Starting phenix.real_space_refine on Thu Mar 5 23:10:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tf8_25865/03_2026/7tf8_25865_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf8_25865/03_2026/7tf8_25865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tf8_25865/03_2026/7tf8_25865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf8_25865/03_2026/7tf8_25865.map" model { file = "/net/cci-nas-00/data/ceres_data/7tf8_25865/03_2026/7tf8_25865_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf8_25865/03_2026/7tf8_25865_neut.cif" } resolution = 3.36 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= -0.002 sd= 0.170 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16401 2.51 5 N 4164 2.21 5 O 5056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25732 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8226 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 51, 'TRANS': 998} Chain breaks: 5 Chain: "B" Number of atoms: 8251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8251 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 51, 'TRANS': 1001} Chain breaks: 5 Chain: "C" Number of atoms: 8226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8226 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 51, 'TRANS': 998} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.78, per 1000 atoms: 0.22 Number of scatterers: 25732 At special positions: 0 Unit cell: (130.68, 136.08, 178.2, 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 111 16.00 O 5056 8.00 N 4164 7.00 C 16401 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 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 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " 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=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " 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=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA U 3 " - " MAN U 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 5 " " BMA o 3 " - " MAN o 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG h 1 " - " NAG h 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG q 1 " - " NAG q 2 " NAG-ASN " NAG A1201 " - " ASN A 343 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 331 " " NAG A1204 " - " ASN A 616 " " NAG A1205 " - " ASN A 709 " " NAG A1206 " - " ASN A1134 " " NAG A1207 " - " ASN A 61 " " NAG A1208 " - " ASN A 165 " " NAG A1209 " - " ASN A 657 " " NAG B1201 " - " ASN B 616 " " NAG B1202 " - " ASN B 657 " " NAG B1203 " - " ASN B 331 " " NAG B1204 " - " ASN B 709 " " NAG B1205 " - " ASN B1098 " " NAG B1206 " - " ASN B1134 " " NAG C1201 " - " ASN C 331 " " NAG C1202 " - " ASN C 282 " " NAG C1203 " - " ASN C 616 " " NAG C1204 " - " ASN C 709 " " NAG C1205 " - " ASN C1134 " " NAG C1206 " - " ASN C1098 " " NAG C1207 " - " ASN C 61 " " NAG C1208 " - " ASN C 165 " " NAG C1209 " - " ASN C 603 " " NAG C1210 " - " ASN C 657 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN C 801 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 282 " " NAG M 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1074 " " NAG S 1 " - " ASN B 61 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 282 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B 801 " " NAG b 1 " - " ASN B1074 " " NAG h 1 " - " ASN C 234 " " NAG o 1 " - " ASN C 717 " " NAG q 1 " - " ASN C1074 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5922 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 44 sheets defined 25.7% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.523A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.915A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 631 through 637 removed outlier: 3.792A pdb=" N ARG A 634 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 635 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.762A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.721A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.538A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 removed outlier: 3.762A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.928A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.669A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.512A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 940 removed outlier: 4.208A pdb=" N ALA A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.678A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 988 through 1032 removed outlier: 3.580A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.995A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.668A pdb=" N LEU B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.274A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.904A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.593A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.576A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.504A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 842 removed outlier: 3.751A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.578A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.689A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.593A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.143A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.890A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.984A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.718A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.637A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.601A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 411' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.512A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.586A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.678A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.619A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.579A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.878A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.093A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.807A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.193A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.656A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.075A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.502A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.077A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.215A 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: 5.764A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.637A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.678A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.072A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.735A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (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 733 through 736 removed outlier: 4.655A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.885A 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 1120 through 1125 removed outlier: 4.483A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.150A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.433A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.064A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.130A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG B 102 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 119 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 316 removed outlier: 3.539A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 327 through 328 removed outlier: 3.715A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.754A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.834A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.889A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.591A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS B1101 " --> pdb=" O ASN B1098 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.976A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.637A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1081 through 1083 removed outlier: 4.337A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.629A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.086A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.679A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.928A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.578A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.352A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.827A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.978A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.524A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.916A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.594A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.590A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2712 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: 5.86 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8037 1.34 - 1.46: 6464 1.46 - 1.58: 11667 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 26303 Sorted by residual: bond pdb=" N VAL B1129 " pdb=" CA VAL B1129 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.69e+00 bond pdb=" N VAL B1122 " pdb=" CA VAL B1122 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.20e-02 6.94e+03 8.76e+00 bond pdb=" N VAL B1128 " pdb=" CA VAL B1128 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.33e+00 bond pdb=" N ASN B1125 " pdb=" CA ASN B1125 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.34e-02 5.57e+03 7.69e+00 bond pdb=" N ILE B1130 " pdb=" CA ILE B1130 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.24e-02 6.50e+03 7.27e+00 ... (remaining 26298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 34948 2.31 - 4.63: 720 4.63 - 6.94: 95 6.94 - 9.26: 12 9.26 - 11.57: 7 Bond angle restraints: 35782 Sorted by residual: angle pdb=" C GLU A 619 " pdb=" N VAL A 620 " pdb=" CA VAL A 620 " ideal model delta sigma weight residual 120.33 123.94 -3.61 8.00e-01 1.56e+00 2.04e+01 angle pdb=" C GLN A 836 " pdb=" N TYR A 837 " pdb=" CA TYR A 837 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 116.34 110.52 5.82 1.40e+00 5.10e-01 1.73e+01 angle pdb=" C GLY C 832 " pdb=" N PHE C 833 " pdb=" CA PHE C 833 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C ASP A 627 " pdb=" N GLN A 628 " pdb=" CA GLN A 628 " ideal model delta sigma weight residual 122.46 127.59 -5.13 1.41e+00 5.03e-01 1.32e+01 ... (remaining 35777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 15730 21.62 - 43.25: 745 43.25 - 64.87: 95 64.87 - 86.50: 78 86.50 - 108.12: 42 Dihedral angle restraints: 16690 sinusoidal: 7492 harmonic: 9198 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -168.98 82.98 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -160.73 74.73 1 1.00e+01 1.00e-02 7.07e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -42.47 -43.53 1 1.00e+01 1.00e-02 2.64e+01 ... (remaining 16687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3635 0.076 - 0.152: 614 0.152 - 0.228: 34 0.228 - 0.304: 15 0.304 - 0.379: 4 Chirality restraints: 4302 Sorted by residual: chirality pdb=" C2 NAG B1206 " pdb=" C1 NAG B1206 " pdb=" C3 NAG B1206 " pdb=" N2 NAG B1206 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" C5 BMA Z 3 " pdb=" C4 BMA Z 3 " pdb=" C6 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.48e+00 ... (remaining 4299 not shown) Planarity restraints: 4542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO A 521 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.46e+00 pdb=" N PRO C 521 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 294 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO B 295 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " -0.034 5.00e-02 4.00e+02 ... (remaining 4539 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6576 2.80 - 3.33: 21398 3.33 - 3.85: 41215 3.85 - 4.38: 47681 4.38 - 4.90: 84894 Nonbonded interactions: 201764 Sorted by model distance: nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.280 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.294 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR B 369 " pdb=" O PRO B 384 " model vdw 2.315 3.040 nonbonded pdb=" OH TYR B 421 " pdb=" O ARG B 457 " model vdw 2.317 3.040 ... (remaining 201759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 1206) selection = (chain 'B' and (resid 27 through 678 or resid 689 through 1206)) selection = (chain 'C' and resid 27 through 1206) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'h' selection = chain 'q' } ncs_group { reference = chain 'M' selection = chain 'S' selection = chain 'a' } ncs_group { reference = chain 'O' selection = chain 'U' selection = chain 'Z' selection = chain 'o' } ncs_group { reference = chain 'P' selection = chain 'V' selection = chain 'b' } 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 individual isotropic 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.680 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 0.049 26423 Z= 0.238 Angle : 0.822 15.821 36100 Z= 0.406 Chirality : 0.056 0.379 4302 Planarity : 0.006 0.066 4501 Dihedral : 14.716 108.120 10642 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.07 % Allowed : 0.15 % Favored : 99.78 % 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: -0.90 (0.14), residues: 3117 helix: -0.82 (0.17), residues: 734 sheet: 0.51 (0.19), residues: 699 loop : -0.95 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 634 TYR 0.024 0.002 TYR B 837 PHE 0.025 0.002 PHE B 906 TRP 0.018 0.002 TRP B 633 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00478 (26303) covalent geometry : angle 0.77744 (35782) SS BOND : bond 0.00350 ( 42) SS BOND : angle 1.00380 ( 84) hydrogen bonds : bond 0.13303 ( 976) hydrogen bonds : angle 6.84873 ( 2712) link_ALPHA1-3 : bond 0.00401 ( 6) link_ALPHA1-3 : angle 1.43218 ( 18) link_ALPHA1-6 : bond 0.00324 ( 5) link_ALPHA1-6 : angle 1.43436 ( 15) link_BETA1-4 : bond 0.01279 ( 26) link_BETA1-4 : angle 4.72035 ( 78) link_NAG-ASN : bond 0.00490 ( 41) link_NAG-ASN : angle 2.65891 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.830 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 75 average time/residue: 0.1564 time to fit residues: 19.7137 Evaluate side-chains 48 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN A 641 ASN A 751 ASN A 926 GLN A1106 GLN B 681 HIS ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.100431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.063746 restraints weight = 62761.256| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.15 r_work: 0.2799 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26423 Z= 0.228 Angle : 0.630 11.218 36100 Z= 0.309 Chirality : 0.047 0.287 4302 Planarity : 0.004 0.049 4501 Dihedral : 10.608 75.979 4982 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.40 % Allowed : 2.98 % Favored : 96.62 % 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: -0.40 (0.15), residues: 3117 helix: 0.51 (0.19), residues: 740 sheet: 0.38 (0.19), residues: 704 loop : -0.89 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 357 TYR 0.021 0.002 TYR C 200 PHE 0.025 0.002 PHE C 906 TRP 0.014 0.001 TRP A 886 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00549 (26303) covalent geometry : angle 0.59366 (35782) SS BOND : bond 0.00430 ( 42) SS BOND : angle 0.83201 ( 84) hydrogen bonds : bond 0.05020 ( 976) hydrogen bonds : angle 5.36247 ( 2712) link_ALPHA1-3 : bond 0.00749 ( 6) link_ALPHA1-3 : angle 3.16078 ( 18) link_ALPHA1-6 : bond 0.00349 ( 5) link_ALPHA1-6 : angle 2.08447 ( 15) link_BETA1-4 : bond 0.00826 ( 26) link_BETA1-4 : angle 3.21187 ( 78) link_NAG-ASN : bond 0.00365 ( 41) link_NAG-ASN : angle 2.19847 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8146 (mm) cc_final: 0.7912 (tt) REVERT: C 473 TYR cc_start: 0.7009 (m-80) cc_final: 0.6708 (m-80) outliers start: 11 outliers final: 5 residues processed: 63 average time/residue: 0.1480 time to fit residues: 16.5987 Evaluate side-chains 57 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 286 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 229 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 chunk 289 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN B 914 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.101443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.065774 restraints weight = 62772.983| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.07 r_work: 0.2840 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26423 Z= 0.138 Angle : 0.544 11.263 36100 Z= 0.266 Chirality : 0.045 0.265 4302 Planarity : 0.003 0.045 4501 Dihedral : 8.934 66.426 4982 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.40 % Allowed : 4.65 % Favored : 94.95 % 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: -0.10 (0.15), residues: 3117 helix: 1.11 (0.20), residues: 740 sheet: 0.42 (0.19), residues: 696 loop : -0.81 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 765 TYR 0.019 0.001 TYR A1067 PHE 0.014 0.001 PHE B 833 TRP 0.008 0.001 TRP A 886 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00319 (26303) covalent geometry : angle 0.51215 (35782) SS BOND : bond 0.00279 ( 42) SS BOND : angle 0.64267 ( 84) hydrogen bonds : bond 0.04187 ( 976) hydrogen bonds : angle 5.04578 ( 2712) link_ALPHA1-3 : bond 0.01134 ( 6) link_ALPHA1-3 : angle 1.99313 ( 18) link_ALPHA1-6 : bond 0.00406 ( 5) link_ALPHA1-6 : angle 1.80804 ( 15) link_BETA1-4 : bond 0.00935 ( 26) link_BETA1-4 : angle 2.92614 ( 78) link_NAG-ASN : bond 0.00350 ( 41) link_NAG-ASN : angle 1.94723 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8244 (mm) cc_final: 0.7979 (tt) REVERT: B 377 PHE cc_start: 0.6253 (m-80) cc_final: 0.5503 (t80) REVERT: C 473 TYR cc_start: 0.6982 (m-80) cc_final: 0.6691 (m-80) outliers start: 11 outliers final: 4 residues processed: 65 average time/residue: 0.1443 time to fit residues: 16.6647 Evaluate side-chains 59 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 64 optimal weight: 3.9990 chunk 313 optimal weight: 8.9990 chunk 191 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 965 GLN C 134 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.099424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.063158 restraints weight = 62613.355| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.09 r_work: 0.2774 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 26423 Z= 0.240 Angle : 0.617 10.664 36100 Z= 0.305 Chirality : 0.047 0.296 4302 Planarity : 0.004 0.046 4501 Dihedral : 8.010 59.729 4981 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.69 % Allowed : 5.93 % Favored : 93.38 % 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: -0.26 (0.15), residues: 3117 helix: 1.03 (0.20), residues: 742 sheet: 0.24 (0.19), residues: 703 loop : -0.90 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.020 0.002 TYR A1067 PHE 0.018 0.002 PHE C 400 TRP 0.010 0.001 TRP A 886 HIS 0.006 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00582 (26303) covalent geometry : angle 0.58568 (35782) SS BOND : bond 0.00458 ( 42) SS BOND : angle 1.33395 ( 84) hydrogen bonds : bond 0.05051 ( 976) hydrogen bonds : angle 5.21463 ( 2712) link_ALPHA1-3 : bond 0.01035 ( 6) link_ALPHA1-3 : angle 2.21226 ( 18) link_ALPHA1-6 : bond 0.00391 ( 5) link_ALPHA1-6 : angle 1.85529 ( 15) link_BETA1-4 : bond 0.00843 ( 26) link_BETA1-4 : angle 2.83474 ( 78) link_NAG-ASN : bond 0.00407 ( 41) link_NAG-ASN : angle 2.11465 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8189 (mm) cc_final: 0.7954 (tt) REVERT: B 377 PHE cc_start: 0.6366 (OUTLIER) cc_final: 0.5608 (t80) REVERT: B 878 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8823 (mt) REVERT: C 473 TYR cc_start: 0.7075 (m-80) cc_final: 0.6759 (m-80) outliers start: 19 outliers final: 12 residues processed: 70 average time/residue: 0.1388 time to fit residues: 17.0697 Evaluate side-chains 67 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 993 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 107 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 257 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 289 optimal weight: 0.9980 chunk 219 optimal weight: 0.5980 chunk 171 optimal weight: 0.8980 chunk 36 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 836 GLN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.100234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.064392 restraints weight = 62587.451| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.05 r_work: 0.2810 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26423 Z= 0.166 Angle : 0.559 10.982 36100 Z= 0.274 Chirality : 0.045 0.280 4302 Planarity : 0.003 0.045 4501 Dihedral : 7.381 58.573 4981 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.91 % Allowed : 6.91 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 3117 helix: 1.32 (0.20), residues: 734 sheet: 0.21 (0.19), residues: 719 loop : -0.90 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 355 TYR 0.019 0.001 TYR A1067 PHE 0.013 0.001 PHE C 400 TRP 0.007 0.001 TRP A 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00397 (26303) covalent geometry : angle 0.52828 (35782) SS BOND : bond 0.00316 ( 42) SS BOND : angle 1.35095 ( 84) hydrogen bonds : bond 0.04330 ( 976) hydrogen bonds : angle 5.03255 ( 2712) link_ALPHA1-3 : bond 0.01055 ( 6) link_ALPHA1-3 : angle 1.97337 ( 18) link_ALPHA1-6 : bond 0.00493 ( 5) link_ALPHA1-6 : angle 1.68844 ( 15) link_BETA1-4 : bond 0.00868 ( 26) link_BETA1-4 : angle 2.68210 ( 78) link_NAG-ASN : bond 0.00344 ( 41) link_NAG-ASN : angle 1.94657 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: B 118 LEU cc_start: 0.8280 (tp) cc_final: 0.7882 (mp) REVERT: B 128 ILE cc_start: 0.8189 (mm) cc_final: 0.7959 (tt) REVERT: B 377 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.5524 (t80) REVERT: C 473 TYR cc_start: 0.6969 (m-80) cc_final: 0.6643 (m-80) outliers start: 25 outliers final: 15 residues processed: 76 average time/residue: 0.1398 time to fit residues: 18.9823 Evaluate side-chains 68 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 993 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 175 optimal weight: 0.9980 chunk 256 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 264 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 237 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.100404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064706 restraints weight = 62875.477| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.01 r_work: 0.2822 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26423 Z= 0.149 Angle : 0.541 11.039 36100 Z= 0.266 Chirality : 0.045 0.264 4302 Planarity : 0.003 0.045 4501 Dihedral : 6.910 57.507 4981 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.84 % Allowed : 7.89 % Favored : 91.28 % 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: -0.08 (0.15), residues: 3117 helix: 1.43 (0.20), residues: 736 sheet: 0.26 (0.19), residues: 723 loop : -0.88 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 765 TYR 0.018 0.001 TYR A1067 PHE 0.013 0.001 PHE B 833 TRP 0.007 0.001 TRP C 64 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00355 (26303) covalent geometry : angle 0.51156 (35782) SS BOND : bond 0.00288 ( 42) SS BOND : angle 1.15150 ( 84) hydrogen bonds : bond 0.04131 ( 976) hydrogen bonds : angle 4.94235 ( 2712) link_ALPHA1-3 : bond 0.01019 ( 6) link_ALPHA1-3 : angle 1.81815 ( 18) link_ALPHA1-6 : bond 0.00552 ( 5) link_ALPHA1-6 : angle 1.71072 ( 15) link_BETA1-4 : bond 0.00864 ( 26) link_BETA1-4 : angle 2.63580 ( 78) link_NAG-ASN : bond 0.00336 ( 41) link_NAG-ASN : angle 1.92386 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: B 118 LEU cc_start: 0.8272 (tp) cc_final: 0.7877 (mp) REVERT: B 128 ILE cc_start: 0.8276 (mm) cc_final: 0.8019 (tt) REVERT: B 377 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.5588 (t80) REVERT: B 878 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8769 (mt) REVERT: C 473 TYR cc_start: 0.7090 (m-80) cc_final: 0.6716 (m-80) outliers start: 23 outliers final: 14 residues processed: 74 average time/residue: 0.1324 time to fit residues: 18.1110 Evaluate side-chains 70 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 993 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 101 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 303 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 292 optimal weight: 6.9990 chunk 217 optimal weight: 0.4980 chunk 225 optimal weight: 30.0000 chunk 240 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 804 GLN B 935 GLN C 239 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1071 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.101527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.066765 restraints weight = 61976.009| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.99 r_work: 0.2851 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26423 Z= 0.092 Angle : 0.503 11.347 36100 Z= 0.246 Chirality : 0.043 0.243 4302 Planarity : 0.003 0.044 4501 Dihedral : 6.468 55.490 4981 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.65 % Allowed : 8.11 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3117 helix: 1.72 (0.20), residues: 734 sheet: 0.40 (0.19), residues: 726 loop : -0.78 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 355 TYR 0.016 0.001 TYR A1067 PHE 0.012 0.001 PHE B 833 TRP 0.008 0.001 TRP C 64 HIS 0.003 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00199 (26303) covalent geometry : angle 0.47466 (35782) SS BOND : bond 0.00194 ( 42) SS BOND : angle 0.90616 ( 84) hydrogen bonds : bond 0.03420 ( 976) hydrogen bonds : angle 4.74934 ( 2712) link_ALPHA1-3 : bond 0.00965 ( 6) link_ALPHA1-3 : angle 1.61992 ( 18) link_ALPHA1-6 : bond 0.00528 ( 5) link_ALPHA1-6 : angle 1.65686 ( 15) link_BETA1-4 : bond 0.00864 ( 26) link_BETA1-4 : angle 2.57045 ( 78) link_NAG-ASN : bond 0.00342 ( 41) link_NAG-ASN : angle 1.80193 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.749 Fit side-chains REVERT: B 118 LEU cc_start: 0.8333 (tp) cc_final: 0.7922 (mp) REVERT: B 377 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.5632 (t80) REVERT: C 473 TYR cc_start: 0.6991 (m-80) cc_final: 0.6708 (m-80) outliers start: 18 outliers final: 11 residues processed: 74 average time/residue: 0.1279 time to fit residues: 16.8747 Evaluate side-chains 65 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 993 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 47 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 288 optimal weight: 0.4980 chunk 112 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 308 optimal weight: 0.6980 chunk 153 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 901 GLN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.100936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.065696 restraints weight = 62531.430| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.05 r_work: 0.2839 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26423 Z= 0.118 Angle : 0.512 11.167 36100 Z= 0.251 Chirality : 0.044 0.245 4302 Planarity : 0.003 0.045 4501 Dihedral : 6.363 55.877 4980 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.62 % Allowed : 8.76 % Favored : 90.62 % 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: 0.18 (0.15), residues: 3117 helix: 1.75 (0.20), residues: 735 sheet: 0.36 (0.18), residues: 728 loop : -0.75 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.020 0.001 TYR B 170 PHE 0.012 0.001 PHE B 833 TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00275 (26303) covalent geometry : angle 0.48385 (35782) SS BOND : bond 0.00241 ( 42) SS BOND : angle 0.95057 ( 84) hydrogen bonds : bond 0.03666 ( 976) hydrogen bonds : angle 4.73810 ( 2712) link_ALPHA1-3 : bond 0.00894 ( 6) link_ALPHA1-3 : angle 1.59341 ( 18) link_ALPHA1-6 : bond 0.00478 ( 5) link_ALPHA1-6 : angle 1.64988 ( 15) link_BETA1-4 : bond 0.00837 ( 26) link_BETA1-4 : angle 2.58617 ( 78) link_NAG-ASN : bond 0.00322 ( 41) link_NAG-ASN : angle 1.82265 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.878 Fit side-chains REVERT: B 377 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.5648 (t80) REVERT: B 878 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8732 (mt) REVERT: C 473 TYR cc_start: 0.6900 (m-80) cc_final: 0.6666 (m-80) outliers start: 17 outliers final: 12 residues processed: 65 average time/residue: 0.1358 time to fit residues: 16.2327 Evaluate side-chains 66 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 993 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 901 GLN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.098811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.062088 restraints weight = 62801.727| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.09 r_work: 0.2772 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 26423 Z= 0.257 Angle : 0.611 10.564 36100 Z= 0.304 Chirality : 0.047 0.255 4302 Planarity : 0.004 0.044 4501 Dihedral : 6.703 59.495 4980 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.87 % Allowed : 8.65 % Favored : 90.48 % 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: -0.15 (0.15), residues: 3117 helix: 1.35 (0.20), residues: 735 sheet: 0.21 (0.19), residues: 696 loop : -0.89 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 355 TYR 0.021 0.002 TYR A1067 PHE 0.018 0.002 PHE C 400 TRP 0.010 0.002 TRP A 886 HIS 0.007 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00627 (26303) covalent geometry : angle 0.58336 (35782) SS BOND : bond 0.00451 ( 42) SS BOND : angle 1.33048 ( 84) hydrogen bonds : bond 0.05043 ( 976) hydrogen bonds : angle 5.10339 ( 2712) link_ALPHA1-3 : bond 0.00831 ( 6) link_ALPHA1-3 : angle 1.69608 ( 18) link_ALPHA1-6 : bond 0.00375 ( 5) link_ALPHA1-6 : angle 1.70273 ( 15) link_BETA1-4 : bond 0.00839 ( 26) link_BETA1-4 : angle 2.66905 ( 78) link_NAG-ASN : bond 0.00432 ( 41) link_NAG-ASN : angle 2.03526 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.841 Fit side-chains REVERT: B 118 LEU cc_start: 0.8398 (tp) cc_final: 0.8035 (mp) REVERT: B 377 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.5435 (t80) REVERT: B 878 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8823 (mt) REVERT: C 473 TYR cc_start: 0.7038 (m-80) cc_final: 0.6664 (m-80) outliers start: 24 outliers final: 13 residues processed: 73 average time/residue: 0.1295 time to fit residues: 16.9416 Evaluate side-chains 64 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 993 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 196 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 79 optimal weight: 0.0970 chunk 268 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 281 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 242 optimal weight: 0.8980 chunk 285 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.101030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.065770 restraints weight = 62235.714| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.13 r_work: 0.2823 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26423 Z= 0.095 Angle : 0.513 11.345 36100 Z= 0.251 Chirality : 0.043 0.244 4302 Planarity : 0.003 0.042 4501 Dihedral : 6.331 58.364 4980 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.47 % Allowed : 9.12 % Favored : 90.40 % 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: 0.13 (0.15), residues: 3117 helix: 1.73 (0.20), residues: 734 sheet: 0.36 (0.19), residues: 725 loop : -0.80 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.017 0.001 TYR C 453 PHE 0.012 0.001 PHE B 833 TRP 0.008 0.001 TRP C 64 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00205 (26303) covalent geometry : angle 0.48550 (35782) SS BOND : bond 0.00207 ( 42) SS BOND : angle 0.95650 ( 84) hydrogen bonds : bond 0.03568 ( 976) hydrogen bonds : angle 4.77086 ( 2712) link_ALPHA1-3 : bond 0.00840 ( 6) link_ALPHA1-3 : angle 1.49233 ( 18) link_ALPHA1-6 : bond 0.00468 ( 5) link_ALPHA1-6 : angle 1.60464 ( 15) link_BETA1-4 : bond 0.00849 ( 26) link_BETA1-4 : angle 2.55223 ( 78) link_NAG-ASN : bond 0.00338 ( 41) link_NAG-ASN : angle 1.79293 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.847 Fit side-chains REVERT: B 118 LEU cc_start: 0.8368 (tp) cc_final: 0.7988 (mp) REVERT: B 377 PHE cc_start: 0.6368 (OUTLIER) cc_final: 0.5496 (t80) REVERT: B 878 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8766 (mt) REVERT: B 902 MET cc_start: 0.8954 (mmt) cc_final: 0.8707 (mmt) REVERT: C 414 GLN cc_start: 0.7848 (mp10) cc_final: 0.7645 (mp10) REVERT: C 473 TYR cc_start: 0.7016 (m-80) cc_final: 0.6695 (m-80) outliers start: 13 outliers final: 8 residues processed: 65 average time/residue: 0.1367 time to fit residues: 16.0509 Evaluate side-chains 64 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 993 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 23 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 287 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 177 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.099250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.063966 restraints weight = 62403.455| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.11 r_work: 0.2785 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26423 Z= 0.221 Angle : 0.580 10.744 36100 Z= 0.286 Chirality : 0.046 0.252 4302 Planarity : 0.003 0.044 4501 Dihedral : 6.517 58.298 4980 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.62 % Allowed : 8.94 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3117 helix: 1.48 (0.20), residues: 736 sheet: 0.28 (0.19), residues: 680 loop : -0.84 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.020 0.001 TYR A1067 PHE 0.019 0.001 PHE C 400 TRP 0.008 0.001 TRP A 886 HIS 0.006 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00533 (26303) covalent geometry : angle 0.55233 (35782) SS BOND : bond 0.00392 ( 42) SS BOND : angle 1.21858 ( 84) hydrogen bonds : bond 0.04624 ( 976) hydrogen bonds : angle 4.98828 ( 2712) link_ALPHA1-3 : bond 0.00794 ( 6) link_ALPHA1-3 : angle 1.60428 ( 18) link_ALPHA1-6 : bond 0.00388 ( 5) link_ALPHA1-6 : angle 1.63700 ( 15) link_BETA1-4 : bond 0.00817 ( 26) link_BETA1-4 : angle 2.62562 ( 78) link_NAG-ASN : bond 0.00384 ( 41) link_NAG-ASN : angle 1.96037 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5019.09 seconds wall clock time: 87 minutes 5.72 seconds (5225.72 seconds total)