Starting phenix.real_space_refine on Wed May 28 17:57:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xz8_38789/05_2025/8xz8_38789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xz8_38789/05_2025/8xz8_38789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xz8_38789/05_2025/8xz8_38789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xz8_38789/05_2025/8xz8_38789.map" model { file = "/net/cci-nas-00/data/ceres_data/8xz8_38789/05_2025/8xz8_38789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xz8_38789/05_2025/8xz8_38789.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.057 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 144 5.16 5 Cl 1 4.86 5 C 19628 2.51 5 N 5017 2.21 5 O 5994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.82s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30785 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4906 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 24, 'TRANS': 571} Chain: "B" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "S" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "U" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 72 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 19.17, per 1000 atoms: 0.62 Number of scatterers: 30785 At special positions: 0 Unit cell: (147, 176, 228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 144 16.00 O 5994 8.00 N 5017 7.00 C 19628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D 840 " - pdb=" SG CYS D 851 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " 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 E 1 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " BMA T 2 " " NAG U 1 " - " BMA U 2 " NAG-ASN " NAG A 902 " - " ASN A 53 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 298 " " NAG A 905 " - " ASN A 431 " " NAG A 906 " - " ASN A 545 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1311 " - " ASN B 343 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 331 " " NAG D1301 " - " ASN D 122 " " NAG D1302 " - " ASN D 61 " " NAG D1303 " - " ASN D 165 " " NAG D1304 " - " ASN D 234 " " NAG D1305 " - " ASN D 616 " " NAG D1306 " - " ASN D 657 " " NAG D1307 " - " ASN D 709 " " NAG D1308 " - " ASN D1074 " " NAG D1309 " - " ASN D 343 " " NAG D1310 " - " ASN D 331 " " NAG E 1 " - " ASN B 282 " " NAG F 1 " - " ASN B1134 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 354 " " NAG K 1 " - " ASN C 282 " " NAG L 1 " - " ASN C1134 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN D 354 " " NAG Q 1 " - " ASN D 282 " " NAG R 1 " - " ASN D1134 " " NAG S 1 " - " ASN D 801 " " NAG T 1 " - " ASN D 717 " " NAG U 1 " - " ASN D1098 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.66 Conformation dependent library (CDL) restraints added in 4.1 seconds 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7090 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 53 sheets defined 32.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.664A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.740A pdb=" N SER A 106 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 108 " --> pdb=" O THR A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 156 through 193 removed outlier: 3.590A pdb=" N ARG A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 219 through 251 Proline residue: A 234 - end of helix Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'A' and resid 302 through 316 Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.919A pdb=" N TRP A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 384 removed outlier: 3.758A pdb=" N TYR A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.979A pdb=" N MET A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.628A pdb=" N LEU A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 444 Processing helix chain 'A' and resid 447 through 465 removed outlier: 4.440A pdb=" N PHE A 451 " --> pdb=" O GLY A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 471 through 484 Processing helix chain 'A' and resid 497 through 502 removed outlier: 4.152A pdb=" N LEU A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 508 removed outlier: 3.593A pdb=" N ASP A 508 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 533 removed outlier: 3.793A pdb=" N TYR A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.739A pdb=" N MET A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 580 through 587 removed outlier: 3.749A pdb=" N PHE A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 598 Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 616 through 627 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.659A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 840 through 844 removed outlier: 4.172A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 857 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.683A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.142A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.690A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 6.124A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 removed outlier: 4.470A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1139 through 1144' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.734A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 619 through 627 Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.513A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 840 through 844 removed outlier: 3.980A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.652A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.406A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.741A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.753A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 403 through 410 removed outlier: 3.604A pdb=" N SER D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.928A pdb=" N GLN D 506 " --> pdb=" O VAL D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 627 removed outlier: 3.517A pdb=" N VAL D 622 " --> pdb=" O THR D 618 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 623 " --> pdb=" O GLU D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 755 removed outlier: 3.508A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 783 Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 848 through 856 removed outlier: 3.604A pdb=" N ASN D 856 " --> pdb=" O ALA D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 909 Processing helix chain 'D' and resid 913 through 918 Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.516A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 966 removed outlier: 3.629A pdb=" N LEU D 966 " --> pdb=" O LEU D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 5.325A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 261 through 262 removed outlier: 6.797A pdb=" N LEU A 261 " --> pdb=" O VAL A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 30 Processing sheet with id=AA3, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.628A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.685A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 188 through 193 Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.600A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 201 through 205 removed outlier: 6.715A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.231A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.988A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.803A pdb=" N ALA B 397 " --> pdb=" O THR B 356 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.263A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AB6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.836A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AB8, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.574A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.264A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.227A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.022A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.855A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AC7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.927A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.368A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.702A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA C 435 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.900A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 448 through 454 removed outlier: 4.998A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.561A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 654 through 660 removed outlier: 3.604A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 701 through 704 Processing sheet with id=AD6, first strand: chain 'C' and resid 713 through 715 Processing sheet with id=AD7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.290A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.118A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 1095 through 1097 Processing sheet with id=AE2, first strand: chain 'D' and resid 27 through 30 removed outlier: 7.272A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 65 " --> pdb=" O TYR D 265 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TYR D 265 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR D 95 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 226 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N HIS D 207 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ALA D 222 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 50 through 55 removed outlier: 3.570A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.794A pdb=" N GLY D 107 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP D 104 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL D 120 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 311 through 316 removed outlier: 3.598A pdb=" N THR D 315 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY D 648 " --> pdb=" O THR D 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 325 through 326 removed outlier: 3.733A pdb=" N THR D 553 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AE8, first strand: chain 'D' and resid 361 through 362 removed outlier: 7.198A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.071A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 713 through 715 removed outlier: 3.594A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 718 through 722 Processing sheet with id=AF5, first strand: chain 'D' and resid 718 through 722 removed outlier: 7.225A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 733 through 734 removed outlier: 3.854A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 1077 through 1078 removed outlier: 3.655A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 1120 through 1122 1179 hydrogen bonds defined for protein. 3330 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: 14.37 Time building geometry restraints manager: 9.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8433 1.33 - 1.46: 7167 1.46 - 1.58: 15727 1.58 - 1.70: 0 1.70 - 1.83: 193 Bond restraints: 31520 Sorted by residual: bond pdb=" N ILE A 467 " pdb=" CA ILE A 467 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.67e+01 bond pdb=" N ILE D 210 " pdb=" CA ILE D 210 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.21e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" CA PRO C 792 " pdb=" C PRO C 792 " ideal model delta sigma weight residual 1.514 1.531 -0.017 5.50e-03 3.31e+04 9.32e+00 bond pdb=" N LEU B 303 " pdb=" CA LEU B 303 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.18e-02 7.18e+03 9.05e+00 ... (remaining 31515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 41740 2.09 - 4.18: 918 4.18 - 6.28: 179 6.28 - 8.37: 27 8.37 - 10.46: 9 Bond angle restraints: 42873 Sorted by residual: angle pdb=" N VAL D 570 " pdb=" CA VAL D 570 " pdb=" C VAL D 570 " ideal model delta sigma weight residual 106.21 112.41 -6.20 1.07e+00 8.73e-01 3.36e+01 angle pdb=" CA ASP D 979 " pdb=" CB ASP D 979 " pdb=" CG ASP D 979 " ideal model delta sigma weight residual 112.60 117.97 -5.37 1.00e+00 1.00e+00 2.89e+01 angle pdb=" N PRO B 527 " pdb=" CA PRO B 527 " pdb=" C PRO B 527 " ideal model delta sigma weight residual 112.47 122.84 -10.37 2.06e+00 2.36e-01 2.54e+01 angle pdb=" CA ASN B 334 " pdb=" C ASN B 334 " pdb=" O ASN B 334 " ideal model delta sigma weight residual 121.89 116.24 5.65 1.17e+00 7.31e-01 2.33e+01 angle pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta sigma weight residual 121.90 116.08 5.82 1.26e+00 6.30e-01 2.13e+01 ... (remaining 42868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.92: 17595 23.92 - 47.85: 1533 47.85 - 71.77: 213 71.77 - 95.70: 152 95.70 - 119.62: 128 Dihedral angle restraints: 19621 sinusoidal: 8586 harmonic: 11035 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -152.32 66.32 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS D 131 " pdb=" SG CYS D 131 " pdb=" SG CYS D 166 " pdb=" CB CYS D 166 " ideal model delta sinusoidal sigma weight residual 93.00 29.97 63.03 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 31.36 61.64 1 1.00e+01 1.00e-02 5.04e+01 ... (remaining 19618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 4941 0.188 - 0.377: 39 0.377 - 0.565: 0 0.565 - 0.754: 0 0.754 - 0.942: 3 Chirality restraints: 4983 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN D1098 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.83e+01 ... (remaining 4980 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 498 " 0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO D 499 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 499 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 499 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 330 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C PRO B 330 " 0.046 2.00e-02 2.50e+03 pdb=" O PRO B 330 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN B 331 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 526 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C GLY B 526 " -0.042 2.00e-02 2.50e+03 pdb=" O GLY B 526 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO B 527 " 0.014 2.00e-02 2.50e+03 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 748 2.67 - 3.23: 30165 3.23 - 3.79: 49608 3.79 - 4.34: 65311 4.34 - 4.90: 105542 Nonbonded interactions: 251374 Sorted by model distance: nonbonded pdb=" O VAL D 503 " pdb=" OH TYR D 508 " model vdw 2.113 3.040 nonbonded pdb=" OH TYR A 242 " pdb=" O LEU A 594 " model vdw 2.146 3.040 nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.152 3.040 nonbonded pdb=" O CYS C 590 " pdb=" OH TYR D 837 " model vdw 2.154 3.040 nonbonded pdb=" O PHE C1075 " pdb=" OG1 THR C1076 " model vdw 2.165 3.040 ... (remaining 251369 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 'B' and (resid 23 through 1144 or resid 1301 through 1310)) selection = chain 'C' selection = chain 'D' } ncs_group { reference = 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' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 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: 0.040 Extract box with map and model: 1.130 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 73.390 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.200 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.004 0.067 31628 Z= 0.202 Angle : 0.794 19.257 43156 Z= 0.391 Chirality : 0.056 0.942 4983 Planarity : 0.004 0.069 5438 Dihedral : 21.400 119.625 12417 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.01 % Favored : 92.78 % Rotamer: Outliers : 0.82 % Allowed : 26.52 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3753 helix: 1.03 (0.16), residues: 1086 sheet: -0.79 (0.21), residues: 610 loop : -1.76 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 452 HIS 0.008 0.001 HIS A 377 PHE 0.019 0.001 PHE C 592 TYR 0.031 0.001 TYR C 351 ARG 0.003 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00935 ( 52) link_NAG-ASN : angle 4.27946 ( 156) link_BETA1-4 : bond 0.00503 ( 17) link_BETA1-4 : angle 2.21934 ( 51) hydrogen bonds : bond 0.14608 ( 1175) hydrogen bonds : angle 7.10401 ( 3330) SS BOND : bond 0.00248 ( 38) SS BOND : angle 1.74922 ( 76) covalent geometry : bond 0.00382 (31520) covalent geometry : angle 0.74662 (42873) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 3.426 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 111 GLU cc_start: 0.6134 (tp30) cc_final: 0.5524 (mp0) REVERT: A 248 MET cc_start: 0.3384 (mtt) cc_final: 0.1482 (ptt) REVERT: B 613 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8659 (mp10) REVERT: D 121 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7623 (t0) REVERT: D 740 MET cc_start: 0.8343 (tpp) cc_final: 0.8132 (tpp) REVERT: D 1050 MET cc_start: 0.7398 (mtm) cc_final: 0.7043 (mtm) outliers start: 27 outliers final: 6 residues processed: 194 average time/residue: 0.4084 time to fit residues: 132.1085 Evaluate side-chains 159 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 968 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 4.9990 chunk 285 optimal weight: 0.1980 chunk 158 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 192 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 295 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 342 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 321 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.100447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.071679 restraints weight = 130789.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.073512 restraints weight = 63662.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.074634 restraints weight = 39704.462| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31628 Z= 0.153 Angle : 0.739 18.795 43156 Z= 0.345 Chirality : 0.051 0.716 4983 Planarity : 0.005 0.065 5438 Dihedral : 14.517 113.101 5523 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 3.70 % Allowed : 23.73 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3753 helix: 1.08 (0.16), residues: 1087 sheet: -0.75 (0.21), residues: 623 loop : -1.69 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 104 HIS 0.005 0.001 HIS A 377 PHE 0.013 0.001 PHE C 592 TYR 0.019 0.001 TYR D1067 ARG 0.008 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00869 ( 52) link_NAG-ASN : angle 4.23250 ( 156) link_BETA1-4 : bond 0.00449 ( 17) link_BETA1-4 : angle 3.47340 ( 51) hydrogen bonds : bond 0.03986 ( 1175) hydrogen bonds : angle 5.75643 ( 3330) SS BOND : bond 0.00374 ( 38) SS BOND : angle 1.37059 ( 76) covalent geometry : bond 0.00339 (31520) covalent geometry : angle 0.68281 (42873) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 164 time to evaluate : 3.190 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 111 GLU cc_start: 0.5830 (tp30) cc_final: 0.5544 (mp0) REVERT: A 296 MET cc_start: -0.1600 (ptt) cc_final: -0.2938 (ptt) REVERT: A 365 MET cc_start: 0.3555 (mmm) cc_final: 0.0984 (tpt) REVERT: B 164 ASN cc_start: 0.2137 (OUTLIER) cc_final: 0.1085 (m110) REVERT: B 189 LEU cc_start: 0.7259 (tt) cc_final: 0.6736 (mp) REVERT: B 613 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8693 (mp10) REVERT: B 994 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8294 (t70) REVERT: C 613 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.8016 (mt0) REVERT: C 705 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8419 (p) REVERT: C 740 MET cc_start: 0.7878 (ttm) cc_final: 0.7269 (ttm) REVERT: D 121 ASN cc_start: 0.8209 (m-40) cc_final: 0.7769 (t0) REVERT: D 327 VAL cc_start: 0.9520 (OUTLIER) cc_final: 0.9171 (p) outliers start: 122 outliers final: 43 residues processed: 269 average time/residue: 0.3704 time to fit residues: 170.4395 Evaluate side-chains 193 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1101 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 316 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 376 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 223 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 202 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 292 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C1036 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1036 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.096917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.068037 restraints weight = 131224.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.069832 restraints weight = 63340.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.070989 restraints weight = 39563.188| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 31628 Z= 0.282 Angle : 0.806 18.687 43156 Z= 0.386 Chirality : 0.053 0.757 4983 Planarity : 0.005 0.058 5438 Dihedral : 10.408 113.721 5518 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.78 % Favored : 92.09 % Rotamer: Outliers : 5.27 % Allowed : 23.58 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3753 helix: 0.91 (0.16), residues: 1084 sheet: -0.92 (0.20), residues: 652 loop : -1.79 (0.14), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 104 HIS 0.011 0.002 HIS A 400 PHE 0.030 0.002 PHE B 592 TYR 0.019 0.002 TYR D1067 ARG 0.011 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.01154 ( 52) link_NAG-ASN : angle 4.56903 ( 156) link_BETA1-4 : bond 0.00394 ( 17) link_BETA1-4 : angle 3.30236 ( 51) hydrogen bonds : bond 0.04295 ( 1175) hydrogen bonds : angle 5.79745 ( 3330) SS BOND : bond 0.00550 ( 38) SS BOND : angle 1.63872 ( 76) covalent geometry : bond 0.00622 (31520) covalent geometry : angle 0.74860 (42873) Misc. bond : bond 0.00099 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 154 time to evaluate : 3.370 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 66 ARG cc_start: 0.5412 (OUTLIER) cc_final: 0.4904 (mmt180) REVERT: A 111 GLU cc_start: 0.5664 (tp30) cc_final: 0.5372 (mp0) REVERT: A 317 ILE cc_start: 0.2721 (OUTLIER) cc_final: 0.2437 (mt) REVERT: A 321 TYR cc_start: 0.2996 (OUTLIER) cc_final: 0.2653 (m-80) REVERT: A 365 MET cc_start: 0.3369 (mmm) cc_final: 0.0830 (tpt) REVERT: B 164 ASN cc_start: 0.1653 (OUTLIER) cc_final: -0.0029 (m110) REVERT: B 588 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.8750 (p) REVERT: B 994 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8288 (t70) REVERT: C 195 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8372 (ptpp) REVERT: C 869 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8957 (ptm) REVERT: D 327 VAL cc_start: 0.9557 (OUTLIER) cc_final: 0.9181 (p) outliers start: 174 outliers final: 90 residues processed: 312 average time/residue: 0.3749 time to fit residues: 197.5457 Evaluate side-chains 232 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 133 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 405 ASN Chi-restraints excluded: chain D residue 460 LYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1101 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 219 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 259 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 51 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 487 ASN C 804 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.097931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.069023 restraints weight = 131345.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.070847 restraints weight = 63382.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.072025 restraints weight = 39616.281| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31628 Z= 0.183 Angle : 0.720 19.044 43156 Z= 0.343 Chirality : 0.051 0.725 4983 Planarity : 0.005 0.058 5438 Dihedral : 8.977 109.040 5513 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.11 % Favored : 92.73 % Rotamer: Outliers : 4.55 % Allowed : 24.45 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3753 helix: 1.03 (0.16), residues: 1086 sheet: -0.88 (0.21), residues: 635 loop : -1.73 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 104 HIS 0.006 0.001 HIS A 400 PHE 0.018 0.001 PHE D1075 TYR 0.016 0.001 TYR D1067 ARG 0.006 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00864 ( 52) link_NAG-ASN : angle 4.45943 ( 156) link_BETA1-4 : bond 0.00347 ( 17) link_BETA1-4 : angle 2.96512 ( 51) hydrogen bonds : bond 0.03763 ( 1175) hydrogen bonds : angle 5.57772 ( 3330) SS BOND : bond 0.00412 ( 38) SS BOND : angle 1.65463 ( 76) covalent geometry : bond 0.00407 (31520) covalent geometry : angle 0.65850 (42873) Misc. bond : bond 0.00100 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 151 time to evaluate : 3.361 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 66 ARG cc_start: 0.5197 (OUTLIER) cc_final: 0.4698 (mmt180) REVERT: A 111 GLU cc_start: 0.5729 (tp30) cc_final: 0.5459 (mp0) REVERT: A 296 MET cc_start: -0.2174 (ptt) cc_final: -0.2888 (ptt) REVERT: A 317 ILE cc_start: 0.2598 (OUTLIER) cc_final: 0.2190 (mt) REVERT: A 321 TYR cc_start: 0.2607 (OUTLIER) cc_final: 0.2303 (m-80) REVERT: A 365 MET cc_start: 0.3149 (mmm) cc_final: 0.0842 (tpt) REVERT: B 80 ASP cc_start: 0.3360 (OUTLIER) cc_final: 0.2868 (t0) REVERT: B 115 GLN cc_start: 0.4930 (OUTLIER) cc_final: 0.4554 (tp-100) REVERT: B 164 ASN cc_start: 0.1823 (OUTLIER) cc_final: 0.0225 (m110) REVERT: B 265 TYR cc_start: 0.8229 (t80) cc_final: 0.8023 (t80) REVERT: B 588 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.8713 (p) REVERT: B 994 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8343 (t70) REVERT: C 127 PHE cc_start: 0.8123 (t80) cc_final: 0.7883 (m-80) REVERT: C 239 GLN cc_start: 0.6188 (OUTLIER) cc_final: 0.5980 (mm110) REVERT: C 853 GLN cc_start: 0.7719 (pt0) cc_final: 0.7180 (pp30) REVERT: D 300 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.9142 (ttmt) REVERT: D 327 VAL cc_start: 0.9468 (OUTLIER) cc_final: 0.9125 (p) REVERT: D 529 LYS cc_start: 0.8101 (mmtm) cc_final: 0.7851 (mmtm) REVERT: D 584 ILE cc_start: 0.7392 (mt) cc_final: 0.7129 (mt) REVERT: D 734 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8785 (m) outliers start: 150 outliers final: 80 residues processed: 286 average time/residue: 0.3800 time to fit residues: 184.2605 Evaluate side-chains 234 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 142 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 405 ASN Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1101 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 257 optimal weight: 0.9990 chunk 11 optimal weight: 0.0770 chunk 63 optimal weight: 1.9990 chunk 299 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 313 optimal weight: 10.0000 chunk 306 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 357 optimal weight: 0.4980 chunk 182 optimal weight: 8.9990 overall best weight: 0.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 276 ASN B 321 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 487 ASN C 519 HIS C 955 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.100497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.070614 restraints weight = 125265.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.072463 restraints weight = 62087.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.073661 restraints weight = 39283.380| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31628 Z= 0.125 Angle : 0.688 18.985 43156 Z= 0.326 Chirality : 0.050 0.700 4983 Planarity : 0.004 0.059 5438 Dihedral : 8.362 106.521 5513 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.27 % Favored : 92.57 % Rotamer: Outliers : 4.18 % Allowed : 24.67 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3753 helix: 1.15 (0.16), residues: 1086 sheet: -0.94 (0.20), residues: 663 loop : -1.66 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 104 HIS 0.006 0.001 HIS A 377 PHE 0.036 0.001 PHE D 497 TYR 0.026 0.001 TYR B 170 ARG 0.008 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00833 ( 52) link_NAG-ASN : angle 4.30687 ( 156) link_BETA1-4 : bond 0.00405 ( 17) link_BETA1-4 : angle 2.60156 ( 51) hydrogen bonds : bond 0.03549 ( 1175) hydrogen bonds : angle 5.41084 ( 3330) SS BOND : bond 0.00331 ( 38) SS BOND : angle 1.52219 ( 76) covalent geometry : bond 0.00281 (31520) covalent geometry : angle 0.63034 (42873) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 154 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.5172 (OUTLIER) cc_final: 0.4738 (mmt180) REVERT: A 111 GLU cc_start: 0.5671 (tp30) cc_final: 0.5423 (mp0) REVERT: A 296 MET cc_start: -0.2445 (ptt) cc_final: -0.3122 (ptt) REVERT: A 321 TYR cc_start: 0.2916 (OUTLIER) cc_final: 0.2706 (m-80) REVERT: A 365 MET cc_start: 0.2998 (mmm) cc_final: 0.0937 (tpt) REVERT: B 80 ASP cc_start: 0.3263 (OUTLIER) cc_final: 0.2950 (t0) REVERT: B 104 TRP cc_start: 0.7566 (m-10) cc_final: 0.7341 (m-10) REVERT: B 164 ASN cc_start: 0.1874 (OUTLIER) cc_final: 0.0370 (m110) REVERT: B 189 LEU cc_start: 0.8091 (tt) cc_final: 0.7444 (pp) REVERT: B 265 TYR cc_start: 0.8096 (t80) cc_final: 0.7852 (t80) REVERT: B 588 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8686 (p) REVERT: B 994 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8353 (t70) REVERT: C 853 GLN cc_start: 0.7800 (pt0) cc_final: 0.7179 (pp30) REVERT: D 121 ASN cc_start: 0.8184 (m-40) cc_final: 0.7725 (t0) REVERT: D 300 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9073 (ttmt) REVERT: D 327 VAL cc_start: 0.9480 (OUTLIER) cc_final: 0.9146 (p) REVERT: D 495 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7887 (t80) REVERT: D 529 LYS cc_start: 0.8013 (mmtm) cc_final: 0.7713 (mmtm) REVERT: D 584 ILE cc_start: 0.7419 (mt) cc_final: 0.7051 (mt) REVERT: D 805 ILE cc_start: 0.9535 (pt) cc_final: 0.9205 (mm) outliers start: 138 outliers final: 82 residues processed: 278 average time/residue: 0.3609 time to fit residues: 171.7668 Evaluate side-chains 236 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 145 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1101 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 0 optimal weight: 30.0000 chunk 253 optimal weight: 1.9990 chunk 350 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 370 optimal weight: 0.9980 chunk 136 optimal weight: 0.0870 chunk 141 optimal weight: 0.7980 chunk 258 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 344 HIS ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 613 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.098814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.070363 restraints weight = 129592.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.072189 restraints weight = 62823.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.073383 restraints weight = 39201.960| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31628 Z= 0.130 Angle : 0.674 18.661 43156 Z= 0.320 Chirality : 0.049 0.683 4983 Planarity : 0.004 0.058 5438 Dihedral : 7.937 101.218 5513 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.22 % Favored : 92.62 % Rotamer: Outliers : 4.27 % Allowed : 24.70 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3753 helix: 1.20 (0.16), residues: 1086 sheet: -0.75 (0.21), residues: 629 loop : -1.60 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 104 HIS 0.006 0.001 HIS A 377 PHE 0.021 0.001 PHE D 497 TYR 0.015 0.001 TYR D 837 ARG 0.004 0.000 ARG D1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00799 ( 52) link_NAG-ASN : angle 4.23948 ( 156) link_BETA1-4 : bond 0.00409 ( 17) link_BETA1-4 : angle 2.33329 ( 51) hydrogen bonds : bond 0.03493 ( 1175) hydrogen bonds : angle 5.28369 ( 3330) SS BOND : bond 0.00409 ( 38) SS BOND : angle 1.47727 ( 76) covalent geometry : bond 0.00293 (31520) covalent geometry : angle 0.61761 (42873) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 157 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.5405 (OUTLIER) cc_final: 0.4861 (mmt180) REVERT: A 111 GLU cc_start: 0.5563 (tp30) cc_final: 0.5224 (mp0) REVERT: A 248 MET cc_start: 0.2991 (mtt) cc_final: 0.1202 (ptt) REVERT: A 296 MET cc_start: -0.2117 (ptt) cc_final: -0.2817 (ptt) REVERT: A 321 TYR cc_start: 0.2821 (OUTLIER) cc_final: 0.2527 (m-80) REVERT: A 323 THR cc_start: -0.0205 (OUTLIER) cc_final: -0.0610 (m) REVERT: A 365 MET cc_start: 0.2662 (mmm) cc_final: 0.0692 (tpt) REVERT: B 92 PHE cc_start: 0.7470 (t80) cc_final: 0.7072 (t80) REVERT: B 115 GLN cc_start: 0.4736 (OUTLIER) cc_final: 0.4419 (tp-100) REVERT: B 164 ASN cc_start: 0.1881 (OUTLIER) cc_final: 0.0518 (m110) REVERT: B 189 LEU cc_start: 0.8164 (tt) cc_final: 0.7536 (pp) REVERT: B 265 TYR cc_start: 0.8076 (t80) cc_final: 0.7859 (t80) REVERT: B 588 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.8820 (p) REVERT: B 904 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.8300 (m-80) REVERT: B 994 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8305 (t70) REVERT: C 127 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: C 853 GLN cc_start: 0.7739 (pt0) cc_final: 0.7144 (pp30) REVERT: D 26 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7912 (pp30) REVERT: D 121 ASN cc_start: 0.8206 (m-40) cc_final: 0.7783 (t0) REVERT: D 246 ARG cc_start: 0.3170 (OUTLIER) cc_final: 0.1317 (mmt90) REVERT: D 300 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9080 (ttmt) REVERT: D 327 VAL cc_start: 0.9460 (OUTLIER) cc_final: 0.9098 (p) REVERT: D 529 LYS cc_start: 0.7988 (mmtm) cc_final: 0.7654 (mmtm) REVERT: D 584 ILE cc_start: 0.7551 (mt) cc_final: 0.7137 (mt) REVERT: D 805 ILE cc_start: 0.9525 (pt) cc_final: 0.9217 (mm) outliers start: 141 outliers final: 95 residues processed: 284 average time/residue: 0.3855 time to fit residues: 185.6553 Evaluate side-chains 252 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 144 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 102 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 309 optimal weight: 8.9990 chunk 317 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 343 optimal weight: 0.7980 chunk 230 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 955 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN D 239 GLN D1036 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.098731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.070400 restraints weight = 129942.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.072260 restraints weight = 62395.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.073437 restraints weight = 38524.818| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31628 Z= 0.134 Angle : 0.679 18.444 43156 Z= 0.322 Chirality : 0.049 0.677 4983 Planarity : 0.004 0.060 5438 Dihedral : 7.725 99.058 5513 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.22 % Favored : 92.62 % Rotamer: Outliers : 4.36 % Allowed : 24.58 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3753 helix: 1.27 (0.16), residues: 1078 sheet: -0.75 (0.21), residues: 629 loop : -1.59 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 104 HIS 0.027 0.001 HIS A 344 PHE 0.021 0.001 PHE B 192 TYR 0.025 0.001 TYR B 170 ARG 0.003 0.000 ARG D1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00790 ( 52) link_NAG-ASN : angle 4.21399 ( 156) link_BETA1-4 : bond 0.00398 ( 17) link_BETA1-4 : angle 2.19426 ( 51) hydrogen bonds : bond 0.03456 ( 1175) hydrogen bonds : angle 5.24144 ( 3330) SS BOND : bond 0.00337 ( 38) SS BOND : angle 1.79113 ( 76) covalent geometry : bond 0.00302 (31520) covalent geometry : angle 0.62301 (42873) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 158 time to evaluate : 3.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.5174 (OUTLIER) cc_final: 0.4822 (mtm-85) REVERT: A 248 MET cc_start: 0.3065 (mtt) cc_final: 0.1207 (ptt) REVERT: A 296 MET cc_start: -0.2134 (ptt) cc_final: -0.2823 (ptt) REVERT: A 321 TYR cc_start: 0.2699 (OUTLIER) cc_final: 0.2435 (m-80) REVERT: A 323 THR cc_start: -0.0369 (OUTLIER) cc_final: -0.0744 (m) REVERT: A 365 MET cc_start: 0.2535 (mmm) cc_final: -0.0111 (tpp) REVERT: B 80 ASP cc_start: 0.3189 (OUTLIER) cc_final: 0.2943 (t0) REVERT: B 92 PHE cc_start: 0.7551 (t80) cc_final: 0.7196 (t80) REVERT: B 164 ASN cc_start: 0.1977 (OUTLIER) cc_final: 0.0629 (m110) REVERT: B 170 TYR cc_start: 0.7395 (t80) cc_final: 0.6993 (m-10) REVERT: B 189 LEU cc_start: 0.8238 (tt) cc_final: 0.7625 (pp) REVERT: B 265 TYR cc_start: 0.8050 (t80) cc_final: 0.7829 (t80) REVERT: B 588 THR cc_start: 0.9389 (OUTLIER) cc_final: 0.8838 (p) REVERT: B 904 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8277 (m-80) REVERT: B 994 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8299 (t70) REVERT: C 127 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: C 660 TYR cc_start: 0.9241 (OUTLIER) cc_final: 0.9034 (m-80) REVERT: C 853 GLN cc_start: 0.7761 (pt0) cc_final: 0.7168 (pp30) REVERT: D 26 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7928 (pp30) REVERT: D 119 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8044 (mp) REVERT: D 121 ASN cc_start: 0.8239 (m-40) cc_final: 0.7827 (t0) REVERT: D 246 ARG cc_start: 0.3224 (OUTLIER) cc_final: 0.1277 (mmt-90) REVERT: D 300 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9087 (ttmt) REVERT: D 327 VAL cc_start: 0.9454 (OUTLIER) cc_final: 0.9087 (p) REVERT: D 529 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7576 (mmtm) REVERT: D 584 ILE cc_start: 0.7627 (mt) cc_final: 0.7193 (mt) REVERT: D 740 MET cc_start: 0.8494 (tpp) cc_final: 0.8271 (tpp) outliers start: 144 outliers final: 102 residues processed: 289 average time/residue: 0.3782 time to fit residues: 185.8375 Evaluate side-chains 267 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 150 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 153 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 355 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 252 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 307 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 276 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** 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 = 0.4011 r_free = 0.4011 target = 0.098325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.069515 restraints weight = 129848.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.071322 restraints weight = 62875.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.072505 restraints weight = 39397.343| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31628 Z= 0.144 Angle : 0.688 18.285 43156 Z= 0.326 Chirality : 0.050 0.677 4983 Planarity : 0.004 0.061 5438 Dihedral : 7.603 97.948 5513 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.17 % Favored : 92.67 % Rotamer: Outliers : 4.12 % Allowed : 24.76 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3753 helix: 1.21 (0.16), residues: 1090 sheet: -0.83 (0.21), residues: 633 loop : -1.60 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 104 HIS 0.006 0.001 HIS A 34 PHE 0.019 0.001 PHE B 338 TYR 0.024 0.001 TYR B 170 ARG 0.003 0.000 ARG D1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 52) link_NAG-ASN : angle 4.46609 ( 156) link_BETA1-4 : bond 0.00383 ( 17) link_BETA1-4 : angle 2.11968 ( 51) hydrogen bonds : bond 0.03457 ( 1175) hydrogen bonds : angle 5.25643 ( 3330) SS BOND : bond 0.00316 ( 38) SS BOND : angle 1.73402 ( 76) covalent geometry : bond 0.00323 (31520) covalent geometry : angle 0.62755 (42873) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 151 time to evaluate : 3.347 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 62 MET cc_start: -0.0775 (mmm) cc_final: -0.0981 (tmm) REVERT: A 248 MET cc_start: 0.3164 (mtt) cc_final: 0.1428 (ptt) REVERT: A 296 MET cc_start: -0.2241 (ptt) cc_final: -0.2895 (ptt) REVERT: A 321 TYR cc_start: 0.2673 (OUTLIER) cc_final: 0.2435 (m-80) REVERT: A 323 THR cc_start: -0.0412 (OUTLIER) cc_final: -0.0770 (m) REVERT: A 365 MET cc_start: 0.2614 (mmm) cc_final: 0.0751 (tpt) REVERT: B 92 PHE cc_start: 0.7603 (t80) cc_final: 0.7271 (t80) REVERT: B 164 ASN cc_start: 0.1819 (OUTLIER) cc_final: 0.0420 (m110) REVERT: B 170 TYR cc_start: 0.7350 (t80) cc_final: 0.7010 (m-10) REVERT: B 189 LEU cc_start: 0.8197 (tt) cc_final: 0.7528 (pp) REVERT: B 265 TYR cc_start: 0.8040 (t80) cc_final: 0.7830 (t80) REVERT: B 346 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.5527 (mmp80) REVERT: B 588 THR cc_start: 0.9396 (OUTLIER) cc_final: 0.8845 (p) REVERT: B 904 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: B 994 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8295 (t70) REVERT: C 127 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: C 660 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8998 (m-80) REVERT: C 853 GLN cc_start: 0.7844 (pt0) cc_final: 0.7233 (pp30) REVERT: D 26 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7904 (pp30) REVERT: D 119 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8039 (mp) REVERT: D 121 ASN cc_start: 0.8231 (m-40) cc_final: 0.7812 (t0) REVERT: D 246 ARG cc_start: 0.3212 (OUTLIER) cc_final: 0.1258 (mmt-90) REVERT: D 327 VAL cc_start: 0.9459 (OUTLIER) cc_final: 0.9090 (p) REVERT: D 529 LYS cc_start: 0.7925 (mmtm) cc_final: 0.7535 (mmtm) REVERT: D 584 ILE cc_start: 0.7676 (mt) cc_final: 0.7209 (mt) REVERT: D 805 ILE cc_start: 0.9512 (pt) cc_final: 0.9219 (mm) outliers start: 136 outliers final: 108 residues processed: 274 average time/residue: 0.3825 time to fit residues: 179.0254 Evaluate side-chains 269 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 148 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 676 THR Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 85 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 356 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 328 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 258 optimal weight: 0.8980 chunk 332 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** 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 = 0.4000 r_free = 0.4000 target = 0.097838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.069268 restraints weight = 128876.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.071057 restraints weight = 63094.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.072213 restraints weight = 39379.795| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31628 Z= 0.160 Angle : 0.695 18.136 43156 Z= 0.330 Chirality : 0.050 0.682 4983 Planarity : 0.004 0.058 5438 Dihedral : 7.519 97.050 5513 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.33 % Favored : 92.51 % Rotamer: Outliers : 4.15 % Allowed : 24.79 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3753 helix: 1.23 (0.16), residues: 1082 sheet: -0.89 (0.20), residues: 646 loop : -1.59 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP B 104 HIS 0.014 0.001 HIS A 34 PHE 0.020 0.001 PHE A 32 TYR 0.024 0.001 TYR B 170 ARG 0.006 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00775 ( 52) link_NAG-ASN : angle 4.34461 ( 156) link_BETA1-4 : bond 0.00381 ( 17) link_BETA1-4 : angle 2.05906 ( 51) hydrogen bonds : bond 0.03532 ( 1175) hydrogen bonds : angle 5.25160 ( 3330) SS BOND : bond 0.00384 ( 38) SS BOND : angle 1.61147 ( 76) covalent geometry : bond 0.00360 (31520) covalent geometry : angle 0.63919 (42873) Misc. bond : bond 0.00066 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 153 time to evaluate : 3.445 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 33 ASN cc_start: 0.1798 (OUTLIER) cc_final: 0.1592 (t0) REVERT: A 62 MET cc_start: -0.0507 (mmm) cc_final: -0.0730 (tmm) REVERT: A 248 MET cc_start: 0.3233 (mtt) cc_final: 0.1498 (ptt) REVERT: A 296 MET cc_start: -0.2226 (ptt) cc_final: -0.2878 (ptt) REVERT: A 323 THR cc_start: -0.0614 (OUTLIER) cc_final: -0.0987 (m) REVERT: A 365 MET cc_start: 0.2555 (mmm) cc_final: 0.0737 (tpt) REVERT: B 92 PHE cc_start: 0.7644 (t80) cc_final: 0.7309 (t80) REVERT: B 164 ASN cc_start: 0.1935 (OUTLIER) cc_final: 0.0521 (m110) REVERT: B 170 TYR cc_start: 0.7324 (t80) cc_final: 0.6997 (m-10) REVERT: B 189 LEU cc_start: 0.8233 (tt) cc_final: 0.7887 (pp) REVERT: B 265 TYR cc_start: 0.8077 (t80) cc_final: 0.7775 (t80) REVERT: B 588 THR cc_start: 0.9407 (OUTLIER) cc_final: 0.8876 (p) REVERT: B 867 ASP cc_start: 0.8210 (m-30) cc_final: 0.7914 (m-30) REVERT: B 904 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: B 994 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8297 (t70) REVERT: C 127 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: C 328 ARG cc_start: 0.4699 (OUTLIER) cc_final: 0.3449 (tmt170) REVERT: C 660 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.9003 (m-80) REVERT: C 853 GLN cc_start: 0.7982 (pt0) cc_final: 0.7363 (pp30) REVERT: D 26 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7911 (pp30) REVERT: D 119 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.8002 (mp) REVERT: D 121 ASN cc_start: 0.8271 (m-40) cc_final: 0.7853 (t0) REVERT: D 246 ARG cc_start: 0.3189 (OUTLIER) cc_final: 0.1257 (mmt-90) REVERT: D 327 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9076 (p) REVERT: D 584 ILE cc_start: 0.7769 (mt) cc_final: 0.7293 (mt) outliers start: 137 outliers final: 106 residues processed: 280 average time/residue: 0.3794 time to fit residues: 180.8743 Evaluate side-chains 264 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 145 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 676 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 216 optimal weight: 0.4980 chunk 156 optimal weight: 0.7980 chunk 263 optimal weight: 0.8980 chunk 291 optimal weight: 0.9980 chunk 282 optimal weight: 20.0000 chunk 345 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 344 optimal weight: 0.9980 chunk 331 optimal weight: 9.9990 chunk 362 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.099203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.070644 restraints weight = 130405.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.072519 restraints weight = 62156.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.073731 restraints weight = 38432.023| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31628 Z= 0.121 Angle : 0.683 18.167 43156 Z= 0.323 Chirality : 0.049 0.672 4983 Planarity : 0.004 0.060 5438 Dihedral : 7.373 96.175 5513 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.09 % Favored : 92.75 % Rotamer: Outliers : 3.36 % Allowed : 25.61 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3753 helix: 1.25 (0.16), residues: 1091 sheet: -0.81 (0.21), residues: 632 loop : -1.61 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 104 HIS 0.014 0.001 HIS A 34 PHE 0.031 0.001 PHE B 238 TYR 0.025 0.001 TYR D 495 ARG 0.003 0.000 ARG D1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00780 ( 52) link_NAG-ASN : angle 4.26226 ( 156) link_BETA1-4 : bond 0.00436 ( 17) link_BETA1-4 : angle 1.98995 ( 51) hydrogen bonds : bond 0.03406 ( 1175) hydrogen bonds : angle 5.16664 ( 3330) SS BOND : bond 0.00312 ( 38) SS BOND : angle 1.46691 ( 76) covalent geometry : bond 0.00271 (31520) covalent geometry : angle 0.62899 (42873) Misc. bond : bond 0.00060 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 156 time to evaluate : 3.476 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 62 MET cc_start: -0.0471 (mmm) cc_final: -0.0695 (tmm) REVERT: A 248 MET cc_start: 0.3005 (mtt) cc_final: 0.1184 (ptt) REVERT: A 296 MET cc_start: -0.2095 (ptt) cc_final: -0.2669 (ptt) REVERT: A 323 THR cc_start: -0.0740 (OUTLIER) cc_final: -0.1145 (m) REVERT: A 365 MET cc_start: 0.2422 (mmm) cc_final: 0.0536 (tpt) REVERT: B 92 PHE cc_start: 0.7707 (t80) cc_final: 0.7403 (t80) REVERT: B 164 ASN cc_start: 0.1894 (OUTLIER) cc_final: 0.0509 (m-40) REVERT: B 170 TYR cc_start: 0.7318 (t80) cc_final: 0.7033 (m-10) REVERT: B 189 LEU cc_start: 0.8242 (tt) cc_final: 0.7917 (pp) REVERT: B 265 TYR cc_start: 0.7970 (t80) cc_final: 0.7719 (t80) REVERT: B 588 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.8875 (p) REVERT: B 867 ASP cc_start: 0.8220 (m-30) cc_final: 0.7889 (m-30) REVERT: B 904 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: B 994 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8316 (t70) REVERT: C 853 GLN cc_start: 0.7914 (pt0) cc_final: 0.7305 (pp30) REVERT: D 26 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7956 (pp30) REVERT: D 119 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7991 (mp) REVERT: D 121 ASN cc_start: 0.8208 (m-40) cc_final: 0.7814 (t0) REVERT: D 246 ARG cc_start: 0.3360 (OUTLIER) cc_final: 0.1352 (mmt-90) REVERT: D 327 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9063 (p) REVERT: D 584 ILE cc_start: 0.7689 (mt) cc_final: 0.7207 (mt) REVERT: D 740 MET cc_start: 0.8454 (tpp) cc_final: 0.8146 (tpp) REVERT: D 805 ILE cc_start: 0.9518 (pt) cc_final: 0.9217 (mm) outliers start: 111 outliers final: 91 residues processed: 255 average time/residue: 0.4068 time to fit residues: 179.1701 Evaluate side-chains 249 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 149 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 241 optimal weight: 10.0000 chunk 277 optimal weight: 0.0070 chunk 21 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 257 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 255 optimal weight: 0.7980 chunk 130 optimal weight: 0.0980 chunk 153 optimal weight: 6.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** 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 = 0.4035 r_free = 0.4035 target = 0.099855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.071669 restraints weight = 129628.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.073555 restraints weight = 61921.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.074779 restraints weight = 38180.663| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31628 Z= 0.116 Angle : 0.678 18.039 43156 Z= 0.322 Chirality : 0.049 0.663 4983 Planarity : 0.004 0.059 5438 Dihedral : 7.225 94.396 5513 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.98 % Favored : 92.86 % Rotamer: Outliers : 3.03 % Allowed : 25.76 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3753 helix: 1.27 (0.16), residues: 1091 sheet: -0.81 (0.21), residues: 629 loop : -1.59 (0.14), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 104 HIS 0.011 0.001 HIS A 34 PHE 0.029 0.001 PHE B 238 TYR 0.026 0.001 TYR A 41 ARG 0.008 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00775 ( 52) link_NAG-ASN : angle 4.18941 ( 156) link_BETA1-4 : bond 0.00446 ( 17) link_BETA1-4 : angle 1.95919 ( 51) hydrogen bonds : bond 0.03416 ( 1175) hydrogen bonds : angle 5.11546 ( 3330) SS BOND : bond 0.00233 ( 38) SS BOND : angle 1.33788 ( 76) covalent geometry : bond 0.00260 (31520) covalent geometry : angle 0.62593 (42873) Misc. bond : bond 0.00042 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10440.75 seconds wall clock time: 184 minutes 14.12 seconds (11054.12 seconds total)