Starting phenix.real_space_refine on Fri Mar 6 06:46:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru5_24697/03_2026/7ru5_24697.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru5_24697/03_2026/7ru5_24697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ru5_24697/03_2026/7ru5_24697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru5_24697/03_2026/7ru5_24697.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru5_24697/03_2026/7ru5_24697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru5_24697/03_2026/7ru5_24697.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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 138 5.16 5 C 18216 2.51 5 N 4734 2.21 5 O 5585 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: 28673 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 8527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1093, 8527 Classifications: {'peptide': 1093} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1036} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8025 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 11 Chain: "B" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8025 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 11 Chain: "H" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 956 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "D" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 956 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" 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: 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: "N" 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: 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: "P" 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: "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: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" 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: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.01, per 1000 atoms: 0.24 Number of scatterers: 28673 At special positions: 0 Unit cell: (146.26, 151.41, 229.69, 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 138 16.00 O 5585 8.00 N 4734 7.00 C 18216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.12 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 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 705 " - pdb=" SG CYS A 883 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.06 Simple disulfide: pdb=" SG CYS C 883 " - pdb=" SG CYS B 705 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.10 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 100D" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 100D" distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 148 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG F 1 " - " ASN C 717 " " NAG G 1 " - " ASN C 801 " " NAG I 1 " - " ASN C1098 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6742 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 64 sheets defined 23.7% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.484A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 843 removed outlier: 4.091A pdb=" N CYS C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.785A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.647A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.550A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.536A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 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 967 removed outlier: 3.980A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 84 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 84 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.139A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.122A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.423A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.438A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.894A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.936A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.874A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.874A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.773A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.782A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.479A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.807A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.798A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'C' and resid 787 through 789 Processing sheet with id=AC2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.698A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.993A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.565A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.207A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.427A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.541A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.325A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.919A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.919A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.542A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AD4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.763A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.616A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.512A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.512A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.563A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.380A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.399A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.971A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.951A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 134 through 135 removed outlier: 6.631A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.414A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 355 through 357 Processing sheet with id=AE9, first strand: chain 'B' and resid 423 through 424 Processing sheet with id=AF1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.670A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.434A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.100A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.795A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.790A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 96 through 100 Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AG3, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.810A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AG5, first strand: chain 'D' and resid 58 through 59 removed outlier: 5.758A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 96 through 100 Processing sheet with id=AG7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AG9, first strand: chain 'E' and resid 45 through 46 removed outlier: 4.284A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 48 through 49 1231 hydrogen bonds defined for protein. 3363 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: 8.57 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5423 1.32 - 1.46: 10892 1.46 - 1.61: 12804 1.61 - 1.76: 38 1.76 - 1.91: 152 Bond restraints: 29309 Sorted by residual: bond pdb=" CB LEU B 387 " pdb=" CG LEU B 387 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" CB HIS C1048 " pdb=" CG HIS C1048 " ideal model delta sigma weight residual 1.497 1.409 0.088 1.40e-02 5.10e+03 3.93e+01 bond pdb=" CB LEU A 387 " pdb=" CG LEU A 387 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" CB HIS C1064 " pdb=" CG HIS C1064 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.03e+01 bond pdb=" NE ARG L 96 " pdb=" CZ ARG L 96 " ideal model delta sigma weight residual 1.326 1.386 -0.060 1.10e-02 8.26e+03 3.02e+01 ... (remaining 29304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.44: 39741 7.44 - 14.88: 113 14.88 - 22.33: 0 22.33 - 29.77: 0 29.77 - 37.21: 1 Bond angle restraints: 39855 Sorted by residual: angle pdb=" C2 NAG B1303 " pdb=" N2 NAG B1303 " pdb=" C7 NAG B1303 " ideal model delta sigma weight residual 124.56 161.77 -37.21 3.00e+00 1.11e-01 1.54e+02 angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 110.82 100.29 10.53 9.70e-01 1.06e+00 1.18e+02 angle pdb=" CA ASN A 422 " pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 112.60 122.96 -10.36 1.00e+00 1.00e+00 1.07e+02 angle pdb=" N ARG D 94 " pdb=" CA ARG D 94 " pdb=" C ARG D 94 " ideal model delta sigma weight residual 113.17 125.10 -11.93 1.26e+00 6.30e-01 8.96e+01 angle pdb=" N ARG H 94 " pdb=" CA ARG H 94 " pdb=" C ARG H 94 " ideal model delta sigma weight residual 113.17 124.80 -11.63 1.26e+00 6.30e-01 8.52e+01 ... (remaining 39850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17379 17.96 - 35.92: 426 35.92 - 53.88: 140 53.88 - 71.84: 52 71.84 - 89.80: 24 Dihedral angle restraints: 18021 sinusoidal: 7540 harmonic: 10481 Sorted by residual: dihedral pdb=" CB CYS C 705 " pdb=" SG CYS C 705 " pdb=" SG CYS A 883 " pdb=" CB CYS A 883 " ideal model delta sinusoidal sigma weight residual 93.00 174.27 -81.27 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 164.90 -71.90 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 160.91 -67.91 1 1.00e+01 1.00e-02 5.99e+01 ... (remaining 18018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3336 0.107 - 0.214: 992 0.214 - 0.321: 211 0.321 - 0.428: 61 0.428 - 0.535: 23 Chirality restraints: 4623 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.50e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.45e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.18e+02 ... (remaining 4620 not shown) Planarity restraints: 5132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " 0.089 2.00e-02 2.50e+03 9.47e-02 1.12e+02 pdb=" CG ASN A 616 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.148 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.065 2.00e-02 2.50e+03 6.89e-02 5.93e+01 pdb=" CG ASN A 331 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.108 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " 0.055 2.00e-02 2.50e+03 5.91e-02 4.37e+01 pdb=" CG ASN B 616 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " -0.093 2.00e-02 2.50e+03 pdb=" C1 NAG B1304 " 0.072 2.00e-02 2.50e+03 ... (remaining 5129 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 12127 2.91 - 3.41: 27104 3.41 - 3.91: 50650 3.91 - 4.40: 58477 4.40 - 4.90: 92068 Nonbonded interactions: 240426 Sorted by model distance: nonbonded pdb=" N ASN C 149 " pdb=" N LYS C 150 " model vdw 2.413 2.560 nonbonded pdb=" N ASP A1084 " pdb=" OD1 ASP A1084 " model vdw 2.430 3.120 nonbonded pdb=" N ARG C 44 " pdb=" O ARG C 44 " model vdw 2.440 2.496 nonbonded pdb=" O GLN B 498 " pdb=" ND2 ASN B 501 " model vdw 2.440 3.120 nonbonded pdb=" N ASP A 111 " pdb=" OD1 ASP A 111 " model vdw 2.449 3.120 ... (remaining 240421 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' selection = (chain 'B' and resid 14 through 1306) selection = (chain 'C' and (resid 14 through 66 or resid 79 through 143 or resid 153 through \ 175 or resid 185 through 260 or resid 263 through 387 or resid 395 through 426 \ or resid 429 through 515 or resid 522 through 637 or resid 641 through 827 or re \ sid 848 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 8.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.730 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.020 0.128 29399 Z= 1.078 Angle : 1.829 37.211 40075 Z= 1.223 Chirality : 0.115 0.535 4623 Planarity : 0.009 0.047 5102 Dihedral : 10.142 89.802 11129 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.06 % Allowed : 0.54 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.47 (0.13), residues: 3545 helix: 0.68 (0.17), residues: 704 sheet: 0.90 (0.18), residues: 764 loop : 0.04 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 457 TYR 0.083 0.010 TYR A 489 PHE 0.060 0.007 PHE B 342 TRP 0.069 0.012 TRP H 47 HIS 0.012 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.02021 (29309) covalent geometry : angle 1.81837 (39855) SS BOND : bond 0.01840 ( 50) SS BOND : angle 3.01659 ( 100) hydrogen bonds : bond 0.16301 ( 1216) hydrogen bonds : angle 8.37027 ( 3363) link_BETA1-4 : bond 0.07037 ( 10) link_BETA1-4 : angle 5.06578 ( 30) link_NAG-ASN : bond 0.08176 ( 30) link_NAG-ASN : angle 2.54766 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 740 MET cc_start: 0.9210 (mtp) cc_final: 0.8941 (mtt) REVERT: C 780 GLU cc_start: 0.8537 (tp30) cc_final: 0.8149 (tp30) REVERT: C 1121 PHE cc_start: 0.6782 (t80) cc_final: 0.6581 (t80) REVERT: A 140 PHE cc_start: 0.6808 (m-80) cc_final: 0.6534 (m-80) REVERT: A 153 MET cc_start: 0.7288 (ttp) cc_final: 0.5117 (ptt) REVERT: B 731 MET cc_start: 0.8820 (ttp) cc_final: 0.8614 (ttm) REVERT: H 36 TRP cc_start: 0.6112 (m100) cc_final: 0.4866 (m100) REVERT: H 47 TRP cc_start: 0.4745 (t60) cc_final: 0.3721 (t60) REVERT: H 63 PHE cc_start: 0.6224 (m-80) cc_final: 0.5628 (m-80) REVERT: H 100 TYR cc_start: 0.4997 (m-80) cc_final: 0.4686 (m-80) REVERT: H 100 PHE cc_start: 0.6485 (m-10) cc_final: 0.5639 (m-80) REVERT: D 82 LEU cc_start: 0.3850 (mt) cc_final: 0.3170 (mp) REVERT: E 48 ILE cc_start: 0.9026 (mt) cc_final: 0.8503 (mp) REVERT: E 98 PHE cc_start: 0.0354 (m-80) cc_final: -0.0029 (m-80) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.2217 time to fit residues: 51.1617 Evaluate side-chains 91 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 414 GLN C 955 ASN A 321 GLN A1010 GLN B 856 ASN B 901 GLN H 1 GLN H 64 GLN L 37 GLN D 1 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.075086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.048241 restraints weight = 188490.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.048920 restraints weight = 88883.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.049471 restraints weight = 55012.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.050007 restraints weight = 42956.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.050313 restraints weight = 36177.021| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 29399 Z= 0.169 Angle : 0.679 10.101 40075 Z= 0.366 Chirality : 0.046 0.344 4623 Planarity : 0.005 0.068 5102 Dihedral : 5.662 41.954 4706 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.67 % Allowed : 2.19 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.61 (0.13), residues: 3545 helix: 2.31 (0.19), residues: 710 sheet: 0.48 (0.17), residues: 826 loop : -0.29 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 38 TYR 0.029 0.002 TYR D 98 PHE 0.030 0.002 PHE L 62 TRP 0.027 0.002 TRP C 258 HIS 0.005 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00371 (29309) covalent geometry : angle 0.66270 (39855) SS BOND : bond 0.00343 ( 50) SS BOND : angle 1.06917 ( 100) hydrogen bonds : bond 0.05697 ( 1216) hydrogen bonds : angle 6.67713 ( 3363) link_BETA1-4 : bond 0.00494 ( 10) link_BETA1-4 : angle 2.63673 ( 30) link_NAG-ASN : bond 0.00604 ( 30) link_NAG-ASN : angle 2.68322 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8536 (ppt170) REVERT: C 740 MET cc_start: 0.8857 (mtp) cc_final: 0.8528 (mtt) REVERT: A 153 MET cc_start: 0.7400 (ttp) cc_final: 0.6379 (tpp) REVERT: B 755 GLN cc_start: 0.8351 (mt0) cc_final: 0.8149 (tp-100) REVERT: H 48 MET cc_start: 0.4538 (OUTLIER) cc_final: 0.4035 (mpp) REVERT: D 80 MET cc_start: 0.0533 (ttp) cc_final: 0.0318 (ttm) REVERT: E 98 PHE cc_start: 0.5616 (m-80) cc_final: 0.5319 (m-10) outliers start: 21 outliers final: 10 residues processed: 126 average time/residue: 0.1856 time to fit residues: 39.4471 Evaluate side-chains 94 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 246 optimal weight: 0.1980 chunk 143 optimal weight: 10.0000 chunk 178 optimal weight: 0.0370 chunk 108 optimal weight: 5.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 519 HIS B 207 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.074039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.050689 restraints weight = 188409.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.051696 restraints weight = 90662.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.051664 restraints weight = 52138.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.051869 restraints weight = 39796.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.051958 restraints weight = 36754.719| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29399 Z= 0.123 Angle : 0.571 9.832 40075 Z= 0.305 Chirality : 0.044 0.350 4623 Planarity : 0.004 0.038 5102 Dihedral : 5.043 50.758 4706 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.46 % Rotamer: Outliers : 0.70 % Allowed : 3.24 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.51 (0.14), residues: 3545 helix: 2.67 (0.19), residues: 713 sheet: 0.17 (0.17), residues: 871 loop : -0.44 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.019 0.002 TYR A1067 PHE 0.026 0.002 PHE H 100F TRP 0.019 0.002 TRP C 258 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00253 (29309) covalent geometry : angle 0.55804 (39855) SS BOND : bond 0.00349 ( 50) SS BOND : angle 0.87047 ( 100) hydrogen bonds : bond 0.04667 ( 1216) hydrogen bonds : angle 6.05731 ( 3363) link_BETA1-4 : bond 0.00739 ( 10) link_BETA1-4 : angle 2.03689 ( 30) link_NAG-ASN : bond 0.00575 ( 30) link_NAG-ASN : angle 2.25640 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4701 (tmm) cc_final: 0.4340 (tmm) REVERT: C 408 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8741 (ppt170) REVERT: A 153 MET cc_start: 0.7471 (ttp) cc_final: 0.6605 (tpp) REVERT: H 36 TRP cc_start: 0.6651 (m100) cc_final: 0.5035 (m100) REVERT: H 62 LYS cc_start: 0.6360 (tptp) cc_final: 0.5402 (pttm) REVERT: H 63 PHE cc_start: 0.5425 (m-80) cc_final: 0.4206 (m-80) REVERT: H 100 TYR cc_start: 0.5348 (m-80) cc_final: 0.4799 (m-80) REVERT: H 100 TRP cc_start: 0.4966 (m100) cc_final: 0.3783 (m100) REVERT: D 98 TYR cc_start: 0.8316 (m-80) cc_final: 0.7883 (m-80) REVERT: E 78 LEU cc_start: 0.3986 (mm) cc_final: 0.3723 (mm) outliers start: 22 outliers final: 12 residues processed: 113 average time/residue: 0.1783 time to fit residues: 34.2384 Evaluate side-chains 99 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 242 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 316 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 302 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 655 HIS C 914 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 655 HIS A 914 ASN B 487 ASN B 655 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 64 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.070631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.046872 restraints weight = 187733.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.047998 restraints weight = 92982.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.047391 restraints weight = 49708.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.047635 restraints weight = 42973.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.047568 restraints weight = 42129.502| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.154 29399 Z= 0.385 Angle : 0.822 12.688 40075 Z= 0.419 Chirality : 0.049 0.327 4623 Planarity : 0.005 0.050 5102 Dihedral : 5.759 53.810 4706 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.14 % Rotamer: Outliers : 0.98 % Allowed : 4.07 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.11 (0.13), residues: 3545 helix: 1.92 (0.19), residues: 720 sheet: -0.18 (0.17), residues: 901 loop : -0.79 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 319 TYR 0.030 0.003 TYR C 904 PHE 0.050 0.003 PHE B 906 TRP 0.017 0.003 TRP A1102 HIS 0.011 0.003 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00877 (29309) covalent geometry : angle 0.81007 (39855) SS BOND : bond 0.00412 ( 50) SS BOND : angle 1.22137 ( 100) hydrogen bonds : bond 0.05578 ( 1216) hydrogen bonds : angle 6.50296 ( 3363) link_BETA1-4 : bond 0.00645 ( 10) link_BETA1-4 : angle 2.10077 ( 30) link_NAG-ASN : bond 0.00820 ( 30) link_NAG-ASN : angle 2.67840 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8655 (ppt170) REVERT: A 153 MET cc_start: 0.7939 (ttp) cc_final: 0.7413 (tpp) REVERT: D 98 TYR cc_start: 0.8297 (m-80) cc_final: 0.8005 (m-80) REVERT: E 35 TRP cc_start: 0.4316 (OUTLIER) cc_final: 0.3242 (m-90) REVERT: E 98 PHE cc_start: 0.4070 (m-80) cc_final: 0.3789 (m-80) outliers start: 31 outliers final: 20 residues processed: 107 average time/residue: 0.1767 time to fit residues: 32.8336 Evaluate side-chains 101 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 72 optimal weight: 0.9980 chunk 146 optimal weight: 50.0000 chunk 246 optimal weight: 0.0010 chunk 164 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 281 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 chunk 356 optimal weight: 10.0000 chunk 264 optimal weight: 0.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN C 913 GLN C 914 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.072000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.048232 restraints weight = 187476.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.049494 restraints weight = 89370.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.048691 restraints weight = 51655.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.049197 restraints weight = 40488.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.049025 restraints weight = 38630.355| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29399 Z= 0.125 Angle : 0.558 9.625 40075 Z= 0.291 Chirality : 0.044 0.328 4623 Planarity : 0.004 0.043 5102 Dihedral : 5.110 52.068 4706 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 0.79 % Allowed : 4.76 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.20 (0.14), residues: 3545 helix: 2.81 (0.19), residues: 696 sheet: -0.22 (0.17), residues: 902 loop : -0.69 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 96 TYR 0.021 0.001 TYR B 170 PHE 0.028 0.001 PHE D 96 TRP 0.014 0.001 TRP C 258 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00270 (29309) covalent geometry : angle 0.54595 (39855) SS BOND : bond 0.00554 ( 50) SS BOND : angle 0.84007 ( 100) hydrogen bonds : bond 0.04465 ( 1216) hydrogen bonds : angle 5.94461 ( 3363) link_BETA1-4 : bond 0.00418 ( 10) link_BETA1-4 : angle 1.60313 ( 30) link_NAG-ASN : bond 0.00461 ( 30) link_NAG-ASN : angle 2.23497 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4512 (tmm) cc_final: 0.4170 (tmm) REVERT: C 740 MET cc_start: 0.9001 (mtp) cc_final: 0.8543 (mtp) REVERT: C 805 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8864 (tp) REVERT: A 153 MET cc_start: 0.7754 (ttp) cc_final: 0.7235 (tpp) REVERT: L 36 TYR cc_start: 0.0477 (OUTLIER) cc_final: 0.0101 (t80) REVERT: D 58 ASN cc_start: -0.0062 (OUTLIER) cc_final: -0.0438 (t0) REVERT: D 98 TYR cc_start: 0.8336 (m-80) cc_final: 0.8042 (m-80) outliers start: 25 outliers final: 12 residues processed: 107 average time/residue: 0.1862 time to fit residues: 34.0333 Evaluate side-chains 96 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 89 optimal weight: 5.9990 chunk 329 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 243 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1119 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.070857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.046926 restraints weight = 187109.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.046464 restraints weight = 87477.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.046980 restraints weight = 55299.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.047127 restraints weight = 41198.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.047127 restraints weight = 35958.740| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 29399 Z= 0.273 Angle : 0.663 10.087 40075 Z= 0.337 Chirality : 0.045 0.315 4623 Planarity : 0.004 0.045 5102 Dihedral : 5.287 53.776 4706 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.66 % Rotamer: Outliers : 0.73 % Allowed : 5.43 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.01 (0.14), residues: 3545 helix: 2.59 (0.19), residues: 706 sheet: -0.38 (0.17), residues: 907 loop : -0.81 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.023 0.002 TYR B1067 PHE 0.027 0.002 PHE D 96 TRP 0.025 0.002 TRP E 35 HIS 0.008 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00621 (29309) covalent geometry : angle 0.65008 (39855) SS BOND : bond 0.00533 ( 50) SS BOND : angle 1.03812 ( 100) hydrogen bonds : bond 0.04703 ( 1216) hydrogen bonds : angle 6.08259 ( 3363) link_BETA1-4 : bond 0.00396 ( 10) link_BETA1-4 : angle 1.62067 ( 30) link_NAG-ASN : bond 0.00548 ( 30) link_NAG-ASN : angle 2.50835 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7779 (ttp) cc_final: 0.7099 (tpp) REVERT: H 100 TYR cc_start: 0.5064 (OUTLIER) cc_final: 0.4699 (m-80) outliers start: 23 outliers final: 16 residues processed: 105 average time/residue: 0.1748 time to fit residues: 31.9802 Evaluate side-chains 103 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 270 optimal weight: 4.9990 chunk 289 optimal weight: 0.5980 chunk 291 optimal weight: 0.6980 chunk 248 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 315 optimal weight: 30.0000 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 294 optimal weight: 4.9990 chunk 344 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS D 6 GLN D 58 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.071504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.045447 restraints weight = 187431.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.044820 restraints weight = 92326.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.045218 restraints weight = 57816.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.045721 restraints weight = 46903.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 89)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.045091 restraints weight = 39856.581| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29399 Z= 0.151 Angle : 0.558 9.144 40075 Z= 0.288 Chirality : 0.044 0.306 4623 Planarity : 0.004 0.044 5102 Dihedral : 5.026 53.202 4706 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.93 % Rotamer: Outliers : 0.76 % Allowed : 5.78 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.14), residues: 3545 helix: 2.95 (0.19), residues: 696 sheet: -0.39 (0.17), residues: 883 loop : -0.74 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.020 0.001 TYR A1067 PHE 0.028 0.001 PHE H 100F TRP 0.025 0.002 TRP E 35 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00339 (29309) covalent geometry : angle 0.54529 (39855) SS BOND : bond 0.00248 ( 50) SS BOND : angle 0.92025 ( 100) hydrogen bonds : bond 0.04267 ( 1216) hydrogen bonds : angle 5.83020 ( 3363) link_BETA1-4 : bond 0.00312 ( 10) link_BETA1-4 : angle 1.43287 ( 30) link_NAG-ASN : bond 0.00422 ( 30) link_NAG-ASN : angle 2.25789 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4523 (tmm) cc_final: 0.4232 (tmm) REVERT: C 805 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8887 (tp) REVERT: A 153 MET cc_start: 0.7732 (ttp) cc_final: 0.6844 (tpp) REVERT: H 100 TYR cc_start: 0.4532 (OUTLIER) cc_final: 0.4303 (m-80) REVERT: L 36 TYR cc_start: 0.0016 (OUTLIER) cc_final: -0.0403 (t80) REVERT: E 32 TYR cc_start: 0.6040 (m-10) cc_final: 0.5775 (m-10) outliers start: 24 outliers final: 13 residues processed: 106 average time/residue: 0.1812 time to fit residues: 33.0910 Evaluate side-chains 102 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 18 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 146 optimal weight: 40.0000 chunk 232 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 340 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B1088 HIS D 6 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.071543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.046539 restraints weight = 189126.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.045675 restraints weight = 88703.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.046200 restraints weight = 56340.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.046612 restraints weight = 43369.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.046809 restraints weight = 37726.874| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29399 Z= 0.139 Angle : 0.553 8.858 40075 Z= 0.286 Chirality : 0.043 0.301 4623 Planarity : 0.004 0.045 5102 Dihedral : 4.917 53.696 4706 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 0.73 % Allowed : 6.07 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.14), residues: 3545 helix: 3.00 (0.19), residues: 705 sheet: -0.32 (0.17), residues: 863 loop : -0.77 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.021 0.001 TYR L 36 PHE 0.026 0.001 PHE H 100F TRP 0.030 0.002 TRP E 35 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00314 (29309) covalent geometry : angle 0.54015 (39855) SS BOND : bond 0.00287 ( 50) SS BOND : angle 1.20716 ( 100) hydrogen bonds : bond 0.04124 ( 1216) hydrogen bonds : angle 5.72963 ( 3363) link_BETA1-4 : bond 0.00272 ( 10) link_BETA1-4 : angle 1.38270 ( 30) link_NAG-ASN : bond 0.00392 ( 30) link_NAG-ASN : angle 2.16299 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4491 (tmm) cc_final: 0.4206 (tmm) REVERT: A 153 MET cc_start: 0.7679 (ttp) cc_final: 0.6735 (tpp) REVERT: H 100 TYR cc_start: 0.4620 (OUTLIER) cc_final: 0.4340 (m-80) REVERT: L 36 TYR cc_start: 0.0457 (OUTLIER) cc_final: 0.0041 (t80) REVERT: E 32 TYR cc_start: 0.6201 (m-10) cc_final: 0.5916 (m-10) outliers start: 23 outliers final: 15 residues processed: 107 average time/residue: 0.1768 time to fit residues: 32.8795 Evaluate side-chains 103 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 30 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 353 optimal weight: 20.0000 chunk 272 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 300 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 321 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1119 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.070649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045772 restraints weight = 189800.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.044907 restraints weight = 90334.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.045406 restraints weight = 58692.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.045711 restraints weight = 45075.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.045711 restraints weight = 38067.316| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 29399 Z= 0.263 Angle : 0.664 10.555 40075 Z= 0.337 Chirality : 0.045 0.293 4623 Planarity : 0.004 0.046 5102 Dihedral : 5.236 54.815 4706 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.68 % Favored : 95.23 % Rotamer: Outliers : 0.67 % Allowed : 6.07 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.11 (0.14), residues: 3545 helix: 2.60 (0.19), residues: 706 sheet: -0.45 (0.17), residues: 871 loop : -0.90 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 408 TYR 0.029 0.002 TYR H 98 PHE 0.028 0.002 PHE H 100F TRP 0.029 0.002 TRP E 35 HIS 0.009 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00601 (29309) covalent geometry : angle 0.65078 (39855) SS BOND : bond 0.00380 ( 50) SS BOND : angle 1.58446 ( 100) hydrogen bonds : bond 0.04601 ( 1216) hydrogen bonds : angle 6.03337 ( 3363) link_BETA1-4 : bond 0.00379 ( 10) link_BETA1-4 : angle 1.52973 ( 30) link_NAG-ASN : bond 0.00540 ( 30) link_NAG-ASN : angle 2.33654 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4375 (tmm) cc_final: 0.4059 (tmm) REVERT: A 153 MET cc_start: 0.7754 (ttp) cc_final: 0.6956 (tpp) REVERT: H 100 TYR cc_start: 0.4593 (OUTLIER) cc_final: 0.4289 (m-80) REVERT: D 92 CYS cc_start: 0.2010 (OUTLIER) cc_final: 0.1326 (m) REVERT: E 32 TYR cc_start: 0.6522 (m-10) cc_final: 0.6164 (m-10) outliers start: 21 outliers final: 12 residues processed: 104 average time/residue: 0.1703 time to fit residues: 30.4538 Evaluate side-chains 96 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 30 optimal weight: 4.9990 chunk 247 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 292 optimal weight: 5.9990 chunk 253 optimal weight: 30.0000 chunk 355 optimal weight: 40.0000 chunk 114 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 234 optimal weight: 2.9990 chunk 264 optimal weight: 0.0870 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.070933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.044913 restraints weight = 187785.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.044992 restraints weight = 92037.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.045527 restraints weight = 58158.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.045916 restraints weight = 44187.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046164 restraints weight = 37407.311| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 29399 Z= 0.201 Angle : 0.597 9.639 40075 Z= 0.306 Chirality : 0.044 0.290 4623 Planarity : 0.004 0.045 5102 Dihedral : 5.150 54.504 4706 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 0.51 % Allowed : 6.39 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.09 (0.14), residues: 3545 helix: 2.71 (0.19), residues: 702 sheet: -0.49 (0.17), residues: 843 loop : -0.90 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.021 0.002 TYR A1067 PHE 0.026 0.002 PHE H 100F TRP 0.023 0.002 TRP E 35 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00457 (29309) covalent geometry : angle 0.58481 (39855) SS BOND : bond 0.00284 ( 50) SS BOND : angle 1.29844 ( 100) hydrogen bonds : bond 0.04339 ( 1216) hydrogen bonds : angle 5.90700 ( 3363) link_BETA1-4 : bond 0.00225 ( 10) link_BETA1-4 : angle 1.37666 ( 30) link_NAG-ASN : bond 0.00435 ( 30) link_NAG-ASN : angle 2.23397 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4546 (tmm) cc_final: 0.4283 (tmm) REVERT: C 805 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8841 (tp) REVERT: A 153 MET cc_start: 0.7785 (ttp) cc_final: 0.7165 (tpp) REVERT: H 80 MET cc_start: 0.3941 (ptt) cc_final: 0.3642 (ptt) REVERT: H 100 TYR cc_start: 0.4450 (OUTLIER) cc_final: 0.3969 (m-80) REVERT: D 92 CYS cc_start: 0.2242 (OUTLIER) cc_final: 0.1650 (m) REVERT: E 32 TYR cc_start: 0.6324 (m-10) cc_final: 0.6064 (m-10) outliers start: 16 outliers final: 11 residues processed: 96 average time/residue: 0.1744 time to fit residues: 29.0189 Evaluate side-chains 99 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 1 optimal weight: 6.9990 chunk 206 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 319 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 347 optimal weight: 30.0000 chunk 145 optimal weight: 30.0000 chunk 16 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 153 optimal weight: 8.9990 chunk 272 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.071563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.047331 restraints weight = 186137.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.046617 restraints weight = 86863.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.047279 restraints weight = 54289.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.047492 restraints weight = 39822.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.047716 restraints weight = 34719.464| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29399 Z= 0.115 Angle : 0.539 8.826 40075 Z= 0.278 Chirality : 0.044 0.292 4623 Planarity : 0.004 0.043 5102 Dihedral : 4.880 54.133 4706 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 0.41 % Allowed : 6.67 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.11 (0.14), residues: 3545 helix: 2.98 (0.19), residues: 703 sheet: -0.38 (0.17), residues: 835 loop : -0.80 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 38 TYR 0.019 0.001 TYR A1067 PHE 0.025 0.001 PHE D 96 TRP 0.024 0.002 TRP E 35 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00251 (29309) covalent geometry : angle 0.52755 (39855) SS BOND : bond 0.00217 ( 50) SS BOND : angle 1.08778 ( 100) hydrogen bonds : bond 0.03998 ( 1216) hydrogen bonds : angle 5.67624 ( 3363) link_BETA1-4 : bond 0.00321 ( 10) link_BETA1-4 : angle 1.30802 ( 30) link_NAG-ASN : bond 0.00397 ( 30) link_NAG-ASN : angle 2.09458 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7167.25 seconds wall clock time: 123 minutes 58.18 seconds (7438.18 seconds total)