0.7816 (mtm) cc_final: 0.7570 (mpp) REVERT: D 65 ASN cc_start: 0.9502 (p0) cc_final: 0.9227 (p0) REVERT: D 161 TYR cc_start: 0.8279 (m-10) cc_final: 0.8011 (m-10) REVERT: D 347 GLN cc_start: 0.8847 (tt0) cc_final: 0.8509 (tm-30) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.1553 time to fit residues: 57.8849 Evaluate side-chains 195 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 chunk 171 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 196 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 chunk 153 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 983 ASN A 997 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** 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 = 0.3404 r_free = 0.3404 target = 0.062656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.041505 restraints weight = 196828.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.043496 restraints weight = 94739.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.044800 restraints weight = 59539.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.045679 restraints weight = 43510.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046282 restraints weight = 35078.887| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17999 Z= 0.169 Angle : 0.693 8.939 24728 Z= 0.371 Chirality : 0.042 0.176 2694 Planarity : 0.005 0.064 2854 Dihedral : 21.871 179.673 3229 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.18 % Allowed : 1.06 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.18), residues: 1921 helix: -0.10 (0.20), residues: 661 sheet: -1.14 (0.28), residues: 338 loop : -1.89 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 523 TYR 0.016 0.002 TYR A1020 PHE 0.028 0.002 PHE A 826 TRP 0.021 0.002 TRP C 560 HIS 0.010 0.001 HIS A 959 Details of bonding type rmsd covalent geometry : bond 0.00364 (17992) covalent geometry : angle 0.69090 (24726) hydrogen bonds : bond 0.04604 ( 746) hydrogen bonds : angle 5.10276 ( 2107) metal coordination : bond 0.00794 ( 7) metal coordination : angle 6.24625 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 CYS cc_start: 0.9480 (m) cc_final: 0.9263 (m) REVERT: A 526 GLU cc_start: 0.9124 (pm20) cc_final: 0.8917 (pm20) REVERT: A 578 TYR cc_start: 0.8869 (t80) cc_final: 0.8492 (t80) REVERT: A 590 GLU cc_start: 0.9597 (tt0) cc_final: 0.9059 (tp30) REVERT: A 667 LYS cc_start: 0.9602 (mtpt) cc_final: 0.9363 (ptpt) REVERT: A 684 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8421 (tm-30) REVERT: A 731 GLU cc_start: 0.9122 (tp30) cc_final: 0.8630 (tt0) REVERT: A 733 MET cc_start: 0.9319 (ttm) cc_final: 0.7963 (tmm) REVERT: A 736 GLU cc_start: 0.9264 (pp20) cc_final: 0.8341 (pp20) REVERT: A 737 MET cc_start: 0.7938 (ttm) cc_final: 0.7507 (ttm) REVERT: A 738 GLU cc_start: 0.8866 (tp30) cc_final: 0.7823 (tm-30) REVERT: A 802 SER cc_start: 0.9163 (p) cc_final: 0.8869 (t) REVERT: A 831 GLN cc_start: 0.9211 (tt0) cc_final: 0.8726 (tm-30) REVERT: A 847 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8585 (mp0) REVERT: A 912 LYS cc_start: 0.9795 (pptt) cc_final: 0.9516 (pptt) REVERT: A 933 TYR cc_start: 0.8943 (m-80) cc_final: 0.8723 (m-80) REVERT: A 995 LYS cc_start: 0.8539 (ttmm) cc_final: 0.8171 (pttt) REVERT: A 1006 LEU cc_start: 0.9584 (tp) cc_final: 0.9305 (tp) REVERT: A 1024 PHE cc_start: 0.9065 (m-80) cc_final: 0.8831 (m-80) REVERT: B 1 MET cc_start: 0.6826 (ttm) cc_final: 0.6166 (pmm) REVERT: B 197 LEU cc_start: 0.9064 (mt) cc_final: 0.8769 (tp) REVERT: B 219 LEU cc_start: 0.9111 (tp) cc_final: 0.8796 (tp) REVERT: B 253 HIS cc_start: 0.8674 (t-90) cc_final: 0.8458 (t-90) REVERT: C 454 PHE cc_start: 0.7494 (t80) cc_final: 0.7072 (t80) REVERT: C 523 ARG cc_start: 0.9130 (mmm160) cc_final: 0.8643 (mmm-85) REVERT: C 527 LYS cc_start: 0.9522 (mttt) cc_final: 0.9215 (mtmm) REVERT: C 594 MET cc_start: 0.9330 (mmm) cc_final: 0.8512 (mmm) REVERT: C 598 ARG cc_start: 0.9635 (mmt-90) cc_final: 0.9317 (mmp80) REVERT: C 616 LYS cc_start: 0.9566 (ptmt) cc_final: 0.9049 (ptmt) REVERT: C 680 MET cc_start: 0.9330 (pmm) cc_final: 0.8794 (pmm) REVERT: C 700 GLU cc_start: 0.9336 (tt0) cc_final: 0.8622 (tm-30) REVERT: C 733 MET cc_start: 0.9398 (mmt) cc_final: 0.9114 (mmm) REVERT: C 737 MET cc_start: 0.9090 (tmm) cc_final: 0.8869 (tmm) REVERT: C 875 TYR cc_start: 0.9410 (t80) cc_final: 0.9138 (t80) REVERT: C 878 ARG cc_start: 0.9243 (mtt90) cc_final: 0.8643 (ptp-110) REVERT: C 938 PHE cc_start: 0.9364 (t80) cc_final: 0.9082 (t80) REVERT: C 1013 HIS cc_start: 0.9478 (t-90) cc_final: 0.8787 (t-170) REVERT: C 1026 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8754 (tp30) REVERT: D 1 MET cc_start: 0.7885 (mtm) cc_final: 0.7659 (mpp) REVERT: D 65 ASN cc_start: 0.9551 (p0) cc_final: 0.9283 (p0) REVERT: D 161 TYR cc_start: 0.8343 (m-10) cc_final: 0.8026 (m-10) REVERT: D 285 MET cc_start: 0.7698 (mmp) cc_final: 0.6625 (tpt) REVERT: D 347 GLN cc_start: 0.8868 (tt0) cc_final: 0.8549 (tm-30) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1510 time to fit residues: 52.8438 Evaluate side-chains 191 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 178 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 187 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 188 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 687 HIS A1013 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 687 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** 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 = 0.3396 r_free = 0.3396 target = 0.062375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.040430 restraints weight = 266375.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042634 restraints weight = 111866.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.044100 restraints weight = 66738.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.045112 restraints weight = 46914.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045783 restraints weight = 36920.311| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17999 Z= 0.184 Angle : 0.702 10.031 24728 Z= 0.375 Chirality : 0.042 0.206 2694 Planarity : 0.005 0.068 2854 Dihedral : 21.837 179.613 3229 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.24 % Allowed : 0.83 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.18), residues: 1921 helix: -0.13 (0.20), residues: 668 sheet: -1.09 (0.28), residues: 331 loop : -1.87 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 523 TYR 0.016 0.002 TYR A1020 PHE 0.025 0.002 PHE A 826 TRP 0.022 0.002 TRP C 560 HIS 0.010 0.002 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00396 (17992) covalent geometry : angle 0.70066 (24726) hydrogen bonds : bond 0.04551 ( 746) hydrogen bonds : angle 5.14601 ( 2107) metal coordination : bond 0.01293 ( 7) metal coordination : angle 4.22126 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LEU cc_start: 0.9235 (mt) cc_final: 0.8857 (pp) REVERT: A 497 CYS cc_start: 0.9475 (m) cc_final: 0.9257 (m) REVERT: A 526 GLU cc_start: 0.8899 (pm20) cc_final: 0.8641 (pm20) REVERT: A 590 GLU cc_start: 0.9586 (tt0) cc_final: 0.9060 (tp30) REVERT: A 647 MET cc_start: 0.8524 (mmm) cc_final: 0.8237 (mmm) REVERT: A 667 LYS cc_start: 0.9565 (mtpt) cc_final: 0.9357 (ptpt) REVERT: A 731 GLU cc_start: 0.9080 (tp30) cc_final: 0.8751 (tt0) REVERT: A 733 MET cc_start: 0.9251 (ttm) cc_final: 0.8915 (ttp) REVERT: A 738 GLU cc_start: 0.8813 (tp30) cc_final: 0.7817 (tm-30) REVERT: A 802 SER cc_start: 0.9284 (p) cc_final: 0.8894 (t) REVERT: A 817 HIS cc_start: 0.9095 (m90) cc_final: 0.8720 (m-70) REVERT: A 831 GLN cc_start: 0.9207 (tt0) cc_final: 0.8697 (tm-30) REVERT: A 847 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8583 (mp0) REVERT: A 859 LEU cc_start: 0.9338 (mt) cc_final: 0.9138 (pp) REVERT: A 1006 LEU cc_start: 0.9609 (tp) cc_final: 0.9313 (tp) REVERT: A 1024 PHE cc_start: 0.9020 (m-80) cc_final: 0.8800 (m-80) REVERT: B 197 LEU cc_start: 0.9078 (mt) cc_final: 0.8740 (tp) REVERT: B 219 LEU cc_start: 0.9071 (tp) cc_final: 0.8766 (tp) REVERT: B 253 HIS cc_start: 0.8688 (t-90) cc_final: 0.8465 (t-90) REVERT: B 280 GLU cc_start: 0.9194 (tp30) cc_final: 0.8698 (tp30) REVERT: C 454 PHE cc_start: 0.7319 (t80) cc_final: 0.7031 (t80) REVERT: C 527 LYS cc_start: 0.9629 (mttt) cc_final: 0.9426 (UNCLASSIFIED) REVERT: C 594 MET cc_start: 0.9357 (mmm) cc_final: 0.8605 (mmm) REVERT: C 598 ARG cc_start: 0.9604 (mmt-90) cc_final: 0.9311 (mmp80) REVERT: C 606 MET cc_start: 0.9067 (ptt) cc_final: 0.8423 (ppp) REVERT: C 616 LYS cc_start: 0.9540 (ptmt) cc_final: 0.8608 (ptmt) REVERT: C 680 MET cc_start: 0.9262 (pmm) cc_final: 0.8672 (pmm) REVERT: C 700 GLU cc_start: 0.9328 (tt0) cc_final: 0.8568 (tm-30) REVERT: C 705 MET cc_start: 0.9246 (mmt) cc_final: 0.8870 (mpp) REVERT: C 733 MET cc_start: 0.9362 (mmt) cc_final: 0.9071 (mmm) REVERT: C 737 MET cc_start: 0.9111 (tmm) cc_final: 0.8875 (tmm) REVERT: C 869 MET cc_start: 0.0016 (ppp) cc_final: -0.1202 (mpp) REVERT: C 875 TYR cc_start: 0.9403 (t80) cc_final: 0.9130 (t80) REVERT: C 878 ARG cc_start: 0.9274 (mtt90) cc_final: 0.8706 (ptp-110) REVERT: C 911 MET cc_start: 0.8619 (tpt) cc_final: 0.8334 (tpp) REVERT: C 938 PHE cc_start: 0.9343 (t80) cc_final: 0.9076 (t80) REVERT: C 1013 HIS cc_start: 0.9447 (t-90) cc_final: 0.8768 (t-170) REVERT: C 1026 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8777 (tp30) REVERT: D 1 MET cc_start: 0.7853 (mtm) cc_final: 0.7624 (mpp) REVERT: D 65 ASN cc_start: 0.9526 (p0) cc_final: 0.9234 (p0) REVERT: D 161 TYR cc_start: 0.8333 (m-10) cc_final: 0.8066 (m-10) REVERT: D 347 GLN cc_start: 0.8863 (tt0) cc_final: 0.8536 (tm-30) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.1488 time to fit residues: 51.2740 Evaluate side-chains 183 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 171 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 170 optimal weight: 8.9990 chunk 50 optimal weight: 0.0370 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 174 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 85 optimal weight: 0.0030 overall best weight: 0.9270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 HIS B 99 ASN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** 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 = 0.3448 r_free = 0.3448 target = 0.064578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.042955 restraints weight = 233344.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.045159 restraints weight = 105131.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.046627 restraints weight = 63900.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047604 restraints weight = 45474.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048298 restraints weight = 35910.770| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17999 Z= 0.140 Angle : 0.694 10.024 24728 Z= 0.367 Chirality : 0.043 0.209 2694 Planarity : 0.005 0.063 2854 Dihedral : 21.720 179.976 3229 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.18 % Allowed : 0.41 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.19), residues: 1921 helix: -0.08 (0.20), residues: 670 sheet: -0.87 (0.28), residues: 351 loop : -1.80 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 523 TYR 0.019 0.002 TYR A 729 PHE 0.027 0.001 PHE A 826 TRP 0.025 0.002 TRP C 560 HIS 0.008 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00304 (17992) covalent geometry : angle 0.69120 (24726) hydrogen bonds : bond 0.04384 ( 746) hydrogen bonds : angle 5.02139 ( 2107) metal coordination : bond 0.01111 ( 7) metal coordination : angle 7.20782 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LEU cc_start: 0.9246 (mt) cc_final: 0.8957 (pp) REVERT: A 526 GLU cc_start: 0.8977 (pm20) cc_final: 0.8761 (pm20) REVERT: A 578 TYR cc_start: 0.8718 (t80) cc_final: 0.8453 (t80) REVERT: A 590 GLU cc_start: 0.9571 (tt0) cc_final: 0.9118 (tp30) REVERT: A 622 MET cc_start: 0.8586 (mmm) cc_final: 0.8137 (mmt) REVERT: A 684 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8595 (tm-30) REVERT: A 705 MET cc_start: 0.8705 (tmm) cc_final: 0.8495 (tmm) REVERT: A 731 GLU cc_start: 0.9124 (tp30) cc_final: 0.8708 (tt0) REVERT: A 733 MET cc_start: 0.9181 (ttm) cc_final: 0.8100 (tmm) REVERT: A 736 GLU cc_start: 0.9491 (pp20) cc_final: 0.8767 (pp20) REVERT: A 738 GLU cc_start: 0.8753 (tp30) cc_final: 0.7769 (tm-30) REVERT: A 802 SER cc_start: 0.9234 (p) cc_final: 0.8828 (t) REVERT: A 831 GLN cc_start: 0.9173 (tt0) cc_final: 0.8676 (tm-30) REVERT: A 847 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8612 (mp0) REVERT: A 859 LEU cc_start: 0.9333 (mt) cc_final: 0.9072 (pp) REVERT: A 912 LYS cc_start: 0.9365 (ptpp) cc_final: 0.9094 (ptpt) REVERT: A 997 ASN cc_start: 0.7415 (m110) cc_final: 0.7109 (m110) REVERT: A 1006 LEU cc_start: 0.9603 (tp) cc_final: 0.9345 (tp) REVERT: A 1008 ASP cc_start: 0.8589 (m-30) cc_final: 0.8345 (m-30) REVERT: A 1024 PHE cc_start: 0.9019 (m-80) cc_final: 0.8817 (m-80) REVERT: B 1 MET cc_start: 0.6415 (ptm) cc_final: 0.6008 (ttt) REVERT: B 84 ASP cc_start: 0.9031 (m-30) cc_final: 0.8686 (t70) REVERT: B 142 LEU cc_start: 0.9015 (tt) cc_final: 0.8776 (pt) REVERT: B 197 LEU cc_start: 0.9014 (mt) cc_final: 0.8660 (tp) REVERT: B 219 LEU cc_start: 0.9084 (tp) cc_final: 0.8875 (tp) REVERT: B 253 HIS cc_start: 0.8663 (t-90) cc_final: 0.8453 (t-90) REVERT: B 280 GLU cc_start: 0.9203 (tp30) cc_final: 0.8755 (tp30) REVERT: C 454 PHE cc_start: 0.7318 (t80) cc_final: 0.7068 (t80) REVERT: C 526 GLU cc_start: 0.8679 (pm20) cc_final: 0.8399 (pm20) REVERT: C 527 LYS cc_start: 0.9631 (mttt) cc_final: 0.9197 (UNCLASSIFIED) REVERT: C 594 MET cc_start: 0.9300 (mmm) cc_final: 0.8568 (mmm) REVERT: C 598 ARG cc_start: 0.9613 (mmt-90) cc_final: 0.9344 (mmp80) REVERT: C 606 MET cc_start: 0.9023 (ptt) cc_final: 0.8363 (ppp) REVERT: C 616 LYS cc_start: 0.9574 (ptmt) cc_final: 0.8607 (ptmt) REVERT: C 680 MET cc_start: 0.9299 (pmm) cc_final: 0.8842 (pmm) REVERT: C 700 GLU cc_start: 0.9303 (tt0) cc_final: 0.8440 (tm-30) REVERT: C 704 MET cc_start: 0.9015 (mmp) cc_final: 0.8792 (mmm) REVERT: C 705 MET cc_start: 0.9195 (mmt) cc_final: 0.8820 (mpp) REVERT: C 733 MET cc_start: 0.9375 (mmt) cc_final: 0.9031 (mmp) REVERT: C 737 MET cc_start: 0.9091 (tmm) cc_final: 0.8848 (tmm) REVERT: C 863 MET cc_start: 0.7314 (mtt) cc_final: 0.6923 (mtt) REVERT: C 869 MET cc_start: 0.0262 (ppp) cc_final: -0.1006 (mpp) REVERT: C 874 ASN cc_start: 0.8980 (p0) cc_final: 0.8534 (p0) REVERT: C 875 TYR cc_start: 0.9381 (t80) cc_final: 0.9100 (t80) REVERT: C 878 ARG cc_start: 0.9241 (mtt90) cc_final: 0.8651 (ptp-110) REVERT: C 911 MET cc_start: 0.8582 (tpt) cc_final: 0.8273 (tpp) REVERT: C 938 PHE cc_start: 0.9372 (t80) cc_final: 0.9063 (t80) REVERT: C 994 ARG cc_start: 0.8422 (ppt170) cc_final: 0.8219 (tmm-80) REVERT: C 1013 HIS cc_start: 0.9467 (t-90) cc_final: 0.8866 (t70) REVERT: C 1026 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8768 (tp30) REVERT: D 65 ASN cc_start: 0.9538 (p0) cc_final: 0.9270 (p0) REVERT: D 161 TYR cc_start: 0.8374 (m-10) cc_final: 0.8069 (m-10) REVERT: D 347 GLN cc_start: 0.8864 (tt0) cc_final: 0.8517 (tm-30) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1498 time to fit residues: 55.1616 Evaluate side-chains 199 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 123 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 HIS A 983 ASN A1013 HIS B 99 ASN B 117 ASN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.061565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.040291 restraints weight = 246562.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.042358 restraints weight = 110888.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.043784 restraints weight = 67595.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.044711 restraints weight = 48162.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.045354 restraints weight = 38235.757| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 17999 Z= 0.238 Angle : 0.740 9.706 24728 Z= 0.395 Chirality : 0.043 0.203 2694 Planarity : 0.006 0.069 2854 Dihedral : 21.764 179.191 3229 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.24 % Allowed : 0.41 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.18), residues: 1921 helix: -0.17 (0.20), residues: 668 sheet: -1.05 (0.28), residues: 337 loop : -1.83 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 523 TYR 0.023 0.002 TYR A 729 PHE 0.032 0.002 PHE A 494 TRP 0.021 0.003 TRP C 560 HIS 0.010 0.002 HIS A 959 Details of bonding type rmsd covalent geometry : bond 0.00501 (17992) covalent geometry : angle 0.73917 (24726) hydrogen bonds : bond 0.04851 ( 746) hydrogen bonds : angle 5.21920 ( 2107) metal coordination : bond 0.01425 ( 7) metal coordination : angle 3.93970 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3620.83 seconds wall clock time: 63 minutes 26.26 seconds (3806.26 seconds total)