Starting phenix.real_space_refine on Fri Sep 19 11:07:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9elk_48152/09_2025/9elk_48152.cif Found real_map, /net/cci-nas-00/data/ceres_data/9elk_48152/09_2025/9elk_48152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9elk_48152/09_2025/9elk_48152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9elk_48152/09_2025/9elk_48152.map" model { file = "/net/cci-nas-00/data/ceres_data/9elk_48152/09_2025/9elk_48152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9elk_48152/09_2025/9elk_48152.cif" } resolution = 2.82 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16146 2.51 5 N 4101 2.21 5 O 4941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25299 Number of models: 1 Model: "" Number of chains: 21 Chain: "C" Number of atoms: 8173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8173 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 54, 'TRANS': 986} Chain breaks: 7 Chain: "A" Number of atoms: 8173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8173 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 54, 'TRANS': 986} Chain breaks: 7 Chain: "B" Number of atoms: 8173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8173 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 54, 'TRANS': 986} Chain breaks: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "L" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: "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: 5.30, per 1000 atoms: 0.21 Number of scatterers: 25299 At special positions: 0 Unit cell: (135.702, 140.728, 187.398, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4941 8.00 N 4101 7.00 C 16146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 354 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 30 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 354 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 30 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 354 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 30 " " NAG D 1 " - " ASN C 717 " " NAG E 1 " - " ASN C1098 " " NAG F 1 " - " ASN C1134 " " NAG G 1 " - " ASN C 282 " " NAG H 1 " - " ASN C 801 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN A 282 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 801 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 841.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5862 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 42 sheets defined 27.6% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 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 366 through 372 removed outlier: 3.659A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.653A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.992A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.285A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.023A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.892A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1139 through 1148 removed outlier: 3.610A pdb=" N LEU C1143 " --> pdb=" O ASP C1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.659A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.654A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.992A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.286A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.023A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.892A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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 1139 through 1148 removed outlier: 3.610A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.659A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.654A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.992A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.285A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.022A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.892A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1139 through 1148 removed outlier: 3.610A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.886A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.247A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.585A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 168 through 172 removed outlier: 4.435A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.642A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.455A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.243A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AA9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.980A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 702 through 704 removed outlier: 3.560A pdb=" N LYS B 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.756A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.756A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.543A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 788 through 790 removed outlier: 6.113A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.854A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.886A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.247A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.585A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 168 through 172 removed outlier: 4.435A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.642A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.243A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AC6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.981A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.756A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.756A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.544A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.113A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.854A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.887A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.585A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 168 through 172 removed outlier: 4.435A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.641A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.243A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 451 through 453 Processing sheet with id=AE1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.981A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.756A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.756A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.543A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.854A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 1049 hydrogen bonds defined for protein. 2859 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.49 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6439 1.33 - 1.46: 6518 1.46 - 1.58: 12783 1.58 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 25881 Sorted by residual: bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.48e+00 ... (remaining 25876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 33581 2.53 - 5.06: 1435 5.06 - 7.58: 159 7.58 - 10.11: 24 10.11 - 12.64: 9 Bond angle restraints: 35208 Sorted by residual: angle pdb=" N PHE B 79 " pdb=" CA PHE B 79 " pdb=" C PHE B 79 " ideal model delta sigma weight residual 111.36 118.30 -6.94 1.09e+00 8.42e-01 4.05e+01 angle pdb=" N PHE A 79 " pdb=" CA PHE A 79 " pdb=" C PHE A 79 " ideal model delta sigma weight residual 111.36 118.28 -6.92 1.09e+00 8.42e-01 4.03e+01 angle pdb=" N PHE C 79 " pdb=" CA PHE C 79 " pdb=" C PHE C 79 " ideal model delta sigma weight residual 111.36 118.28 -6.92 1.09e+00 8.42e-01 4.02e+01 angle pdb=" N GLY C 75 " pdb=" CA GLY C 75 " pdb=" C GLY C 75 " ideal model delta sigma weight residual 112.54 105.64 6.90 1.28e+00 6.10e-01 2.91e+01 angle pdb=" N GLY A 75 " pdb=" CA GLY A 75 " pdb=" C GLY A 75 " ideal model delta sigma weight residual 112.54 105.64 6.90 1.28e+00 6.10e-01 2.91e+01 ... (remaining 35203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.44: 15153 21.44 - 42.89: 705 42.89 - 64.33: 186 64.33 - 85.78: 60 85.78 - 107.22: 33 Dihedral angle restraints: 16137 sinusoidal: 7035 harmonic: 9102 Sorted by residual: dihedral pdb=" CD ARG A 454 " pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " pdb=" NH1 ARG A 454 " ideal model delta sinusoidal sigma weight residual 0.00 -47.93 47.93 1 1.00e+01 1.00e-02 3.17e+01 dihedral pdb=" CD ARG C 454 " pdb=" NE ARG C 454 " pdb=" CZ ARG C 454 " pdb=" NH1 ARG C 454 " ideal model delta sinusoidal sigma weight residual 0.00 -47.89 47.89 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CD ARG B 454 " pdb=" NE ARG B 454 " pdb=" CZ ARG B 454 " pdb=" NH1 ARG B 454 " ideal model delta sinusoidal sigma weight residual 0.00 -47.89 47.89 1 1.00e+01 1.00e-02 3.16e+01 ... (remaining 16134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 4003 0.141 - 0.283: 128 0.283 - 0.424: 18 0.424 - 0.566: 0 0.566 - 0.707: 3 Chirality restraints: 4152 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 4149 not shown) Planarity restraints: 4497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 454 " -0.665 9.50e-02 1.11e+02 2.99e-01 6.24e+01 pdb=" NE ARG A 454 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 454 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG A 454 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 454 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 454 " -0.664 9.50e-02 1.11e+02 2.99e-01 6.23e+01 pdb=" NE ARG C 454 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG C 454 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG C 454 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG C 454 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 454 " 0.665 9.50e-02 1.11e+02 2.99e-01 6.23e+01 pdb=" NE ARG B 454 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG B 454 " 0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG B 454 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG B 454 " 0.004 2.00e-02 2.50e+03 ... (remaining 4494 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 12 2.34 - 2.98: 12624 2.98 - 3.62: 35492 3.62 - 4.26: 58920 4.26 - 4.90: 97117 Nonbonded interactions: 204165 Sorted by model distance: nonbonded pdb=" CG PRO A 225 " pdb=" CE1 PHE B 562 " model vdw 1.697 3.740 nonbonded pdb=" CE1 PHE C 562 " pdb=" CG PRO B 225 " model vdw 1.698 3.740 nonbonded pdb=" CG PRO C 225 " pdb=" CE1 PHE A 562 " model vdw 1.698 3.740 nonbonded pdb=" OG SER C 555 " pdb=" OD1 ASP C 586 " model vdw 2.106 3.040 nonbonded pdb=" OG SER B 555 " pdb=" OD1 ASP B 586 " model vdw 2.106 3.040 ... (remaining 204160 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.570 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.007 0.083 25974 Z= 0.316 Angle : 1.206 16.630 35451 Z= 0.657 Chirality : 0.068 0.707 4152 Planarity : 0.011 0.299 4461 Dihedral : 14.591 107.220 10167 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.14), residues: 3075 helix: 1.25 (0.17), residues: 732 sheet: 0.84 (0.19), residues: 624 loop : -0.09 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.003 ARG A 454 TYR 0.043 0.004 TYR B 265 PHE 0.045 0.004 PHE B 371 TRP 0.028 0.003 TRP B 452 HIS 0.009 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00717 (25881) covalent geometry : angle 1.15784 (35208) SS BOND : bond 0.00469 ( 36) SS BOND : angle 1.70314 ( 72) hydrogen bonds : bond 0.13220 ( 1034) hydrogen bonds : angle 7.56088 ( 2859) link_BETA1-4 : bond 0.01556 ( 21) link_BETA1-4 : angle 5.16236 ( 63) link_NAG-ASN : bond 0.00799 ( 36) link_NAG-ASN : angle 4.82242 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 269 TYR cc_start: 0.8063 (m-80) cc_final: 0.7460 (m-80) REVERT: C 335 LEU cc_start: 0.8000 (mm) cc_final: 0.7690 (tp) REVERT: C 386 LYS cc_start: 0.5736 (ttpp) cc_final: 0.5001 (tppt) REVERT: C 574 ASP cc_start: 0.7960 (p0) cc_final: 0.7662 (p0) REVERT: A 269 TYR cc_start: 0.8023 (m-80) cc_final: 0.7470 (m-80) REVERT: A 386 LYS cc_start: 0.5761 (ttpp) cc_final: 0.5012 (tppt) REVERT: A 389 ASP cc_start: 0.8010 (m-30) cc_final: 0.7795 (m-30) REVERT: B 177 MET cc_start: 0.4608 (tpp) cc_final: 0.4113 (tpp) REVERT: B 269 TYR cc_start: 0.7996 (m-80) cc_final: 0.7388 (m-80) REVERT: B 386 LYS cc_start: 0.5637 (ttpp) cc_final: 0.4990 (ttpp) REVERT: B 389 ASP cc_start: 0.7928 (m-30) cc_final: 0.7650 (m-30) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.4745 time to fit residues: 159.4626 Evaluate side-chains 213 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.0270 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 ASN C 978 ASN C1119 ASN A 137 ASN A 703 ASN A 907 ASN A 978 ASN A1119 ASN B 137 ASN B 978 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.193663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131270 restraints weight = 29502.769| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.24 r_work: 0.3276 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25974 Z= 0.148 Angle : 0.669 10.643 35451 Z= 0.342 Chirality : 0.047 0.298 4152 Planarity : 0.005 0.063 4461 Dihedral : 8.374 64.989 4524 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.82 % Allowed : 9.75 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.14), residues: 3075 helix: 2.30 (0.19), residues: 723 sheet: 0.72 (0.19), residues: 624 loop : -0.44 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 357 TYR 0.031 0.001 TYR B 265 PHE 0.021 0.002 PHE A 371 TRP 0.016 0.002 TRP B 452 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00325 (25881) covalent geometry : angle 0.62341 (35208) SS BOND : bond 0.00371 ( 36) SS BOND : angle 1.09285 ( 72) hydrogen bonds : bond 0.05445 ( 1034) hydrogen bonds : angle 6.07917 ( 2859) link_BETA1-4 : bond 0.01102 ( 21) link_BETA1-4 : angle 4.06528 ( 63) link_NAG-ASN : bond 0.00631 ( 36) link_NAG-ASN : angle 3.09565 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 269 TYR cc_start: 0.8101 (m-80) cc_final: 0.7374 (m-80) REVERT: C 358 ILE cc_start: 0.7377 (mt) cc_final: 0.7128 (mp) REVERT: C 386 LYS cc_start: 0.5806 (OUTLIER) cc_final: 0.5533 (ttpp) REVERT: C 1002 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: A 269 TYR cc_start: 0.8047 (m-80) cc_final: 0.7391 (m-80) REVERT: A 357 ARG cc_start: 0.6655 (mtp-110) cc_final: 0.6291 (mtp85) REVERT: A 386 LYS cc_start: 0.5609 (OUTLIER) cc_final: 0.5330 (ttpp) REVERT: B 153 MET cc_start: 0.0908 (ppp) cc_final: -0.0065 (tpt) REVERT: B 269 TYR cc_start: 0.7993 (m-80) cc_final: 0.7295 (m-80) REVERT: B 358 ILE cc_start: 0.7461 (mt) cc_final: 0.7156 (mp) REVERT: B 386 LYS cc_start: 0.5483 (OUTLIER) cc_final: 0.4725 (ttpp) REVERT: B 389 ASP cc_start: 0.7966 (m-30) cc_final: 0.7735 (m-30) REVERT: B 740 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8301 (ttt) REVERT: B 904 TYR cc_start: 0.8155 (m-10) cc_final: 0.7795 (m-10) outliers start: 50 outliers final: 13 residues processed: 281 average time/residue: 0.4791 time to fit residues: 162.2168 Evaluate side-chains 225 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 884 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 104 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 257 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN C 613 GLN C 677 GLN C 703 ASN C 804 GLN C 955 ASN A 125 ASN A 613 GLN A 677 GLN A 703 ASN A 804 GLN B 125 ASN B 613 GLN B 677 GLN B 703 ASN B 804 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.191012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137133 restraints weight = 29491.477| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.87 r_work: 0.3255 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25974 Z= 0.194 Angle : 0.643 9.995 35451 Z= 0.328 Chirality : 0.048 0.246 4152 Planarity : 0.005 0.052 4461 Dihedral : 6.415 41.679 4524 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.69 % Allowed : 11.14 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.14), residues: 3075 helix: 2.51 (0.19), residues: 699 sheet: 0.46 (0.19), residues: 639 loop : -0.64 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 357 TYR 0.034 0.002 TYR B 265 PHE 0.019 0.002 PHE A 192 TRP 0.017 0.002 TRP A 886 HIS 0.007 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00463 (25881) covalent geometry : angle 0.60362 (35208) SS BOND : bond 0.00526 ( 36) SS BOND : angle 1.04139 ( 72) hydrogen bonds : bond 0.05336 ( 1034) hydrogen bonds : angle 5.79586 ( 2859) link_BETA1-4 : bond 0.01079 ( 21) link_BETA1-4 : angle 3.81677 ( 63) link_NAG-ASN : bond 0.00442 ( 36) link_NAG-ASN : angle 2.78586 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 224 time to evaluate : 0.962 Fit side-chains REVERT: C 237 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7515 (mtm110) REVERT: C 269 TYR cc_start: 0.8194 (m-80) cc_final: 0.7717 (m-80) REVERT: C 386 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5552 (ttpp) REVERT: A 269 TYR cc_start: 0.8100 (m-80) cc_final: 0.7681 (m-80) REVERT: A 357 ARG cc_start: 0.6813 (mtp-110) cc_final: 0.6498 (mtp85) REVERT: A 378 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6969 (ptmm) REVERT: A 386 LYS cc_start: 0.6239 (OUTLIER) cc_final: 0.5588 (ttpp) REVERT: A 624 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8512 (mp) REVERT: B 153 MET cc_start: 0.1362 (ppp) cc_final: 0.0157 (tpt) REVERT: B 237 ARG cc_start: 0.7762 (mtm-85) cc_final: 0.7447 (mtm110) REVERT: B 269 TYR cc_start: 0.8051 (m-80) cc_final: 0.7635 (m-80) REVERT: B 576 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8776 (p) REVERT: B 740 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8383 (ttm) REVERT: B 904 TYR cc_start: 0.8169 (m-10) cc_final: 0.7541 (m-10) outliers start: 74 outliers final: 32 residues processed: 269 average time/residue: 0.4766 time to fit residues: 154.4991 Evaluate side-chains 245 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 934 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 93 optimal weight: 0.3980 chunk 219 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 265 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 299 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1119 ASN A1119 ASN B 703 ASN B1119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.192312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.130866 restraints weight = 29401.670| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.37 r_work: 0.3247 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25974 Z= 0.122 Angle : 0.571 9.169 35451 Z= 0.288 Chirality : 0.045 0.222 4152 Planarity : 0.005 0.056 4461 Dihedral : 5.691 41.186 4524 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.89 % Allowed : 12.59 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.14), residues: 3075 helix: 2.68 (0.19), residues: 702 sheet: 0.35 (0.19), residues: 651 loop : -0.71 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 357 TYR 0.027 0.001 TYR C 265 PHE 0.018 0.001 PHE B 192 TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00266 (25881) covalent geometry : angle 0.53162 (35208) SS BOND : bond 0.00670 ( 36) SS BOND : angle 0.83450 ( 72) hydrogen bonds : bond 0.04522 ( 1034) hydrogen bonds : angle 5.53947 ( 2859) link_BETA1-4 : bond 0.01003 ( 21) link_BETA1-4 : angle 3.59251 ( 63) link_NAG-ASN : bond 0.00371 ( 36) link_NAG-ASN : angle 2.61973 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 237 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7571 (mtm110) REVERT: C 269 TYR cc_start: 0.8220 (m-80) cc_final: 0.7696 (m-80) REVERT: C 393 THR cc_start: 0.7924 (m) cc_final: 0.7627 (p) REVERT: C 869 MET cc_start: 0.9171 (mtt) cc_final: 0.8898 (mtt) REVERT: A 237 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7508 (mtm110) REVERT: A 269 TYR cc_start: 0.8158 (m-80) cc_final: 0.7701 (m-80) REVERT: A 357 ARG cc_start: 0.6894 (mtp-110) cc_final: 0.6604 (mtp85) REVERT: A 576 VAL cc_start: 0.9002 (m) cc_final: 0.8796 (p) REVERT: A 624 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8477 (mp) REVERT: A 933 LYS cc_start: 0.8223 (mttm) cc_final: 0.7947 (mtpt) REVERT: B 153 MET cc_start: 0.1182 (ppp) cc_final: 0.0059 (tpt) REVERT: B 237 ARG cc_start: 0.7712 (mtm-85) cc_final: 0.7424 (mtm110) REVERT: B 269 TYR cc_start: 0.8088 (m-80) cc_final: 0.7627 (m-80) REVERT: B 280 ASN cc_start: 0.7630 (t0) cc_final: 0.7423 (t0) REVERT: B 314 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: B 386 LYS cc_start: 0.6329 (ttpt) cc_final: 0.5869 (ttpt) REVERT: B 576 VAL cc_start: 0.8971 (m) cc_final: 0.8759 (p) REVERT: B 740 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8382 (ttm) REVERT: B 904 TYR cc_start: 0.8184 (m-10) cc_final: 0.7475 (m-10) REVERT: B 933 LYS cc_start: 0.8223 (mttm) cc_final: 0.7834 (mtmm) outliers start: 52 outliers final: 28 residues processed: 273 average time/residue: 0.4827 time to fit residues: 158.0626 Evaluate side-chains 249 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 934 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 275 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 181 optimal weight: 0.0980 chunk 209 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 703 ASN A 703 ASN A1010 GLN A1088 HIS A1119 ASN B 703 ASN B1088 HIS B1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.188660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133226 restraints weight = 29270.344| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.80 r_work: 0.3219 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 25974 Z= 0.232 Angle : 0.640 10.079 35451 Z= 0.325 Chirality : 0.048 0.214 4152 Planarity : 0.005 0.061 4461 Dihedral : 5.794 44.851 4524 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.17 % Allowed : 12.01 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.14), residues: 3075 helix: 2.37 (0.19), residues: 723 sheet: 0.37 (0.19), residues: 663 loop : -0.80 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 357 TYR 0.031 0.002 TYR A 265 PHE 0.022 0.002 PHE C 898 TRP 0.014 0.002 TRP C 633 HIS 0.009 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00565 (25881) covalent geometry : angle 0.60557 (35208) SS BOND : bond 0.00438 ( 36) SS BOND : angle 0.93922 ( 72) hydrogen bonds : bond 0.05432 ( 1034) hydrogen bonds : angle 5.71902 ( 2859) link_BETA1-4 : bond 0.01106 ( 21) link_BETA1-4 : angle 3.60743 ( 63) link_NAG-ASN : bond 0.00414 ( 36) link_NAG-ASN : angle 2.57851 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 198 time to evaluate : 0.932 Fit side-chains REVERT: C 153 MET cc_start: 0.1571 (ppp) cc_final: 0.0390 (tpt) REVERT: C 237 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7596 (mtm110) REVERT: C 269 TYR cc_start: 0.8212 (m-80) cc_final: 0.7735 (m-80) REVERT: C 294 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6938 (t70) REVERT: C 904 TYR cc_start: 0.8118 (m-10) cc_final: 0.7821 (m-10) REVERT: A 191 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: A 269 TYR cc_start: 0.8158 (m-80) cc_final: 0.7721 (m-80) REVERT: A 378 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6976 (ptmm) REVERT: A 576 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8887 (p) REVERT: A 624 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8455 (mp) REVERT: B 153 MET cc_start: 0.1358 (ppp) cc_final: 0.0280 (tpt) REVERT: B 269 TYR cc_start: 0.8125 (m-80) cc_final: 0.7691 (m-80) REVERT: B 576 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8833 (p) REVERT: B 740 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8431 (ttm) REVERT: B 904 TYR cc_start: 0.8160 (m-10) cc_final: 0.7509 (m-10) outliers start: 87 outliers final: 53 residues processed: 248 average time/residue: 0.4752 time to fit residues: 142.1410 Evaluate side-chains 246 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 230 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 216 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 307 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 625 HIS A 625 HIS B 625 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.188950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123179 restraints weight = 29441.257| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.28 r_work: 0.3235 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25974 Z= 0.130 Angle : 0.564 9.088 35451 Z= 0.285 Chirality : 0.045 0.215 4152 Planarity : 0.004 0.068 4461 Dihedral : 5.383 44.136 4524 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.84 % Allowed : 12.88 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.15), residues: 3075 helix: 2.75 (0.19), residues: 699 sheet: 0.36 (0.20), residues: 630 loop : -0.77 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 357 TYR 0.023 0.001 TYR C 265 PHE 0.016 0.001 PHE B 192 TRP 0.011 0.001 TRP C 64 HIS 0.011 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00299 (25881) covalent geometry : angle 0.52964 (35208) SS BOND : bond 0.00270 ( 36) SS BOND : angle 0.82044 ( 72) hydrogen bonds : bond 0.04498 ( 1034) hydrogen bonds : angle 5.41822 ( 2859) link_BETA1-4 : bond 0.01020 ( 21) link_BETA1-4 : angle 3.32290 ( 63) link_NAG-ASN : bond 0.00393 ( 36) link_NAG-ASN : angle 2.46624 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 212 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.1235 (ppp) cc_final: 0.0241 (tpt) REVERT: C 237 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.7240 (mtm110) REVERT: C 269 TYR cc_start: 0.8185 (m-80) cc_final: 0.7444 (m-80) REVERT: C 294 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6450 (t70) REVERT: C 393 THR cc_start: 0.7905 (m) cc_final: 0.7572 (p) REVERT: C 904 TYR cc_start: 0.8079 (m-10) cc_final: 0.7746 (m-10) REVERT: A 191 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: A 269 TYR cc_start: 0.8149 (m-80) cc_final: 0.7494 (m-80) REVERT: A 321 GLN cc_start: 0.8316 (mm-40) cc_final: 0.8096 (mm-40) REVERT: A 357 ARG cc_start: 0.6986 (ttp-110) cc_final: 0.6366 (mtp85) REVERT: A 576 VAL cc_start: 0.8861 (m) cc_final: 0.8657 (p) REVERT: A 624 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8117 (mp) REVERT: A 904 TYR cc_start: 0.8131 (m-10) cc_final: 0.7924 (m-10) REVERT: B 153 MET cc_start: 0.0994 (ppp) cc_final: 0.0109 (tpt) REVERT: B 237 ARG cc_start: 0.7427 (mtm-85) cc_final: 0.7163 (mtm110) REVERT: B 269 TYR cc_start: 0.8116 (m-80) cc_final: 0.7445 (m-80) REVERT: B 314 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: B 740 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8152 (ttm) REVERT: B 904 TYR cc_start: 0.8138 (m-10) cc_final: 0.7260 (m-10) outliers start: 78 outliers final: 45 residues processed: 258 average time/residue: 0.4598 time to fit residues: 142.7695 Evaluate side-chains 253 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 203 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 14 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 230 optimal weight: 0.4980 chunk 97 optimal weight: 0.0980 chunk 291 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 0.3980 chunk 177 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 625 HIS C1119 ASN A 625 HIS A 703 ASN A1119 ASN B 625 HIS B 703 ASN B1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.189843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125047 restraints weight = 29343.090| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.07 r_work: 0.3269 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25974 Z= 0.115 Angle : 0.548 8.597 35451 Z= 0.276 Chirality : 0.044 0.308 4152 Planarity : 0.004 0.074 4461 Dihedral : 5.163 42.807 4524 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.51 % Allowed : 13.72 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.15), residues: 3075 helix: 2.85 (0.19), residues: 699 sheet: 0.44 (0.20), residues: 630 loop : -0.73 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 357 TYR 0.023 0.001 TYR B 266 PHE 0.018 0.001 PHE A 192 TRP 0.012 0.001 TRP B 64 HIS 0.028 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00259 (25881) covalent geometry : angle 0.51501 (35208) SS BOND : bond 0.00256 ( 36) SS BOND : angle 0.86317 ( 72) hydrogen bonds : bond 0.04242 ( 1034) hydrogen bonds : angle 5.29923 ( 2859) link_BETA1-4 : bond 0.00976 ( 21) link_BETA1-4 : angle 3.18204 ( 63) link_NAG-ASN : bond 0.00379 ( 36) link_NAG-ASN : angle 2.40014 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 215 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.1383 (ppp) cc_final: 0.0417 (tpt) REVERT: C 237 ARG cc_start: 0.7619 (mtm-85) cc_final: 0.7361 (mtm110) REVERT: C 269 TYR cc_start: 0.8131 (m-80) cc_final: 0.7461 (m-80) REVERT: C 393 THR cc_start: 0.7943 (m) cc_final: 0.7594 (p) REVERT: C 904 TYR cc_start: 0.8096 (m-10) cc_final: 0.7762 (m-10) REVERT: A 191 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: A 269 TYR cc_start: 0.8140 (m-80) cc_final: 0.7552 (m-80) REVERT: A 357 ARG cc_start: 0.6992 (ttp-110) cc_final: 0.6378 (mtp85) REVERT: A 624 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8196 (mp) REVERT: A 904 TYR cc_start: 0.8124 (m-10) cc_final: 0.7907 (m-10) REVERT: B 153 MET cc_start: 0.1119 (ppp) cc_final: 0.0174 (tpt) REVERT: B 237 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.7211 (mtm110) REVERT: B 269 TYR cc_start: 0.8083 (m-80) cc_final: 0.7471 (m-80) REVERT: B 280 ASN cc_start: 0.7482 (t0) cc_final: 0.7257 (t0) REVERT: B 334 ASN cc_start: 0.6430 (t0) cc_final: 0.6051 (p0) REVERT: B 386 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.6053 (ttpt) REVERT: B 740 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8147 (ttm) REVERT: B 904 TYR cc_start: 0.8120 (m-10) cc_final: 0.7245 (m-10) outliers start: 69 outliers final: 39 residues processed: 257 average time/residue: 0.4871 time to fit residues: 150.5792 Evaluate side-chains 243 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 268 optimal weight: 3.9990 chunk 300 optimal weight: 0.4980 chunk 154 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 122 optimal weight: 0.4980 chunk 225 optimal weight: 0.0770 chunk 159 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 242 optimal weight: 0.0970 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 625 HIS C 703 ASN C1088 HIS A1119 ASN B 625 HIS B1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.191337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127473 restraints weight = 29480.727| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.22 r_work: 0.3279 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25974 Z= 0.103 Angle : 0.536 8.877 35451 Z= 0.270 Chirality : 0.044 0.242 4152 Planarity : 0.004 0.074 4461 Dihedral : 4.928 40.852 4524 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.86 % Allowed : 14.59 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.15), residues: 3075 helix: 2.97 (0.19), residues: 708 sheet: 0.46 (0.20), residues: 642 loop : -0.74 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 357 TYR 0.022 0.001 TYR B 266 PHE 0.019 0.001 PHE B 192 TRP 0.010 0.001 TRP C 64 HIS 0.006 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00224 (25881) covalent geometry : angle 0.50548 (35208) SS BOND : bond 0.00318 ( 36) SS BOND : angle 0.92523 ( 72) hydrogen bonds : bond 0.03917 ( 1034) hydrogen bonds : angle 5.13596 ( 2859) link_BETA1-4 : bond 0.00913 ( 21) link_BETA1-4 : angle 3.00903 ( 63) link_NAG-ASN : bond 0.00349 ( 36) link_NAG-ASN : angle 2.23688 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.1305 (ppp) cc_final: 0.0359 (tpt) REVERT: C 237 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7300 (mtm110) REVERT: C 269 TYR cc_start: 0.8134 (m-80) cc_final: 0.7436 (m-80) REVERT: C 393 THR cc_start: 0.7916 (m) cc_final: 0.7567 (p) REVERT: C 904 TYR cc_start: 0.8075 (m-10) cc_final: 0.7730 (m-10) REVERT: C 933 LYS cc_start: 0.7947 (mttm) cc_final: 0.7475 (mtmm) REVERT: A 269 TYR cc_start: 0.8142 (m-80) cc_final: 0.7505 (m-80) REVERT: A 624 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8141 (mp) REVERT: A 933 LYS cc_start: 0.7972 (mttm) cc_final: 0.7517 (mtmm) REVERT: B 153 MET cc_start: 0.1145 (ppp) cc_final: 0.0217 (tpt) REVERT: B 237 ARG cc_start: 0.7425 (mtm-85) cc_final: 0.7153 (mtm110) REVERT: B 269 TYR cc_start: 0.8122 (m-80) cc_final: 0.7472 (m-80) REVERT: B 294 ASP cc_start: 0.6335 (t70) cc_final: 0.6060 (t70) REVERT: B 334 ASN cc_start: 0.6433 (t0) cc_final: 0.6171 (p0) REVERT: B 386 LYS cc_start: 0.6279 (OUTLIER) cc_final: 0.5936 (ttpt) REVERT: B 740 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8062 (ttm) REVERT: B 904 TYR cc_start: 0.8105 (m-10) cc_final: 0.7307 (m-10) REVERT: B 933 LYS cc_start: 0.7993 (mttm) cc_final: 0.7515 (mtmm) outliers start: 51 outliers final: 34 residues processed: 265 average time/residue: 0.4706 time to fit residues: 150.3371 Evaluate side-chains 249 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 934 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 299 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 262 optimal weight: 0.7980 chunk 282 optimal weight: 0.0060 chunk 105 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 287 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 300 optimal weight: 0.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 625 HIS A 625 HIS A 703 ASN A1119 ASN B 625 HIS B1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.190120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126021 restraints weight = 29537.811| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.08 r_work: 0.3248 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25974 Z= 0.124 Angle : 0.549 8.176 35451 Z= 0.277 Chirality : 0.044 0.232 4152 Planarity : 0.004 0.081 4461 Dihedral : 4.959 40.997 4524 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.15 % Allowed : 14.74 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.15), residues: 3075 helix: 2.98 (0.19), residues: 696 sheet: 0.48 (0.20), residues: 630 loop : -0.71 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 357 TYR 0.022 0.001 TYR B 266 PHE 0.018 0.001 PHE A 192 TRP 0.011 0.001 TRP C 64 HIS 0.011 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00289 (25881) covalent geometry : angle 0.51977 (35208) SS BOND : bond 0.00267 ( 36) SS BOND : angle 0.98543 ( 72) hydrogen bonds : bond 0.04142 ( 1034) hydrogen bonds : angle 5.17020 ( 2859) link_BETA1-4 : bond 0.00941 ( 21) link_BETA1-4 : angle 2.94982 ( 63) link_NAG-ASN : bond 0.00327 ( 36) link_NAG-ASN : angle 2.24461 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.1332 (ppp) cc_final: 0.0404 (tpt) REVERT: C 237 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7358 (mtm110) REVERT: C 269 TYR cc_start: 0.8143 (m-80) cc_final: 0.7501 (m-80) REVERT: C 393 THR cc_start: 0.8004 (m) cc_final: 0.7648 (p) REVERT: C 904 TYR cc_start: 0.8105 (m-10) cc_final: 0.7823 (m-10) REVERT: C 933 LYS cc_start: 0.8042 (mttm) cc_final: 0.7582 (mtmm) REVERT: A 191 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: A 269 TYR cc_start: 0.8185 (m-80) cc_final: 0.7588 (m-80) REVERT: A 624 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8173 (mp) REVERT: A 933 LYS cc_start: 0.8038 (mttm) cc_final: 0.7609 (mtmm) REVERT: B 153 MET cc_start: 0.1195 (ppp) cc_final: 0.0235 (tpt) REVERT: B 237 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.7231 (mtm110) REVERT: B 269 TYR cc_start: 0.8116 (m-80) cc_final: 0.7464 (m-80) REVERT: B 294 ASP cc_start: 0.6443 (t70) cc_final: 0.6186 (t70) REVERT: B 740 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8139 (ttm) REVERT: B 904 TYR cc_start: 0.8143 (m-10) cc_final: 0.7356 (m-10) REVERT: B 933 LYS cc_start: 0.8058 (mttm) cc_final: 0.7595 (mtmm) outliers start: 59 outliers final: 42 residues processed: 249 average time/residue: 0.5078 time to fit residues: 151.7659 Evaluate side-chains 251 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 934 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 77 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 185 optimal weight: 0.7980 chunk 176 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 310 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 625 HIS A 625 HIS A1119 ASN B 625 HIS B1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.189701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123714 restraints weight = 29469.105| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.23 r_work: 0.3237 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25974 Z= 0.136 Angle : 0.557 8.315 35451 Z= 0.282 Chirality : 0.045 0.219 4152 Planarity : 0.004 0.085 4461 Dihedral : 5.006 41.772 4524 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.97 % Allowed : 15.14 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.15), residues: 3075 helix: 2.93 (0.19), residues: 696 sheet: 0.46 (0.20), residues: 630 loop : -0.73 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 357 TYR 0.024 0.001 TYR C 266 PHE 0.018 0.001 PHE B 192 TRP 0.012 0.001 TRP C 64 HIS 0.036 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00320 (25881) covalent geometry : angle 0.52898 (35208) SS BOND : bond 0.00272 ( 36) SS BOND : angle 0.91830 ( 72) hydrogen bonds : bond 0.04283 ( 1034) hydrogen bonds : angle 5.19464 ( 2859) link_BETA1-4 : bond 0.00939 ( 21) link_BETA1-4 : angle 2.94852 ( 63) link_NAG-ASN : bond 0.00316 ( 36) link_NAG-ASN : angle 2.22368 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 206 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.1345 (ppp) cc_final: 0.0425 (tpt) REVERT: C 237 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7388 (mtm110) REVERT: C 269 TYR cc_start: 0.8183 (m-80) cc_final: 0.7535 (m-80) REVERT: C 358 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7089 (mp) REVERT: C 393 THR cc_start: 0.8041 (m) cc_final: 0.7688 (p) REVERT: C 904 TYR cc_start: 0.8142 (m-10) cc_final: 0.7861 (m-10) REVERT: C 933 LYS cc_start: 0.8077 (mttm) cc_final: 0.7618 (mtmm) REVERT: A 128 ILE cc_start: 0.7523 (mp) cc_final: 0.7320 (mt) REVERT: A 269 TYR cc_start: 0.8216 (m-80) cc_final: 0.7623 (m-80) REVERT: A 357 ARG cc_start: 0.7130 (ttp-110) cc_final: 0.6482 (mtp85) REVERT: A 624 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8155 (mp) REVERT: A 933 LYS cc_start: 0.8095 (mttm) cc_final: 0.7668 (mtmm) REVERT: B 153 MET cc_start: 0.1130 (ppp) cc_final: 0.0188 (tpt) REVERT: B 237 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.7209 (mtm110) REVERT: B 269 TYR cc_start: 0.8127 (m-80) cc_final: 0.7456 (m-80) REVERT: B 294 ASP cc_start: 0.6513 (t70) cc_final: 0.6246 (t70) REVERT: B 740 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8152 (ttm) REVERT: B 904 TYR cc_start: 0.8143 (m-10) cc_final: 0.7382 (m-10) REVERT: B 933 LYS cc_start: 0.8071 (mttm) cc_final: 0.7603 (mtmm) outliers start: 54 outliers final: 41 residues processed: 238 average time/residue: 0.4690 time to fit residues: 134.1484 Evaluate side-chains 247 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 203 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 934 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 47 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 127 optimal weight: 0.0070 chunk 83 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 297 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 308 optimal weight: 0.6980 chunk 288 optimal weight: 0.5980 chunk 187 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 625 HIS A1119 ASN B 625 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.191050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127259 restraints weight = 29331.360| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.14 r_work: 0.3253 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25974 Z= 0.109 Angle : 0.538 7.905 35451 Z= 0.271 Chirality : 0.044 0.207 4152 Planarity : 0.004 0.081 4461 Dihedral : 4.869 41.098 4524 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.89 % Allowed : 15.21 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.15), residues: 3075 helix: 2.98 (0.19), residues: 705 sheet: 0.48 (0.20), residues: 648 loop : -0.77 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 357 TYR 0.022 0.001 TYR C 266 PHE 0.020 0.001 PHE A 192 TRP 0.011 0.001 TRP C 64 HIS 0.011 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00246 (25881) covalent geometry : angle 0.51042 (35208) SS BOND : bond 0.00235 ( 36) SS BOND : angle 0.86828 ( 72) hydrogen bonds : bond 0.03965 ( 1034) hydrogen bonds : angle 5.09210 ( 2859) link_BETA1-4 : bond 0.00913 ( 21) link_BETA1-4 : angle 2.85167 ( 63) link_NAG-ASN : bond 0.00317 ( 36) link_NAG-ASN : angle 2.16665 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9749.57 seconds wall clock time: 166 minutes 25.72 seconds (9985.72 seconds total)