Starting phenix.real_space_refine on Fri Mar 6 14:58:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rq6_24628/03_2026/7rq6_24628.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rq6_24628/03_2026/7rq6_24628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rq6_24628/03_2026/7rq6_24628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rq6_24628/03_2026/7rq6_24628.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rq6_24628/03_2026/7rq6_24628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rq6_24628/03_2026/7rq6_24628.map" } resolution = 4.18 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= -0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 504 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 19944 2.51 5 N 5151 2.21 5 O 6138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31368 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8464 Classifications: {'peptide': 1086} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "B" Number of atoms: 8464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8464 Classifications: {'peptide': 1086} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "C" Number of atoms: 8464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8464 Classifications: {'peptide': 1086} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "K" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 7.31, per 1000 atoms: 0.23 Number of scatterers: 31368 At special positions: 0 Unit cell: (208.096, 200.092, 176.081, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 6138 8.00 N 5151 7.00 C 19944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 165 " " NAG A2003 " - " ASN A 234 " " NAG A2004 " - " ASN A 282 " " NAG A2005 " - " ASN A 331 " " NAG A2006 " - " ASN A 616 " " NAG A2007 " - " ASN A 657 " " NAG A2008 " - " ASN A 709 " " NAG A2009 " - " ASN A 717 " " NAG A2010 " - " ASN A 801 " " NAG A2011 " - " ASN A1074 " " NAG A2012 " - " ASN A1134 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 165 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 282 " " NAG B2005 " - " ASN B 331 " " NAG B2006 " - " ASN B 616 " " NAG B2007 " - " ASN B 657 " " NAG B2008 " - " ASN B 709 " " NAG B2009 " - " ASN B 717 " " NAG B2010 " - " ASN B 801 " " NAG B2011 " - " ASN B1074 " " NAG B2012 " - " ASN B1134 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 165 " " NAG C2003 " - " ASN C 234 " " NAG C2004 " - " ASN C 282 " " NAG C2005 " - " ASN C 331 " " NAG C2006 " - " ASN C 616 " " NAG C2007 " - " ASN C 657 " " NAG C2008 " - " ASN C 709 " " NAG C2009 " - " ASN C 717 " " NAG C2010 " - " ASN C 801 " " NAG C2011 " - " ASN C1074 " " NAG C2012 " - " ASN C1134 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B1098 " " NAG I 1 " - " ASN C1098 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7368 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 65 sheets defined 20.0% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.703A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.506A pdb=" N ALA A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.532A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.709A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.591A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.128A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 906 removed outlier: 4.194A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 909 No H-bonds generated for 'chain 'A' and resid 907 through 909' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.576A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.821A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.643A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 86 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.599A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.700A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.500A pdb=" N ALA B 623 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.536A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.702A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 800 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.602A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.519A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 906 removed outlier: 4.142A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 909 No H-bonds generated for 'chain 'B' and resid 907 through 909' Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.539A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.811A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.664A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 86 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.612A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.699A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 416 through 423 Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.503A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.521A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.697A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 800 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.607A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.133A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 906 removed outlier: 4.164A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 909 No H-bonds generated for 'chain 'C' and resid 907 through 909' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.525A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.812A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.673A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 86 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 removed outlier: 3.868A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.900A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.510A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.313A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.565A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 516 through 517 removed outlier: 3.545A pdb=" N GLU A 516 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 4.406A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.650A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.130A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.825A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.288A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.167A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.532A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR H 96 " --> pdb=" O MET H 100F" (cutoff:3.500A) removed outlier: 5.975A pdb=" N MET H 100F" --> pdb=" O TYR H 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.482A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC6, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.411A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 50 through 53 removed outlier: 3.877A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 91 through 93 removed outlier: 4.064A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AD1, first strand: chain 'B' and resid 314 through 319 removed outlier: 6.045A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.505A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 376 through 377 removed outlier: 3.631A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 516 through 517 removed outlier: 3.558A pdb=" N GLU B 516 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 4.402A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.628A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.152A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AE2, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AE3, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.284A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.158A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.678A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR D 100E" --> pdb=" O TYR D 96 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.311A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS E 107 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AF1, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.380A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 50 through 53 removed outlier: 3.866A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 91 through 93 removed outlier: 4.073A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AF5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.492A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.443A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 376 through 377 removed outlier: 3.614A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 516 through 517 removed outlier: 3.536A pdb=" N GLU C 516 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AG1, first strand: chain 'C' and resid 654 through 655 removed outlier: 4.415A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.665A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.146A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AG5, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AG6, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.272A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.168A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.634A pdb=" N VAL J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TYR J 96 " --> pdb=" O MET J 100F" (cutoff:3.500A) removed outlier: 6.106A pdb=" N MET J 100F" --> pdb=" O TYR J 96 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AH2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.326A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 1022 hydrogen bonds defined for protein. 2682 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.70 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9792 1.34 - 1.46: 7981 1.46 - 1.59: 14138 1.59 - 1.71: 0 1.71 - 1.84: 171 Bond restraints: 32082 Sorted by residual: bond pdb=" CA GLY B 184 " pdb=" C GLY B 184 " ideal model delta sigma weight residual 1.518 1.497 0.020 1.07e-02 8.73e+03 3.60e+00 bond pdb=" CA VAL A 70 " pdb=" C VAL A 70 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.27e-02 6.20e+03 2.76e+00 bond pdb=" CA PHE A 543 " pdb=" C PHE A 543 " ideal model delta sigma weight residual 1.526 1.504 0.021 1.30e-02 5.92e+03 2.71e+00 bond pdb=" CA ASN C 185 " pdb=" C ASN C 185 " ideal model delta sigma weight residual 1.528 1.508 0.021 1.28e-02 6.10e+03 2.65e+00 bond pdb=" CA PHE C 543 " pdb=" C PHE C 543 " ideal model delta sigma weight residual 1.525 1.504 0.021 1.28e-02 6.10e+03 2.60e+00 ... (remaining 32077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 42829 2.45 - 4.90: 752 4.90 - 7.36: 73 7.36 - 9.81: 10 9.81 - 12.26: 4 Bond angle restraints: 43668 Sorted by residual: angle pdb=" N THR A 73 " pdb=" CA THR A 73 " pdb=" C THR A 73 " ideal model delta sigma weight residual 112.68 103.25 9.43 1.33e+00 5.65e-01 5.03e+01 angle pdb=" C PHE B 347 " pdb=" CA PHE B 347 " pdb=" CB PHE B 347 " ideal model delta sigma weight residual 116.54 109.69 6.85 1.15e+00 7.56e-01 3.55e+01 angle pdb=" C PHE C 347 " pdb=" CA PHE C 347 " pdb=" CB PHE C 347 " ideal model delta sigma weight residual 116.54 109.71 6.83 1.15e+00 7.56e-01 3.52e+01 angle pdb=" C PHE A 347 " pdb=" CA PHE A 347 " pdb=" CB PHE A 347 " ideal model delta sigma weight residual 116.54 109.72 6.82 1.15e+00 7.56e-01 3.52e+01 angle pdb=" N GLN C 563 " pdb=" CA GLN C 563 " pdb=" C GLN C 563 " ideal model delta sigma weight residual 108.00 116.69 -8.69 1.48e+00 4.57e-01 3.45e+01 ... (remaining 43663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 17765 17.46 - 34.91: 1567 34.91 - 52.37: 205 52.37 - 69.83: 53 69.83 - 87.28: 33 Dihedral angle restraints: 19623 sinusoidal: 8136 harmonic: 11487 Sorted by residual: dihedral pdb=" C GLN C 563 " pdb=" N GLN C 563 " pdb=" CA GLN C 563 " pdb=" CB GLN C 563 " ideal model delta harmonic sigma weight residual -122.60 -135.36 12.76 0 2.50e+00 1.60e-01 2.61e+01 dihedral pdb=" CA ARG B 158 " pdb=" C ARG B 158 " pdb=" N VAL B 159 " pdb=" CA VAL B 159 " ideal model delta harmonic sigma weight residual 180.00 -156.65 -23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ARG A 158 " pdb=" C ARG A 158 " pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta harmonic sigma weight residual -180.00 -157.04 -22.96 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 19620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4762 0.096 - 0.192: 279 0.192 - 0.289: 15 0.289 - 0.385: 4 0.385 - 0.481: 1 Chirality restraints: 5061 Sorted by residual: chirality pdb=" CA GLN C 563 " pdb=" N GLN C 563 " pdb=" C GLN C 563 " pdb=" CB GLN C 563 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" C1 NAG C2008 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C2008 " pdb=" O5 NAG C2008 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C1 NAG B2008 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B2008 " pdb=" O5 NAG B2008 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 5058 not shown) Planarity restraints: 5616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 66 " 0.019 2.00e-02 2.50e+03 3.69e-02 1.37e+01 pdb=" C GLY E 66 " -0.064 2.00e-02 2.50e+03 pdb=" O GLY E 66 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE E 67 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 190 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C ARG B 190 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG B 190 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU B 191 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 190 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ARG A 190 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG A 190 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU A 191 " -0.012 2.00e-02 2.50e+03 ... (remaining 5613 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1226 2.71 - 3.26: 31968 3.26 - 3.80: 49426 3.80 - 4.35: 58990 4.35 - 4.90: 99379 Nonbonded interactions: 240989 Sorted by model distance: nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.159 3.040 nonbonded pdb=" OG1 THR C 618 " pdb=" OE1 GLU C 619 " model vdw 2.160 3.040 nonbonded pdb=" OG1 THR B 618 " pdb=" OE1 GLU B 619 " model vdw 2.168 3.040 nonbonded pdb=" O GLN C 804 " pdb=" OG SER C 816 " model vdw 2.191 3.040 nonbonded pdb=" O GLN B 804 " pdb=" OG SER B 816 " model vdw 2.200 3.040 ... (remaining 240984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.820 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 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 : 0.005 0.062 32163 Z= 0.214 Angle : 0.777 12.260 43872 Z= 0.424 Chirality : 0.050 0.481 5061 Planarity : 0.004 0.043 5577 Dihedral : 13.245 87.283 12138 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.30 % Favored : 91.62 % Rotamer: Outliers : 0.03 % Allowed : 0.93 % Favored : 99.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 3891 helix: 1.44 (0.22), residues: 633 sheet: -0.90 (0.17), residues: 861 loop : -1.95 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.027 0.001 TYR A 265 PHE 0.022 0.002 PHE C 906 TRP 0.020 0.002 TRP D 103 HIS 0.009 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00451 (32082) covalent geometry : angle 0.75980 (43668) SS BOND : bond 0.00379 ( 39) SS BOND : angle 1.16744 ( 78) hydrogen bonds : bond 0.14501 ( 977) hydrogen bonds : angle 6.74923 ( 2682) link_BETA1-4 : bond 0.00062 ( 3) link_BETA1-4 : angle 1.28320 ( 9) link_NAG-ASN : bond 0.00510 ( 39) link_NAG-ASN : angle 3.11318 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.7329 (p90) cc_final: 0.6780 (p90) REVERT: A 333 THR cc_start: 0.8046 (t) cc_final: 0.7825 (m) REVERT: H 100 MET cc_start: 0.7837 (tpp) cc_final: 0.7438 (tpp) REVERT: L 3 ARG cc_start: 0.7292 (mmp-170) cc_final: 0.6858 (tmm160) REVERT: L 74 THR cc_start: 0.6171 (p) cc_final: 0.5914 (p) REVERT: B 869 MET cc_start: 0.7042 (mtm) cc_final: 0.6806 (mtm) REVERT: D 100 MET cc_start: 0.7622 (tpp) cc_final: 0.7394 (tpp) REVERT: E 74 THR cc_start: 0.5246 (p) cc_final: 0.5044 (p) REVERT: J 100 MET cc_start: 0.7904 (tpp) cc_final: 0.7304 (tpp) REVERT: K 74 THR cc_start: 0.5835 (p) cc_final: 0.5566 (p) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.1800 time to fit residues: 80.5316 Evaluate side-chains 173 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.0010 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN A 804 GLN A 895 GLN L 31 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 804 GLN B 895 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN C 460 ASN C 895 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN K 38 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.116900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.097575 restraints weight = 119542.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.093047 restraints weight = 160531.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.090254 restraints weight = 158410.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.090811 restraints weight = 140308.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.090573 restraints weight = 97872.723| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32163 Z= 0.114 Angle : 0.602 10.938 43872 Z= 0.307 Chirality : 0.045 0.298 5061 Planarity : 0.004 0.045 5577 Dihedral : 5.531 54.182 5133 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.86 % Favored : 93.06 % Rotamer: Outliers : 0.12 % Allowed : 4.18 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 3891 helix: 1.60 (0.21), residues: 639 sheet: -0.53 (0.18), residues: 801 loop : -1.82 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 78 TYR 0.022 0.001 TYR B1067 PHE 0.025 0.001 PHE B 186 TRP 0.015 0.001 TRP B 436 HIS 0.009 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00253 (32082) covalent geometry : angle 0.58497 (43668) SS BOND : bond 0.00261 ( 39) SS BOND : angle 0.84176 ( 78) hydrogen bonds : bond 0.04072 ( 977) hydrogen bonds : angle 5.28128 ( 2682) link_BETA1-4 : bond 0.00286 ( 3) link_BETA1-4 : angle 1.19252 ( 9) link_NAG-ASN : bond 0.00590 ( 39) link_NAG-ASN : angle 2.77209 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 268 time to evaluate : 1.108 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: H 102 VAL cc_start: 0.7786 (t) cc_final: 0.7532 (t) REVERT: L 38 GLN cc_start: 0.6916 (mm110) cc_final: 0.6639 (tp40) REVERT: L 74 THR cc_start: 0.6290 (p) cc_final: 0.6011 (p) REVERT: B 1029 MET cc_start: 0.9045 (tpp) cc_final: 0.8841 (tpp) REVERT: C 265 TYR cc_start: 0.7050 (p90) cc_final: 0.6676 (p90) REVERT: J 3 GLN cc_start: 0.7677 (pm20) cc_final: 0.6870 (tm-30) REVERT: J 100 MET cc_start: 0.7855 (tpp) cc_final: 0.7395 (tpp) REVERT: J 102 VAL cc_start: 0.7480 (t) cc_final: 0.7072 (t) REVERT: K 74 THR cc_start: 0.5988 (p) cc_final: 0.5762 (p) outliers start: 4 outliers final: 0 residues processed: 272 average time/residue: 0.1822 time to fit residues: 82.8359 Evaluate side-chains 179 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 96 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 277 optimal weight: 9.9990 chunk 251 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 385 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 360 ASN A 895 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 422 ASN B 895 GLN B 928 ASN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN C 149 ASN C 360 ASN C 422 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.114831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.095330 restraints weight = 119561.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.092648 restraints weight = 163696.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.089637 restraints weight = 131552.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.088836 restraints weight = 142442.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.088304 restraints weight = 108295.501| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32163 Z= 0.173 Angle : 0.629 10.173 43872 Z= 0.323 Chirality : 0.045 0.277 5061 Planarity : 0.004 0.048 5577 Dihedral : 5.396 56.237 5133 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.74 % Favored : 92.19 % Rotamer: Outliers : 0.20 % Allowed : 4.64 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.41 (0.13), residues: 3891 helix: 1.42 (0.21), residues: 624 sheet: -0.43 (0.18), residues: 843 loop : -1.88 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 3 TYR 0.021 0.001 TYR B1067 PHE 0.022 0.002 PHE B 186 TRP 0.015 0.002 TRP H 35A HIS 0.008 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00392 (32082) covalent geometry : angle 0.61203 (43668) SS BOND : bond 0.00242 ( 39) SS BOND : angle 0.92733 ( 78) hydrogen bonds : bond 0.04282 ( 977) hydrogen bonds : angle 5.34799 ( 2682) link_BETA1-4 : bond 0.00077 ( 3) link_BETA1-4 : angle 1.06765 ( 9) link_NAG-ASN : bond 0.00572 ( 39) link_NAG-ASN : angle 2.79709 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 272 time to evaluate : 1.087 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: A 265 TYR cc_start: 0.7108 (p90) cc_final: 0.6778 (p90) REVERT: A 849 LEU cc_start: 0.8293 (mp) cc_final: 0.8088 (mt) REVERT: H 102 VAL cc_start: 0.7717 (t) cc_final: 0.7301 (t) REVERT: L 38 GLN cc_start: 0.6911 (mm110) cc_final: 0.6578 (tp40) REVERT: L 74 THR cc_start: 0.6349 (p) cc_final: 0.6062 (p) REVERT: D 102 VAL cc_start: 0.7486 (t) cc_final: 0.6931 (t) REVERT: E 74 THR cc_start: 0.5411 (p) cc_final: 0.5166 (p) REVERT: C 265 TYR cc_start: 0.7028 (p90) cc_final: 0.6642 (p90) REVERT: C 473 TYR cc_start: 0.4898 (p90) cc_final: 0.4625 (p90) REVERT: J 100 MET cc_start: 0.7899 (tpp) cc_final: 0.7550 (tpp) REVERT: J 102 VAL cc_start: 0.7596 (t) cc_final: 0.7106 (t) REVERT: K 74 THR cc_start: 0.6175 (p) cc_final: 0.5946 (p) outliers start: 7 outliers final: 0 residues processed: 279 average time/residue: 0.1936 time to fit residues: 88.2442 Evaluate side-chains 174 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 104 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 236 optimal weight: 0.6980 chunk 221 optimal weight: 0.6980 chunk 388 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 374 optimal weight: 2.9990 chunk 325 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 895 GLN B 895 GLN B 978 ASN E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN K 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.115392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.095119 restraints weight = 119010.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.090524 restraints weight = 165371.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.088192 restraints weight = 158781.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.088582 restraints weight = 129938.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.088831 restraints weight = 99812.744| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32163 Z= 0.140 Angle : 0.606 10.284 43872 Z= 0.309 Chirality : 0.045 0.281 5061 Planarity : 0.004 0.074 5577 Dihedral : 5.121 55.194 5133 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.99 % Favored : 92.93 % Rotamer: Outliers : 0.12 % Allowed : 3.22 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.14), residues: 3891 helix: 1.65 (0.21), residues: 609 sheet: -0.46 (0.18), residues: 810 loop : -1.82 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 3 TYR 0.016 0.001 TYR C 266 PHE 0.020 0.002 PHE A 377 TRP 0.026 0.002 TRP H 103 HIS 0.009 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00317 (32082) covalent geometry : angle 0.58807 (43668) SS BOND : bond 0.00259 ( 39) SS BOND : angle 0.91741 ( 78) hydrogen bonds : bond 0.03984 ( 977) hydrogen bonds : angle 5.18038 ( 2682) link_BETA1-4 : bond 0.00093 ( 3) link_BETA1-4 : angle 0.99864 ( 9) link_NAG-ASN : bond 0.00549 ( 39) link_NAG-ASN : angle 2.84288 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 270 time to evaluate : 1.133 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: A 265 TYR cc_start: 0.7013 (p90) cc_final: 0.6710 (p90) REVERT: A 849 LEU cc_start: 0.8215 (mp) cc_final: 0.7942 (mt) REVERT: H 102 VAL cc_start: 0.7680 (t) cc_final: 0.7401 (t) REVERT: L 38 GLN cc_start: 0.6828 (mm110) cc_final: 0.6435 (tp40) REVERT: L 74 THR cc_start: 0.6281 (p) cc_final: 0.6019 (p) REVERT: L 78 LEU cc_start: 0.4715 (mm) cc_final: 0.4353 (mt) REVERT: D 102 VAL cc_start: 0.7315 (t) cc_final: 0.6821 (t) REVERT: E 38 GLN cc_start: 0.7693 (mm110) cc_final: 0.6715 (tt0) REVERT: E 74 THR cc_start: 0.5217 (p) cc_final: 0.4966 (p) REVERT: C 265 TYR cc_start: 0.6934 (p90) cc_final: 0.6615 (p90) REVERT: C 473 TYR cc_start: 0.4752 (p90) cc_final: 0.4484 (p90) REVERT: J 3 GLN cc_start: 0.7588 (pm20) cc_final: 0.7301 (tm-30) REVERT: J 102 VAL cc_start: 0.7509 (t) cc_final: 0.7155 (t) REVERT: K 74 THR cc_start: 0.6087 (p) cc_final: 0.5853 (p) outliers start: 4 outliers final: 0 residues processed: 274 average time/residue: 0.1815 time to fit residues: 82.9413 Evaluate side-chains 187 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 25 optimal weight: 0.8980 chunk 308 optimal weight: 0.0980 chunk 335 optimal weight: 0.2980 chunk 288 optimal weight: 0.0970 chunk 246 optimal weight: 40.0000 chunk 52 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 373 optimal weight: 10.0000 chunk 241 optimal weight: 20.0000 chunk 387 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 978 ASN E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 895 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.116312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.096753 restraints weight = 119307.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.092339 restraints weight = 152412.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.089861 restraints weight = 142734.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.090763 restraints weight = 127188.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.090259 restraints weight = 88810.027| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32163 Z= 0.113 Angle : 0.591 11.128 43872 Z= 0.299 Chirality : 0.045 0.287 5061 Planarity : 0.004 0.060 5577 Dihedral : 4.827 53.902 5133 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.66 % Favored : 93.27 % Rotamer: Outliers : 0.09 % Allowed : 2.09 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.14), residues: 3891 helix: 1.85 (0.22), residues: 609 sheet: -0.40 (0.18), residues: 777 loop : -1.80 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 3 TYR 0.016 0.001 TYR C1067 PHE 0.018 0.001 PHE A 377 TRP 0.023 0.002 TRP B 436 HIS 0.008 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00253 (32082) covalent geometry : angle 0.57369 (43668) SS BOND : bond 0.00346 ( 39) SS BOND : angle 0.83190 ( 78) hydrogen bonds : bond 0.03742 ( 977) hydrogen bonds : angle 4.98956 ( 2682) link_BETA1-4 : bond 0.00204 ( 3) link_BETA1-4 : angle 1.06249 ( 9) link_NAG-ASN : bond 0.00534 ( 39) link_NAG-ASN : angle 2.73795 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 268 time to evaluate : 1.155 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: A 265 TYR cc_start: 0.6991 (p90) cc_final: 0.6753 (p90) REVERT: A 849 LEU cc_start: 0.8244 (mp) cc_final: 0.7967 (mt) REVERT: H 102 VAL cc_start: 0.7652 (t) cc_final: 0.7204 (t) REVERT: L 74 THR cc_start: 0.6214 (p) cc_final: 0.5923 (p) REVERT: B 869 MET cc_start: 0.7047 (mtm) cc_final: 0.6817 (mtm) REVERT: D 3 GLN cc_start: 0.7764 (pm20) cc_final: 0.7247 (tm-30) REVERT: D 66 ARG cc_start: 0.7269 (mpp80) cc_final: 0.7017 (mmm160) REVERT: D 102 VAL cc_start: 0.7283 (t) cc_final: 0.6854 (t) REVERT: E 38 GLN cc_start: 0.7560 (mm110) cc_final: 0.6562 (tt0) REVERT: E 74 THR cc_start: 0.5176 (p) cc_final: 0.4915 (p) REVERT: C 265 TYR cc_start: 0.6856 (p90) cc_final: 0.6587 (p90) REVERT: J 100 MET cc_start: 0.7956 (tpp) cc_final: 0.7245 (tpp) REVERT: J 102 VAL cc_start: 0.7571 (t) cc_final: 0.6849 (t) REVERT: K 38 GLN cc_start: 0.7672 (mm110) cc_final: 0.7343 (tp40) REVERT: K 74 THR cc_start: 0.5979 (p) cc_final: 0.5765 (p) outliers start: 3 outliers final: 0 residues processed: 271 average time/residue: 0.1721 time to fit residues: 79.5900 Evaluate side-chains 189 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 76 optimal weight: 1.9990 chunk 382 optimal weight: 20.0000 chunk 210 optimal weight: 3.9990 chunk 318 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 286 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 355 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 895 GLN B 978 ASN E 27 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 895 GLN C 928 ASN K 38 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.115439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.095667 restraints weight = 118985.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.092847 restraints weight = 163352.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.090501 restraints weight = 135400.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.090598 restraints weight = 134074.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.090010 restraints weight = 104105.970| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32163 Z= 0.142 Angle : 0.605 9.810 43872 Z= 0.306 Chirality : 0.045 0.277 5061 Planarity : 0.004 0.054 5577 Dihedral : 4.863 55.189 5133 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.14 % Favored : 92.78 % Rotamer: Outliers : 0.09 % Allowed : 1.80 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.14), residues: 3891 helix: 1.53 (0.22), residues: 627 sheet: -0.43 (0.18), residues: 825 loop : -1.83 (0.13), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 3 TYR 0.025 0.001 TYR B 265 PHE 0.015 0.002 PHE C 800 TRP 0.022 0.002 TRP B 436 HIS 0.008 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00325 (32082) covalent geometry : angle 0.58704 (43668) SS BOND : bond 0.00216 ( 39) SS BOND : angle 1.08974 ( 78) hydrogen bonds : bond 0.03837 ( 977) hydrogen bonds : angle 5.10175 ( 2682) link_BETA1-4 : bond 0.00175 ( 3) link_BETA1-4 : angle 1.00540 ( 9) link_NAG-ASN : bond 0.00520 ( 39) link_NAG-ASN : angle 2.74570 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 255 time to evaluate : 1.178 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: A 849 LEU cc_start: 0.8371 (mp) cc_final: 0.8055 (mt) REVERT: H 102 VAL cc_start: 0.7729 (t) cc_final: 0.7286 (t) REVERT: L 38 GLN cc_start: 0.6227 (mm110) cc_final: 0.5532 (tt0) REVERT: L 74 THR cc_start: 0.6275 (p) cc_final: 0.5991 (p) REVERT: D 102 VAL cc_start: 0.7320 (t) cc_final: 0.6867 (t) REVERT: E 38 GLN cc_start: 0.7576 (mm110) cc_final: 0.6522 (tt0) REVERT: E 74 THR cc_start: 0.5187 (p) cc_final: 0.4930 (p) REVERT: C 265 TYR cc_start: 0.6898 (p90) cc_final: 0.6630 (p90) REVERT: J 3 GLN cc_start: 0.7552 (pm20) cc_final: 0.7264 (tm-30) REVERT: J 100 MET cc_start: 0.8018 (tpp) cc_final: 0.7654 (tpp) REVERT: J 102 VAL cc_start: 0.7633 (t) cc_final: 0.7000 (t) REVERT: K 74 THR cc_start: 0.5964 (p) cc_final: 0.5739 (p) outliers start: 3 outliers final: 1 residues processed: 258 average time/residue: 0.1829 time to fit residues: 79.2307 Evaluate side-chains 177 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 155 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 322 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 chunk 345 optimal weight: 0.9990 chunk 176 optimal weight: 0.1980 chunk 196 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 334 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 928 ASN B 978 ASN E 27 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.116151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.096167 restraints weight = 119353.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.093048 restraints weight = 157905.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.090362 restraints weight = 132838.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.090323 restraints weight = 132831.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.089926 restraints weight = 98820.283| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32163 Z= 0.113 Angle : 0.594 10.327 43872 Z= 0.301 Chirality : 0.045 0.278 5061 Planarity : 0.004 0.050 5577 Dihedral : 4.720 54.089 5133 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 0.06 % Allowed : 1.07 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.14), residues: 3891 helix: 1.75 (0.22), residues: 609 sheet: -0.40 (0.18), residues: 825 loop : -1.81 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 94 TYR 0.023 0.001 TYR A 265 PHE 0.015 0.001 PHE C 888 TRP 0.023 0.002 TRP C 436 HIS 0.009 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00254 (32082) covalent geometry : angle 0.57693 (43668) SS BOND : bond 0.00475 ( 39) SS BOND : angle 1.14471 ( 78) hydrogen bonds : bond 0.03710 ( 977) hydrogen bonds : angle 4.99576 ( 2682) link_BETA1-4 : bond 0.00064 ( 3) link_BETA1-4 : angle 0.96575 ( 9) link_NAG-ASN : bond 0.00534 ( 39) link_NAG-ASN : angle 2.70808 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 1.124 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: A 265 TYR cc_start: 0.7142 (p90) cc_final: 0.6642 (p90) REVERT: A 849 LEU cc_start: 0.8420 (mp) cc_final: 0.8100 (mt) REVERT: H 102 VAL cc_start: 0.7770 (t) cc_final: 0.7409 (t) REVERT: L 38 GLN cc_start: 0.6261 (mm110) cc_final: 0.5564 (tt0) REVERT: L 74 THR cc_start: 0.6362 (p) cc_final: 0.6088 (p) REVERT: D 3 GLN cc_start: 0.7848 (pm20) cc_final: 0.7290 (tm-30) REVERT: D 102 VAL cc_start: 0.7348 (t) cc_final: 0.6940 (t) REVERT: E 3 ARG cc_start: 0.8094 (tmm160) cc_final: 0.7563 (tmm160) REVERT: E 38 GLN cc_start: 0.7565 (mm110) cc_final: 0.6457 (tt0) REVERT: E 74 THR cc_start: 0.5263 (p) cc_final: 0.4993 (p) REVERT: C 473 TYR cc_start: 0.4994 (p90) cc_final: 0.4697 (p90) REVERT: C 900 MET cc_start: 0.8203 (ptm) cc_final: 0.7934 (ptm) REVERT: J 3 GLN cc_start: 0.7629 (pm20) cc_final: 0.7312 (tm-30) REVERT: J 100 MET cc_start: 0.7886 (tpp) cc_final: 0.7606 (tpp) REVERT: J 102 VAL cc_start: 0.7679 (t) cc_final: 0.7064 (t) REVERT: K 74 THR cc_start: 0.5955 (p) cc_final: 0.5742 (p) outliers start: 2 outliers final: 0 residues processed: 263 average time/residue: 0.1726 time to fit residues: 76.9822 Evaluate side-chains 183 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 283 optimal weight: 0.0050 chunk 263 optimal weight: 3.9990 chunk 200 optimal weight: 0.5980 chunk 221 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 310 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 326 optimal weight: 0.6980 chunk 257 optimal weight: 30.0000 chunk 381 optimal weight: 20.0000 chunk 309 optimal weight: 10.0000 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 895 GLN B 978 ASN E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.119614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.097846 restraints weight = 111780.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.092434 restraints weight = 155758.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.090430 restraints weight = 131465.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.090257 restraints weight = 116453.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.090446 restraints weight = 92555.333| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32163 Z= 0.140 Angle : 0.611 9.730 43872 Z= 0.310 Chirality : 0.045 0.266 5061 Planarity : 0.004 0.052 5577 Dihedral : 4.822 55.476 5133 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.45 % Favored : 92.47 % Rotamer: Outliers : 0.06 % Allowed : 1.13 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3891 helix: 1.45 (0.22), residues: 627 sheet: -0.39 (0.18), residues: 822 loop : -1.85 (0.13), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.022 0.001 TYR A 265 PHE 0.023 0.002 PHE A 888 TRP 0.023 0.002 TRP C 436 HIS 0.009 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00318 (32082) covalent geometry : angle 0.59367 (43668) SS BOND : bond 0.00276 ( 39) SS BOND : angle 1.01743 ( 78) hydrogen bonds : bond 0.03818 ( 977) hydrogen bonds : angle 5.08099 ( 2682) link_BETA1-4 : bond 0.00098 ( 3) link_BETA1-4 : angle 0.96373 ( 9) link_NAG-ASN : bond 0.00524 ( 39) link_NAG-ASN : angle 2.75779 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 259 time to evaluate : 0.776 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: A 265 TYR cc_start: 0.7173 (p90) cc_final: 0.6674 (p90) REVERT: A 849 LEU cc_start: 0.8381 (mp) cc_final: 0.8026 (mt) REVERT: H 102 VAL cc_start: 0.8342 (t) cc_final: 0.7778 (t) REVERT: L 74 THR cc_start: 0.6813 (p) cc_final: 0.6547 (p) REVERT: D 3 GLN cc_start: 0.8066 (pm20) cc_final: 0.7458 (tm-30) REVERT: D 100 MET cc_start: 0.7871 (tpp) cc_final: 0.7640 (tpp) REVERT: D 102 VAL cc_start: 0.7693 (t) cc_final: 0.7144 (t) REVERT: E 38 GLN cc_start: 0.7927 (mm110) cc_final: 0.6516 (tt0) REVERT: E 74 THR cc_start: 0.5829 (p) cc_final: 0.5564 (p) REVERT: J 3 GLN cc_start: 0.8009 (pm20) cc_final: 0.7580 (tm-30) REVERT: J 100 MET cc_start: 0.7926 (tpp) cc_final: 0.7714 (tpp) REVERT: J 102 VAL cc_start: 0.8086 (t) cc_final: 0.7477 (t) REVERT: K 38 GLN cc_start: 0.6013 (tt0) cc_final: 0.5707 (mm110) REVERT: K 74 THR cc_start: 0.6557 (p) cc_final: 0.6340 (p) outliers start: 2 outliers final: 0 residues processed: 261 average time/residue: 0.1783 time to fit residues: 78.1468 Evaluate side-chains 180 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 183 optimal weight: 0.6980 chunk 367 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 255 optimal weight: 0.9990 chunk 260 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 204 optimal weight: 0.0570 chunk 232 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 336 optimal weight: 0.0030 overall best weight: 0.5110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 978 ASN E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 895 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.120843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.100078 restraints weight = 111429.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.094426 restraints weight = 154173.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.091643 restraints weight = 153109.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.092403 restraints weight = 130989.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.092438 restraints weight = 91170.172| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32163 Z= 0.107 Angle : 0.595 11.324 43872 Z= 0.299 Chirality : 0.045 0.279 5061 Planarity : 0.004 0.050 5577 Dihedral : 4.640 53.580 5133 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.53 % Favored : 93.40 % Rotamer: Outliers : 0.06 % Allowed : 0.44 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.14), residues: 3891 helix: 1.56 (0.22), residues: 627 sheet: -0.30 (0.19), residues: 756 loop : -1.76 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1019 TYR 0.021 0.001 TYR A 265 PHE 0.018 0.001 PHE C 888 TRP 0.024 0.001 TRP C 436 HIS 0.009 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00239 (32082) covalent geometry : angle 0.57263 (43668) SS BOND : bond 0.00210 ( 39) SS BOND : angle 0.93129 ( 78) hydrogen bonds : bond 0.03594 ( 977) hydrogen bonds : angle 4.94460 ( 2682) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 1.06435 ( 9) link_NAG-ASN : bond 0.00555 ( 39) link_NAG-ASN : angle 3.10626 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 1.191 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: A 265 TYR cc_start: 0.7086 (p90) cc_final: 0.6606 (p90) REVERT: A 849 LEU cc_start: 0.8406 (mp) cc_final: 0.8042 (mt) REVERT: H 100 MET cc_start: 0.7847 (tpp) cc_final: 0.7273 (tpp) REVERT: H 102 VAL cc_start: 0.8204 (t) cc_final: 0.7709 (t) REVERT: L 74 THR cc_start: 0.6631 (p) cc_final: 0.6355 (p) REVERT: D 3 GLN cc_start: 0.7959 (pm20) cc_final: 0.7415 (tm-30) REVERT: D 102 VAL cc_start: 0.7451 (t) cc_final: 0.6917 (t) REVERT: E 3 ARG cc_start: 0.8229 (tmm160) cc_final: 0.7590 (tmm160) REVERT: E 38 GLN cc_start: 0.7748 (mm110) cc_final: 0.6547 (tt0) REVERT: E 74 THR cc_start: 0.5647 (p) cc_final: 0.5379 (p) REVERT: J 3 GLN cc_start: 0.7855 (pm20) cc_final: 0.7470 (tm-30) REVERT: J 102 VAL cc_start: 0.7890 (t) cc_final: 0.7339 (t) REVERT: K 74 THR cc_start: 0.6312 (p) cc_final: 0.6022 (p) outliers start: 2 outliers final: 0 residues processed: 268 average time/residue: 0.1788 time to fit residues: 81.1274 Evaluate side-chains 181 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 42 optimal weight: 0.0980 chunk 214 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 205 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 253 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 978 ASN E 27 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.115042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.094683 restraints weight = 119208.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.089705 restraints weight = 167511.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.087244 restraints weight = 159158.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.087775 restraints weight = 125974.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.087173 restraints weight = 105842.020| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32163 Z= 0.145 Angle : 0.617 9.928 43872 Z= 0.313 Chirality : 0.045 0.268 5061 Planarity : 0.004 0.051 5577 Dihedral : 4.840 55.600 5133 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.45 % Favored : 92.47 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3891 helix: 1.39 (0.21), residues: 627 sheet: -0.31 (0.18), residues: 876 loop : -1.83 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 3 TYR 0.021 0.001 TYR A 265 PHE 0.024 0.002 PHE A 888 TRP 0.023 0.002 TRP C 436 HIS 0.009 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00330 (32082) covalent geometry : angle 0.59811 (43668) SS BOND : bond 0.00239 ( 39) SS BOND : angle 0.88564 ( 78) hydrogen bonds : bond 0.03809 ( 977) hydrogen bonds : angle 5.10989 ( 2682) link_BETA1-4 : bond 0.00159 ( 3) link_BETA1-4 : angle 0.91077 ( 9) link_NAG-ASN : bond 0.00510 ( 39) link_NAG-ASN : angle 2.95263 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 261 time to evaluate : 1.118 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: A 265 TYR cc_start: 0.7136 (p90) cc_final: 0.6632 (p90) REVERT: A 849 LEU cc_start: 0.8461 (mp) cc_final: 0.8061 (mt) REVERT: H 100 MET cc_start: 0.7903 (tpp) cc_final: 0.7358 (tpp) REVERT: H 102 VAL cc_start: 0.8324 (t) cc_final: 0.7762 (t) REVERT: L 3 ARG cc_start: 0.7945 (tmm160) cc_final: 0.7731 (tmm160) REVERT: L 38 GLN cc_start: 0.6528 (mm110) cc_final: 0.4654 (tt0) REVERT: L 74 THR cc_start: 0.6749 (p) cc_final: 0.6476 (p) REVERT: D 3 GLN cc_start: 0.8186 (pm20) cc_final: 0.7576 (tm-30) REVERT: D 102 VAL cc_start: 0.7755 (t) cc_final: 0.7180 (t) REVERT: E 3 ARG cc_start: 0.8405 (tmm160) cc_final: 0.7821 (tmm160) REVERT: E 74 THR cc_start: 0.5662 (p) cc_final: 0.5386 (p) REVERT: J 3 GLN cc_start: 0.7993 (pm20) cc_final: 0.7619 (tm-30) REVERT: J 102 VAL cc_start: 0.8074 (t) cc_final: 0.7429 (t) REVERT: K 38 GLN cc_start: 0.7741 (mm110) cc_final: 0.6379 (tt0) REVERT: K 44 PRO cc_start: 0.6855 (Cg_exo) cc_final: 0.6305 (Cg_endo) REVERT: K 74 THR cc_start: 0.6262 (p) cc_final: 0.5975 (p) outliers start: 3 outliers final: 1 residues processed: 264 average time/residue: 0.1735 time to fit residues: 76.9785 Evaluate side-chains 188 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 283 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 chunk 348 optimal weight: 0.0970 chunk 375 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 236 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN E 27 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.115143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.095738 restraints weight = 119740.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.092803 restraints weight = 155772.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.089695 restraints weight = 134735.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.089293 restraints weight = 140575.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.088336 restraints weight = 109332.333| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32163 Z= 0.140 Angle : 0.615 11.729 43872 Z= 0.311 Chirality : 0.045 0.274 5061 Planarity : 0.004 0.050 5577 Dihedral : 4.844 55.060 5133 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.32 % Favored : 92.60 % Rotamer: Outliers : 0.06 % Allowed : 0.35 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.14), residues: 3891 helix: 1.38 (0.21), residues: 627 sheet: -0.33 (0.18), residues: 876 loop : -1.83 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 94 TYR 0.024 0.001 TYR B 265 PHE 0.024 0.002 PHE A 888 TRP 0.022 0.002 TRP C 436 HIS 0.009 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00319 (32082) covalent geometry : angle 0.59381 (43668) SS BOND : bond 0.00239 ( 39) SS BOND : angle 0.89533 ( 78) hydrogen bonds : bond 0.03764 ( 977) hydrogen bonds : angle 5.08680 ( 2682) link_BETA1-4 : bond 0.00147 ( 3) link_BETA1-4 : angle 0.97607 ( 9) link_NAG-ASN : bond 0.00488 ( 39) link_NAG-ASN : angle 3.11487 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4605.62 seconds wall clock time: 80 minutes 58.73 seconds (4858.73 seconds total)