Starting phenix.real_space_refine on Sat Sep 12 18:05:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbw_7852/09_2026/6dbw_7852_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbw_7852/09_2026/6dbw_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_7852/09_2026/6dbw_7852_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbw_7852/09_2026/6dbw_7852_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dbw_7852/09_2026/6dbw_7852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbw_7852/09_2026/6dbw_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 4.36, per 1000 atoms: 0.25 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: 1.67 Conformation dependent library (CDL) restraints added in 799.7 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: 2.06 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: 4.06 Time building geometry restraints manager: 2.17 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.900 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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= 0.456 Angle : 1.304 58.794 24728 Z= 0.901 Chirality : 0.064 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/Z covalent geometry : bond 0.00626 / 0.42 (17992) covalent geometry : angle 1.29936 / 0.90 (24726) hydrogen bonds : bond 0.15057 / 9.92 ( 746) hydrogen bonds : angle 7.15452 / 5.01 ( 2107) metal coordination : bond 0.27130 / 14.97 ( 7) metal coordination : angle 11.80133 / 4.87 ( 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 : 0.643 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: 0.8879 (pp) REVERT: A 522 LEU cc_start: 0.9609 (mt) cc_final: 0.9407 (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: 0.9042 (tm-30) REVERT: A 732 LYS cc_start: 0.9394 (ttpt) cc_final: 0.9179 (tmtt) REVERT: A 733 MET cc_start: 0.9203 (ttm) cc_final: 0.8878 (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: 0.8601 (t) REVERT: A 820 ILE cc_start: 0.9642 (mt) cc_final: 0.9193 (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: 0.8730 (tpp) REVERT: A 995 LYS cc_start: 0.9006 (mttp) cc_final: 0.8513 (mtpp) REVERT: A 1005 GLU cc_start: 0.9577 (pt0) cc_final: 0.9040 (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: 0.8332 (tp) REVERT: B 23 ASP cc_start: 0.9058 (t0) cc_final: 0.8833 (t0) REVERT: B 56 LYS cc_start: 0.9033 (mptp) cc_final: 0.8704 (mmtt) REVERT: B 84 ASP cc_start: 0.9344 (m-30) cc_final: 0.8900 (t70) REVERT: B 126 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8188 (tm-30) REVERT: B 129 LEU cc_start: 0.8928 (mt) cc_final: 0.8652 (pt) REVERT: B 197 LEU cc_start: 0.8955 (mt) cc_final: 0.8669 (tp) REVERT: B 227 ASP cc_start: 0.9389 (m-30) cc_final: 0.9077 (t0) REVERT: B 280 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9187 (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: 0.8481 (ptm) REVERT: C 519 LEU cc_start: 0.9188 (mt) cc_final: 0.8794 (tt) REVERT: C 527 LYS cc_start: 0.9517 (mttt) cc_final: 0.9199 (tptp) REVERT: C 560 TRP cc_start: 0.8638 (t60) cc_final: 0.8434 (t-100) REVERT: C 566 ASP cc_start: 0.9230 (m-30) cc_final: 0.8222 (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: 0.9409 (mmp80) REVERT: C 616 LYS cc_start: 0.9226 (ptmt) cc_final: 0.9024 (ptmt) REVERT: C 642 PHE cc_start: 0.8370 (t80) cc_final: 0.8169 (t80) REVERT: C 748 ILE cc_start: 0.9019 (pt) cc_final: 0.8806 (pt) REVERT: C 763 MET cc_start: 0.8393 (mtt) cc_final: 0.8143 (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: 0.8786 (pp) REVERT: C 871 MET cc_start: 0.7013 (ttp) cc_final: 0.6485 (ttm) REVERT: C 875 TYR cc_start: 0.8729 (t80) cc_final: 0.8341 (t80) REVERT: C 1007 GLU cc_start: 0.9234 (tt0) cc_final: 0.8575 (tp30) REVERT: D 65 ASN cc_start: 0.9394 (p0) cc_final: 0.9112 (p0) REVERT: D 84 ASP cc_start: 0.9276 (m-30) cc_final: 0.8608 (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: 0.1557 time to fit residues: 82.4178 Evaluate side-chains 225 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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: 20.0000 chunk 107 optimal weight: 30.0000 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: 10.0000 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 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 501 HIS C 520 HIS C 687 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN C 831 GLN C 927 GLN ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.062254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.041463 restraints weight = 216453.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.043399 restraints weight = 101633.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.044710 restraints weight = 63322.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.045579 restraints weight = 45701.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046192 restraints weight = 36563.133| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 29 (52 function evaluations) r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 17999 Z= 0.320 Angle : 0.915 11.519 24728 Z= 0.490 Chirality : 0.051 0.284 2694 Planarity : 0.008 0.091 2854 Dihedral : 22.450 178.586 3229 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 26.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.41 % Allowed : 4.31 % Favored : 95.28 % 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: -3.34 (0.16), residues: 1921 helix: -1.76 (0.17), residues: 672 sheet: -2.26 (0.26), residues: 328 loop : -2.50 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 284 TYR 0.025 0.003 TYR B 277 PHE 0.025 0.003 PHE C 644 TRP 0.019 0.003 TRP C 560 HIS 0.018 0.003 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.32 (17992) covalent geometry : angle 0.91360 / 0.49 (24726) hydrogen bonds : bond 0.07215 / 4.85 ( 746) hydrogen bonds : angle 6.12117 / 4.28 ( 2107) metal coordination : bond 0.05521 / 2.97 ( 7) metal coordination : angle 4.94854 / 2.36 ( 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: 4 poor density : 279 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8943 (t) cc_final: 0.8616 (t) REVERT: A 594 MET cc_start: 0.9499 (mmm) cc_final: 0.9270 (mmt) REVERT: A 624 ASP cc_start: 0.7398 (m-30) cc_final: 0.7137 (t0) REVERT: A 647 MET cc_start: 0.9009 (mmm) cc_final: 0.8713 (mmm) REVERT: A 729 TYR cc_start: 0.8447 (m-80) cc_final: 0.7545 (m-80) REVERT: A 731 GLU cc_start: 0.8853 (tp30) cc_final: 0.8297 (tm-30) REVERT: A 732 LYS cc_start: 0.9562 (ttpt) cc_final: 0.9154 (tmtt) REVERT: A 733 MET cc_start: 0.9702 (ttm) cc_final: 0.8785 (tmm) REVERT: A 738 GLU cc_start: 0.8718 (tp30) cc_final: 0.7994 (tm-30) REVERT: A 802 SER cc_start: 0.9088 (p) cc_final: 0.8755 (t) REVERT: A 806 PHE cc_start: 0.9023 (p90) cc_final: 0.8029 (p90) REVERT: A 828 LYS cc_start: 0.9439 (tttt) cc_final: 0.8924 (tptm) REVERT: A 911 MET cc_start: 0.8280 (ptm) cc_final: 0.7989 (ptm) REVERT: A 989 LEU cc_start: 0.9773 (mt) cc_final: 0.9271 (mt) REVERT: A 995 LYS cc_start: 0.8505 (ttmm) cc_final: 0.7765 (ttmm) REVERT: A 1005 GLU cc_start: 0.9206 (pt0) cc_final: 0.8925 (pt0) REVERT: B 22 LEU cc_start: 0.9245 (mt) cc_final: 0.8863 (tp) REVERT: B 84 ASP cc_start: 0.9051 (m-30) cc_final: 0.8680 (t70) REVERT: B 185 ILE cc_start: 0.9551 (tt) cc_final: 0.9292 (mp) REVERT: B 197 LEU cc_start: 0.9044 (mt) cc_final: 0.8808 (tp) REVERT: B 219 LEU cc_start: 0.9041 (tp) cc_final: 0.8817 (tp) REVERT: B 232 ARG cc_start: 0.9325 (pmt-80) cc_final: 0.9123 (ptm160) REVERT: C 474 MET cc_start: 0.6285 (tpp) cc_final: 0.6077 (tpt) REVERT: C 495 LEU cc_start: 0.9397 (mm) cc_final: 0.9046 (mm) REVERT: C 499 GLN cc_start: 0.9472 (mt0) cc_final: 0.9196 (mp10) REVERT: C 522 LEU cc_start: 0.9182 (mt) cc_final: 0.8867 (mt) REVERT: C 527 LYS cc_start: 0.9697 (mttt) cc_final: 0.9128 (tptp) REVERT: C 530 LEU cc_start: 0.9325 (mt) cc_final: 0.9118 (mt) REVERT: C 594 MET cc_start: 0.9194 (mmm) cc_final: 0.8255 (mmm) REVERT: C 598 ARG cc_start: 0.9557 (mmt-90) cc_final: 0.9247 (mmp80) REVERT: C 606 MET cc_start: 0.8861 (ptt) cc_final: 0.8379 (ppp) REVERT: C 616 LYS cc_start: 0.9468 (ptmt) cc_final: 0.8775 (ptpt) REVERT: C 677 LEU cc_start: 0.9227 (tp) cc_final: 0.9005 (tp) REVERT: C 680 MET cc_start: 0.9207 (pmm) cc_final: 0.8957 (pmm) REVERT: C 700 GLU cc_start: 0.9214 (tt0) cc_final: 0.8672 (tm-30) REVERT: C 733 MET cc_start: 0.9079 (mmt) cc_final: 0.8834 (mmp) REVERT: C 737 MET cc_start: 0.9492 (ttm) cc_final: 0.9281 (ttp) REVERT: C 863 MET cc_start: 0.7250 (mmm) cc_final: 0.6916 (mmm) REVERT: C 875 TYR cc_start: 0.9232 (t80) cc_final: 0.8913 (t80) REVERT: C 938 PHE cc_start: 0.9356 (t80) cc_final: 0.8978 (t80) REVERT: C 1007 GLU cc_start: 0.8966 (tt0) cc_final: 0.8445 (tm-30) REVERT: D 65 ASN cc_start: 0.9587 (p0) cc_final: 0.9353 (p0) REVERT: D 173 ASN cc_start: 0.9482 (m-40) cc_final: 0.9068 (m-40) REVERT: D 288 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7769 (m) REVERT: D 347 GLN cc_start: 0.8760 (tt0) cc_final: 0.8293 (tm-30) outliers start: 4 outliers final: 1 residues processed: 283 average time/residue: 0.1499 time to fit residues: 62.3012 Evaluate side-chains 198 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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: 10.0000 chunk 172 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 199 optimal weight: 30.0000 chunk 6 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 201 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 GLN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 HIS ** B 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.060312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.039406 restraints weight = 249868.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.041397 restraints weight = 110798.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.042734 restraints weight = 67365.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043633 restraints weight = 48034.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.044251 restraints weight = 38001.495| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 20 (27 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.132 17999 Z= 0.332 Angle : 0.873 11.241 24728 Z= 0.471 Chirality : 0.048 0.289 2694 Planarity : 0.007 0.059 2854 Dihedral : 22.440 179.924 3229 Min Nonbonded Distance : 1.531 Molprobity Statistics. All-atom Clashscore : 27.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.29 % Allowed : 5.43 % Favored : 94.28 % 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: -3.03 (0.17), residues: 1921 helix: -1.50 (0.18), residues: 678 sheet: -2.11 (0.26), residues: 342 loop : -2.31 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 778 TYR 0.024 0.003 TYR C 875 PHE 0.023 0.003 PHE A 642 TRP 0.036 0.003 TRP C 915 HIS 0.013 0.002 HIS A 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.33 (17992) covalent geometry : angle 0.87245 / 0.47 (24726) hydrogen bonds : bond 0.06546 / 4.38 ( 746) hydrogen bonds : angle 6.04491 / 4.25 ( 2107) metal coordination : bond 0.02400 / 1.63 ( 7) metal coordination : angle 2.56896 / 1.18 ( 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 230 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 228 time to evaluate : 0.672 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: A 503 MET cc_start: 0.9179 (ppp) cc_final: 0.8967 (ppp) REVERT: A 522 LEU cc_start: 0.9580 (mt) cc_final: 0.9295 (mt) REVERT: A 624 ASP cc_start: 0.7270 (m-30) cc_final: 0.7016 (t0) REVERT: A 667 LYS cc_start: 0.9538 (mtpt) cc_final: 0.9237 (ptpt) REVERT: A 729 TYR cc_start: 0.8184 (m-80) cc_final: 0.7446 (m-80) REVERT: A 731 GLU cc_start: 0.8897 (tp30) cc_final: 0.8564 (tm-30) REVERT: A 733 MET cc_start: 0.9516 (ttm) cc_final: 0.8746 (tmm) REVERT: A 738 GLU cc_start: 0.8712 (tp30) cc_final: 0.7980 (tm-30) REVERT: A 802 SER cc_start: 0.9151 (p) cc_final: 0.8800 (t) REVERT: A 828 LYS cc_start: 0.9489 (tttt) cc_final: 0.8986 (tptm) REVERT: A 863 MET cc_start: 0.7207 (mmm) cc_final: 0.6547 (mmm) REVERT: A 911 MET cc_start: 0.8501 (ptm) cc_final: 0.8179 (ptm) REVERT: A 912 LYS cc_start: 0.9766 (pptt) cc_final: 0.9540 (pptt) REVERT: A 945 MET cc_start: 0.8998 (ttt) cc_final: 0.8724 (tpp) REVERT: A 989 LEU cc_start: 0.9708 (mt) cc_final: 0.9507 (mt) REVERT: A 995 LYS cc_start: 0.8619 (ttmm) cc_final: 0.7758 (ttmm) REVERT: A 1006 LEU cc_start: 0.9718 (mt) cc_final: 0.9483 (mt) REVERT: B 22 LEU cc_start: 0.9227 (mt) cc_final: 0.8765 (tp) REVERT: B 129 LEU cc_start: 0.8686 (mp) cc_final: 0.8319 (mp) REVERT: B 185 ILE cc_start: 0.9625 (tt) cc_final: 0.9286 (mp) REVERT: B 197 LEU cc_start: 0.8992 (mt) cc_final: 0.8767 (tt) REVERT: C 495 LEU cc_start: 0.9404 (mm) cc_final: 0.8983 (tp) REVERT: C 522 LEU cc_start: 0.9234 (mt) cc_final: 0.8829 (mp) REVERT: C 526 GLU cc_start: 0.8703 (pt0) cc_final: 0.8323 (pt0) REVERT: C 594 MET cc_start: 0.9171 (mmm) cc_final: 0.7870 (mmm) REVERT: C 598 ARG cc_start: 0.9653 (mmt-90) cc_final: 0.9229 (mmp-170) REVERT: C 606 MET cc_start: 0.9001 (ptt) cc_final: 0.8631 (ppp) REVERT: C 616 LYS cc_start: 0.9470 (ptmt) cc_final: 0.9077 (ptmt) REVERT: C 680 MET cc_start: 0.9236 (pmm) cc_final: 0.8751 (pmm) REVERT: C 700 GLU cc_start: 0.9343 (tt0) cc_final: 0.8667 (tm-30) REVERT: C 705 MET cc_start: 0.9423 (mmt) cc_final: 0.9055 (mpp) REVERT: C 733 MET cc_start: 0.9222 (mmt) cc_final: 0.8963 (mmm) REVERT: C 737 MET cc_start: 0.9528 (ttm) cc_final: 0.9284 (ttp) REVERT: C 807 MET cc_start: 0.9169 (tmm) cc_final: 0.8668 (tmm) REVERT: C 863 MET cc_start: 0.7433 (mmm) cc_final: 0.7215 (mtp) REVERT: C 871 MET cc_start: 0.7096 (ttp) cc_final: 0.6520 (tmm) REVERT: C 938 PHE cc_start: 0.9344 (t80) cc_final: 0.9015 (t80) REVERT: C 1007 GLU cc_start: 0.9002 (tt0) cc_final: 0.8430 (mm-30) REVERT: C 1010 LEU cc_start: 0.9808 (tp) cc_final: 0.9574 (tp) REVERT: D 1 MET cc_start: 0.8400 (mtm) cc_final: 0.7877 (mpp) REVERT: D 65 ASN cc_start: 0.9558 (p0) cc_final: 0.9330 (p0) REVERT: D 173 ASN cc_start: 0.9385 (m-40) cc_final: 0.8980 (m-40) REVERT: D 347 GLN cc_start: 0.8809 (tt0) cc_final: 0.8509 (tm-30) outliers start: 2 outliers final: 1 residues processed: 230 average time/residue: 0.1442 time to fit residues: 49.8704 Evaluate side-chains 181 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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: 6.9990 chunk 59 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 192 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** A 858 GLN ** 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 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 = 0.3398 r_free = 0.3398 target = 0.062452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.041884 restraints weight = 198828.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.043843 restraints weight = 94933.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.045140 restraints weight = 59176.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.046018 restraints weight = 42753.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046623 restraints weight = 34058.310| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17999 Z= 0.201 Angle : 0.770 10.217 24728 Z= 0.414 Chirality : 0.048 0.295 2694 Planarity : 0.005 0.062 2854 Dihedral : 22.358 179.338 3229 Min Nonbonded Distance : 1.520 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.18 % Allowed : 2.95 % Favored : 96.87 % 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: -2.55 (0.18), residues: 1921 helix: -1.01 (0.19), residues: 669 sheet: -1.81 (0.26), residues: 347 loop : -2.11 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 994 TYR 0.032 0.003 TYR B 107 PHE 0.017 0.002 PHE B 156 TRP 0.044 0.002 TRP C 915 HIS 0.008 0.002 HIS A 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 (17992) covalent geometry : angle 0.77012 / 0.41 (24726) hydrogen bonds : bond 0.05433 / 3.59 ( 746) hydrogen bonds : angle 5.65191 / 3.94 ( 2107) metal coordination : bond 0.00917 / 0.59 ( 7) metal coordination : angle 2.35186 / 0.84 ( 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 241 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.651 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: A 495 LEU cc_start: 0.9267 (mt) cc_final: 0.8799 (pp) REVERT: A 503 MET cc_start: 0.9161 (ppp) cc_final: 0.8904 (ppp) REVERT: A 522 LEU cc_start: 0.9487 (mt) cc_final: 0.9110 (mt) REVERT: A 526 GLU cc_start: 0.8976 (pm20) cc_final: 0.8717 (pm20) REVERT: A 590 GLU cc_start: 0.9608 (tt0) cc_final: 0.8953 (pp20) REVERT: A 667 LYS cc_start: 0.9582 (mtpt) cc_final: 0.9275 (ptpt) REVERT: A 677 LEU cc_start: 0.9408 (pt) cc_final: 0.9140 (pt) REVERT: A 684 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8763 (tm-30) REVERT: A 731 GLU cc_start: 0.8906 (tp30) cc_final: 0.8469 (tm-30) REVERT: A 732 LYS cc_start: 0.9352 (tmtt) cc_final: 0.8863 (tptp) REVERT: A 733 MET cc_start: 0.9492 (ttm) cc_final: 0.8769 (tmm) REVERT: A 738 GLU cc_start: 0.8833 (tp30) cc_final: 0.7982 (tm-30) REVERT: A 802 SER cc_start: 0.9120 (p) cc_final: 0.8763 (t) REVERT: A 806 PHE cc_start: 0.9112 (p90) cc_final: 0.8011 (p90) REVERT: A 817 HIS cc_start: 0.9322 (m90) cc_final: 0.8943 (m90) REVERT: A 828 LYS cc_start: 0.9451 (tttt) cc_final: 0.8910 (tptp) REVERT: A 911 MET cc_start: 0.8550 (ptm) cc_final: 0.8012 (mtp) REVERT: A 912 LYS cc_start: 0.9772 (pptt) cc_final: 0.9538 (pptt) REVERT: A 945 MET cc_start: 0.9005 (ttt) cc_final: 0.8721 (tpp) REVERT: A 995 LYS cc_start: 0.8518 (ttmm) cc_final: 0.7728 (ttmm) REVERT: A 1024 PHE cc_start: 0.9154 (m-80) cc_final: 0.8899 (m-80) REVERT: B 1 MET cc_start: 0.6223 (pmm) cc_final: 0.5974 (ptm) REVERT: B 129 LEU cc_start: 0.8712 (mp) cc_final: 0.8483 (mp) REVERT: B 197 LEU cc_start: 0.8976 (mt) cc_final: 0.8708 (tt) REVERT: C 522 LEU cc_start: 0.9186 (mt) cc_final: 0.8670 (mp) REVERT: C 526 GLU cc_start: 0.8664 (pt0) cc_final: 0.8463 (pt0) REVERT: C 594 MET cc_start: 0.9176 (mmm) cc_final: 0.8284 (mmm) REVERT: C 598 ARG cc_start: 0.9643 (mmt-90) cc_final: 0.9263 (mmp80) REVERT: C 606 MET cc_start: 0.8893 (ptt) cc_final: 0.8138 (ppp) REVERT: C 616 LYS cc_start: 0.9504 (ptmt) cc_final: 0.9020 (ptmt) REVERT: C 680 MET cc_start: 0.9196 (pmm) cc_final: 0.8692 (pmm) REVERT: C 700 GLU cc_start: 0.9300 (tt0) cc_final: 0.8638 (tm-30) REVERT: C 733 MET cc_start: 0.9334 (mmt) cc_final: 0.9043 (mmp) REVERT: C 737 MET cc_start: 0.9566 (ttm) cc_final: 0.9205 (ttp) REVERT: C 763 MET cc_start: 0.8425 (mtm) cc_final: 0.8217 (mtm) REVERT: C 807 MET cc_start: 0.9220 (tmm) cc_final: 0.8587 (tmm) REVERT: C 871 MET cc_start: 0.6979 (ttp) cc_final: 0.6586 (tmm) REVERT: C 875 TYR cc_start: 0.9458 (t80) cc_final: 0.9177 (t80) REVERT: C 877 ARG cc_start: 0.9546 (tpt90) cc_final: 0.9244 (tpt-90) REVERT: C 880 MET cc_start: 0.8780 (mmp) cc_final: 0.8530 (mmm) REVERT: C 911 MET cc_start: 0.8499 (tpt) cc_final: 0.7747 (tpp) REVERT: C 938 PHE cc_start: 0.9344 (t80) cc_final: 0.9032 (t80) REVERT: C 1010 LEU cc_start: 0.9819 (tp) cc_final: 0.9593 (tp) REVERT: C 1025 MET cc_start: 0.8637 (mpp) cc_final: 0.8407 (mpp) REVERT: C 1026 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8697 (tp30) REVERT: D 65 ASN cc_start: 0.9540 (p0) cc_final: 0.9279 (p0) REVERT: D 72 LEU cc_start: 0.9430 (mp) cc_final: 0.9141 (mp) REVERT: D 173 ASN cc_start: 0.9367 (m-40) cc_final: 0.8988 (m-40) REVERT: D 347 GLN cc_start: 0.8904 (tt0) cc_final: 0.8575 (tm-30) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1455 time to fit residues: 52.9471 Evaluate side-chains 190 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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: 5.9990 chunk 78 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** 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** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.060963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.040270 restraints weight = 212699.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.042241 restraints weight = 100115.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.043543 restraints weight = 62004.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.044424 restraints weight = 44674.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.045029 restraints weight = 35601.409| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 17999 Z= 0.254 Angle : 0.790 12.019 24728 Z= 0.422 Chirality : 0.047 0.302 2694 Planarity : 0.005 0.062 2854 Dihedral : 22.273 179.439 3229 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 24.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.18 % Allowed : 3.19 % Favored : 96.64 % 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: -2.43 (0.18), residues: 1921 helix: -0.87 (0.19), residues: 674 sheet: -1.79 (0.26), residues: 347 loop : -2.07 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 167 TYR 0.020 0.003 TYR B 29 PHE 0.021 0.002 PHE B 156 TRP 0.026 0.002 TRP C 915 HIS 0.017 0.002 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.25 (17992) covalent geometry : angle 0.79011 / 0.42 (24726) hydrogen bonds : bond 0.05568 / 3.71 ( 746) hydrogen bonds : angle 5.66159 / 3.96 ( 2107) metal coordination : bond 0.01319 / 0.89 ( 7) metal coordination : angle 2.39088 / 1.13 ( 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 221 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.616 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 503 MET cc_start: 0.9170 (ppp) cc_final: 0.8921 (ppp) REVERT: A 590 GLU cc_start: 0.9577 (tt0) cc_final: 0.8917 (pp20) REVERT: A 667 LYS cc_start: 0.9566 (mtpt) cc_final: 0.9271 (ptpt) REVERT: A 684 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8675 (tm-30) REVERT: A 731 GLU cc_start: 0.8939 (tp30) cc_final: 0.8580 (tm-30) REVERT: A 732 LYS cc_start: 0.9331 (tmtt) cc_final: 0.8994 (tptp) REVERT: A 733 MET cc_start: 0.9390 (ttm) cc_final: 0.8648 (tmm) REVERT: A 737 MET cc_start: 0.8253 (ttm) cc_final: 0.7970 (ttm) REVERT: A 738 GLU cc_start: 0.8793 (tp30) cc_final: 0.7995 (tm-30) REVERT: A 802 SER cc_start: 0.9292 (p) cc_final: 0.9010 (t) REVERT: A 817 HIS cc_start: 0.9345 (m90) cc_final: 0.9072 (m90) REVERT: A 828 LYS cc_start: 0.9481 (tttt) cc_final: 0.8933 (tptp) REVERT: A 911 MET cc_start: 0.8643 (ptm) cc_final: 0.8096 (mtp) REVERT: A 912 LYS cc_start: 0.9784 (pptt) cc_final: 0.9545 (pptt) REVERT: A 945 MET cc_start: 0.8932 (ttt) cc_final: 0.8719 (tpp) REVERT: A 995 LYS cc_start: 0.8530 (ttmm) cc_final: 0.7513 (ttmm) REVERT: A 996 MET cc_start: 0.8196 (mpp) cc_final: 0.7794 (mpp) REVERT: A 1024 PHE cc_start: 0.9157 (m-80) cc_final: 0.8878 (m-80) REVERT: B 1 MET cc_start: 0.6495 (pmm) cc_final: 0.6261 (ptm) REVERT: B 129 LEU cc_start: 0.8778 (mp) cc_final: 0.8538 (mp) REVERT: B 197 LEU cc_start: 0.9030 (mt) cc_final: 0.8734 (tt) REVERT: B 219 LEU cc_start: 0.9198 (tp) cc_final: 0.8917 (tp) REVERT: C 473 MET cc_start: 0.4886 (ttt) cc_final: 0.4578 (ttt) REVERT: C 522 LEU cc_start: 0.9299 (mt) cc_final: 0.8799 (mp) REVERT: C 526 GLU cc_start: 0.9008 (pt0) cc_final: 0.8608 (pt0) REVERT: C 594 MET cc_start: 0.9250 (mmm) cc_final: 0.8233 (mmm) REVERT: C 598 ARG cc_start: 0.9649 (mmt-90) cc_final: 0.9268 (mmp80) REVERT: C 606 MET cc_start: 0.8926 (ptt) cc_final: 0.8184 (ppp) REVERT: C 616 LYS cc_start: 0.9512 (ptmt) cc_final: 0.9032 (ptmt) REVERT: C 680 MET cc_start: 0.9271 (pmm) cc_final: 0.8744 (pmm) REVERT: C 700 GLU cc_start: 0.9312 (tt0) cc_final: 0.8615 (tm-30) REVERT: C 733 MET cc_start: 0.9334 (mmt) cc_final: 0.9013 (mmm) REVERT: C 737 MET cc_start: 0.9571 (ttm) cc_final: 0.9292 (ttp) REVERT: C 807 MET cc_start: 0.9223 (tmm) cc_final: 0.8754 (tmm) REVERT: C 871 MET cc_start: 0.7159 (ttp) cc_final: 0.6777 (tmm) REVERT: C 875 TYR cc_start: 0.9463 (t80) cc_final: 0.9210 (t80) REVERT: C 877 ARG cc_start: 0.9526 (tpt90) cc_final: 0.9324 (tpt-90) REVERT: C 878 ARG cc_start: 0.9291 (mtt90) cc_final: 0.8813 (ptp-110) REVERT: C 880 MET cc_start: 0.8858 (mmp) cc_final: 0.8595 (mmm) REVERT: C 911 MET cc_start: 0.8677 (tpt) cc_final: 0.7932 (tpp) REVERT: C 938 PHE cc_start: 0.9356 (t80) cc_final: 0.9092 (t80) REVERT: C 1007 GLU cc_start: 0.8934 (tt0) cc_final: 0.8634 (tt0) REVERT: D 1 MET cc_start: 0.7957 (mtm) cc_final: 0.7447 (mpp) REVERT: D 65 ASN cc_start: 0.9541 (p0) cc_final: 0.9287 (p0) REVERT: D 72 LEU cc_start: 0.9434 (mp) cc_final: 0.9213 (mp) REVERT: D 173 ASN cc_start: 0.9260 (m-40) cc_final: 0.8910 (m-40) REVERT: D 347 GLN cc_start: 0.8914 (tt0) cc_final: 0.8560 (tm-30) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1466 time to fit residues: 48.7262 Evaluate side-chains 181 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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: 8.9990 chunk 69 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 152 optimal weight: 0.0060 chunk 58 optimal weight: 0.6980 chunk 99 optimal weight: 30.0000 chunk 195 optimal weight: 50.0000 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** 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 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.063245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.041600 restraints weight = 237355.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.043774 restraints weight = 103127.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045240 restraints weight = 61820.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046193 restraints weight = 43518.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.046825 restraints weight = 34215.012| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17999 Z= 0.161 Angle : 0.726 9.457 24728 Z= 0.389 Chirality : 0.046 0.300 2694 Planarity : 0.005 0.062 2854 Dihedral : 22.171 179.545 3229 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.18 % Allowed : 1.59 % Favored : 98.23 % 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: -2.16 (0.18), residues: 1921 helix: -0.56 (0.19), residues: 666 sheet: -1.58 (0.27), residues: 337 loop : -2.00 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 575 TYR 0.024 0.002 TYR C 933 PHE 0.017 0.002 PHE C 720 TRP 0.025 0.002 TRP C 915 HIS 0.013 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (17992) covalent geometry : angle 0.72586 / 0.39 (24726) hydrogen bonds : bond 0.04837 / 3.15 ( 746) hydrogen bonds : angle 5.36220 / 3.72 ( 2107) metal coordination : bond 0.00889 / 0.48 ( 7) metal coordination : angle 3.19711 / 1.13 ( 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 237 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.591 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 495 LEU cc_start: 0.9328 (mt) cc_final: 0.9016 (pp) REVERT: A 503 MET cc_start: 0.9080 (ppp) cc_final: 0.8874 (ppp) REVERT: A 522 LEU cc_start: 0.9470 (mt) cc_final: 0.9092 (mt) REVERT: A 526 GLU cc_start: 0.8989 (pm20) cc_final: 0.8681 (pm20) REVERT: A 667 LYS cc_start: 0.9585 (mtpt) cc_final: 0.9332 (ptpt) REVERT: A 675 ARG cc_start: 0.8624 (mtp180) cc_final: 0.8394 (mtp180) REVERT: A 731 GLU cc_start: 0.8920 (tp30) cc_final: 0.8669 (tm-30) REVERT: A 733 MET cc_start: 0.9306 (ttm) cc_final: 0.8781 (tmm) REVERT: A 737 MET cc_start: 0.8076 (ttm) cc_final: 0.7843 (ttm) REVERT: A 738 GLU cc_start: 0.8885 (tp30) cc_final: 0.8076 (tm-30) REVERT: A 802 SER cc_start: 0.9208 (p) cc_final: 0.8857 (t) REVERT: A 817 HIS cc_start: 0.9242 (m90) cc_final: 0.8948 (m90) REVERT: A 828 LYS cc_start: 0.9443 (tttt) cc_final: 0.8876 (tptp) REVERT: A 912 LYS cc_start: 0.9784 (pptt) cc_final: 0.9545 (pptt) REVERT: A 945 MET cc_start: 0.8905 (ttt) cc_final: 0.8699 (tpp) REVERT: A 991 ARG cc_start: 0.9504 (mmp80) cc_final: 0.9048 (mmm160) REVERT: A 995 LYS cc_start: 0.8627 (ttmm) cc_final: 0.7714 (ttmm) REVERT: B 1 MET cc_start: 0.6386 (pmm) cc_final: 0.6153 (ttp) REVERT: B 129 LEU cc_start: 0.8727 (mp) cc_final: 0.8480 (mp) REVERT: B 197 LEU cc_start: 0.8976 (mt) cc_final: 0.8722 (tt) REVERT: C 519 LEU cc_start: 0.9666 (tp) cc_final: 0.9407 (tp) REVERT: C 526 GLU cc_start: 0.8943 (pt0) cc_final: 0.8483 (pt0) REVERT: C 594 MET cc_start: 0.9221 (mmm) cc_final: 0.8346 (mmm) REVERT: C 598 ARG cc_start: 0.9630 (mmt-90) cc_final: 0.9344 (mmp80) REVERT: C 606 MET cc_start: 0.8839 (ptt) cc_final: 0.8108 (ppp) REVERT: C 616 LYS cc_start: 0.9574 (ptmt) cc_final: 0.9190 (ptmt) REVERT: C 680 MET cc_start: 0.9261 (pmm) cc_final: 0.8782 (pmm) REVERT: C 700 GLU cc_start: 0.9274 (tt0) cc_final: 0.8530 (tm-30) REVERT: C 705 MET cc_start: 0.9357 (mmt) cc_final: 0.9011 (mpp) REVERT: C 733 MET cc_start: 0.9325 (mmt) cc_final: 0.9045 (mmp) REVERT: C 737 MET cc_start: 0.9543 (ttm) cc_final: 0.9172 (ttp) REVERT: C 807 MET cc_start: 0.9128 (tmm) cc_final: 0.8515 (tmm) REVERT: C 871 MET cc_start: 0.7149 (ttp) cc_final: 0.6612 (tmm) REVERT: C 875 TYR cc_start: 0.9417 (t80) cc_final: 0.9186 (t80) REVERT: C 877 ARG cc_start: 0.9496 (tpt90) cc_final: 0.9209 (tpt-90) REVERT: C 878 ARG cc_start: 0.9261 (mtt90) cc_final: 0.8659 (ptp-110) REVERT: C 880 MET cc_start: 0.8825 (mmp) cc_final: 0.8550 (mmm) REVERT: C 911 MET cc_start: 0.8455 (tpt) cc_final: 0.7677 (tpp) REVERT: C 938 PHE cc_start: 0.9348 (t80) cc_final: 0.9046 (t80) REVERT: C 1010 LEU cc_start: 0.9809 (tp) cc_final: 0.9567 (tp) REVERT: C 1013 HIS cc_start: 0.9380 (t-90) cc_final: 0.8812 (t-170) REVERT: D 1 MET cc_start: 0.7851 (mtm) cc_final: 0.7404 (mpp) REVERT: D 65 ASN cc_start: 0.9524 (p0) cc_final: 0.9265 (p0) REVERT: D 72 LEU cc_start: 0.9392 (mp) cc_final: 0.9142 (mp) REVERT: D 173 ASN cc_start: 0.9221 (m-40) cc_final: 0.8896 (m-40) REVERT: D 347 GLN cc_start: 0.8886 (tt0) cc_final: 0.8553 (tm-30) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1411 time to fit residues: 50.2696 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 : 0.621 ------------------------------------------------------------------------------- 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: 7.9990 chunk 11 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 196 optimal weight: 50.0000 chunk 76 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A 997 ASN ** 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 204 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.061582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.040936 restraints weight = 189170.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.042865 restraints weight = 92374.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.044112 restraints weight = 58093.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.044970 restraints weight = 42305.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.045568 restraints weight = 33976.888| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (21 function evaluations) r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 17999 Z= 0.221 Angle : 0.744 10.139 24728 Z= 0.400 Chirality : 0.045 0.304 2694 Planarity : 0.005 0.063 2854 Dihedral : 22.108 179.521 3229 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.18 % Allowed : 1.71 % Favored : 98.11 % 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: -2.15 (0.18), residues: 1921 helix: -0.60 (0.19), residues: 671 sheet: -1.59 (0.27), residues: 345 loop : -1.96 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 167 TYR 0.018 0.002 TYR B 277 PHE 0.030 0.002 PHE A 826 TRP 0.056 0.003 TRP A 782 HIS 0.012 0.002 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 (17992) covalent geometry : angle 0.74266 / 0.40 (24726) hydrogen bonds : bond 0.05125 / 3.41 ( 746) hydrogen bonds : angle 5.39663 / 3.77 ( 2107) metal coordination : bond 0.01863 / 1.18 ( 7) metal coordination : angle 5.31724 / 2.53 ( 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 215 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.665 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 495 LEU cc_start: 0.9293 (mt) cc_final: 0.8962 (pp) REVERT: A 503 MET cc_start: 0.9136 (ppp) cc_final: 0.8910 (ppp) REVERT: A 522 LEU cc_start: 0.9519 (mt) cc_final: 0.9142 (mt) REVERT: A 526 GLU cc_start: 0.8997 (pm20) cc_final: 0.8721 (pm20) REVERT: A 667 LYS cc_start: 0.9561 (mtpt) cc_final: 0.9333 (ptpt) REVERT: A 684 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8572 (tm-30) REVERT: A 731 GLU cc_start: 0.9040 (tp30) cc_final: 0.8490 (tm-30) REVERT: A 733 MET cc_start: 0.9310 (ttm) cc_final: 0.8611 (tmm) REVERT: A 738 GLU cc_start: 0.8859 (tp30) cc_final: 0.8041 (tm-30) REVERT: A 802 SER cc_start: 0.9040 (p) cc_final: 0.8742 (t) REVERT: A 817 HIS cc_start: 0.9295 (m90) cc_final: 0.8996 (m90) REVERT: A 828 LYS cc_start: 0.9489 (tttt) cc_final: 0.8928 (tptp) REVERT: A 912 LYS cc_start: 0.9786 (pptt) cc_final: 0.9546 (pptt) REVERT: A 945 MET cc_start: 0.8845 (ttt) cc_final: 0.8637 (tpp) REVERT: A 995 LYS cc_start: 0.8600 (ttmm) cc_final: 0.7837 (ttmm) REVERT: A 1006 LEU cc_start: 0.9607 (tp) cc_final: 0.9404 (tp) REVERT: B 129 LEU cc_start: 0.8762 (mp) cc_final: 0.8486 (mp) REVERT: B 219 LEU cc_start: 0.9132 (tp) cc_final: 0.8826 (tp) REVERT: C 473 MET cc_start: 0.5164 (ttt) cc_final: 0.4926 (ttt) REVERT: C 519 LEU cc_start: 0.9673 (tp) cc_final: 0.9383 (tp) REVERT: C 526 GLU cc_start: 0.8951 (pt0) cc_final: 0.8676 (pt0) REVERT: C 594 MET cc_start: 0.9267 (mmm) cc_final: 0.8319 (mmm) REVERT: C 598 ARG cc_start: 0.9627 (mmt-90) cc_final: 0.9306 (mmp80) REVERT: C 606 MET cc_start: 0.8887 (ptt) cc_final: 0.8155 (ppp) REVERT: C 616 LYS cc_start: 0.9557 (ptmt) cc_final: 0.9108 (ptmt) REVERT: C 680 MET cc_start: 0.9296 (pmm) cc_final: 0.8791 (pmm) REVERT: C 700 GLU cc_start: 0.9324 (tt0) cc_final: 0.8614 (tm-30) REVERT: C 733 MET cc_start: 0.9316 (mmt) cc_final: 0.9110 (mmm) REVERT: C 737 MET cc_start: 0.9592 (ttm) cc_final: 0.9341 (ttp) REVERT: C 807 MET cc_start: 0.9137 (tmm) cc_final: 0.8691 (tmm) REVERT: C 871 MET cc_start: 0.7337 (ttp) cc_final: 0.6767 (tmm) REVERT: C 875 TYR cc_start: 0.9443 (t80) cc_final: 0.9168 (t80) REVERT: C 878 ARG cc_start: 0.9285 (mtt90) cc_final: 0.8706 (ptp-110) REVERT: C 880 MET cc_start: 0.8871 (mmp) cc_final: 0.8613 (mmm) REVERT: C 911 MET cc_start: 0.8474 (tpt) cc_final: 0.7735 (tpp) REVERT: C 938 PHE cc_start: 0.9358 (t80) cc_final: 0.9082 (t80) REVERT: C 1010 LEU cc_start: 0.9799 (tp) cc_final: 0.9551 (tp) REVERT: C 1013 HIS cc_start: 0.9344 (t-90) cc_final: 0.8849 (t-170) REVERT: C 1026 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8448 (tp30) REVERT: D 1 MET cc_start: 0.7847 (mtm) cc_final: 0.7438 (mpp) REVERT: D 65 ASN cc_start: 0.9511 (p0) cc_final: 0.9244 (p0) REVERT: D 72 LEU cc_start: 0.9427 (mp) cc_final: 0.9202 (mp) REVERT: D 173 ASN cc_start: 0.9197 (m-40) cc_final: 0.8887 (m-40) REVERT: D 347 GLN cc_start: 0.8931 (tt0) cc_final: 0.8601 (tm-30) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1489 time to fit residues: 47.9407 Evaluate side-chains 172 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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: 10.0000 chunk 22 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 196 optimal weight: 50.0000 chunk 86 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.061396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.040723 restraints weight = 194416.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042658 restraints weight = 93126.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.043943 restraints weight = 58161.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.044823 restraints weight = 42084.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045376 restraints weight = 33600.109| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- 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: 52 | |-----------------------------------------------------------------------------| |-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: 52 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17999 Z= 0.215 Angle : 0.742 10.150 24728 Z= 0.398 Chirality : 0.046 0.301 2694 Planarity : 0.005 0.073 2854 Dihedral : 22.070 179.423 3229 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.18 % Allowed : 1.12 % Favored : 98.70 % 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: -2.12 (0.18), residues: 1921 helix: -0.56 (0.19), residues: 670 sheet: -1.61 (0.27), residues: 350 loop : -1.92 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 426 TYR 0.022 0.002 TYR C 933 PHE 0.021 0.002 PHE B 156 TRP 0.030 0.002 TRP A 782 HIS 0.012 0.002 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 (17992) covalent geometry : angle 0.74027 / 0.40 (24726) hydrogen bonds : bond 0.05038 / 3.36 ( 746) hydrogen bonds : angle 5.38818 / 3.78 ( 2107) metal coordination : bond 0.04012 / 2.17 ( 7) metal coordination : angle 5.17133 / 2.38 ( 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 216 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.592 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 503 MET cc_start: 0.9147 (ppp) cc_final: 0.8926 (ppp) REVERT: A 526 GLU cc_start: 0.8982 (pm20) cc_final: 0.8775 (pm20) REVERT: A 667 LYS cc_start: 0.9544 (mtpt) cc_final: 0.9342 (ptpt) REVERT: A 684 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8678 (tm-30) REVERT: A 729 TYR cc_start: 0.8560 (m-80) cc_final: 0.8203 (m-80) REVERT: A 731 GLU cc_start: 0.9110 (tp30) cc_final: 0.8547 (tm-30) REVERT: A 732 LYS cc_start: 0.9234 (tmtt) cc_final: 0.9001 (tmtt) REVERT: A 733 MET cc_start: 0.9159 (ttm) cc_final: 0.8806 (tmm) REVERT: A 738 GLU cc_start: 0.8877 (tp30) cc_final: 0.7881 (tm-30) REVERT: A 802 SER cc_start: 0.9059 (p) cc_final: 0.8747 (t) REVERT: A 817 HIS cc_start: 0.9225 (m90) cc_final: 0.8962 (m90) REVERT: A 828 LYS cc_start: 0.9454 (tttt) cc_final: 0.8904 (tptp) REVERT: A 912 LYS cc_start: 0.9786 (pptt) cc_final: 0.9550 (pptt) REVERT: A 995 LYS cc_start: 0.8586 (ttmm) cc_final: 0.7763 (ttmm) REVERT: A 996 MET cc_start: 0.8109 (mpp) cc_final: 0.7841 (mpp) REVERT: A 1006 LEU cc_start: 0.9572 (tp) cc_final: 0.9347 (tp) REVERT: B 129 LEU cc_start: 0.8788 (mp) cc_final: 0.8496 (mp) REVERT: B 219 LEU cc_start: 0.9128 (tp) cc_final: 0.8829 (tp) REVERT: B 285 MET cc_start: 0.7743 (tpp) cc_final: 0.7526 (tpp) REVERT: C 486 CYS cc_start: 0.9257 (t) cc_final: 0.8895 (t) REVERT: C 519 LEU cc_start: 0.9681 (tp) cc_final: 0.9398 (tp) REVERT: C 526 GLU cc_start: 0.8973 (pt0) cc_final: 0.8617 (pt0) REVERT: C 594 MET cc_start: 0.9323 (mmm) cc_final: 0.8434 (mmm) REVERT: C 598 ARG cc_start: 0.9619 (mmt-90) cc_final: 0.9312 (mmp80) REVERT: C 606 MET cc_start: 0.8890 (ptt) cc_final: 0.8152 (ppp) REVERT: C 616 LYS cc_start: 0.9543 (ptmt) cc_final: 0.8587 (ptmt) REVERT: C 680 MET cc_start: 0.9309 (pmm) cc_final: 0.8786 (pmm) REVERT: C 700 GLU cc_start: 0.9335 (tt0) cc_final: 0.8645 (tm-30) REVERT: C 705 MET cc_start: 0.9336 (mmt) cc_final: 0.8939 (mpp) REVERT: C 733 MET cc_start: 0.9297 (mmt) cc_final: 0.9090 (mmm) REVERT: C 737 MET cc_start: 0.9574 (ttm) cc_final: 0.9305 (ttp) REVERT: C 807 MET cc_start: 0.9074 (tmm) cc_final: 0.8671 (tmm) REVERT: C 878 ARG cc_start: 0.9244 (mtt90) cc_final: 0.8689 (ptp-110) REVERT: C 938 PHE cc_start: 0.9369 (t80) cc_final: 0.9109 (t80) REVERT: C 1010 LEU cc_start: 0.9793 (tp) cc_final: 0.9584 (tp) REVERT: C 1013 HIS cc_start: 0.9393 (t-90) cc_final: 0.8807 (t-170) REVERT: C 1026 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8677 (tp30) REVERT: D 1 MET cc_start: 0.7857 (mtm) cc_final: 0.7507 (mpp) REVERT: D 65 ASN cc_start: 0.9521 (p0) cc_final: 0.9246 (p0) REVERT: D 72 LEU cc_start: 0.9416 (mp) cc_final: 0.9205 (mp) REVERT: D 173 ASN cc_start: 0.9087 (m-40) cc_final: 0.8876 (m-40) REVERT: D 347 GLN cc_start: 0.8906 (tt0) cc_final: 0.8576 (tm-30) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1465 time to fit residues: 47.5853 Evaluate side-chains 178 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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: 7.9990 chunk 82 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 188 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 45 optimal weight: 40.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 HIS ** B 33 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.062472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.040792 restraints weight = 260925.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.042987 restraints weight = 110825.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.044435 restraints weight = 65742.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045426 restraints weight = 46130.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.046074 restraints weight = 36028.538| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17999 Z= 0.170 Angle : 0.722 9.538 24728 Z= 0.386 Chirality : 0.045 0.301 2694 Planarity : 0.005 0.065 2854 Dihedral : 22.043 179.684 3229 Min Nonbonded Distance : 1.624 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.24 % Allowed : 0.35 % 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: -2.03 (0.18), residues: 1921 helix: -0.47 (0.19), residues: 670 sheet: -1.55 (0.27), residues: 354 loop : -1.89 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 897 TYR 0.022 0.002 TYR C 500 PHE 0.030 0.002 PHE A 826 TRP 0.024 0.002 TRP A 782 HIS 0.012 0.002 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (17992) covalent geometry : angle 0.71899 / 0.39 (24726) hydrogen bonds : bond 0.04769 / 3.16 ( 746) hydrogen bonds : angle 5.25378 / 3.67 ( 2107) metal coordination : bond 0.01404 / 0.80 ( 7) metal coordination : angle 7.25743 / 2.98 ( 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 221 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.656 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 495 LEU cc_start: 0.9309 (mt) cc_final: 0.9069 (pp) REVERT: A 522 LEU cc_start: 0.9489 (mt) cc_final: 0.9107 (mt) REVERT: A 526 GLU cc_start: 0.9033 (pm20) cc_final: 0.8800 (pm20) REVERT: A 731 GLU cc_start: 0.9082 (tp30) cc_final: 0.8574 (tm-30) REVERT: A 732 LYS cc_start: 0.9245 (tmtt) cc_final: 0.8822 (tppt) REVERT: A 733 MET cc_start: 0.9110 (ttm) cc_final: 0.8867 (tmm) REVERT: A 738 GLU cc_start: 0.8960 (tp30) cc_final: 0.7927 (tm-30) REVERT: A 802 SER cc_start: 0.9001 (p) cc_final: 0.8630 (t) REVERT: A 817 HIS cc_start: 0.9227 (m90) cc_final: 0.8907 (m90) REVERT: A 828 LYS cc_start: 0.9435 (tttt) cc_final: 0.8833 (tptp) REVERT: A 912 LYS cc_start: 0.9797 (pptt) cc_final: 0.9529 (pptt) REVERT: A 987 ASN cc_start: 0.9630 (p0) cc_final: 0.9403 (p0) REVERT: A 995 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8067 (tppt) REVERT: A 1006 LEU cc_start: 0.9607 (tp) cc_final: 0.9346 (tp) REVERT: B 129 LEU cc_start: 0.8783 (mp) cc_final: 0.8489 (mp) REVERT: B 197 LEU cc_start: 0.8668 (tp) cc_final: 0.8044 (tt) REVERT: B 219 LEU cc_start: 0.9168 (tp) cc_final: 0.8957 (tp) REVERT: B 285 MET cc_start: 0.7768 (tpp) cc_final: 0.7544 (tpp) REVERT: C 519 LEU cc_start: 0.9653 (tp) cc_final: 0.9375 (tp) REVERT: C 526 GLU cc_start: 0.9116 (pt0) cc_final: 0.8560 (pt0) REVERT: C 527 LYS cc_start: 0.9682 (mttt) cc_final: 0.8926 (tptm) REVERT: C 594 MET cc_start: 0.9324 (mmm) cc_final: 0.8376 (mmm) REVERT: C 598 ARG cc_start: 0.9641 (mmt-90) cc_final: 0.9301 (mmp80) REVERT: C 606 MET cc_start: 0.8842 (ptt) cc_final: 0.8436 (ppp) REVERT: C 616 LYS cc_start: 0.9551 (ptmt) cc_final: 0.8619 (ptmt) REVERT: C 680 MET cc_start: 0.9312 (pmm) cc_final: 0.8793 (pmm) REVERT: C 700 GLU cc_start: 0.9334 (tt0) cc_final: 0.8598 (tm-30) REVERT: C 733 MET cc_start: 0.9319 (mmt) cc_final: 0.9108 (mmm) REVERT: C 737 MET cc_start: 0.9587 (ttm) cc_final: 0.9319 (ttp) REVERT: C 807 MET cc_start: 0.9076 (tmm) cc_final: 0.8706 (tmm) REVERT: C 878 ARG cc_start: 0.9223 (mtt90) cc_final: 0.8629 (ptp-110) REVERT: C 911 MET cc_start: 0.8669 (tpp) cc_final: 0.7722 (tpp) REVERT: C 938 PHE cc_start: 0.9373 (t80) cc_final: 0.9111 (t80) REVERT: C 1013 HIS cc_start: 0.9398 (t-90) cc_final: 0.8800 (t-170) REVERT: C 1026 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8690 (tp30) REVERT: D 1 MET cc_start: 0.7801 (mtm) cc_final: 0.7423 (mpp) REVERT: D 65 ASN cc_start: 0.9520 (p0) cc_final: 0.9246 (p0) REVERT: D 72 LEU cc_start: 0.9424 (mp) cc_final: 0.9206 (mp) REVERT: D 173 ASN cc_start: 0.9061 (m-40) cc_final: 0.8848 (m-40) REVERT: D 347 GLN cc_start: 0.8908 (tt0) cc_final: 0.8555 (tm-30) outliers start: 1 outliers final: 1 residues processed: 220 average time/residue: 0.1431 time to fit residues: 47.2771 Evaluate side-chains 185 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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: 8.9990 chunk 110 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 170 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.061722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.040274 restraints weight = 246033.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.042391 restraints weight = 108754.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.043829 restraints weight = 65556.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.044756 restraints weight = 46360.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045398 restraints weight = 36616.750| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- 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: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (17 function evaluations) r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17999 Z= 0.201 Angle : 0.741 9.438 24728 Z= 0.395 Chirality : 0.046 0.445 2694 Planarity : 0.005 0.065 2854 Dihedral : 22.005 179.513 3229 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % 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: -2.02 (0.18), residues: 1921 helix: -0.43 (0.19), residues: 668 sheet: -1.53 (0.27), residues: 358 loop : -1.92 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 96 TYR 0.032 0.002 TYR D 90 PHE 0.029 0.002 PHE A 826 TRP 0.022 0.002 TRP C 560 HIS 0.012 0.002 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (17992) covalent geometry : angle 0.73904 / 0.40 (24726) hydrogen bonds : bond 0.04912 / 3.29 ( 746) hydrogen bonds : angle 5.29742 / 3.71 ( 2107) metal coordination : bond 0.01149 / 0.72 ( 7) metal coordination : angle 5.64837 / 2.37 ( 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 213 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.676 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: A 526 GLU cc_start: 0.9040 (pm20) cc_final: 0.8812 (pm20) REVERT: A 622 MET cc_start: 0.8891 (mmm) cc_final: 0.8684 (mmm) REVERT: A 667 LYS cc_start: 0.9523 (ptmt) cc_final: 0.9265 (ttpp) REVERT: A 731 GLU cc_start: 0.9183 (tp30) cc_final: 0.8553 (tm-30) REVERT: A 732 LYS cc_start: 0.9311 (tmtt) cc_final: 0.9063 (tppt) REVERT: A 733 MET cc_start: 0.9144 (ttm) cc_final: 0.8876 (tmm) REVERT: A 738 GLU cc_start: 0.8978 (tp30) cc_final: 0.7955 (tm-30) REVERT: A 802 SER cc_start: 0.9032 (p) cc_final: 0.8648 (t) REVERT: A 817 HIS cc_start: 0.9263 (m90) cc_final: 0.8951 (m90) REVERT: A 828 LYS cc_start: 0.9444 (tttt) cc_final: 0.8838 (tptp) REVERT: A 912 LYS cc_start: 0.9790 (pptt) cc_final: 0.9524 (pptt) REVERT: A 987 ASN cc_start: 0.9585 (p0) cc_final: 0.9358 (p0) REVERT: A 995 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8276 (tppt) REVERT: A 1006 LEU cc_start: 0.9619 (tp) cc_final: 0.9351 (tp) REVERT: B 129 LEU cc_start: 0.8795 (mp) cc_final: 0.8485 (mp) REVERT: B 219 LEU cc_start: 0.9173 (tp) cc_final: 0.8855 (tp) REVERT: B 285 MET cc_start: 0.7805 (tpp) cc_final: 0.7575 (tpp) REVERT: C 454 PHE cc_start: 0.7501 (t80) cc_final: 0.7148 (t80) REVERT: C 519 LEU cc_start: 0.9667 (tp) cc_final: 0.9402 (tp) REVERT: C 527 LYS cc_start: 0.9674 (mttt) cc_final: 0.9090 (mtmm) REVERT: C 594 MET cc_start: 0.9349 (mmm) cc_final: 0.8467 (mmm) REVERT: C 598 ARG cc_start: 0.9632 (mmt-90) cc_final: 0.9323 (mmp80) REVERT: C 606 MET cc_start: 0.8833 (ptt) cc_final: 0.8417 (ppp) REVERT: C 616 LYS cc_start: 0.9551 (ptmt) cc_final: 0.8640 (ptmt) REVERT: C 680 MET cc_start: 0.9349 (pmm) cc_final: 0.8811 (pmm) REVERT: C 700 GLU cc_start: 0.9369 (tt0) cc_final: 0.8668 (tm-30) REVERT: C 705 MET cc_start: 0.9250 (mmt) cc_final: 0.8862 (mpp) REVERT: C 737 MET cc_start: 0.9599 (ttm) cc_final: 0.9167 (ppp) REVERT: C 807 MET cc_start: 0.9130 (tmm) cc_final: 0.8761 (ppp) REVERT: C 878 ARG cc_start: 0.9288 (mtt90) cc_final: 0.8707 (ptp-110) REVERT: C 911 MET cc_start: 0.8692 (tpp) cc_final: 0.7731 (tpp) REVERT: C 938 PHE cc_start: 0.9382 (t80) cc_final: 0.9049 (t80) REVERT: C 1010 LEU cc_start: 0.9808 (tp) cc_final: 0.9605 (tp) REVERT: C 1013 HIS cc_start: 0.9405 (t-90) cc_final: 0.8840 (t-170) REVERT: C 1025 MET cc_start: 0.8687 (mmt) cc_final: 0.8323 (mmm) REVERT: C 1026 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8694 (tp30) REVERT: D 1 MET cc_start: 0.7955 (mtm) cc_final: 0.7601 (mpp) REVERT: D 65 ASN cc_start: 0.9550 (p0) cc_final: 0.9293 (p0) REVERT: D 72 LEU cc_start: 0.9417 (mp) cc_final: 0.9215 (mp) REVERT: D 173 ASN cc_start: 0.9026 (m-40) cc_final: 0.8811 (m-40) REVERT: D 347 GLN cc_start: 0.8876 (tt0) cc_final: 0.8550 (tm-30) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1417 time to fit residues: 45.6136 Evaluate side-chains 171 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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: 9.9990 chunk 85 optimal weight: 3.9990 chunk 180 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 97 optimal weight: 40.0000 chunk 118 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN ** 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 = 0.3430 r_free = 0.3430 target = 0.063846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.041864 restraints weight = 247561.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.044106 restraints weight = 105870.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.045598 restraints weight = 63056.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046584 restraints weight = 44265.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047258 restraints weight = 34640.468| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (18 function evaluations) r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17999 Z= 0.140 Angle : 0.715 10.613 24728 Z= 0.380 Chirality : 0.045 0.298 2694 Planarity : 0.005 0.066 2854 Dihedral : 21.928 179.908 3229 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.18 % Allowed : 0.24 % Favored : 99.59 % 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: -1.79 (0.18), residues: 1921 helix: -0.17 (0.20), residues: 659 sheet: -1.32 (0.28), residues: 352 loop : -1.87 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 897 TYR 0.043 0.002 TYR D 90 PHE 0.028 0.002 PHE A 826 TRP 0.031 0.002 TRP C 560 HIS 0.010 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (17992) covalent geometry : angle 0.71123 / 0.38 (24726) hydrogen bonds : bond 0.04518 / 2.96 ( 746) hydrogen bonds : angle 5.09277 / 3.57 ( 2107) metal coordination : bond 0.01269 / 0.76 ( 7) metal coordination : angle 8.17826 / 3.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3318.88 seconds wall clock time: 58 minutes 17.61 seconds (3497.61 seconds total)