Starting phenix.real_space_refine on Thu Mar 5 12:50:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7keb_22837/03_2026/7keb_22837.cif Found real_map, /net/cci-nas-00/data/ceres_data/7keb_22837/03_2026/7keb_22837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7keb_22837/03_2026/7keb_22837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7keb_22837/03_2026/7keb_22837.map" model { file = "/net/cci-nas-00/data/ceres_data/7keb_22837/03_2026/7keb_22837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7keb_22837/03_2026/7keb_22837.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.041 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 96 5.16 5 C 14244 2.51 5 N 3683 2.21 5 O 4342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 181 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22365 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7394 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 45, 'TRANS': 920} Chain breaks: 12 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 6863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6863 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 44, 'TRANS': 904} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7282 Classifications: {'peptide': 960} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 914} Chain breaks: 11 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 12, 'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.46, per 1000 atoms: 0.24 Number of scatterers: 22365 At special positions: 0 Unit cell: (140.714, 129.076, 173.512, 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 96 16.00 O 4342 8.00 N 3683 7.00 C 14244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 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=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.00 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=1.96 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 I 1 " - " NAG I 2 " " 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 N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 845.6 milliseconds 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5398 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 44 sheets defined 28.5% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 138 through 142 removed outlier: 4.144A pdb=" N LEU A 141 " --> pdb=" O ASP A 138 " (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 349 through 353 removed outlier: 4.197A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.248A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.938A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.250A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.857A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 4.643A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.185A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.752A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.587A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 988 through 1032 removed outlier: 3.709A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 4.067A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 336 through 341 removed outlier: 3.991A pdb=" N GLY B 339 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.138A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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 801 through 805 removed outlier: 4.576A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.672A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.612A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.611A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.751A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.664A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1033 Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 4.217A pdb=" N VAL B1128 " --> pdb=" O ASN B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.086A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.907A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.533A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 439 through 442 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.822A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.596A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.041A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.825A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.739A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.647A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.509A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1129 removed outlier: 4.133A pdb=" N VAL C1128 " --> pdb=" O ASN C1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.289A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 52 removed outlier: 3.828A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.901A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.593A pdb=" N LEU A 611 " --> pdb=" O SER A 596 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.838A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.962A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.720A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.227A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 719 removed outlier: 6.352A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 722 through 727 removed outlier: 3.537A pdb=" N PHE A1052 " --> pdb=" O LEU A1063 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.182A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.501A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.086A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.781A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.159A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.257A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE B 584 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 355 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 removed outlier: 4.352A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.352A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 703 through 704 removed outlier: 6.637A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 719 removed outlier: 3.915A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.237A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.029A pdb=" N TYR C 279 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.785A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.827A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.643A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.591A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.795A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.786A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 712 Processing sheet with id=AE6, first strand: chain 'C' and resid 715 through 728 removed outlier: 6.091A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.747A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2643 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: 5.09 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6522 1.34 - 1.46: 4521 1.46 - 1.59: 11650 1.59 - 1.71: 0 1.71 - 1.84: 120 Bond restraints: 22813 Sorted by residual: bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C5 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG C1312 " pdb=" O5 NAG C1312 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.484 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 22808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 30066 3.93 - 7.86: 1016 7.86 - 11.80: 8 11.80 - 15.73: 1 15.73 - 19.66: 1 Bond angle restraints: 31092 Sorted by residual: angle pdb=" N CYS C 166 " pdb=" CA CYS C 166 " pdb=" C CYS C 166 " ideal model delta sigma weight residual 109.85 123.03 -13.18 1.58e+00 4.01e-01 6.96e+01 angle pdb=" OE1 GLN C 913 " pdb=" CD GLN C 913 " pdb=" NE2 GLN C 913 " ideal model delta sigma weight residual 122.60 115.64 6.96 1.00e+00 1.00e+00 4.85e+01 angle pdb=" CA ASP C 40 " pdb=" CB ASP C 40 " pdb=" CG ASP C 40 " ideal model delta sigma weight residual 112.60 119.17 -6.57 1.00e+00 1.00e+00 4.31e+01 angle pdb=" CB LEU B 699 " pdb=" CG LEU B 699 " pdb=" CD1 LEU B 699 " ideal model delta sigma weight residual 110.70 130.36 -19.66 3.00e+00 1.11e-01 4.30e+01 angle pdb=" CA PHE A 55 " pdb=" CB PHE A 55 " pdb=" CG PHE A 55 " ideal model delta sigma weight residual 113.80 119.74 -5.94 1.00e+00 1.00e+00 3.53e+01 ... (remaining 31087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 13298 17.89 - 35.78: 813 35.78 - 53.67: 109 53.67 - 71.56: 42 71.56 - 89.45: 32 Dihedral angle restraints: 14294 sinusoidal: 5953 harmonic: 8341 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 176.74 -83.74 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 173.98 -80.98 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -166.32 80.32 1 1.00e+01 1.00e-02 7.99e+01 ... (remaining 14291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 3810 0.315 - 0.630: 9 0.630 - 0.945: 1 0.945 - 1.261: 1 1.261 - 1.576: 1 Chirality restraints: 3822 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.60e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.35e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.31e+01 ... (remaining 3819 not shown) Planarity restraints: 3976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " -0.207 2.00e-02 2.50e+03 2.41e-01 7.26e+02 pdb=" CG ASN A1074 " 0.129 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " 0.385 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.287 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.193 2.00e-02 2.50e+03 2.23e-01 6.20e+02 pdb=" CG ASN B 603 " -0.112 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.358 2.00e-02 2.50e+03 pdb=" C1 NAG B1307 " 0.265 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " 0.184 2.00e-02 2.50e+03 2.05e-01 5.26e+02 pdb=" CG ASN A 603 " -0.112 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.323 2.00e-02 2.50e+03 pdb=" C1 NAG A1306 " 0.244 2.00e-02 2.50e+03 ... (remaining 3973 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 9003 2.92 - 3.41: 22428 3.41 - 3.91: 38156 3.91 - 4.40: 43325 4.40 - 4.90: 71447 Nonbonded interactions: 184359 Sorted by model distance: nonbonded pdb=" ND2 ASN C 165 " pdb=" O7 NAG C1312 " model vdw 2.421 3.120 nonbonded pdb=" CA GLY B 339 " pdb=" C8 NAG B1306 " model vdw 2.453 3.088 nonbonded pdb=" O GLY B 339 " pdb=" OD1 ASN B 343 " model vdw 2.473 3.040 nonbonded pdb=" O GLY B 339 " pdb=" O7 NAG B1306 " model vdw 2.516 2.432 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.533 3.040 ... (remaining 184354 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 345 or (resid 346 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 or (res \ id 382 through 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 404 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 427 or (resid 428 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 442 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 450 through 451 and \ (name N or name CA or name C or name O or name CB )) or (resid 453 and (name N \ or name CA or name C or name O or name CB )) or resid 463 or (resid 464 through \ 466 and (name N or name CA or name C or name O or name CB )) or resid 491 or (re \ sid 492 through 495 and (name N or name CA or name C or name O or name CB )) or \ resid 496 or (resid 497 through 498 and (name N or name CA or name C or name O o \ r name CB )) or resid 499 or (resid 500 through 503 and (name N or name CA or na \ me C or name O or name CB )) or (resid 504 through 506 and (name N or name CA or \ name C or name O or name CB )) or resid 507 or (resid 508 through 515 and (name \ N or name CA or name C or name O or name CB )) or (resid 522 through 524 and (n \ ame N or name CA or name C or name O or name CB )) or resid 525 through 528 or ( \ resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ through 553 or (resid 554 and (name N or name CA or name C or name O or name CB \ )) or resid 555 through 793 or (resid 794 and (name N or name CA or name C or na \ me O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C o \ r name O or name CB )) or resid 797 through 810 or (resid 811 and (name N or nam \ e CA or name C or name O or name CB )) or resid 813 through 827 or resid 856 thr \ ough 866 or (resid 867 through 868 and (name N or name CA or name C or name O or \ name CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or nam \ e C or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N o \ r name CA or name C or name O or name CB )) or resid 986 through 987 or (resid 9 \ 88 through 989 and (name N or name CA or name C or name O or name CB )) or resid \ 990 through 1141 or (resid 1142 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147 through 1310)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 442 or resid 450 through 451 or resid 453 or resid 46 \ 3 through 501 or resid 503 through 567 or (resid 568 and (name N or name CA or n \ ame C or name O or name CB )) or resid 569 through 570 or (resid 571 and (name N \ or name CA or name C or name O or name CB )) or resid 572 through 581 or (resid \ 582 through 583 and (name N or name CA or name C or name O or name CB )) or res \ id 584 through 585 or (resid 586 and (name N or name CA or name C or name O or n \ ame CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name \ C or name O or name CB )) or resid 620 through 676 or resid 690 through 744 or ( \ resid 745 and (name N or name CA or name C or name O or name CB )) or resid 746 \ through 810 or (resid 811 and (name N or name CA or name C or name O or name CB \ )) or resid 813 through 827 or resid 856 through 866 or (resid 867 through 868 a \ nd (name N or name CA or name C or name O or name CB )) or resid 869 through 920 \ or (resid 921 and (name N or name CA or name C or name O or name CB )) or resid \ 922 through 939 or (resid 940 and (name N or name CA or name C or name O or nam \ e CB )) or resid 941 through 984 or (resid 985 and (name N or name CA or name C \ or name O or name CB )) or resid 986 through 987 or (resid 988 through 989 and ( \ name N or name CA or name C or name O or name CB )) or resid 990 through 1072 or \ (resid 1073 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 074 through 1117 or (resid 1118 and (name N or name CA or name C or name O or na \ me CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1147 through 1310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 344 or (resid 345 through 360 and (name N or name CA or name C or name O o \ r name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name C or name O or name CB )) \ or (resid 404 through 411 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or (resid 416 through 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 through 442 and (name N or name CA or name C or name O or name CB )) o \ r (resid 448 through 449 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 451 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 or (resid 464 through 466 and (name N or name CA or name C or name O or na \ me CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 through 500 or (resid 501 \ and (name N or name CA or name C or name O or name CB )) or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (n \ ame N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 th \ rough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 25 through 527 or (resid 528 through 529 and (name N or name CA or name C or nam \ e O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA \ or name C or name O or name CB )) or resid 555 through 567 or (resid 568 and (na \ me N or name CA or name C or name O or name CB )) or resid 569 through 570 or (r \ esid 571 and (name N or name CA or name C or name O or name CB )) or resid 572 t \ hrough 581 or (resid 582 through 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or n \ ame C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 645 or (resid \ 646 through 647 and (name N or name CA or name C or name O or name CB )) or res \ id 648 through 793 or (resid 794 and (name N or name CA or name C or name O or n \ ame CB )) or resid 795 or (resid 796 and (name N or name CA or name C or name O \ or name CB )) or resid 797 through 920 or (resid 921 and (name N or name CA or n \ ame C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (r \ esid 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 \ through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or name C \ or name O or name CB )) or resid 1147 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 1.990 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.770 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 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 : 0.014 0.320 22908 Z= 0.797 Angle : 1.851 36.455 31339 Z= 1.196 Chirality : 0.102 1.576 3822 Planarity : 0.016 0.175 3929 Dihedral : 12.736 89.451 8791 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.08 % Favored : 90.31 % Rotamer: Outliers : 0.13 % Allowed : 0.27 % Favored : 99.60 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.14), residues: 2797 helix: -1.34 (0.17), residues: 642 sheet: 0.05 (0.26), residues: 384 loop : -1.75 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 328 TYR 0.162 0.025 TYR A 789 PHE 0.104 0.014 PHE A 55 TRP 0.284 0.035 TRP C 104 HIS 0.014 0.004 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.01353 (22813) covalent geometry : angle 1.80966 (31092) SS BOND : bond 0.01591 ( 35) SS BOND : angle 2.53858 ( 70) hydrogen bonds : bond 0.14939 ( 982) hydrogen bonds : angle 8.58363 ( 2643) Misc. bond : bond 0.32036 ( 1) link_BETA1-4 : bond 0.02430 ( 12) link_BETA1-4 : angle 4.14539 ( 36) link_NAG-ASN : bond 0.02088 ( 47) link_NAG-ASN : angle 5.65246 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 213 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 315 THR cc_start: 0.7752 (p) cc_final: 0.7522 (t) outliers start: 3 outliers final: 3 residues processed: 216 average time/residue: 0.1635 time to fit residues: 55.4458 Evaluate side-chains 100 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain C residue 873 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 901 GLN A 935 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN B 901 GLN B1005 GLN C 764 ASN C 926 GLN C 953 ASN C1005 GLN C1135 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.069126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.049196 restraints weight = 95519.131| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 4.62 r_work: 0.3036 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 22908 Z= 0.288 Angle : 0.851 13.325 31339 Z= 0.432 Chirality : 0.049 0.321 3822 Planarity : 0.005 0.052 3929 Dihedral : 7.481 54.946 4270 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.72 % Favored : 94.21 % Rotamer: Outliers : 1.28 % Allowed : 5.45 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 2797 helix: -0.38 (0.18), residues: 654 sheet: -0.37 (0.21), residues: 612 loop : -1.38 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 319 TYR 0.025 0.002 TYR B1067 PHE 0.029 0.002 PHE C1089 TRP 0.022 0.003 TRP C 886 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00623 (22813) covalent geometry : angle 0.79716 (31092) SS BOND : bond 0.00549 ( 35) SS BOND : angle 1.96859 ( 70) hydrogen bonds : bond 0.06797 ( 982) hydrogen bonds : angle 6.92808 ( 2643) Misc. bond : bond 0.00314 ( 1) link_BETA1-4 : bond 0.00318 ( 12) link_BETA1-4 : angle 1.85445 ( 36) link_NAG-ASN : bond 0.00575 ( 47) link_NAG-ASN : angle 4.25882 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7067 (m-90) cc_final: 0.6411 (m-90) REVERT: A 740 MET cc_start: 0.8819 (tpt) cc_final: 0.8505 (tpt) REVERT: A 886 TRP cc_start: 0.6912 (p-90) cc_final: 0.6502 (p-90) REVERT: A 900 MET cc_start: 0.7525 (mmm) cc_final: 0.7146 (mmm) REVERT: B 986 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7519 (tppp) REVERT: C 759 PHE cc_start: 0.8069 (m-80) cc_final: 0.7826 (m-80) outliers start: 29 outliers final: 22 residues processed: 117 average time/residue: 0.1699 time to fit residues: 31.3030 Evaluate side-chains 100 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 144 optimal weight: 0.6980 chunk 140 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 232 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 901 GLN B1135 ASN C 764 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.070344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.050486 restraints weight = 93298.674| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 4.68 r_work: 0.3078 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22908 Z= 0.157 Angle : 0.645 12.334 31339 Z= 0.332 Chirality : 0.045 0.292 3822 Planarity : 0.004 0.051 3929 Dihedral : 6.555 59.268 4270 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 1.55 % Allowed : 6.20 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 2797 helix: 0.15 (0.19), residues: 663 sheet: -0.33 (0.21), residues: 583 loop : -1.15 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 319 TYR 0.017 0.002 TYR B1067 PHE 0.017 0.001 PHE C1075 TRP 0.014 0.002 TRP A 64 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00326 (22813) covalent geometry : angle 0.60819 (31092) SS BOND : bond 0.00400 ( 35) SS BOND : angle 1.42486 ( 70) hydrogen bonds : bond 0.05262 ( 982) hydrogen bonds : angle 6.39079 ( 2643) Misc. bond : bond 0.00309 ( 1) link_BETA1-4 : bond 0.00356 ( 12) link_BETA1-4 : angle 1.45880 ( 36) link_NAG-ASN : bond 0.00481 ( 47) link_NAG-ASN : angle 3.04943 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8659 (m-30) cc_final: 0.8005 (t70) REVERT: A 104 TRP cc_start: 0.6990 (m-90) cc_final: 0.6174 (m-90) REVERT: A 396 TYR cc_start: 0.8881 (m-80) cc_final: 0.8603 (m-80) REVERT: A 740 MET cc_start: 0.8716 (tpt) cc_final: 0.8413 (tpt) REVERT: A 886 TRP cc_start: 0.7008 (p-90) cc_final: 0.6525 (p-90) REVERT: A 900 MET cc_start: 0.7564 (mmm) cc_final: 0.7275 (mmm) REVERT: A 979 ASP cc_start: 0.9096 (m-30) cc_final: 0.8764 (t0) REVERT: A 1029 MET cc_start: 0.8710 (tpp) cc_final: 0.8475 (tpp) REVERT: A 1095 PHE cc_start: 0.8256 (m-10) cc_final: 0.7978 (m-80) REVERT: A 1135 ASN cc_start: 0.7547 (t0) cc_final: 0.6972 (t0) REVERT: B 1113 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7866 (mp10) REVERT: C 740 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8632 (tpt) REVERT: C 759 PHE cc_start: 0.7906 (m-80) cc_final: 0.7660 (m-80) REVERT: C 973 ILE cc_start: 0.9440 (tt) cc_final: 0.9009 (pt) outliers start: 35 outliers final: 13 residues processed: 128 average time/residue: 0.1492 time to fit residues: 31.4267 Evaluate side-chains 97 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 873 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 3 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 48 optimal weight: 0.3980 chunk 131 optimal weight: 50.0000 chunk 30 optimal weight: 7.9990 chunk 256 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 188 ASN B 779 GLN B 901 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 87 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.068380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.048397 restraints weight = 95568.950| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 4.59 r_work: 0.3022 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 22908 Z= 0.258 Angle : 0.695 15.207 31339 Z= 0.356 Chirality : 0.045 0.298 3822 Planarity : 0.004 0.053 3929 Dihedral : 6.387 58.799 4270 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.03 % Rotamer: Outliers : 1.95 % Allowed : 7.75 % Favored : 90.30 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 2797 helix: 0.30 (0.19), residues: 659 sheet: -0.45 (0.20), residues: 614 loop : -1.18 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.022 0.002 TYR B1067 PHE 0.026 0.002 PHE C1089 TRP 0.012 0.002 TRP A 64 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00556 (22813) covalent geometry : angle 0.66240 (31092) SS BOND : bond 0.00504 ( 35) SS BOND : angle 1.94969 ( 70) hydrogen bonds : bond 0.05633 ( 982) hydrogen bonds : angle 6.39318 ( 2643) Misc. bond : bond 0.00188 ( 1) link_BETA1-4 : bond 0.00263 ( 12) link_BETA1-4 : angle 1.44958 ( 36) link_NAG-ASN : bond 0.00523 ( 47) link_NAG-ASN : angle 2.88161 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 84 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8663 (m-30) cc_final: 0.7970 (t70) REVERT: A 396 TYR cc_start: 0.8912 (m-80) cc_final: 0.8609 (m-80) REVERT: A 697 MET cc_start: 0.7927 (ptm) cc_final: 0.7515 (ppp) REVERT: A 740 MET cc_start: 0.8659 (tpt) cc_final: 0.8351 (tpt) REVERT: A 957 GLN cc_start: 0.9468 (mt0) cc_final: 0.9200 (pt0) REVERT: A 979 ASP cc_start: 0.9077 (m-30) cc_final: 0.8756 (t0) REVERT: A 1135 ASN cc_start: 0.7860 (t0) cc_final: 0.7238 (t0) REVERT: B 63 THR cc_start: 0.5801 (OUTLIER) cc_final: 0.5519 (p) REVERT: B 318 PHE cc_start: 0.9035 (t80) cc_final: 0.8619 (t80) REVERT: B 864 LEU cc_start: 0.8565 (tt) cc_final: 0.8304 (tp) REVERT: B 1113 GLN cc_start: 0.8392 (mm110) cc_final: 0.7980 (mp10) REVERT: C 764 ASN cc_start: 0.9504 (OUTLIER) cc_final: 0.9065 (m-40) REVERT: C 900 MET cc_start: 0.8344 (mtp) cc_final: 0.7989 (mtp) REVERT: C 973 ILE cc_start: 0.9481 (tt) cc_final: 0.9064 (pt) outliers start: 44 outliers final: 26 residues processed: 120 average time/residue: 0.1420 time to fit residues: 28.4674 Evaluate side-chains 107 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 40 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 271 optimal weight: 6.9990 chunk 284 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.069750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.049705 restraints weight = 92750.647| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 4.61 r_work: 0.3058 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22908 Z= 0.144 Angle : 0.601 11.658 31339 Z= 0.306 Chirality : 0.043 0.286 3822 Planarity : 0.004 0.053 3929 Dihedral : 5.908 56.861 4270 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.89 % Rotamer: Outliers : 1.28 % Allowed : 8.77 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 2797 helix: 0.51 (0.20), residues: 655 sheet: -0.35 (0.21), residues: 587 loop : -1.01 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.017 0.001 TYR C1067 PHE 0.019 0.001 PHE A 759 TRP 0.011 0.001 TRP A 64 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00304 (22813) covalent geometry : angle 0.56992 (31092) SS BOND : bond 0.00322 ( 35) SS BOND : angle 1.81837 ( 70) hydrogen bonds : bond 0.04797 ( 982) hydrogen bonds : angle 6.13147 ( 2643) Misc. bond : bond 0.00032 ( 1) link_BETA1-4 : bond 0.00325 ( 12) link_BETA1-4 : angle 1.27079 ( 36) link_NAG-ASN : bond 0.00437 ( 47) link_NAG-ASN : angle 2.57151 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8943 (m-80) cc_final: 0.8599 (m-80) REVERT: A 697 MET cc_start: 0.7887 (ptm) cc_final: 0.7547 (ppp) REVERT: A 737 ASP cc_start: 0.8722 (p0) cc_final: 0.8437 (p0) REVERT: A 740 MET cc_start: 0.8435 (tpt) cc_final: 0.7619 (tpt) REVERT: A 957 GLN cc_start: 0.9440 (mt0) cc_final: 0.9175 (pt0) REVERT: A 979 ASP cc_start: 0.9065 (m-30) cc_final: 0.8752 (t0) REVERT: A 1135 ASN cc_start: 0.7568 (t0) cc_final: 0.6864 (t0) REVERT: B 864 LEU cc_start: 0.8551 (tt) cc_final: 0.8257 (tt) REVERT: B 1113 GLN cc_start: 0.8266 (mm110) cc_final: 0.7860 (mp10) REVERT: C 900 MET cc_start: 0.8282 (mtp) cc_final: 0.7866 (mtp) REVERT: C 973 ILE cc_start: 0.9503 (tt) cc_final: 0.9120 (pt) outliers start: 29 outliers final: 22 residues processed: 117 average time/residue: 0.1476 time to fit residues: 29.0217 Evaluate side-chains 104 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 873 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 89 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 270 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 134 optimal weight: 0.0970 chunk 252 optimal weight: 7.9990 chunk 268 optimal weight: 4.9990 chunk 180 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.068580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.048508 restraints weight = 94463.446| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 4.63 r_work: 0.3020 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 22908 Z= 0.212 Angle : 0.623 14.943 31339 Z= 0.319 Chirality : 0.043 0.285 3822 Planarity : 0.004 0.054 3929 Dihedral : 5.837 56.076 4270 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.61 % Favored : 94.35 % Rotamer: Outliers : 1.82 % Allowed : 8.64 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.15), residues: 2797 helix: 0.60 (0.20), residues: 654 sheet: -0.31 (0.21), residues: 603 loop : -1.03 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.019 0.002 TYR C1067 PHE 0.020 0.002 PHE C1089 TRP 0.010 0.001 TRP A 64 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00455 (22813) covalent geometry : angle 0.59452 (31092) SS BOND : bond 0.00400 ( 35) SS BOND : angle 1.94546 ( 70) hydrogen bonds : bond 0.05107 ( 982) hydrogen bonds : angle 6.11532 ( 2643) Misc. bond : bond 0.00011 ( 1) link_BETA1-4 : bond 0.00248 ( 12) link_BETA1-4 : angle 1.27938 ( 36) link_NAG-ASN : bond 0.00460 ( 47) link_NAG-ASN : angle 2.46933 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8961 (m-80) cc_final: 0.8629 (m-80) REVERT: A 737 ASP cc_start: 0.8747 (p0) cc_final: 0.8504 (p0) REVERT: A 740 MET cc_start: 0.8397 (tpt) cc_final: 0.7555 (tpt) REVERT: A 979 ASP cc_start: 0.9025 (m-30) cc_final: 0.8732 (t0) REVERT: A 1135 ASN cc_start: 0.7764 (t0) cc_final: 0.7140 (t0) REVERT: B 63 THR cc_start: 0.5695 (OUTLIER) cc_final: 0.5303 (p) REVERT: B 318 PHE cc_start: 0.9017 (t80) cc_final: 0.8676 (t80) REVERT: B 1113 GLN cc_start: 0.8308 (mm110) cc_final: 0.7930 (mp10) REVERT: C 568 ASP cc_start: 0.8211 (t0) cc_final: 0.7595 (p0) REVERT: C 764 ASN cc_start: 0.9466 (OUTLIER) cc_final: 0.8869 (m-40) REVERT: C 973 ILE cc_start: 0.9525 (tt) cc_final: 0.9202 (pt) outliers start: 41 outliers final: 28 residues processed: 119 average time/residue: 0.1510 time to fit residues: 30.0076 Evaluate side-chains 109 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 72 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 283 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 138 optimal weight: 0.0270 chunk 273 optimal weight: 0.9980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 913 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.070255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.050411 restraints weight = 92218.818| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 4.63 r_work: 0.3081 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22908 Z= 0.119 Angle : 0.565 10.788 31339 Z= 0.289 Chirality : 0.043 0.275 3822 Planarity : 0.004 0.053 3929 Dihedral : 5.481 55.371 4270 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.86 % Favored : 95.10 % Rotamer: Outliers : 1.51 % Allowed : 9.13 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.16), residues: 2797 helix: 0.73 (0.20), residues: 652 sheet: -0.31 (0.21), residues: 560 loop : -0.86 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 237 TYR 0.016 0.001 TYR B 741 PHE 0.012 0.001 PHE A 759 TRP 0.011 0.001 TRP B 886 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00251 (22813) covalent geometry : angle 0.53868 (31092) SS BOND : bond 0.00301 ( 35) SS BOND : angle 1.63552 ( 70) hydrogen bonds : bond 0.04425 ( 982) hydrogen bonds : angle 5.93369 ( 2643) Misc. bond : bond 0.00012 ( 1) link_BETA1-4 : bond 0.00337 ( 12) link_BETA1-4 : angle 1.17631 ( 36) link_NAG-ASN : bond 0.00418 ( 47) link_NAG-ASN : angle 2.29253 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8954 (m-80) cc_final: 0.8602 (m-80) REVERT: A 737 ASP cc_start: 0.8769 (p0) cc_final: 0.8479 (p0) REVERT: A 900 MET cc_start: 0.7062 (mmm) cc_final: 0.6747 (mmt) REVERT: A 957 GLN cc_start: 0.9442 (mt0) cc_final: 0.9176 (pt0) REVERT: A 979 ASP cc_start: 0.9103 (m-30) cc_final: 0.8771 (t0) REVERT: A 1002 GLN cc_start: 0.9074 (tt0) cc_final: 0.8594 (tp-100) REVERT: A 1135 ASN cc_start: 0.7478 (t0) cc_final: 0.6775 (t0) REVERT: B 63 THR cc_start: 0.5320 (OUTLIER) cc_final: 0.4975 (p) REVERT: B 740 MET cc_start: 0.8913 (tpp) cc_final: 0.8539 (mmm) REVERT: B 869 MET cc_start: 0.8447 (mtm) cc_final: 0.7933 (ttm) REVERT: B 988 GLU cc_start: 0.9044 (mp0) cc_final: 0.8750 (mp0) REVERT: B 1050 MET cc_start: 0.8415 (ptt) cc_final: 0.8167 (ptm) REVERT: B 1113 GLN cc_start: 0.8178 (mm110) cc_final: 0.7977 (mp10) REVERT: C 568 ASP cc_start: 0.8207 (t0) cc_final: 0.7543 (p0) REVERT: C 697 MET cc_start: 0.7638 (tmm) cc_final: 0.7428 (tmm) REVERT: C 764 ASN cc_start: 0.9463 (OUTLIER) cc_final: 0.8878 (m-40) REVERT: C 900 MET cc_start: 0.8154 (mtp) cc_final: 0.7791 (mtp) REVERT: C 973 ILE cc_start: 0.9492 (tt) cc_final: 0.9132 (pt) REVERT: C 1113 GLN cc_start: 0.8405 (mt0) cc_final: 0.7840 (mp10) outliers start: 34 outliers final: 22 residues processed: 121 average time/residue: 0.1431 time to fit residues: 29.3011 Evaluate side-chains 109 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 873 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 223 optimal weight: 0.9980 chunk 62 optimal weight: 0.1980 chunk 166 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 216 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN B 901 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.070316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.051118 restraints weight = 92788.559| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.87 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22908 Z= 0.124 Angle : 0.548 10.187 31339 Z= 0.280 Chirality : 0.042 0.267 3822 Planarity : 0.004 0.053 3929 Dihedral : 5.250 55.181 4270 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.28 % Rotamer: Outliers : 1.60 % Allowed : 9.30 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2797 helix: 0.69 (0.20), residues: 667 sheet: -0.20 (0.21), residues: 560 loop : -0.86 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.015 0.001 TYR C1067 PHE 0.019 0.001 PHE A 759 TRP 0.010 0.001 TRP B 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00264 (22813) covalent geometry : angle 0.52508 (31092) SS BOND : bond 0.00302 ( 35) SS BOND : angle 1.37878 ( 70) hydrogen bonds : bond 0.04368 ( 982) hydrogen bonds : angle 5.83681 ( 2643) Misc. bond : bond 0.00002 ( 1) link_BETA1-4 : bond 0.00308 ( 12) link_BETA1-4 : angle 1.17205 ( 36) link_NAG-ASN : bond 0.00405 ( 47) link_NAG-ASN : angle 2.17924 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8865 (m-80) cc_final: 0.8585 (m-80) REVERT: A 737 ASP cc_start: 0.8138 (p0) cc_final: 0.7914 (p0) REVERT: A 900 MET cc_start: 0.7030 (mmm) cc_final: 0.6719 (mmt) REVERT: A 979 ASP cc_start: 0.9065 (m-30) cc_final: 0.8740 (t0) REVERT: A 1002 GLN cc_start: 0.8986 (tt0) cc_final: 0.8505 (tp-100) REVERT: A 1135 ASN cc_start: 0.7430 (t0) cc_final: 0.6653 (t0) REVERT: B 63 THR cc_start: 0.5191 (OUTLIER) cc_final: 0.4887 (p) REVERT: B 740 MET cc_start: 0.8495 (tpp) cc_final: 0.7909 (mmm) REVERT: B 869 MET cc_start: 0.8253 (mtm) cc_final: 0.7734 (ttm) REVERT: C 237 ARG cc_start: 0.9403 (mmm-85) cc_final: 0.9146 (mmm-85) REVERT: C 568 ASP cc_start: 0.8142 (t0) cc_final: 0.7458 (p0) REVERT: C 697 MET cc_start: 0.7556 (tmm) cc_final: 0.7317 (tmm) REVERT: C 764 ASN cc_start: 0.9267 (OUTLIER) cc_final: 0.8514 (m-40) REVERT: C 973 ILE cc_start: 0.9506 (tt) cc_final: 0.9135 (pt) REVERT: C 1113 GLN cc_start: 0.8085 (mt0) cc_final: 0.7602 (mp10) outliers start: 36 outliers final: 26 residues processed: 120 average time/residue: 0.1427 time to fit residues: 29.0730 Evaluate side-chains 112 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 93 optimal weight: 0.5980 chunk 266 optimal weight: 0.7980 chunk 260 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 45 optimal weight: 0.0570 chunk 246 optimal weight: 3.9990 chunk 206 optimal weight: 20.0000 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.070543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.051225 restraints weight = 92816.150| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.77 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22908 Z= 0.123 Angle : 0.551 10.179 31339 Z= 0.282 Chirality : 0.042 0.263 3822 Planarity : 0.004 0.052 3929 Dihedral : 5.132 55.343 4270 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.24 % Rotamer: Outliers : 1.55 % Allowed : 9.75 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2797 helix: 0.68 (0.20), residues: 674 sheet: -0.21 (0.21), residues: 560 loop : -0.78 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.020 0.001 TYR A 365 PHE 0.019 0.001 PHE A 759 TRP 0.010 0.001 TRP B 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00260 (22813) covalent geometry : angle 0.52752 (31092) SS BOND : bond 0.00294 ( 35) SS BOND : angle 1.64932 ( 70) hydrogen bonds : bond 0.04275 ( 982) hydrogen bonds : angle 5.76602 ( 2643) Misc. bond : bond 0.00001 ( 1) link_BETA1-4 : bond 0.00326 ( 12) link_BETA1-4 : angle 1.13519 ( 36) link_NAG-ASN : bond 0.00409 ( 47) link_NAG-ASN : angle 2.13177 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.9339 (p0) cc_final: 0.8514 (t0) REVERT: A 396 TYR cc_start: 0.8846 (m-80) cc_final: 0.8589 (m-80) REVERT: A 900 MET cc_start: 0.6985 (mmm) cc_final: 0.6689 (mmt) REVERT: A 979 ASP cc_start: 0.9040 (m-30) cc_final: 0.8707 (t0) REVERT: A 1002 GLN cc_start: 0.8954 (tt0) cc_final: 0.8476 (tp-100) REVERT: A 1135 ASN cc_start: 0.7416 (t0) cc_final: 0.6645 (t0) REVERT: B 63 THR cc_start: 0.5487 (OUTLIER) cc_final: 0.5193 (p) REVERT: B 740 MET cc_start: 0.8451 (tpp) cc_final: 0.7816 (mmm) REVERT: B 869 MET cc_start: 0.8225 (mtm) cc_final: 0.7749 (ttm) REVERT: C 237 ARG cc_start: 0.9407 (mmm-85) cc_final: 0.9131 (mmm-85) REVERT: C 568 ASP cc_start: 0.8184 (t0) cc_final: 0.7536 (p0) REVERT: C 764 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8504 (m-40) REVERT: C 973 ILE cc_start: 0.9501 (tt) cc_final: 0.9139 (pt) REVERT: C 1031 GLU cc_start: 0.7931 (mt-10) cc_final: 0.6721 (tp30) REVERT: C 1113 GLN cc_start: 0.8093 (mt0) cc_final: 0.7609 (mp10) outliers start: 35 outliers final: 28 residues processed: 117 average time/residue: 0.1484 time to fit residues: 29.0828 Evaluate side-chains 112 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 175 optimal weight: 4.9990 chunk 120 optimal weight: 50.0000 chunk 227 optimal weight: 8.9990 chunk 156 optimal weight: 0.9980 chunk 265 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 166 optimal weight: 0.5980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 901 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.068575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.048457 restraints weight = 94701.230| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 4.65 r_work: 0.3033 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22908 Z= 0.220 Angle : 0.613 10.437 31339 Z= 0.313 Chirality : 0.044 0.272 3822 Planarity : 0.004 0.052 3929 Dihedral : 5.377 55.327 4270 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 1.42 % Allowed : 10.15 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.16), residues: 2797 helix: 0.76 (0.20), residues: 657 sheet: -0.25 (0.21), residues: 574 loop : -0.80 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 995 TYR 0.020 0.002 TYR C1067 PHE 0.024 0.002 PHE A 65 TRP 0.015 0.001 TRP A 64 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00475 (22813) covalent geometry : angle 0.59114 (31092) SS BOND : bond 0.00403 ( 35) SS BOND : angle 1.60258 ( 70) hydrogen bonds : bond 0.04844 ( 982) hydrogen bonds : angle 5.94040 ( 2643) Misc. bond : bond 0.00012 ( 1) link_BETA1-4 : bond 0.00259 ( 12) link_BETA1-4 : angle 1.19604 ( 36) link_NAG-ASN : bond 0.00447 ( 47) link_NAG-ASN : angle 2.17777 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.9335 (p0) cc_final: 0.8568 (t0) REVERT: A 396 TYR cc_start: 0.8975 (m-80) cc_final: 0.8681 (m-80) REVERT: A 564 GLN cc_start: 0.7284 (tp40) cc_final: 0.7082 (mp10) REVERT: A 697 MET cc_start: 0.7845 (ptm) cc_final: 0.7565 (ppp) REVERT: A 731 MET cc_start: 0.9008 (ttp) cc_final: 0.8640 (ttm) REVERT: A 878 LEU cc_start: 0.8708 (tp) cc_final: 0.8469 (mp) REVERT: A 979 ASP cc_start: 0.9026 (m-30) cc_final: 0.8717 (t0) REVERT: A 1002 GLN cc_start: 0.9052 (tt0) cc_final: 0.8608 (tp-100) REVERT: A 1135 ASN cc_start: 0.7781 (t0) cc_final: 0.7109 (t0) REVERT: B 63 THR cc_start: 0.5627 (OUTLIER) cc_final: 0.5312 (p) REVERT: B 740 MET cc_start: 0.8773 (tpp) cc_final: 0.8205 (mmm) REVERT: B 864 LEU cc_start: 0.8548 (tt) cc_final: 0.8332 (tp) REVERT: C 568 ASP cc_start: 0.8452 (t0) cc_final: 0.7798 (p0) REVERT: C 764 ASN cc_start: 0.9417 (OUTLIER) cc_final: 0.8943 (m-40) REVERT: C 973 ILE cc_start: 0.9525 (tt) cc_final: 0.9244 (pt) REVERT: C 1017 GLU cc_start: 0.9040 (tt0) cc_final: 0.8723 (tp30) outliers start: 32 outliers final: 25 residues processed: 104 average time/residue: 0.1455 time to fit residues: 25.6609 Evaluate side-chains 104 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 40 optimal weight: 0.0770 chunk 259 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.069558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.049483 restraints weight = 93470.252| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.66 r_work: 0.3063 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22908 Z= 0.149 Angle : 0.565 10.215 31339 Z= 0.289 Chirality : 0.043 0.267 3822 Planarity : 0.004 0.052 3929 Dihedral : 5.241 55.615 4270 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 1.37 % Allowed : 10.23 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2797 helix: 0.77 (0.20), residues: 655 sheet: -0.27 (0.21), residues: 567 loop : -0.72 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 995 TYR 0.018 0.001 TYR A 365 PHE 0.019 0.001 PHE A 759 TRP 0.016 0.001 TRP A 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00318 (22813) covalent geometry : angle 0.54208 (31092) SS BOND : bond 0.00385 ( 35) SS BOND : angle 1.67660 ( 70) hydrogen bonds : bond 0.04479 ( 982) hydrogen bonds : angle 5.82875 ( 2643) Misc. bond : bond 0.00000 ( 1) link_BETA1-4 : bond 0.00259 ( 12) link_BETA1-4 : angle 1.13913 ( 36) link_NAG-ASN : bond 0.00417 ( 47) link_NAG-ASN : angle 2.12910 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5517.57 seconds wall clock time: 95 minutes 29.62 seconds (5729.62 seconds total)