Starting phenix.real_space_refine on Thu Jun 26 22:03:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xz8_38789/06_2025/8xz8_38789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xz8_38789/06_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_38789/06_2025/8xz8_38789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xz8_38789/06_2025/8xz8_38789.map" model { file = "/net/cci-nas-00/data/ceres_data/8xz8_38789/06_2025/8xz8_38789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xz8_38789/06_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): 0.89s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.92, per 1000 atoms: 0.58 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: 8.31 Conformation dependent library (CDL) restraints added in 3.9 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: 4.44 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: 12.95 Time building geometry restraints manager: 9.14 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.150 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 69.580 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.210 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.680 ------------------------------------------------------------------------------- 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 : 3.132 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: 0.3883 time to fit residues: 125.8300 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 : 3.094 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.100375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.071625 restraints weight = 130074.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.073474 restraints weight = 62289.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.074678 restraints weight = 38594.981| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 3.478 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: 0.5844 (tp30) cc_final: 0.5540 (mp0) REVERT: A 296 MET cc_start: -0.1540 (ptt) cc_final: -0.2871 (ptt) REVERT: A 365 MET cc_start: 0.3518 (mmm) cc_final: 0.0915 (tpt) REVERT: B 164 ASN cc_start: 0.2059 (OUTLIER) cc_final: 0.0985 (m110) REVERT: B 189 LEU cc_start: 0.7225 (tt) cc_final: 0.6728 (mp) REVERT: B 613 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8714 (mp10) REVERT: B 994 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8271 (t70) REVERT: C 740 MET cc_start: 0.7853 (ttm) cc_final: 0.7240 (ttm) REVERT: D 121 ASN cc_start: 0.8184 (m-40) cc_final: 0.7774 (t0) REVERT: D 327 VAL cc_start: 0.9531 (OUTLIER) cc_final: 0.9186 (p) outliers start: 122 outliers final: 43 residues processed: 269 average time/residue: 0.3843 time to fit residues: 177.3939 Evaluate side-chains 191 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 3.449 ------------------------------------------------------------------------------- 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 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE 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: 30.0000 chunk 21 optimal weight: 4.9990 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: 10.0000 chunk 107 optimal weight: 5.9990 chunk 292 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 314 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.112925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.080168 restraints weight = 107736.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.081849 restraints weight = 64424.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.082853 restraints weight = 46989.124| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 31628 Z= 0.277 Angle : 0.810 18.728 43156 Z= 0.386 Chirality : 0.053 0.761 4983 Planarity : 0.005 0.058 5438 Dihedral : 10.194 113.519 5518 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.81 % Favored : 92.06 % Rotamer: Outliers : 5.30 % Allowed : 23.67 % Favored : 71.03 % 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: -1.18 (0.14), residues: 3753 helix: 0.92 (0.16), residues: 1080 sheet: -0.83 (0.21), residues: 643 loop : -1.78 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 104 HIS 0.008 0.002 HIS A 377 PHE 0.033 0.002 PHE D1075 TYR 0.019 0.002 TYR D1067 ARG 0.011 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.01013 ( 52) link_NAG-ASN : angle 4.62672 ( 156) link_BETA1-4 : bond 0.00397 ( 17) link_BETA1-4 : angle 3.28091 ( 51) hydrogen bonds : bond 0.04323 ( 1175) hydrogen bonds : angle 5.79591 ( 3330) SS BOND : bond 0.00559 ( 38) SS BOND : angle 1.61085 ( 76) covalent geometry : bond 0.00617 (31520) covalent geometry : angle 0.75154 (42873) Misc. bond : bond 0.00101 ( 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 329 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 154 time to evaluate : 3.069 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: 0.5175 (OUTLIER) cc_final: 0.4712 (mmt180) REVERT: A 111 GLU cc_start: 0.5620 (tp30) cc_final: 0.5418 (mp0) REVERT: A 317 ILE cc_start: 0.2740 (OUTLIER) cc_final: 0.2456 (mt) REVERT: A 321 TYR cc_start: 0.3048 (OUTLIER) cc_final: 0.2723 (m-80) REVERT: A 365 MET cc_start: 0.3311 (mmm) cc_final: 0.0778 (tpt) REVERT: B 164 ASN cc_start: 0.1894 (OUTLIER) cc_final: 0.0278 (m110) REVERT: B 588 THR cc_start: 0.9376 (OUTLIER) cc_final: 0.8857 (p) REVERT: B 994 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8215 (t70) REVERT: C 195 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8359 (ptpp) REVERT: C 869 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8947 (ptm) REVERT: D 327 VAL cc_start: 0.9450 (OUTLIER) cc_final: 0.9064 (p) REVERT: D 529 LYS cc_start: 0.8305 (mmtm) cc_final: 0.8036 (mmtm) REVERT: D 740 MET cc_start: 0.8573 (tpp) cc_final: 0.8368 (tpp) outliers start: 175 outliers final: 92 residues processed: 313 average time/residue: 0.3928 time to fit residues: 208.0099 Evaluate side-chains 233 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 132 time to evaluate : 3.177 ------------------------------------------------------------------------------- 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 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 528 LYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 615 VAL 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 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 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: 0.9980 chunk 159 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 346 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 259 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 94 optimal weight: 0.0670 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 239 GLN C 487 ASN C 519 HIS C 804 GLN C1036 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.100978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.072011 restraints weight = 127215.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.073916 restraints weight = 62182.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.075128 restraints weight = 39225.821| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31628 Z= 0.125 Angle : 0.694 19.228 43156 Z= 0.329 Chirality : 0.051 0.696 4983 Planarity : 0.004 0.057 5438 Dihedral : 8.669 108.546 5513 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.74 % Favored : 93.13 % Rotamer: Outliers : 3.88 % Allowed : 24.94 % Favored : 71.18 % 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: -1.04 (0.14), residues: 3753 helix: 1.13 (0.16), residues: 1086 sheet: -0.96 (0.20), residues: 671 loop : -1.68 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 104 HIS 0.006 0.001 HIS A 400 PHE 0.017 0.001 PHE C 592 TYR 0.016 0.001 TYR D 837 ARG 0.007 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00868 ( 52) link_NAG-ASN : angle 4.39784 ( 156) link_BETA1-4 : bond 0.00478 ( 17) link_BETA1-4 : angle 2.84079 ( 51) hydrogen bonds : bond 0.03586 ( 1175) hydrogen bonds : angle 5.42625 ( 3330) SS BOND : bond 0.00343 ( 38) SS BOND : angle 1.49763 ( 76) covalent geometry : bond 0.00276 (31520) covalent geometry : angle 0.63336 (42873) Misc. bond : bond 0.00071 ( 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 288 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 160 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.5426 (OUTLIER) cc_final: 0.4898 (mmt180) REVERT: A 111 GLU cc_start: 0.5651 (tp30) cc_final: 0.5362 (mp0) REVERT: A 296 MET cc_start: -0.2073 (ptt) cc_final: -0.2782 (ptt) REVERT: A 321 TYR cc_start: 0.2807 (OUTLIER) cc_final: 0.2390 (m-80) REVERT: A 365 MET cc_start: 0.2888 (mmm) cc_final: 0.0614 (tpt) REVERT: B 80 ASP cc_start: 0.3253 (OUTLIER) cc_final: 0.2960 (t0) REVERT: B 104 TRP cc_start: 0.7584 (m-10) cc_final: 0.7266 (m-10) REVERT: B 164 ASN cc_start: 0.1954 (OUTLIER) cc_final: 0.0623 (m110) REVERT: B 265 TYR cc_start: 0.8134 (t80) cc_final: 0.7921 (t80) REVERT: B 588 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.8699 (p) REVERT: B 994 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8321 (t70) REVERT: C 740 MET cc_start: 0.8212 (ttm) cc_final: 0.7653 (ttm) REVERT: C 853 GLN cc_start: 0.7550 (pt0) cc_final: 0.7044 (pp30) REVERT: D 121 ASN cc_start: 0.8112 (m-40) cc_final: 0.7711 (t0) REVERT: D 327 VAL cc_start: 0.9483 (OUTLIER) cc_final: 0.9144 (p) REVERT: D 584 ILE cc_start: 0.7200 (mt) cc_final: 0.6945 (mt) outliers start: 128 outliers final: 57 residues processed: 275 average time/residue: 0.3870 time to fit residues: 181.0084 Evaluate side-chains 213 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 149 time to evaluate : 3.367 ------------------------------------------------------------------------------- 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 108 LEU Chi-restraints excluded: chain A residue 120 LEU 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 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 353 TRP 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 636 TYR Chi-restraints excluded: chain B residue 816 SER 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 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 487 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 858 LEU 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 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 229 LEU 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 401 VAL Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 534 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 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: 0.8980 chunk 63 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 313 optimal weight: 0.6980 chunk 306 optimal weight: 0.0070 chunk 192 optimal weight: 6.9990 chunk 357 optimal weight: 6.9990 chunk 182 optimal weight: 8.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- 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 321 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 487 ASN C 955 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.101004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.072311 restraints weight = 126776.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.074161 restraints weight = 62950.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.075356 restraints weight = 40157.781| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31628 Z= 0.119 Angle : 0.672 18.877 43156 Z= 0.319 Chirality : 0.050 0.677 4983 Planarity : 0.004 0.057 5438 Dihedral : 8.135 105.132 5513 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.09 % Favored : 92.75 % Rotamer: Outliers : 3.91 % Allowed : 24.85 % Favored : 71.24 % 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: -0.89 (0.14), residues: 3753 helix: 1.25 (0.16), residues: 1084 sheet: -0.82 (0.21), residues: 643 loop : -1.60 (0.14), residues: 2026 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 0.034 0.001 PHE D 497 TYR 0.026 0.001 TYR B 170 ARG 0.007 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00826 ( 52) link_NAG-ASN : angle 4.24401 ( 156) link_BETA1-4 : bond 0.00412 ( 17) link_BETA1-4 : angle 2.51893 ( 51) hydrogen bonds : bond 0.03466 ( 1175) hydrogen bonds : angle 5.30157 ( 3330) SS BOND : bond 0.00364 ( 38) SS BOND : angle 1.41761 ( 76) covalent geometry : bond 0.00267 (31520) covalent geometry : angle 0.61455 (42873) Misc. bond : bond 0.00049 ( 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 287 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 158 time to evaluate : 3.380 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 66 ARG cc_start: 0.5521 (OUTLIER) cc_final: 0.5030 (mmt180) REVERT: A 111 GLU cc_start: 0.5518 (tp30) cc_final: 0.5200 (mp0) REVERT: A 248 MET cc_start: 0.3285 (mtt) cc_final: 0.1632 (ptt) REVERT: A 296 MET cc_start: -0.2065 (ptt) cc_final: -0.2718 (ptt) REVERT: A 321 TYR cc_start: 0.2770 (OUTLIER) cc_final: 0.2474 (m-80) REVERT: A 365 MET cc_start: 0.2784 (mmm) cc_final: 0.0585 (tpt) REVERT: B 164 ASN cc_start: 0.1906 (OUTLIER) cc_final: 0.0597 (m-40) REVERT: B 189 LEU cc_start: 0.8133 (tt) cc_final: 0.7489 (pp) REVERT: B 265 TYR cc_start: 0.8034 (t80) cc_final: 0.7810 (t80) REVERT: B 588 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.8732 (p) REVERT: B 994 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8296 (t70) REVERT: C 127 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: C 740 MET cc_start: 0.8140 (ttm) cc_final: 0.7826 (ttm) REVERT: C 853 GLN cc_start: 0.7590 (pt0) cc_final: 0.7006 (pp30) REVERT: C 1050 MET cc_start: 0.7865 (mtt) cc_final: 0.7398 (mtp) REVERT: D 26 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7953 (pp30) REVERT: D 121 ASN cc_start: 0.8197 (m-40) cc_final: 0.7776 (t0) REVERT: D 327 VAL cc_start: 0.9467 (OUTLIER) cc_final: 0.9128 (p) REVERT: D 584 ILE cc_start: 0.7353 (mt) cc_final: 0.7017 (mt) REVERT: D 805 ILE cc_start: 0.9500 (pt) cc_final: 0.9204 (mm) outliers start: 129 outliers final: 71 residues processed: 273 average time/residue: 0.3886 time to fit residues: 181.4961 Evaluate side-chains 227 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 148 time to evaluate : 3.846 ------------------------------------------------------------------------------- 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 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 27 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 ASN 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 636 TYR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 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 C residue 127 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 430 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 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1001 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 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 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 401 VAL Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 534 VAL 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 931 ILE 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: 3.9990 chunk 350 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 370 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C1036 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN ** D 188 ASN ** 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 = 0.4016 r_free = 0.4016 target = 0.112898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.081479 restraints weight = 106788.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.083757 restraints weight = 65349.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.083154 restraints weight = 51268.062| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31628 Z= 0.222 Angle : 0.721 18.347 43156 Z= 0.346 Chirality : 0.051 0.712 4983 Planarity : 0.005 0.058 5438 Dihedral : 7.975 100.845 5513 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.49 % Favored : 92.35 % Rotamer: Outliers : 4.21 % Allowed : 24.88 % Favored : 70.91 % 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: -0.96 (0.14), residues: 3753 helix: 1.16 (0.16), residues: 1078 sheet: -0.78 (0.21), residues: 620 loop : -1.63 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 633 HIS 0.035 0.001 HIS A 344 PHE 0.018 0.002 PHE D 497 TYR 0.020 0.001 TYR D 495 ARG 0.004 0.000 ARG D 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00801 ( 52) link_NAG-ASN : angle 4.32267 ( 156) link_BETA1-4 : bond 0.00352 ( 17) link_BETA1-4 : angle 2.35645 ( 51) hydrogen bonds : bond 0.03729 ( 1175) hydrogen bonds : angle 5.41343 ( 3330) SS BOND : bond 0.00563 ( 38) SS BOND : angle 1.79322 ( 76) covalent geometry : bond 0.00494 (31520) covalent geometry : angle 0.66575 (42873) Misc. bond : bond 0.00083 ( 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 289 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 150 time to evaluate : 3.128 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 66 ARG cc_start: 0.5181 (OUTLIER) cc_final: 0.4654 (mmt180) REVERT: A 111 GLU cc_start: 0.5544 (tp30) cc_final: 0.5252 (mp0) REVERT: A 248 MET cc_start: 0.3034 (mtt) cc_final: 0.1208 (ptt) REVERT: A 296 MET cc_start: -0.1928 (ptt) cc_final: -0.2617 (ptt) REVERT: A 317 ILE cc_start: 0.2764 (OUTLIER) cc_final: 0.2480 (mt) REVERT: A 323 THR cc_start: -0.0093 (OUTLIER) cc_final: -0.0419 (m) REVERT: A 365 MET cc_start: 0.2763 (mmm) cc_final: 0.0687 (tpt) REVERT: B 80 ASP cc_start: 0.2792 (OUTLIER) cc_final: 0.2465 (t0) REVERT: B 92 PHE cc_start: 0.7411 (t80) cc_final: 0.6937 (t80) REVERT: B 115 GLN cc_start: 0.4827 (OUTLIER) cc_final: 0.4570 (tp40) REVERT: B 164 ASN cc_start: 0.1922 (OUTLIER) cc_final: 0.0337 (m110) REVERT: B 265 TYR cc_start: 0.8158 (t80) cc_final: 0.7887 (t80) REVERT: B 588 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.9027 (p) REVERT: B 994 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8297 (t70) REVERT: C 853 GLN cc_start: 0.7908 (pt0) cc_final: 0.7293 (pp30) REVERT: D 121 ASN cc_start: 0.8158 (m-40) cc_final: 0.7795 (t0) REVERT: D 327 VAL cc_start: 0.9400 (OUTLIER) cc_final: 0.9026 (p) REVERT: D 584 ILE cc_start: 0.7845 (mt) cc_final: 0.7405 (mt) REVERT: D 731 MET cc_start: 0.8632 (ptp) cc_final: 0.8403 (ptt) REVERT: D 740 MET cc_start: 0.8539 (tpp) cc_final: 0.8325 (tpp) outliers start: 139 outliers final: 95 residues processed: 277 average time/residue: 0.3962 time to fit residues: 190.3396 Evaluate side-chains 249 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 145 time to evaluate : 3.070 ------------------------------------------------------------------------------- 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 317 ILE 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 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 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 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 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 214 ARG 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 367 VAL 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 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 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 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 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 1108 ASN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 61 ASN 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 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 585 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 770 ILE 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 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: 7.9990 chunk 5 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 309 optimal weight: 7.9990 chunk 317 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 343 optimal weight: 0.4980 chunk 230 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 285 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.098422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.070161 restraints weight = 129402.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.071968 restraints weight = 62666.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.073146 restraints weight = 39113.194| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2344 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= 0.137 Angle : 0.684 18.461 43156 Z= 0.326 Chirality : 0.050 0.689 4983 Planarity : 0.004 0.059 5438 Dihedral : 7.757 99.379 5513 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.22 % Favored : 92.62 % Rotamer: Outliers : 3.82 % Allowed : 25.21 % Favored : 70.97 % 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: -0.96 (0.14), residues: 3753 helix: 1.20 (0.16), residues: 1084 sheet: -0.90 (0.20), residues: 649 loop : -1.62 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 633 HIS 0.006 0.001 HIS A 377 PHE 0.034 0.001 PHE B 135 TYR 0.015 0.001 TYR D 495 ARG 0.005 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00790 ( 52) link_NAG-ASN : angle 4.24494 ( 156) link_BETA1-4 : bond 0.00416 ( 17) link_BETA1-4 : angle 2.12960 ( 51) hydrogen bonds : bond 0.03533 ( 1175) hydrogen bonds : angle 5.29328 ( 3330) SS BOND : bond 0.00321 ( 38) SS BOND : angle 1.86039 ( 76) covalent geometry : bond 0.00312 (31520) covalent geometry : angle 0.62811 (42873) Misc. bond : bond 0.00072 ( 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 283 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 157 time to evaluate : 3.698 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 66 ARG cc_start: 0.5248 (OUTLIER) cc_final: 0.4879 (mtm-85) REVERT: A 248 MET cc_start: 0.3151 (mtt) cc_final: 0.1346 (ptt) REVERT: A 296 MET cc_start: -0.2116 (ptt) cc_final: -0.2792 (ptt) REVERT: A 323 THR cc_start: -0.0418 (OUTLIER) cc_final: -0.0821 (m) REVERT: A 365 MET cc_start: 0.2548 (mmm) cc_final: -0.0110 (tpp) REVERT: B 80 ASP cc_start: 0.3338 (OUTLIER) cc_final: 0.3032 (t0) REVERT: B 92 PHE cc_start: 0.7536 (t80) cc_final: 0.7166 (t80) REVERT: B 115 GLN cc_start: 0.4775 (OUTLIER) cc_final: 0.4537 (tp-100) REVERT: B 164 ASN cc_start: 0.1840 (OUTLIER) cc_final: 0.0264 (m110) REVERT: B 189 LEU cc_start: 0.8173 (tt) cc_final: 0.7876 (pp) REVERT: B 265 TYR cc_start: 0.8097 (t80) cc_final: 0.7879 (t80) REVERT: B 588 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.8845 (p) REVERT: B 740 MET cc_start: 0.8419 (ttp) cc_final: 0.8110 (ttp) REVERT: B 994 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8352 (t70) REVERT: C 853 GLN cc_start: 0.7808 (pt0) cc_final: 0.7213 (pp30) REVERT: D 26 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7890 (pp30) REVERT: D 119 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8019 (mp) REVERT: D 121 ASN cc_start: 0.8304 (m-40) cc_final: 0.7864 (t0) REVERT: D 246 ARG cc_start: 0.3204 (OUTLIER) cc_final: 0.1260 (mmt-90) REVERT: D 327 VAL cc_start: 0.9453 (OUTLIER) cc_final: 0.9103 (p) REVERT: D 584 ILE cc_start: 0.7744 (mt) cc_final: 0.7285 (mt) REVERT: D 740 MET cc_start: 0.8505 (tpp) cc_final: 0.8253 (tpp) REVERT: D 805 ILE cc_start: 0.9536 (pt) cc_final: 0.9221 (mm) outliers start: 126 outliers final: 89 residues processed: 272 average time/residue: 0.3923 time to fit residues: 182.1501 Evaluate side-chains 250 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 150 time to evaluate : 3.236 ------------------------------------------------------------------------------- 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 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 80 ASP 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 193 VAL 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 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 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 214 ARG 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 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 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 869 MET 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 1101 HIS 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 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 515 PHE 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 770 ILE 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 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: 0.8980 chunk 205 optimal weight: 0.0570 chunk 44 optimal weight: 9.9990 chunk 355 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 252 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 307 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1036 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.100686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.072886 restraints weight = 130478.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.075382 restraints weight = 66355.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.075484 restraints weight = 39022.032| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31628 Z= 0.121 Angle : 0.679 18.241 43156 Z= 0.321 Chirality : 0.049 0.675 4983 Planarity : 0.005 0.082 5438 Dihedral : 7.540 97.185 5513 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.87 % Favored : 92.97 % Rotamer: Outliers : 3.48 % Allowed : 25.67 % Favored : 70.85 % 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: -0.89 (0.14), residues: 3753 helix: 1.26 (0.16), residues: 1088 sheet: -0.88 (0.20), residues: 641 loop : -1.58 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 633 HIS 0.006 0.001 HIS A 377 PHE 0.043 0.001 PHE D 592 TYR 0.026 0.001 TYR B 170 ARG 0.008 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00797 ( 52) link_NAG-ASN : angle 4.36239 ( 156) link_BETA1-4 : bond 0.00433 ( 17) link_BETA1-4 : angle 2.03644 ( 51) hydrogen bonds : bond 0.03413 ( 1175) hydrogen bonds : angle 5.20388 ( 3330) SS BOND : bond 0.00302 ( 38) SS BOND : angle 1.58866 ( 76) covalent geometry : bond 0.00272 (31520) covalent geometry : angle 0.62051 (42873) Misc. bond : bond 0.00053 ( 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 280 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 165 time to evaluate : 3.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.3252 (mtt) cc_final: 0.1456 (ptt) REVERT: A 296 MET cc_start: -0.1994 (ptt) cc_final: -0.2643 (ptt) REVERT: A 323 THR cc_start: -0.0707 (OUTLIER) cc_final: -0.1113 (m) REVERT: A 365 MET cc_start: 0.2470 (mmm) cc_final: 0.0525 (tpt) REVERT: B 92 PHE cc_start: 0.7547 (t80) cc_final: 0.7286 (t80) REVERT: B 164 ASN cc_start: 0.2428 (OUTLIER) cc_final: 0.1235 (m-40) REVERT: B 170 TYR cc_start: 0.7452 (t80) cc_final: 0.7014 (m-10) REVERT: B 189 LEU cc_start: 0.8241 (tt) cc_final: 0.7508 (pp) REVERT: B 265 TYR cc_start: 0.8012 (t80) cc_final: 0.7799 (t80) REVERT: B 588 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.8853 (p) REVERT: B 878 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9068 (mt) REVERT: B 994 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8312 (t70) REVERT: C 195 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8297 (ptpp) REVERT: C 853 GLN cc_start: 0.7854 (pt0) cc_final: 0.7256 (pp30) REVERT: D 26 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7941 (pp30) REVERT: D 119 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.8026 (mp) REVERT: D 121 ASN cc_start: 0.8181 (m-40) cc_final: 0.7777 (t0) REVERT: D 246 ARG cc_start: 0.3161 (OUTLIER) cc_final: 0.1287 (mmt-90) REVERT: D 327 VAL cc_start: 0.9444 (OUTLIER) cc_final: 0.9100 (p) REVERT: D 584 ILE cc_start: 0.7681 (mt) cc_final: 0.7222 (mt) REVERT: D 740 MET cc_start: 0.8514 (tpp) cc_final: 0.8269 (tpp) REVERT: D 805 ILE cc_start: 0.9511 (pt) cc_final: 0.9207 (mm) outliers start: 115 outliers final: 86 residues processed: 267 average time/residue: 0.3906 time to fit residues: 177.7202 Evaluate side-chains 252 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 156 time to evaluate : 3.811 ------------------------------------------------------------------------------- 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 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 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 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 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 878 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 195 LYS Chi-restraints excluded: chain C residue 214 ARG 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 517 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 705 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 869 MET 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 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 246 ARG 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 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 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: 0.0670 chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 289 optimal weight: 5.9990 chunk 356 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 328 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 258 optimal weight: 0.6980 chunk 332 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 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 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 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 = 0.4024 r_free = 0.4024 target = 0.099768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.073015 restraints weight = 129948.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.075462 restraints weight = 67184.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.075950 restraints weight = 35890.020| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31628 Z= 0.142 Angle : 0.683 18.064 43156 Z= 0.323 Chirality : 0.049 0.673 4983 Planarity : 0.004 0.061 5438 Dihedral : 7.431 96.098 5513 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.09 % Favored : 92.75 % Rotamer: Outliers : 3.61 % Allowed : 25.58 % Favored : 70.82 % 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: -0.88 (0.14), residues: 3753 helix: 1.30 (0.16), residues: 1082 sheet: -0.88 (0.20), residues: 643 loop : -1.59 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 167 HIS 0.006 0.001 HIS A 377 PHE 0.029 0.001 PHE B 135 TYR 0.024 0.001 TYR B 170 ARG 0.007 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00770 ( 52) link_NAG-ASN : angle 4.29346 ( 156) link_BETA1-4 : bond 0.00395 ( 17) link_BETA1-4 : angle 2.01988 ( 51) hydrogen bonds : bond 0.03434 ( 1175) hydrogen bonds : angle 5.19305 ( 3330) SS BOND : bond 0.00306 ( 38) SS BOND : angle 1.54313 ( 76) covalent geometry : bond 0.00320 (31520) covalent geometry : angle 0.62751 (42873) Misc. bond : bond 0.00057 ( 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 273 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 154 time to evaluate : 3.430 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 248 MET cc_start: 0.2996 (mtt) cc_final: 0.1101 (ptt) REVERT: A 296 MET cc_start: -0.1884 (ptt) cc_final: -0.2512 (ptt) REVERT: A 323 THR cc_start: -0.0842 (OUTLIER) cc_final: -0.1274 (m) REVERT: A 365 MET cc_start: 0.2416 (mmm) cc_final: 0.0395 (tpt) REVERT: B 92 PHE cc_start: 0.7600 (t80) cc_final: 0.7302 (t80) REVERT: B 164 ASN cc_start: 0.1980 (OUTLIER) cc_final: 0.0605 (m-40) REVERT: B 170 TYR cc_start: 0.7374 (t80) cc_final: 0.7013 (m-10) REVERT: B 189 LEU cc_start: 0.8276 (tt) cc_final: 0.7900 (pp) REVERT: B 265 TYR cc_start: 0.8020 (t80) cc_final: 0.7799 (t80) REVERT: B 346 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.5715 (mmp80) REVERT: B 588 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.8860 (p) REVERT: B 994 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8275 (t70) REVERT: C 195 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8345 (ptpp) REVERT: C 853 GLN cc_start: 0.8008 (pt0) cc_final: 0.7383 (pp30) REVERT: D 26 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7870 (pp30) REVERT: D 119 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7957 (mp) REVERT: D 121 ASN cc_start: 0.8196 (m-40) cc_final: 0.7797 (t0) REVERT: D 246 ARG cc_start: 0.3214 (OUTLIER) cc_final: 0.1291 (mmt-90) REVERT: D 327 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9104 (p) REVERT: D 584 ILE cc_start: 0.7705 (mt) cc_final: 0.7233 (mt) REVERT: D 740 MET cc_start: 0.8518 (tpp) cc_final: 0.8273 (tpp) REVERT: D 805 ILE cc_start: 0.9517 (pt) cc_final: 0.9224 (mm) outliers start: 119 outliers final: 95 residues processed: 262 average time/residue: 0.3861 time to fit residues: 172.6049 Evaluate side-chains 255 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 150 time to evaluate : 3.591 ------------------------------------------------------------------------------- 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 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 400 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 91 TYR 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 193 VAL 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 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 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 214 ARG 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 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 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 1101 HIS 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 246 ARG 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 760 CYS 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 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: 9.9990 chunk 156 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 282 optimal weight: 20.0000 chunk 345 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 344 optimal weight: 2.9990 chunk 331 optimal weight: 8.9990 chunk 362 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.100137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.070325 restraints weight = 124365.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.072172 restraints weight = 62335.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.073359 restraints weight = 40042.609| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31628 Z= 0.182 Angle : 0.710 17.875 43156 Z= 0.338 Chirality : 0.050 0.701 4983 Planarity : 0.005 0.064 5438 Dihedral : 7.441 95.156 5513 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.62 % Favored : 92.22 % Rotamer: Outliers : 3.33 % Allowed : 25.94 % Favored : 70.73 % 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: -0.95 (0.14), residues: 3753 helix: 1.23 (0.16), residues: 1081 sheet: -0.94 (0.20), residues: 643 loop : -1.62 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 167 HIS 0.006 0.001 HIS A 400 PHE 0.029 0.001 PHE B 135 TYR 0.025 0.001 TYR B 170 ARG 0.009 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00764 ( 52) link_NAG-ASN : angle 4.32700 ( 156) link_BETA1-4 : bond 0.00363 ( 17) link_BETA1-4 : angle 2.00756 ( 51) hydrogen bonds : bond 0.03597 ( 1175) hydrogen bonds : angle 5.27614 ( 3330) SS BOND : bond 0.00361 ( 38) SS BOND : angle 1.64505 ( 76) covalent geometry : bond 0.00407 (31520) covalent geometry : angle 0.65577 (42873) Misc. bond : bond 0.00089 ( 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 269 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 159 time to evaluate : 3.340 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 159 ARG cc_start: 0.1924 (mtt180) cc_final: 0.1597 (tpm170) REVERT: A 248 MET cc_start: 0.3139 (mtt) cc_final: 0.1392 (ptt) REVERT: A 323 THR cc_start: -0.0672 (OUTLIER) cc_final: -0.1026 (m) REVERT: A 365 MET cc_start: 0.2670 (mmm) cc_final: 0.0921 (tpt) REVERT: B 92 PHE cc_start: 0.7668 (t80) cc_final: 0.7387 (t80) REVERT: B 164 ASN cc_start: 0.1837 (OUTLIER) cc_final: 0.0309 (m110) REVERT: B 170 TYR cc_start: 0.7283 (t80) cc_final: 0.6957 (m-10) REVERT: B 265 TYR cc_start: 0.8024 (t80) cc_final: 0.7768 (t80) REVERT: B 588 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.8955 (p) REVERT: C 195 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8400 (ptpp) REVERT: D 121 ASN cc_start: 0.8195 (m-40) cc_final: 0.7761 (t0) REVERT: D 246 ARG cc_start: 0.3544 (OUTLIER) cc_final: 0.1401 (mmt-90) REVERT: D 327 VAL cc_start: 0.9474 (OUTLIER) cc_final: 0.9127 (p) REVERT: D 584 ILE cc_start: 0.7875 (mt) cc_final: 0.7401 (mt) REVERT: D 731 MET cc_start: 0.8560 (ptp) cc_final: 0.8323 (ptt) REVERT: D 740 MET cc_start: 0.8524 (tpp) cc_final: 0.8305 (tpp) outliers start: 110 outliers final: 90 residues processed: 256 average time/residue: 0.3854 time to fit residues: 168.7946 Evaluate side-chains 245 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 149 time to evaluate : 3.066 ------------------------------------------------------------------------------- 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 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 400 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 91 TYR Chi-restraints excluded: chain B residue 108 THR 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 293 LEU Chi-restraints excluded: chain B residue 353 TRP 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 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 1001 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 308 VAL 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 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 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 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 1101 HIS 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 162 SER Chi-restraints excluded: chain D residue 246 ARG 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 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 760 CYS 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 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: 0.7980 chunk 277 optimal weight: 0.0770 chunk 21 optimal weight: 3.9990 chunk 165 optimal weight: 9.9990 chunk 257 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 255 optimal weight: 5.9990 chunk 130 optimal weight: 0.0470 chunk 153 optimal weight: 3.9990 overall best weight: 0.9838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.103224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.072967 restraints weight = 119270.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.074790 restraints weight = 61088.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.076015 restraints weight = 40189.972| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31628 Z= 0.124 Angle : 0.683 17.957 43156 Z= 0.324 Chirality : 0.049 0.678 4983 Planarity : 0.004 0.061 5438 Dihedral : 7.234 93.127 5513 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.17 % Favored : 92.67 % Rotamer: Outliers : 2.94 % Allowed : 26.39 % Favored : 70.67 % 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: -0.90 (0.14), residues: 3753 helix: 1.28 (0.16), residues: 1088 sheet: -0.92 (0.20), residues: 643 loop : -1.60 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 167 HIS 0.006 0.001 HIS A 377 PHE 0.032 0.001 PHE B 238 TYR 0.025 0.001 TYR B 170 ARG 0.006 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00763 ( 52) link_NAG-ASN : angle 4.24590 ( 156) link_BETA1-4 : bond 0.00441 ( 17) link_BETA1-4 : angle 1.90477 ( 51) hydrogen bonds : bond 0.03408 ( 1175) hydrogen bonds : angle 5.15043 ( 3330) SS BOND : bond 0.00273 ( 38) SS BOND : angle 1.47565 ( 76) covalent geometry : bond 0.00281 (31520) covalent geometry : angle 0.62863 (42873) Misc. bond : bond 0.00061 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10518.05 seconds wall clock time: 183 minutes 49.30 seconds (11029.30 seconds total)