Starting phenix.real_space_refine on Mon Jul 6 01:56:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rq6_24628/07_2026/7rq6_24628.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rq6_24628/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rq6_24628/07_2026/7rq6_24628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rq6_24628/07_2026/7rq6_24628.map" model { file = "/net/cci-nas-00/data/ceres_data/7rq6_24628/07_2026/7rq6_24628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rq6_24628/07_2026/7rq6_24628.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rq6_24628/07_2026/7rq6_24628.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rq6_24628/07_2026/7rq6_24628.cif" } 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-6108/lib/python3.11/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 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 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 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 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 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 chiralities: 12 Time building chain proxies: 6.35, per 1000 atoms: 0.20 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: 2.46 Conformation dependent library (CDL) restraints added in 1.4 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: 1.13 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: 7.44 Time building geometry restraints manager: 3.33 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: 16963 17.46 - 34.91: 1524 34.91 - 52.37: 186 52.37 - 69.83: 35 69.83 - 87.28: 33 Dihedral angle restraints: 18741 sinusoidal: 7254 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 18738 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: 0.04 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: 9.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 28.100 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 13.317 87.283 11256 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/Z covalent geometry : bond 0.00451 / 0.21 (32082) covalent geometry : angle 0.75980 / 0.42 (43668) SS BOND : bond 0.00379 / 0.26 ( 39) SS BOND : angle 1.16744 / 0.80 ( 78) hydrogen bonds : bond 0.14501 / 9.50 ( 977) hydrogen bonds : angle 6.74923 / 4.69 ( 2682) link_BETA1-4 : bond 0.00062 / 0.03 ( 3) link_BETA1-4 : angle 1.28320 / 0.68 ( 9) link_NAG-ASN : bond 0.00510 / 0.33 ( 39) link_NAG-ASN : angle 3.11318 / 2.27 ( 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 : 1.155 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: 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: 0.1891 time to fit residues: 83.6666 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 : 0.989 ------------------------------------------------------------------------------- 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... 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 = 0.4156 r_free = 0.4156 target = 0.116763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.097407 restraints weight = 119535.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.092605 restraints weight = 161536.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.090343 restraints weight = 161041.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.091100 restraints weight = 133794.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.090732 restraints weight = 98610.281| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.0882 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= 0.117 Angle : 0.606 10.858 43872 Z= 0.310 Chirality : 0.045 0.275 5061 Planarity : 0.004 0.047 5577 Dihedral : 4.463 20.512 4251 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.84 % Favored : 93.09 % Rotamer: Outliers : 0.12 % Allowed : 3.83 % Favored : 96.05 % 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 (0.13), residues: 3891 helix: 1.57 (0.21), residues: 639 sheet: -0.54 (0.18), residues: 801 loop : -1.83 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.021 0.001 TYR A 265 PHE 0.024 0.001 PHE B 186 TRP 0.021 0.002 TRP B 258 HIS 0.009 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (32082) covalent geometry : angle 0.58900 / 0.31 (43668) SS BOND : bond 0.00161 / 0.11 ( 39) SS BOND : angle 0.83364 / 0.52 ( 78) hydrogen bonds : bond 0.04277 / 2.81 ( 977) hydrogen bonds : angle 5.35901 / 3.72 ( 2682) link_BETA1-4 : bond 0.00317 / 0.16 ( 3) link_BETA1-4 : angle 1.04619 / 0.58 ( 9) link_NAG-ASN : bond 0.00558 / 0.34 ( 39) link_NAG-ASN : angle 2.77440 / 2.01 ( 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 : 1.287 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: H 102 VAL cc_start: 0.7807 (t) cc_final: 0.7542 (t) REVERT: L 38 GLN cc_start: 0.6922 (mm110) cc_final: 0.6644 (tp40) REVERT: L 74 THR cc_start: 0.6317 (p) cc_final: 0.6048 (p) REVERT: B 1029 MET cc_start: 0.9077 (tpp) cc_final: 0.8848 (tpp) REVERT: D 102 VAL cc_start: 0.7426 (t) cc_final: 0.7067 (t) REVERT: E 38 GLN cc_start: 0.7872 (mm110) cc_final: 0.7343 (mm110) REVERT: C 265 TYR cc_start: 0.7082 (p90) cc_final: 0.6677 (p90) REVERT: J 3 GLN cc_start: 0.7730 (pm20) cc_final: 0.6872 (tm-30) REVERT: J 100 MET cc_start: 0.7880 (tpp) cc_final: 0.7359 (tpp) REVERT: J 102 VAL cc_start: 0.7549 (t) cc_final: 0.7156 (t) REVERT: K 74 THR cc_start: 0.5913 (p) cc_final: 0.5682 (p) outliers start: 4 outliers final: 0 residues processed: 272 average time/residue: 0.1787 time to fit residues: 81.0778 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 : 1.132 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 277 optimal weight: 10.0000 chunk 251 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 385 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 360 ASN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 422 ASN B 895 GLN ** 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.119934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.098788 restraints weight = 111769.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.092013 restraints weight = 159321.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.089955 restraints weight = 139266.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.089770 restraints weight = 106614.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.089994 restraints weight = 91630.364| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1108 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= 0.169 Angle : 0.622 10.364 43872 Z= 0.319 Chirality : 0.045 0.261 5061 Planarity : 0.004 0.046 5577 Dihedral : 4.519 20.089 4251 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.66 % Favored : 92.26 % Rotamer: Outliers : 0.20 % Allowed : 4.26 % Favored : 95.53 % 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: 1.46 (0.21), residues: 627 sheet: -0.45 (0.18), residues: 813 loop : -1.86 (0.12), residues: 2451 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 0.014 0.002 TRP H 35A HIS 0.009 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (32082) covalent geometry : angle 0.60555 / 0.32 (43668) SS BOND : bond 0.00362 / 0.22 ( 39) SS BOND : angle 0.93876 / 0.58 ( 78) hydrogen bonds : bond 0.04213 / 2.76 ( 977) hydrogen bonds : angle 5.36161 / 3.73 ( 2682) link_BETA1-4 : bond 0.00101 / 0.05 ( 3) link_BETA1-4 : angle 0.89897 / 0.51 ( 9) link_NAG-ASN : bond 0.00541 / 0.34 ( 39) link_NAG-ASN : angle 2.76229 / 2.00 ( 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 278 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 271 time to evaluate : 1.143 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: 0.7138 (p90) cc_final: 0.6755 (p90) REVERT: A 849 LEU cc_start: 0.8201 (mp) cc_final: 0.7995 (mt) REVERT: H 102 VAL cc_start: 0.8154 (t) cc_final: 0.7808 (t) REVERT: L 38 GLN cc_start: 0.7006 (mm110) cc_final: 0.6648 (tp40) REVERT: L 74 THR cc_start: 0.6850 (p) cc_final: 0.6579 (p) REVERT: B 869 MET cc_start: 0.7447 (mtm) cc_final: 0.7190 (mtm) REVERT: D 102 VAL cc_start: 0.7774 (t) cc_final: 0.7295 (t) REVERT: E 74 THR cc_start: 0.6040 (p) cc_final: 0.5802 (p) REVERT: C 265 TYR cc_start: 0.7032 (p90) cc_final: 0.6636 (p90) REVERT: C 473 TYR cc_start: 0.5213 (p90) cc_final: 0.4910 (p90) REVERT: J 100 MET cc_start: 0.7983 (tpp) cc_final: 0.7505 (tpp) REVERT: J 102 VAL cc_start: 0.7941 (t) cc_final: 0.7404 (t) REVERT: K 74 THR cc_start: 0.6608 (p) cc_final: 0.6379 (p) outliers start: 7 outliers final: 0 residues processed: 278 average time/residue: 0.1979 time to fit residues: 89.8127 Evaluate side-chains 178 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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: 0.6980 chunk 188 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 189 optimal weight: 9.9990 chunk 236 optimal weight: 0.6980 chunk 221 optimal weight: 5.9990 chunk 388 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 374 optimal weight: 9.9990 chunk 325 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN B 895 GLN E 27 GLN C 895 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.115854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.095586 restraints weight = 118877.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.091792 restraints weight = 158971.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.089477 restraints weight = 157189.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.089945 restraints weight = 128192.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.090148 restraints weight = 98411.447| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1399 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= 0.126 Angle : 0.597 10.383 43872 Z= 0.304 Chirality : 0.045 0.272 5061 Planarity : 0.004 0.071 5577 Dihedral : 4.417 19.486 4251 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.76 % Favored : 93.16 % Rotamer: Outliers : 0.12 % Allowed : 3.08 % Favored : 96.81 % 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: -1.29 (0.14), residues: 3891 helix: 1.75 (0.22), residues: 609 sheet: -0.41 (0.18), residues: 810 loop : -1.81 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 3 TYR 0.016 0.001 TYR B 266 PHE 0.021 0.001 PHE A 377 TRP 0.023 0.002 TRP C 436 HIS 0.009 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (32082) covalent geometry : angle 0.58080 / 0.30 (43668) SS BOND : bond 0.00225 / 0.14 ( 39) SS BOND : angle 0.86733 / 0.54 ( 78) hydrogen bonds : bond 0.03892 / 2.56 ( 977) hydrogen bonds : angle 5.10643 / 3.55 ( 2682) link_BETA1-4 : bond 0.00260 / 0.13 ( 3) link_BETA1-4 : angle 0.96314 / 0.53 ( 9) link_NAG-ASN : bond 0.00521 / 0.31 ( 39) link_NAG-ASN : angle 2.71501 / 1.97 ( 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 277 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 273 time to evaluate : 1.266 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: 0.7050 (p90) cc_final: 0.6769 (p90) REVERT: A 849 LEU cc_start: 0.8194 (mp) cc_final: 0.7914 (mt) REVERT: H 102 VAL cc_start: 0.7646 (t) cc_final: 0.7143 (t) REVERT: L 38 GLN cc_start: 0.6832 (mm110) cc_final: 0.6498 (tp40) REVERT: L 74 THR cc_start: 0.6191 (p) cc_final: 0.5905 (p) REVERT: D 2 VAL cc_start: 0.7193 (t) cc_final: 0.6887 (m) REVERT: E 74 THR cc_start: 0.5130 (p) cc_final: 0.4905 (p) REVERT: C 265 TYR cc_start: 0.6969 (p90) cc_final: 0.6660 (p90) REVERT: C 473 TYR cc_start: 0.4770 (p90) cc_final: 0.4483 (p90) REVERT: J 102 VAL cc_start: 0.7447 (t) cc_final: 0.7114 (t) REVERT: K 74 THR cc_start: 0.6037 (p) cc_final: 0.5752 (p) outliers start: 4 outliers final: 0 residues processed: 277 average time/residue: 0.1951 time to fit residues: 89.6980 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 : 1.233 ------------------------------------------------------------------------------- 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: 4.9990 chunk 308 optimal weight: 0.0670 chunk 335 optimal weight: 0.7980 chunk 288 optimal weight: 0.6980 chunk 246 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 373 optimal weight: 8.9990 chunk 241 optimal weight: 20.0000 chunk 387 optimal weight: 20.0000 overall best weight: 2.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 895 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 895 GLN E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN K 6 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 = 0.4112 r_free = 0.4112 target = 0.118932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.099306 restraints weight = 112523.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.095521 restraints weight = 147412.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.092756 restraints weight = 130086.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.092090 restraints weight = 131398.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.091757 restraints weight = 98673.558| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 32163 Z= 0.217 Angle : 0.675 10.610 43872 Z= 0.346 Chirality : 0.046 0.247 5061 Planarity : 0.005 0.066 5577 Dihedral : 4.671 20.370 4251 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.53 % Favored : 91.39 % Rotamer: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.81 % 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: -1.50 (0.13), residues: 3891 helix: 1.38 (0.21), residues: 606 sheet: -0.53 (0.18), residues: 804 loop : -1.89 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 78 TYR 0.021 0.002 TYR C1067 PHE 0.024 0.002 PHE B1121 TRP 0.021 0.002 TRP B 436 HIS 0.008 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (32082) covalent geometry : angle 0.65765 / 0.34 (43668) SS BOND : bond 0.00576 / 0.43 ( 39) SS BOND : angle 0.91212 / 0.58 ( 78) hydrogen bonds : bond 0.04462 / 2.93 ( 977) hydrogen bonds : angle 5.45914 / 3.79 ( 2682) link_BETA1-4 : bond 0.00159 / 0.08 ( 3) link_BETA1-4 : angle 0.77598 / 0.44 ( 9) link_NAG-ASN : bond 0.00614 / 0.40 ( 39) link_NAG-ASN : angle 2.94982 / 2.12 ( 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 257 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 254 time to evaluate : 1.271 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: 0.7034 (p90) cc_final: 0.6754 (p90) REVERT: A 333 THR cc_start: 0.7863 (t) cc_final: 0.7662 (m) REVERT: A 849 LEU cc_start: 0.8405 (mp) cc_final: 0.8086 (mt) REVERT: H 102 VAL cc_start: 0.7780 (t) cc_final: 0.7522 (t) REVERT: L 38 GLN cc_start: 0.6784 (mm110) cc_final: 0.6411 (tp40) REVERT: L 74 THR cc_start: 0.6274 (p) cc_final: 0.5991 (p) REVERT: D 2 VAL cc_start: 0.7106 (t) cc_final: 0.6669 (m) REVERT: D 3 GLN cc_start: 0.7664 (pm20) cc_final: 0.7075 (tm-30) REVERT: E 3 ARG cc_start: 0.8069 (tmm160) cc_final: 0.7837 (tmm160) REVERT: E 38 GLN cc_start: 0.7618 (mm110) cc_final: 0.6683 (tt0) REVERT: E 74 THR cc_start: 0.5295 (p) cc_final: 0.5037 (p) REVERT: C 265 TYR cc_start: 0.6952 (p90) cc_final: 0.6601 (p90) REVERT: J 3 GLN cc_start: 0.7702 (pm20) cc_final: 0.7370 (tm-30) REVERT: J 100 MET cc_start: 0.8051 (tpp) cc_final: 0.7271 (tpp) REVERT: J 102 VAL cc_start: 0.7635 (t) cc_final: 0.6896 (t) REVERT: K 38 GLN cc_start: 0.7626 (mm110) cc_final: 0.7420 (tp40) REVERT: K 74 THR cc_start: 0.6054 (p) cc_final: 0.5739 (p) outliers start: 3 outliers final: 1 residues processed: 257 average time/residue: 0.1782 time to fit residues: 77.0026 Evaluate side-chains 176 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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: 2.9990 chunk 382 optimal weight: 20.0000 chunk 210 optimal weight: 0.8980 chunk 318 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 286 optimal weight: 7.9990 chunk 245 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 355 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 38 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 = 0.4119 r_free = 0.4119 target = 0.114567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.094724 restraints weight = 118790.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.090791 restraints weight = 166565.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.087941 restraints weight = 156868.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.088753 restraints weight = 139298.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.088356 restraints weight = 100795.682| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1713 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= 0.154 Angle : 0.625 9.921 43872 Z= 0.317 Chirality : 0.045 0.264 5061 Planarity : 0.004 0.059 5577 Dihedral : 4.540 20.022 4251 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.30 % Favored : 92.62 % Rotamer: Outliers : 0.06 % Allowed : 1.62 % Favored : 98.32 % 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: -1.47 (0.13), residues: 3891 helix: 1.57 (0.21), residues: 606 sheet: -0.59 (0.18), residues: 825 loop : -1.89 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.016 0.001 TYR B 266 PHE 0.024 0.002 PHE B 800 TRP 0.022 0.002 TRP C 436 HIS 0.008 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (32082) covalent geometry : angle 0.60762 / 0.31 (43668) SS BOND : bond 0.00224 / 0.16 ( 39) SS BOND : angle 1.03944 / 0.64 ( 78) hydrogen bonds : bond 0.04075 / 2.68 ( 977) hydrogen bonds : angle 5.27906 / 3.66 ( 2682) link_BETA1-4 : bond 0.00129 / 0.07 ( 3) link_BETA1-4 : angle 0.77214 / 0.44 ( 9) link_NAG-ASN : bond 0.00485 / 0.30 ( 39) link_NAG-ASN : angle 2.79754 / 2.00 ( 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 259 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 257 time to evaluate : 1.258 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: 0.6963 (p90) cc_final: 0.6696 (p90) REVERT: A 849 LEU cc_start: 0.8503 (mp) cc_final: 0.8184 (mt) REVERT: H 102 VAL cc_start: 0.7822 (t) cc_final: 0.7301 (t) REVERT: L 74 THR cc_start: 0.6382 (p) cc_final: 0.6089 (p) REVERT: E 38 GLN cc_start: 0.7673 (mm110) cc_final: 0.6536 (tt0) REVERT: E 74 THR cc_start: 0.5330 (p) cc_final: 0.5076 (p) REVERT: C 265 TYR cc_start: 0.6929 (p90) cc_final: 0.6595 (p90) REVERT: J 3 GLN cc_start: 0.7739 (pm20) cc_final: 0.7437 (tm-30) REVERT: J 100 MET cc_start: 0.8111 (tpp) cc_final: 0.7620 (tpp) REVERT: J 102 VAL cc_start: 0.7838 (t) cc_final: 0.7204 (t) REVERT: K 74 THR cc_start: 0.5996 (p) cc_final: 0.5699 (p) outliers start: 2 outliers final: 0 residues processed: 259 average time/residue: 0.1874 time to fit residues: 81.4033 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 : 1.224 ------------------------------------------------------------------------------- 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: 1.9990 chunk 148 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 chunk 322 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 345 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 chunk 196 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 334 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 978 ASN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.115348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.096065 restraints weight = 119189.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.091604 restraints weight = 155815.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.088790 restraints weight = 157375.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.089209 restraints weight = 129255.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.089336 restraints weight = 92080.106| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32163 Z= 0.123 Angle : 0.606 10.351 43872 Z= 0.309 Chirality : 0.045 0.271 5061 Planarity : 0.004 0.055 5577 Dihedral : 4.406 20.058 4251 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.38 % Favored : 92.55 % Rotamer: Outliers : 0.06 % Allowed : 1.25 % Favored : 98.69 % 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: -1.44 (0.13), residues: 3891 helix: 1.38 (0.21), residues: 627 sheet: -0.56 (0.18), residues: 825 loop : -1.84 (0.13), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 3 TYR 0.023 0.001 TYR C 266 PHE 0.018 0.001 PHE A 888 TRP 0.023 0.002 TRP C 436 HIS 0.008 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (32082) covalent geometry : angle 0.58916 / 0.31 (43668) SS BOND : bond 0.00632 / 0.37 ( 39) SS BOND : angle 1.07977 / 0.66 ( 78) hydrogen bonds : bond 0.03904 / 2.54 ( 977) hydrogen bonds : angle 5.13904 / 3.57 ( 2682) link_BETA1-4 : bond 0.00159 / 0.08 ( 3) link_BETA1-4 : angle 0.79380 / 0.44 ( 9) link_NAG-ASN : bond 0.00491 / 0.30 ( 39) link_NAG-ASN : angle 2.72735 / 1.96 ( 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 260 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 258 time to evaluate : 1.111 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 849 LEU cc_start: 0.8441 (mp) cc_final: 0.8092 (mt) REVERT: H 102 VAL cc_start: 0.7763 (t) cc_final: 0.7239 (t) REVERT: L 38 GLN cc_start: 0.6348 (mm110) cc_final: 0.5498 (tt0) REVERT: L 44 PRO cc_start: 0.6390 (Cg_exo) cc_final: 0.5986 (Cg_endo) REVERT: L 74 THR cc_start: 0.6377 (p) cc_final: 0.6096 (p) REVERT: B 869 MET cc_start: 0.7329 (mtm) cc_final: 0.7028 (mtm) REVERT: D 3 GLN cc_start: 0.7844 (pm20) cc_final: 0.7247 (tm-30) REVERT: D 66 ARG cc_start: 0.7298 (mpp80) cc_final: 0.7054 (mmm160) REVERT: E 38 GLN cc_start: 0.7600 (mm110) cc_final: 0.6474 (tt0) REVERT: E 74 THR cc_start: 0.5324 (p) cc_final: 0.5055 (p) REVERT: C 473 TYR cc_start: 0.5030 (p90) cc_final: 0.4742 (p90) REVERT: J 66 ARG cc_start: 0.7481 (mmt90) cc_final: 0.7209 (mmm160) REVERT: J 100 MET cc_start: 0.7932 (tpp) cc_final: 0.7628 (tpp) REVERT: J 102 VAL cc_start: 0.7762 (t) cc_final: 0.7135 (t) REVERT: K 44 PRO cc_start: 0.6295 (Cg_exo) cc_final: 0.5998 (Cg_endo) REVERT: K 74 THR cc_start: 0.5918 (p) cc_final: 0.5627 (p) outliers start: 2 outliers final: 0 residues processed: 260 average time/residue: 0.1821 time to fit residues: 79.5205 Evaluate side-chains 178 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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: 0.0670 chunk 263 optimal weight: 6.9990 chunk 200 optimal weight: 0.6980 chunk 221 optimal weight: 0.3980 chunk 329 optimal weight: 2.9990 chunk 310 optimal weight: 0.1980 chunk 178 optimal weight: 6.9990 chunk 326 optimal weight: 0.9990 chunk 257 optimal weight: 30.0000 chunk 381 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 overall best weight: 0.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 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 895 GLN J 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.116190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.096744 restraints weight = 119713.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.092372 restraints weight = 152958.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.089230 restraints weight = 150186.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.090106 restraints weight = 136753.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.089708 restraints weight = 92499.490| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32163 Z= 0.107 Angle : 0.595 10.124 43872 Z= 0.301 Chirality : 0.045 0.276 5061 Planarity : 0.004 0.051 5577 Dihedral : 4.235 19.949 4251 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.71 % Favored : 93.22 % Rotamer: Outliers : 0.06 % Allowed : 0.64 % Favored : 99.30 % 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: -1.34 (0.14), residues: 3891 helix: 1.53 (0.22), residues: 627 sheet: -0.42 (0.19), residues: 756 loop : -1.80 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 3 TYR 0.022 0.001 TYR A 265 PHE 0.018 0.001 PHE D 78 TRP 0.024 0.002 TRP C 436 HIS 0.008 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (32082) covalent geometry : angle 0.57837 / 0.30 (43668) SS BOND : bond 0.00217 / 0.15 ( 39) SS BOND : angle 1.00257 / 0.62 ( 78) hydrogen bonds : bond 0.03653 / 2.39 ( 977) hydrogen bonds : angle 4.97271 / 3.45 ( 2682) link_BETA1-4 : bond 0.00194 / 0.10 ( 3) link_BETA1-4 : angle 0.87674 / 0.47 ( 9) link_NAG-ASN : bond 0.00502 / 0.30 ( 39) link_NAG-ASN : angle 2.65736 / 1.91 ( 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 268 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.7129 (p90) cc_final: 0.6595 (p90) REVERT: A 849 LEU cc_start: 0.8407 (mp) cc_final: 0.8112 (mt) REVERT: H 102 VAL cc_start: 0.7924 (t) cc_final: 0.7373 (t) REVERT: L 38 GLN cc_start: 0.6373 (mm110) cc_final: 0.5483 (tt0) REVERT: L 74 THR cc_start: 0.6439 (p) cc_final: 0.6174 (p) REVERT: B 869 MET cc_start: 0.7260 (mtm) cc_final: 0.6979 (mtm) REVERT: D 3 GLN cc_start: 0.7887 (pm20) cc_final: 0.7302 (tm-30) REVERT: D 102 VAL cc_start: 0.7450 (t) cc_final: 0.6941 (t) REVERT: E 38 GLN cc_start: 0.7629 (mm110) cc_final: 0.6595 (tt0) REVERT: E 74 THR cc_start: 0.5386 (p) cc_final: 0.5126 (p) REVERT: C 473 TYR cc_start: 0.4940 (p90) cc_final: 0.4589 (p90) REVERT: J 102 VAL cc_start: 0.7847 (t) cc_final: 0.7208 (t) REVERT: K 38 GLN cc_start: 0.6133 (tt0) cc_final: 0.5901 (mm110) REVERT: K 74 THR cc_start: 0.6077 (p) cc_final: 0.5794 (p) outliers start: 2 outliers final: 0 residues processed: 268 average time/residue: 0.1761 time to fit residues: 79.0532 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 : 0.934 ------------------------------------------------------------------------------- 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: 1.9990 chunk 367 optimal weight: 0.4980 chunk 130 optimal weight: 20.0000 chunk 255 optimal weight: 6.9990 chunk 260 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 336 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 928 ASN 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 = 0.4128 r_free = 0.4128 target = 0.119424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.098634 restraints weight = 112293.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.091734 restraints weight = 163676.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.089009 restraints weight = 163984.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089793 restraints weight = 122295.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.089237 restraints weight = 104312.578| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32163 Z= 0.154 Angle : 0.622 9.817 43872 Z= 0.316 Chirality : 0.045 0.262 5061 Planarity : 0.004 0.055 5577 Dihedral : 4.398 19.517 4251 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.71 % Favored : 92.21 % Rotamer: Outliers : 0.06 % Allowed : 0.75 % Favored : 99.19 % 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: -1.47 (0.13), residues: 3891 helix: 1.31 (0.21), residues: 627 sheet: -0.50 (0.18), residues: 822 loop : -1.87 (0.13), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 3 TYR 0.023 0.001 TYR A 265 PHE 0.023 0.002 PHE C 888 TRP 0.023 0.002 TRP B 436 HIS 0.009 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (32082) covalent geometry : angle 0.60532 / 0.31 (43668) SS BOND : bond 0.00255 / 0.18 ( 39) SS BOND : angle 0.90142 / 0.56 ( 78) hydrogen bonds : bond 0.03970 / 2.60 ( 977) hydrogen bonds : angle 5.17370 / 3.59 ( 2682) link_BETA1-4 : bond 0.00084 / 0.04 ( 3) link_BETA1-4 : angle 0.77417 / 0.44 ( 9) link_NAG-ASN : bond 0.00499 / 0.32 ( 39) link_NAG-ASN : angle 2.74818 / 1.98 ( 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 256 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 254 time to evaluate : 1.265 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 849 LEU cc_start: 0.8444 (mp) cc_final: 0.8070 (mt) REVERT: H 102 VAL cc_start: 0.8269 (t) cc_final: 0.7880 (t) REVERT: L 38 GLN cc_start: 0.6397 (mm110) cc_final: 0.5436 (tt0) REVERT: L 44 PRO cc_start: 0.6688 (Cg_exo) cc_final: 0.6182 (Cg_endo) REVERT: L 74 THR cc_start: 0.6848 (p) cc_final: 0.6571 (p) REVERT: D 3 GLN cc_start: 0.8019 (pm20) cc_final: 0.7425 (tm-30) REVERT: D 100 MET cc_start: 0.7864 (tpp) cc_final: 0.7619 (tpp) REVERT: D 102 VAL cc_start: 0.7658 (t) cc_final: 0.7188 (t) REVERT: E 38 GLN cc_start: 0.7899 (mm110) cc_final: 0.6587 (tt0) REVERT: E 74 THR cc_start: 0.5820 (p) cc_final: 0.5553 (p) REVERT: C 265 TYR cc_start: 0.6965 (p90) cc_final: 0.6542 (p90) REVERT: J 102 VAL cc_start: 0.8171 (t) cc_final: 0.7618 (t) REVERT: K 38 GLN cc_start: 0.6034 (tt0) cc_final: 0.5811 (tt0) REVERT: K 74 THR cc_start: 0.6427 (p) cc_final: 0.6144 (p) outliers start: 2 outliers final: 0 residues processed: 256 average time/residue: 0.1862 time to fit residues: 79.6106 Evaluate side-chains 175 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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: 4.9990 chunk 214 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** 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 ** 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 = 0.4110 r_free = 0.4110 target = 0.114079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.094106 restraints weight = 119135.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.089878 restraints weight = 162172.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.086950 restraints weight = 147047.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.087540 restraints weight = 136714.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.087213 restraints weight = 98985.515| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32163 Z= 0.173 Angle : 0.642 9.720 43872 Z= 0.328 Chirality : 0.046 0.261 5061 Planarity : 0.004 0.054 5577 Dihedral : 4.472 19.645 4251 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.92 % Favored : 92.01 % 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: -1.54 (0.14), residues: 3891 helix: 1.18 (0.21), residues: 627 sheet: -0.51 (0.18), residues: 846 loop : -1.93 (0.13), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 3 TYR 0.021 0.001 TYR C 904 PHE 0.020 0.002 PHE C 906 TRP 0.022 0.002 TRP C 436 HIS 0.009 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (32082) covalent geometry : angle 0.62594 / 0.32 (43668) SS BOND : bond 0.00285 / 0.20 ( 39) SS BOND : angle 0.93787 / 0.59 ( 78) hydrogen bonds : bond 0.04064 / 2.67 ( 977) hydrogen bonds : angle 5.28550 / 3.66 ( 2682) link_BETA1-4 : bond 0.00118 / 0.06 ( 3) link_BETA1-4 : angle 0.68271 / 0.39 ( 9) link_NAG-ASN : bond 0.00491 / 0.31 ( 39) link_NAG-ASN : angle 2.76876 / 1.98 ( 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 253 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 251 time to evaluate : 1.247 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: 0.7203 (p90) cc_final: 0.6824 (p90) REVERT: A 849 LEU cc_start: 0.8454 (mp) cc_final: 0.8060 (mt) REVERT: H 102 VAL cc_start: 0.7874 (t) cc_final: 0.7297 (t) REVERT: L 38 GLN cc_start: 0.6473 (mm110) cc_final: 0.5653 (tt0) REVERT: L 44 PRO cc_start: 0.6533 (Cg_exo) cc_final: 0.6170 (Cg_endo) REVERT: L 74 THR cc_start: 0.6506 (p) cc_final: 0.6216 (p) REVERT: B 869 MET cc_start: 0.7404 (mtm) cc_final: 0.7094 (mtm) REVERT: D 3 GLN cc_start: 0.7866 (pm20) cc_final: 0.7371 (tm-30) REVERT: D 102 VAL cc_start: 0.7494 (t) cc_final: 0.7015 (t) REVERT: E 38 GLN cc_start: 0.6925 (tp40) cc_final: 0.6587 (tt0) REVERT: E 74 THR cc_start: 0.5863 (p) cc_final: 0.5563 (p) REVERT: C 265 TYR cc_start: 0.6952 (p90) cc_final: 0.6663 (p90) REVERT: J 102 VAL cc_start: 0.7930 (t) cc_final: 0.7288 (t) REVERT: K 3 ARG cc_start: 0.7939 (tmm160) cc_final: 0.7422 (tmm160) REVERT: K 74 THR cc_start: 0.5964 (p) cc_final: 0.5676 (p) outliers start: 2 outliers final: 1 residues processed: 253 average time/residue: 0.1913 time to fit residues: 80.8795 Evaluate side-chains 178 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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: 0.0670 chunk 107 optimal weight: 0.7980 chunk 240 optimal weight: 7.9990 chunk 348 optimal weight: 0.4980 chunk 375 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 236 optimal weight: 0.0870 chunk 52 optimal weight: 0.9990 chunk 102 optimal weight: 0.0980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 978 ASN E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 895 GLN C 978 ASN C 992 GLN ** C1106 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 = 0.4152 r_free = 0.4152 target = 0.120779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.100203 restraints weight = 111765.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.093497 restraints weight = 153872.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.091492 restraints weight = 133113.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.091749 restraints weight = 105978.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.092019 restraints weight = 83806.018| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32163 Z= 0.106 Angle : 0.600 10.055 43872 Z= 0.302 Chirality : 0.045 0.280 5061 Planarity : 0.004 0.052 5577 Dihedral : 4.205 19.938 4251 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.66 % Favored : 93.27 % Rotamer: Outliers : 0.03 % Allowed : 0.38 % 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: -1.30 (0.14), residues: 3891 helix: 1.53 (0.22), residues: 627 sheet: -0.32 (0.19), residues: 774 loop : -1.79 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 905 TYR 0.021 0.001 TYR B 904 PHE 0.016 0.001 PHE A 157 TRP 0.044 0.002 TRP B 886 HIS 0.009 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (32082) covalent geometry : angle 0.58426 / 0.30 (43668) SS BOND : bond 0.00208 / 0.14 ( 39) SS BOND : angle 1.00534 / 0.63 ( 78) hydrogen bonds : bond 0.03575 / 2.35 ( 977) hydrogen bonds : angle 4.91687 / 3.40 ( 2682) link_BETA1-4 : bond 0.00251 / 0.13 ( 3) link_BETA1-4 : angle 0.88896 / 0.47 ( 9) link_NAG-ASN : bond 0.00498 / 0.31 ( 39) link_NAG-ASN : angle 2.61669 / 1.87 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4761.64 seconds wall clock time: 83 minutes 50.39 seconds (5030.39 seconds total)