Starting phenix.real_space_refine on Mon Aug 25 21:47:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xz8_38789/08_2025/8xz8_38789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xz8_38789/08_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_38789/08_2025/8xz8_38789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xz8_38789/08_2025/8xz8_38789.map" model { file = "/net/cci-nas-00/data/ceres_data/8xz8_38789/08_2025/8xz8_38789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xz8_38789/08_2025/8xz8_38789.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.057 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.96, per 1000 atoms: 0.26 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: 3.11 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.30 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: 5.82 Time building geometry restraints manager: 3.97 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 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: 4.140 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: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.890 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- 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 : 13.95 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.003 0.000 ARG C 995 TYR 0.031 0.001 TYR C 351 PHE 0.019 0.001 PHE C 592 TRP 0.028 0.002 TRP C 452 HIS 0.008 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00382 (31520) covalent geometry : angle 0.74662 (42873) SS BOND : bond 0.00248 ( 38) SS BOND : angle 1.74922 ( 76) hydrogen bonds : bond 0.14608 ( 1175) hydrogen bonds : angle 7.10401 ( 3330) Misc. bond : bond 0.00038 ( 1) link_BETA1-4 : bond 0.00503 ( 17) link_BETA1-4 : angle 2.21934 ( 51) link_NAG-ASN : bond 0.00935 ( 52) link_NAG-ASN : angle 4.27946 ( 156) *********************** 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 : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 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: 0.1717 time to fit residues: 55.7540 Evaluate side-chains 160 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 26 GLN 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 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.099613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.071775 restraints weight = 130652.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.074210 restraints weight = 69281.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.074439 restraints weight = 39772.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.074787 restraints weight = 27652.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.074925 restraints weight = 26277.677| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31628 Z= 0.181 Angle : 0.757 18.704 43156 Z= 0.355 Chirality : 0.052 0.719 4983 Planarity : 0.005 0.066 5438 Dihedral : 14.205 113.544 5523 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.19 % Favored : 92.67 % Rotamer: Outliers : 3.94 % Allowed : 23.91 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.14), residues: 3753 helix: 1.01 (0.16), residues: 1097 sheet: -0.89 (0.20), residues: 653 loop : -1.72 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1107 TYR 0.020 0.001 TYR B1067 PHE 0.013 0.001 PHE D 220 TRP 0.025 0.001 TRP B 104 HIS 0.005 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00401 (31520) covalent geometry : angle 0.70125 (42873) SS BOND : bond 0.00396 ( 38) SS BOND : angle 1.47451 ( 76) hydrogen bonds : bond 0.03935 ( 1175) hydrogen bonds : angle 5.76755 ( 3330) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.00514 ( 17) link_BETA1-4 : angle 3.58634 ( 51) link_NAG-ASN : bond 0.00842 ( 52) link_NAG-ASN : angle 4.27893 ( 156) *********************** 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 293 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 163 time to evaluate : 0.888 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: 0.5933 (tp30) cc_final: 0.5534 (mp0) REVERT: A 296 MET cc_start: -0.1313 (ptt) cc_final: -0.2659 (ptt) REVERT: A 365 MET cc_start: 0.3476 (mmm) cc_final: 0.0761 (tpt) REVERT: B 164 ASN cc_start: 0.2254 (OUTLIER) cc_final: 0.1189 (m110) REVERT: B 189 LEU cc_start: 0.7270 (tt) cc_final: 0.6734 (mp) REVERT: B 613 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8804 (mp10) REVERT: B 994 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8264 (t70) REVERT: C 278 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.9186 (ptmt) REVERT: D 121 ASN cc_start: 0.8148 (m-40) cc_final: 0.7782 (t0) REVERT: D 327 VAL cc_start: 0.9535 (OUTLIER) cc_final: 0.9177 (p) outliers start: 130 outliers final: 48 residues processed: 276 average time/residue: 0.1512 time to fit residues: 71.0882 Evaluate side-chains 193 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 140 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 400 HIS 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 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 353 TRP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 636 TYR 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 278 LYS Chi-restraints excluded: chain C residue 308 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 850 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR 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 915 VAL Chi-restraints excluded: chain D residue 931 ILE 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 335 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 136 optimal weight: 0.0980 chunk 236 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN B 26 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 125 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1106 GLN D1011 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.100530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.071676 restraints weight = 130722.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.073571 restraints weight = 61903.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.074798 restraints weight = 38052.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.075566 restraints weight = 27692.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.076020 restraints weight = 22634.930| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 31628 Z= 0.127 Angle : 0.709 19.059 43156 Z= 0.330 Chirality : 0.051 0.670 4983 Planarity : 0.004 0.057 5438 Dihedral : 10.862 110.411 5518 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.87 % Favored : 92.99 % Rotamer: Outliers : 3.42 % Allowed : 24.03 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.14), residues: 3753 helix: 1.08 (0.16), residues: 1106 sheet: -0.88 (0.20), residues: 661 loop : -1.69 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.017 0.001 TYR B 170 PHE 0.020 0.001 PHE B 592 TRP 0.021 0.001 TRP B 104 HIS 0.006 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00279 (31520) covalent geometry : angle 0.64817 (42873) SS BOND : bond 0.00304 ( 38) SS BOND : angle 1.51537 ( 76) hydrogen bonds : bond 0.03716 ( 1175) hydrogen bonds : angle 5.51112 ( 3330) Misc. bond : bond 0.00052 ( 1) link_BETA1-4 : bond 0.00474 ( 17) link_BETA1-4 : angle 3.25641 ( 51) link_NAG-ASN : bond 0.01151 ( 52) link_NAG-ASN : angle 4.35455 ( 156) *********************** 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 282 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 169 time to evaluate : 0.920 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 111 GLU cc_start: 0.5701 (tp30) cc_final: 0.5450 (mp0) REVERT: A 296 MET cc_start: -0.1839 (ptt) cc_final: -0.2687 (ptt) REVERT: A 317 ILE cc_start: 0.2549 (OUTLIER) cc_final: 0.2286 (mt) REVERT: A 321 TYR cc_start: 0.2713 (OUTLIER) cc_final: 0.2411 (m-80) REVERT: A 365 MET cc_start: 0.3322 (mmm) cc_final: 0.0794 (tpt) REVERT: B 164 ASN cc_start: 0.2212 (OUTLIER) cc_final: 0.1169 (m110) REVERT: B 189 LEU cc_start: 0.7284 (tt) cc_final: 0.6799 (mp) REVERT: B 588 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8636 (p) REVERT: B 994 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8154 (t70) REVERT: C 278 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9148 (ptmt) REVERT: D 121 ASN cc_start: 0.8153 (m-40) cc_final: 0.7748 (t0) REVERT: D 300 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8966 (ttmt) REVERT: D 327 VAL cc_start: 0.9534 (OUTLIER) cc_final: 0.9218 (p) REVERT: D 371 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.6242 (m-80) outliers start: 113 outliers final: 48 residues processed: 268 average time/residue: 0.1614 time to fit residues: 73.4086 Evaluate side-chains 205 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 148 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 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 317 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 26 GLN 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 294 ASP Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 858 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 274 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 300 LYS 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 534 VAL Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 1008 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1101 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 272 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 325 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 345 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** C 777 ASN ** 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 = 0.4042 r_free = 0.4042 target = 0.099852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.071161 restraints weight = 130227.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.072963 restraints weight = 63215.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.074146 restraints weight = 39592.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.074908 restraints weight = 29311.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.075308 restraints weight = 23984.547| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31628 Z= 0.145 Angle : 0.688 18.822 43156 Z= 0.325 Chirality : 0.050 0.673 4983 Planarity : 0.004 0.056 5438 Dihedral : 9.040 105.386 5516 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.90 % Favored : 92.97 % Rotamer: Outliers : 3.97 % Allowed : 23.70 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.14), residues: 3753 helix: 1.20 (0.16), residues: 1086 sheet: -0.87 (0.21), residues: 645 loop : -1.62 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1000 TYR 0.016 0.001 TYR D1067 PHE 0.020 0.001 PHE D 562 TRP 0.023 0.001 TRP B 104 HIS 0.007 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00325 (31520) covalent geometry : angle 0.62648 (42873) SS BOND : bond 0.00415 ( 38) SS BOND : angle 1.57245 ( 76) hydrogen bonds : bond 0.03572 ( 1175) hydrogen bonds : angle 5.39301 ( 3330) Misc. bond : bond 0.00043 ( 1) link_BETA1-4 : bond 0.00374 ( 17) link_BETA1-4 : angle 3.11973 ( 51) link_NAG-ASN : bond 0.00844 ( 52) link_NAG-ASN : angle 4.30993 ( 156) *********************** 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 289 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 158 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.5742 (tp30) cc_final: 0.5465 (mp0) REVERT: A 317 ILE cc_start: 0.2524 (OUTLIER) cc_final: 0.2296 (mt) REVERT: A 365 MET cc_start: 0.3338 (mmm) cc_final: 0.0808 (tpt) REVERT: A 494 GLU cc_start: -0.1180 (OUTLIER) cc_final: -0.2808 (pt0) REVERT: A 507 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.5731 (tm-30) REVERT: B 164 ASN cc_start: 0.2181 (OUTLIER) cc_final: 0.1095 (m110) REVERT: B 189 LEU cc_start: 0.7365 (tt) cc_final: 0.6856 (mp) REVERT: B 588 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.8649 (p) REVERT: B 900 MET cc_start: 0.8636 (mtp) cc_final: 0.8351 (mtt) REVERT: B 994 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8224 (t70) REVERT: B 1029 MET cc_start: 0.9220 (tpp) cc_final: 0.8996 (tpp) REVERT: C 239 GLN cc_start: 0.5898 (OUTLIER) cc_final: 0.5694 (mm110) REVERT: C 278 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9135 (ptmt) REVERT: C 853 GLN cc_start: 0.7157 (pt0) cc_final: 0.6670 (pp30) REVERT: D 26 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8042 (pp30) REVERT: D 121 ASN cc_start: 0.8179 (m-40) cc_final: 0.7806 (t0) REVERT: D 300 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.9025 (ttmt) REVERT: D 327 VAL cc_start: 0.9536 (OUTLIER) cc_final: 0.9198 (p) REVERT: D 371 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.6247 (m-80) REVERT: D 568 ASP cc_start: 0.7986 (p0) cc_final: 0.7724 (p0) REVERT: D 805 ILE cc_start: 0.9485 (pt) cc_final: 0.9204 (mm) outliers start: 131 outliers final: 72 residues processed: 276 average time/residue: 0.1512 time to fit residues: 70.7871 Evaluate side-chains 233 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 149 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 306 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain B residue 45 SER 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 164 ASN 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 588 THR 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 697 MET Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 239 GLN 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 343 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL 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 786 LYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 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 274 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 488 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 277 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 316 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 64 optimal weight: 0.2980 chunk 216 optimal weight: 8.9990 chunk 300 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 487 ASN C 519 HIS C 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.099400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.070891 restraints weight = 131116.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.072771 restraints weight = 62484.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.073961 restraints weight = 38616.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.074705 restraints weight = 28217.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.075217 restraints weight = 23090.329| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31628 Z= 0.155 Angle : 0.678 18.641 43156 Z= 0.323 Chirality : 0.050 0.669 4983 Planarity : 0.004 0.055 5438 Dihedral : 8.301 102.675 5516 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.75 % Rotamer: Outliers : 4.27 % Allowed : 23.91 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.14), residues: 3753 helix: 1.23 (0.16), residues: 1086 sheet: -0.86 (0.21), residues: 645 loop : -1.62 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 160 TYR 0.019 0.001 TYR B 265 PHE 0.016 0.001 PHE D 562 TRP 0.042 0.001 TRP B 104 HIS 0.006 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00350 (31520) covalent geometry : angle 0.61953 (42873) SS BOND : bond 0.00382 ( 38) SS BOND : angle 1.58847 ( 76) hydrogen bonds : bond 0.03531 ( 1175) hydrogen bonds : angle 5.33657 ( 3330) Misc. bond : bond 0.00058 ( 1) link_BETA1-4 : bond 0.00362 ( 17) link_BETA1-4 : angle 2.74644 ( 51) link_NAG-ASN : bond 0.00815 ( 52) link_NAG-ASN : angle 4.25093 ( 156) *********************** 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 296 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 155 time to evaluate : 1.073 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: 0.5504 (OUTLIER) cc_final: 0.5263 (mmt180) REVERT: A 111 GLU cc_start: 0.5618 (tp30) cc_final: 0.5338 (mp0) REVERT: A 248 MET cc_start: 0.3166 (mtt) cc_final: 0.1269 (ptt) REVERT: A 296 MET cc_start: -0.2168 (ptt) cc_final: -0.2846 (ptt) REVERT: A 317 ILE cc_start: 0.2686 (OUTLIER) cc_final: 0.2477 (mt) REVERT: A 321 TYR cc_start: 0.2497 (OUTLIER) cc_final: 0.2183 (m-80) REVERT: A 323 THR cc_start: -0.0312 (OUTLIER) cc_final: -0.0706 (m) REVERT: A 365 MET cc_start: 0.2770 (mmm) cc_final: 0.0541 (tpt) REVERT: A 494 GLU cc_start: -0.1097 (OUTLIER) cc_final: -0.2483 (tm-30) REVERT: B 164 ASN cc_start: 0.1726 (OUTLIER) cc_final: 0.0396 (m110) REVERT: B 588 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.8738 (p) REVERT: B 994 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8258 (t70) REVERT: B 1005 GLN cc_start: 0.8989 (tp40) cc_final: 0.8726 (tp-100) REVERT: C 278 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9158 (ptmt) REVERT: C 853 GLN cc_start: 0.7319 (pt0) cc_final: 0.6781 (pp30) REVERT: D 26 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8029 (pp30) REVERT: D 300 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9105 (ttmt) REVERT: D 327 VAL cc_start: 0.9519 (OUTLIER) cc_final: 0.9203 (p) REVERT: D 568 ASP cc_start: 0.7990 (p0) cc_final: 0.7703 (p0) REVERT: D 584 ILE cc_start: 0.7057 (mt) cc_final: 0.6822 (mt) REVERT: D 805 ILE cc_start: 0.9491 (pt) cc_final: 0.9224 (mm) outliers start: 141 outliers final: 82 residues processed: 283 average time/residue: 0.1599 time to fit residues: 76.8744 Evaluate side-chains 241 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 147 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 120 LEU Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 297 GLU 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 323 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 494 GLU 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 45 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 294 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 816 SER 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 996 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 278 LYS 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 517 LEU Chi-restraints excluded: chain C residue 524 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 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 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 274 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 382 VAL 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 539 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 373 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 174 optimal weight: 7.9990 chunk 310 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 344 HIS ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN D 992 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.099636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.071662 restraints weight = 130327.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.073567 restraints weight = 60817.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.074765 restraints weight = 36936.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.075562 restraints weight = 26623.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.075923 restraints weight = 21544.079| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31628 Z= 0.148 Angle : 0.675 18.394 43156 Z= 0.322 Chirality : 0.050 0.668 4983 Planarity : 0.004 0.057 5438 Dihedral : 7.851 98.328 5513 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.17 % Favored : 92.67 % Rotamer: Outliers : 4.12 % Allowed : 24.00 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.14), residues: 3753 helix: 1.25 (0.16), residues: 1087 sheet: -0.79 (0.21), residues: 637 loop : -1.60 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.015 0.001 TYR D1067 PHE 0.021 0.001 PHE B 92 TRP 0.043 0.001 TRP B 104 HIS 0.005 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00333 (31520) covalent geometry : angle 0.61872 (42873) SS BOND : bond 0.00392 ( 38) SS BOND : angle 1.67737 ( 76) hydrogen bonds : bond 0.03505 ( 1175) hydrogen bonds : angle 5.24946 ( 3330) Misc. bond : bond 0.00057 ( 1) link_BETA1-4 : bond 0.00380 ( 17) link_BETA1-4 : angle 2.33839 ( 51) link_NAG-ASN : bond 0.00796 ( 52) link_NAG-ASN : angle 4.21213 ( 156) *********************** 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 302 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 166 time to evaluate : 0.855 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: 0.5422 (OUTLIER) cc_final: 0.4929 (mmt180) REVERT: A 111 GLU cc_start: 0.5502 (tp30) cc_final: 0.5185 (mp0) REVERT: A 248 MET cc_start: 0.3049 (mtt) cc_final: 0.1201 (ptt) REVERT: A 296 MET cc_start: -0.2181 (ptt) cc_final: -0.2876 (ptt) REVERT: A 317 ILE cc_start: 0.2728 (OUTLIER) cc_final: 0.2528 (mt) REVERT: A 323 THR cc_start: -0.0669 (OUTLIER) cc_final: -0.1072 (m) REVERT: A 365 MET cc_start: 0.2641 (mmm) cc_final: 0.0457 (tpt) REVERT: A 494 GLU cc_start: -0.1299 (OUTLIER) cc_final: -0.1517 (tp30) REVERT: B 164 ASN cc_start: 0.1544 (OUTLIER) cc_final: 0.0174 (m-40) REVERT: B 170 TYR cc_start: 0.7254 (t80) cc_final: 0.6876 (m-10) REVERT: B 588 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.8774 (p) REVERT: B 900 MET cc_start: 0.8743 (mtp) cc_final: 0.8451 (mtt) REVERT: B 994 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8243 (t70) REVERT: B 1005 GLN cc_start: 0.8976 (tp40) cc_final: 0.8755 (tp-100) REVERT: B 1029 MET cc_start: 0.9241 (tpp) cc_final: 0.8982 (tpp) REVERT: C 127 PHE cc_start: 0.8075 (t80) cc_final: 0.7633 (m-80) REVERT: C 853 GLN cc_start: 0.7422 (pt0) cc_final: 0.6886 (pp30) REVERT: D 26 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7949 (pp30) REVERT: D 121 ASN cc_start: 0.8094 (m-40) cc_final: 0.7785 (t0) REVERT: D 300 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9123 (ttmt) REVERT: D 327 VAL cc_start: 0.9483 (OUTLIER) cc_final: 0.9183 (p) REVERT: D 568 ASP cc_start: 0.7999 (p0) cc_final: 0.7657 (p0) REVERT: D 584 ILE cc_start: 0.7266 (mt) cc_final: 0.6981 (mt) outliers start: 136 outliers final: 91 residues processed: 287 average time/residue: 0.1512 time to fit residues: 72.9071 Evaluate side-chains 257 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 156 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 297 GLU 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 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 494 GLU 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 45 SER 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 164 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 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 916 LEU 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 1141 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 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 786 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 382 VAL 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 763 LEU Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 59 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 201 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 343 optimal weight: 0.0270 overall best weight: 3.1844 ------------------------------------------------------------------------------- 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** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** 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 = 0.3996 r_free = 0.3996 target = 0.097434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.070168 restraints weight = 130629.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.072452 restraints weight = 68802.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.072787 restraints weight = 37745.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.073131 restraints weight = 28254.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.073252 restraints weight = 26584.160| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31628 Z= 0.222 Angle : 0.722 18.037 43156 Z= 0.345 Chirality : 0.051 0.708 4983 Planarity : 0.005 0.059 5438 Dihedral : 7.856 96.552 5513 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.62 % Favored : 92.22 % Rotamer: Outliers : 4.12 % Allowed : 24.00 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.14), residues: 3753 helix: 1.18 (0.16), residues: 1086 sheet: -0.79 (0.21), residues: 620 loop : -1.63 (0.14), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1000 TYR 0.015 0.001 TYR B1067 PHE 0.025 0.002 PHE B 592 TRP 0.040 0.002 TRP B 104 HIS 0.032 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00497 (31520) covalent geometry : angle 0.66264 (42873) SS BOND : bond 0.00389 ( 38) SS BOND : angle 1.73256 ( 76) hydrogen bonds : bond 0.03656 ( 1175) hydrogen bonds : angle 5.33579 ( 3330) Misc. bond : bond 0.00115 ( 1) link_BETA1-4 : bond 0.00347 ( 17) link_BETA1-4 : angle 2.24103 ( 51) link_NAG-ASN : bond 0.00803 ( 52) link_NAG-ASN : angle 4.53855 ( 156) *********************** 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 290 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 154 time to evaluate : 0.851 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: 0.5214 (OUTLIER) cc_final: 0.4839 (mtm-85) REVERT: A 111 GLU cc_start: 0.5720 (tp30) cc_final: 0.5346 (mp0) REVERT: A 248 MET cc_start: 0.3103 (mtt) cc_final: 0.1178 (ptt) REVERT: A 323 THR cc_start: -0.0421 (OUTLIER) cc_final: -0.0848 (m) REVERT: A 365 MET cc_start: 0.2432 (mmm) cc_final: 0.0228 (tpt) REVERT: A 494 GLU cc_start: -0.2004 (OUTLIER) cc_final: -0.2355 (tp30) REVERT: B 164 ASN cc_start: 0.2302 (OUTLIER) cc_final: 0.0864 (m110) REVERT: B 170 TYR cc_start: 0.7340 (t80) cc_final: 0.6881 (m-10) REVERT: B 588 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.8864 (p) REVERT: B 900 MET cc_start: 0.8780 (mtp) cc_final: 0.8504 (mtt) REVERT: B 994 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8302 (t70) REVERT: C 127 PHE cc_start: 0.8194 (t80) cc_final: 0.7787 (m-80) REVERT: C 328 ARG cc_start: 0.4749 (OUTLIER) cc_final: 0.4467 (tmt170) REVERT: C 334 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.8054 (p0) REVERT: C 740 MET cc_start: 0.8866 (tpp) cc_final: 0.8397 (tpp) REVERT: C 853 GLN cc_start: 0.7716 (pt0) cc_final: 0.7127 (pp30) REVERT: D 26 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7898 (pp30) REVERT: D 121 ASN cc_start: 0.8158 (m-40) cc_final: 0.7767 (t0) REVERT: D 327 VAL cc_start: 0.9476 (OUTLIER) cc_final: 0.9134 (p) REVERT: D 529 LYS cc_start: 0.8033 (mmtm) cc_final: 0.7760 (mmtm) REVERT: D 568 ASP cc_start: 0.8059 (p0) cc_final: 0.7754 (p0) REVERT: D 584 ILE cc_start: 0.7633 (mt) cc_final: 0.7244 (mt) outliers start: 136 outliers final: 93 residues processed: 279 average time/residue: 0.1664 time to fit residues: 79.5384 Evaluate side-chains 253 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 150 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 297 GLU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 THR 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 494 GLU 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 45 SER 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 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 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 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 922 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 400 PHE 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 896 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 61 ASN 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 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 382 VAL 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 620 VAL 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 866 THR 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 358 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 319 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 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 = 0.3999 r_free = 0.3999 target = 0.098659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.071856 restraints weight = 130197.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.074375 restraints weight = 64578.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.074877 restraints weight = 32707.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.075255 restraints weight = 24313.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.075333 restraints weight = 24148.361| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31628 Z= 0.201 Angle : 0.713 18.084 43156 Z= 0.340 Chirality : 0.050 0.715 4983 Planarity : 0.004 0.059 5438 Dihedral : 7.740 95.140 5513 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.70 % Favored : 92.14 % Rotamer: Outliers : 4.09 % Allowed : 24.15 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.14), residues: 3753 helix: 1.13 (0.16), residues: 1086 sheet: -0.86 (0.21), residues: 630 loop : -1.67 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.022 0.001 TYR D 495 PHE 0.039 0.002 PHE D 497 TRP 0.048 0.002 TRP B 104 HIS 0.006 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00449 (31520) covalent geometry : angle 0.65653 (42873) SS BOND : bond 0.00355 ( 38) SS BOND : angle 1.66842 ( 76) hydrogen bonds : bond 0.03670 ( 1175) hydrogen bonds : angle 5.33808 ( 3330) Misc. bond : bond 0.00045 ( 1) link_BETA1-4 : bond 0.00345 ( 17) link_BETA1-4 : angle 2.03371 ( 51) link_NAG-ASN : bond 0.00778 ( 52) link_NAG-ASN : angle 4.41572 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 152 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.3194 (mtt) cc_final: 0.1151 (ptt) REVERT: A 323 THR cc_start: -0.0557 (OUTLIER) cc_final: -0.1007 (m) REVERT: A 365 MET cc_start: 0.2226 (mmm) cc_final: 0.0178 (tpt) REVERT: A 494 GLU cc_start: -0.2050 (OUTLIER) cc_final: -0.2407 (tp30) REVERT: B 92 PHE cc_start: 0.7597 (t80) cc_final: 0.7047 (t80) REVERT: B 164 ASN cc_start: 0.2062 (OUTLIER) cc_final: 0.0467 (m110) REVERT: B 170 TYR cc_start: 0.7376 (t80) cc_final: 0.6851 (m-10) REVERT: B 346 ARG cc_start: 0.5847 (OUTLIER) cc_final: 0.5539 (mmp80) REVERT: B 588 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.8862 (p) REVERT: B 900 MET cc_start: 0.8739 (mtp) cc_final: 0.8432 (mtt) REVERT: B 994 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8326 (t70) REVERT: B 1005 GLN cc_start: 0.8888 (tp40) cc_final: 0.8628 (tp40) REVERT: B 1029 MET cc_start: 0.9256 (tpp) cc_final: 0.9042 (tpp) REVERT: C 127 PHE cc_start: 0.8209 (t80) cc_final: 0.7828 (m-80) REVERT: C 328 ARG cc_start: 0.4793 (OUTLIER) cc_final: 0.4441 (tmt170) REVERT: C 853 GLN cc_start: 0.7849 (pt0) cc_final: 0.7238 (pp30) REVERT: D 121 ASN cc_start: 0.8270 (m-40) cc_final: 0.7867 (t0) REVERT: D 327 VAL cc_start: 0.9456 (OUTLIER) cc_final: 0.9093 (p) REVERT: D 495 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7734 (t80) REVERT: D 568 ASP cc_start: 0.8055 (p0) cc_final: 0.7766 (p0) REVERT: D 584 ILE cc_start: 0.7810 (mt) cc_final: 0.7387 (mt) REVERT: D 822 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9341 (mm) outliers start: 135 outliers final: 93 residues processed: 273 average time/residue: 0.1752 time to fit residues: 81.2394 Evaluate side-chains 246 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 143 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 494 GLU 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 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 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 513 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 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 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 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 400 PHE 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 615 VAL 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 896 ILE 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 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 229 LEU Chi-restraints excluded: chain D residue 238 PHE 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 390 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 760 CYS 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 904 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 273 optimal weight: 5.9990 chunk 181 optimal weight: 0.3980 chunk 327 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 325 optimal weight: 2.9990 chunk 348 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 51 ASN A 276 ASN A 344 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.098567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.071807 restraints weight = 129508.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.073997 restraints weight = 67757.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.074484 restraints weight = 37420.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.074900 restraints weight = 26743.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.075074 restraints weight = 24462.722| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31628 Z= 0.135 Angle : 0.688 18.055 43156 Z= 0.326 Chirality : 0.050 0.696 4983 Planarity : 0.004 0.060 5438 Dihedral : 7.518 93.442 5513 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.17 % Favored : 92.67 % Rotamer: Outliers : 3.18 % Allowed : 25.06 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.14), residues: 3753 helix: 1.22 (0.16), residues: 1086 sheet: -0.90 (0.20), residues: 644 loop : -1.61 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 454 TYR 0.021 0.001 TYR B 495 PHE 0.038 0.001 PHE D 497 TRP 0.047 0.001 TRP B 104 HIS 0.017 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00305 (31520) covalent geometry : angle 0.63289 (42873) SS BOND : bond 0.00298 ( 38) SS BOND : angle 1.41295 ( 76) hydrogen bonds : bond 0.03506 ( 1175) hydrogen bonds : angle 5.20322 ( 3330) Misc. bond : bond 0.00062 ( 1) link_BETA1-4 : bond 0.00404 ( 17) link_BETA1-4 : angle 1.95601 ( 51) link_NAG-ASN : bond 0.00774 ( 52) link_NAG-ASN : angle 4.29826 ( 156) *********************** 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 268 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 163 time to evaluate : 1.121 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 248 MET cc_start: 0.3161 (mtt) cc_final: 0.1235 (ptt) REVERT: A 294 GLU cc_start: 0.6665 (pp20) cc_final: 0.6438 (pp20) REVERT: A 323 THR cc_start: -0.0610 (OUTLIER) cc_final: -0.1062 (m) REVERT: A 365 MET cc_start: 0.2415 (mmm) cc_final: 0.0392 (tpt) REVERT: A 494 GLU cc_start: -0.2007 (OUTLIER) cc_final: -0.2337 (tp30) REVERT: B 92 PHE cc_start: 0.7660 (t80) cc_final: 0.7237 (t80) REVERT: B 164 ASN cc_start: 0.2243 (OUTLIER) cc_final: 0.0791 (m-40) REVERT: B 170 TYR cc_start: 0.7334 (t80) cc_final: 0.6865 (m-10) REVERT: B 346 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5729 (tpp-160) REVERT: B 588 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.8859 (p) REVERT: B 900 MET cc_start: 0.8727 (mtp) cc_final: 0.8426 (mtt) REVERT: B 994 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8281 (t70) REVERT: B 1029 MET cc_start: 0.9216 (tpp) cc_final: 0.8982 (tpp) REVERT: C 127 PHE cc_start: 0.8199 (t80) cc_final: 0.7826 (m-80) REVERT: C 328 ARG cc_start: 0.4688 (OUTLIER) cc_final: 0.4114 (tmt170) REVERT: C 740 MET cc_start: 0.8795 (tpp) cc_final: 0.8246 (tpp) REVERT: C 853 GLN cc_start: 0.7857 (pt0) cc_final: 0.7287 (pp30) REVERT: C 858 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7888 (mm) REVERT: D 121 ASN cc_start: 0.8257 (m-40) cc_final: 0.7852 (t0) REVERT: D 327 VAL cc_start: 0.9449 (OUTLIER) cc_final: 0.9102 (p) REVERT: D 568 ASP cc_start: 0.7959 (p0) cc_final: 0.7693 (p0) REVERT: D 584 ILE cc_start: 0.7781 (mt) cc_final: 0.7342 (mt) REVERT: D 740 MET cc_start: 0.8472 (tpp) cc_final: 0.8124 (tpp) REVERT: D 822 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9286 (mm) outliers start: 105 outliers final: 77 residues processed: 257 average time/residue: 0.1839 time to fit residues: 80.4528 Evaluate side-chains 237 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 150 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 494 GLU 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 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 513 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 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 308 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 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 896 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 162 SER 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 394 ASN 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 699 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 770 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 144 optimal weight: 6.9990 chunk 343 optimal weight: 0.5980 chunk 216 optimal weight: 0.9990 chunk 324 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 45 optimal weight: 0.0020 chunk 293 optimal weight: 0.0870 chunk 121 optimal weight: 0.4980 chunk 295 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.4368 ------------------------------------------------------------------------------- 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 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.114951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.084101 restraints weight = 104910.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.086369 restraints weight = 63149.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.085929 restraints weight = 52617.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.086524 restraints weight = 39553.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.086618 restraints weight = 36108.241| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31628 Z= 0.117 Angle : 0.686 18.033 43156 Z= 0.326 Chirality : 0.049 0.681 4983 Planarity : 0.004 0.063 5438 Dihedral : 7.352 92.039 5513 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.03 % Favored : 92.81 % Rotamer: Outliers : 2.73 % Allowed : 25.70 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.14), residues: 3753 helix: 1.25 (0.16), residues: 1088 sheet: -0.84 (0.21), residues: 632 loop : -1.59 (0.14), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1000 TYR 0.018 0.001 TYR D 495 PHE 0.035 0.001 PHE A 427 TRP 0.047 0.001 TRP B 104 HIS 0.018 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00260 (31520) covalent geometry : angle 0.63382 (42873) SS BOND : bond 0.00250 ( 38) SS BOND : angle 1.29193 ( 76) hydrogen bonds : bond 0.03408 ( 1175) hydrogen bonds : angle 5.13649 ( 3330) Misc. bond : bond 0.00066 ( 1) link_BETA1-4 : bond 0.00462 ( 17) link_BETA1-4 : angle 1.92685 ( 51) link_NAG-ASN : bond 0.00777 ( 52) link_NAG-ASN : angle 4.21803 ( 156) ********************** 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 252 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 162 time to evaluate : 1.201 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 159 ARG cc_start: 0.2328 (mtt180) cc_final: 0.1751 (tpp-160) REVERT: A 248 MET cc_start: 0.3321 (mtt) cc_final: 0.1512 (ptt) REVERT: A 296 MET cc_start: -0.2148 (ptt) cc_final: -0.2725 (ptt) REVERT: A 323 THR cc_start: -0.0508 (OUTLIER) cc_final: -0.0868 (m) REVERT: A 365 MET cc_start: 0.2469 (mmm) cc_final: 0.0442 (tpt) REVERT: A 494 GLU cc_start: -0.2039 (OUTLIER) cc_final: -0.2392 (tp30) REVERT: B 92 PHE cc_start: 0.7613 (t80) cc_final: 0.7197 (t80) REVERT: B 164 ASN cc_start: 0.2320 (OUTLIER) cc_final: 0.0893 (m-40) REVERT: B 346 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.6108 (mmp80) REVERT: B 588 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.8902 (p) REVERT: B 867 ASP cc_start: 0.8117 (m-30) cc_final: 0.7833 (m-30) REVERT: B 900 MET cc_start: 0.8815 (mtp) cc_final: 0.8548 (mtt) REVERT: B 994 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8231 (t70) REVERT: B 1029 MET cc_start: 0.9202 (tpp) cc_final: 0.8953 (tpp) REVERT: C 127 PHE cc_start: 0.8378 (t80) cc_final: 0.8023 (m-80) REVERT: C 853 GLN cc_start: 0.7945 (pt0) cc_final: 0.7390 (pp30) REVERT: C 858 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7859 (mm) REVERT: D 26 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8120 (pp30) REVERT: D 121 ASN cc_start: 0.8217 (m-40) cc_final: 0.7840 (t0) REVERT: D 327 VAL cc_start: 0.9369 (OUTLIER) cc_final: 0.8987 (p) REVERT: D 568 ASP cc_start: 0.8013 (p0) cc_final: 0.7693 (p0) REVERT: D 584 ILE cc_start: 0.7751 (mt) cc_final: 0.7290 (mt) REVERT: D 740 MET cc_start: 0.8457 (tpp) cc_final: 0.8253 (tpp) REVERT: D 805 ILE cc_start: 0.9518 (pt) cc_final: 0.9163 (mm) REVERT: D 822 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9268 (mm) outliers start: 90 outliers final: 70 residues processed: 241 average time/residue: 0.1873 time to fit residues: 76.5640 Evaluate side-chains 234 residues out of total 3309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 154 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 462 VAL Chi-restraints excluded: chain A residue 494 GLU 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 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 513 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 859 THR 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 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 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 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 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 159 VAL Chi-restraints excluded: chain D residue 162 SER 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 390 LEU 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 699 LEU 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 822 LEU Chi-restraints excluded: chain D residue 915 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 353 optimal weight: 0.6980 chunk 374 optimal weight: 0.3980 chunk 174 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 310 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** 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 = 0.4028 r_free = 0.4028 target = 0.100553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.071022 restraints weight = 125907.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.072888 restraints weight = 62487.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.074108 restraints weight = 39588.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.074869 restraints weight = 29478.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.075357 restraints weight = 24422.191| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31628 Z= 0.145 Angle : 0.692 17.741 43156 Z= 0.328 Chirality : 0.049 0.679 4983 Planarity : 0.004 0.065 5438 Dihedral : 7.290 90.563 5513 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.17 % Favored : 92.67 % Rotamer: Outliers : 2.85 % Allowed : 25.73 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.14), residues: 3753 helix: 1.29 (0.16), residues: 1082 sheet: -0.82 (0.21), residues: 635 loop : -1.60 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1000 TYR 0.024 0.001 TYR B 170 PHE 0.031 0.001 PHE D 497 TRP 0.040 0.002 TRP B 104 HIS 0.007 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00327 (31520) covalent geometry : angle 0.64041 (42873) SS BOND : bond 0.00270 ( 38) SS BOND : angle 1.31503 ( 76) hydrogen bonds : bond 0.03479 ( 1175) hydrogen bonds : angle 5.13099 ( 3330) Misc. bond : bond 0.00064 ( 1) link_BETA1-4 : bond 0.00395 ( 17) link_BETA1-4 : angle 1.95247 ( 51) link_NAG-ASN : bond 0.00755 ( 52) link_NAG-ASN : angle 4.21372 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5414.68 seconds wall clock time: 94 minutes 46.16 seconds (5686.16 seconds total)