Starting phenix.real_space_refine on Wed Nov 19 12:46:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cv0_7631/11_2025/6cv0_7631.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cv0_7631/11_2025/6cv0_7631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cv0_7631/11_2025/6cv0_7631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cv0_7631/11_2025/6cv0_7631.map" model { file = "/net/cci-nas-00/data/ceres_data/6cv0_7631/11_2025/6cv0_7631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cv0_7631/11_2025/6cv0_7631.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 15264 2.51 5 N 3960 2.21 5 O 4842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24192 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7658 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 37, 'TRANS': 955} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7658 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 37, 'TRANS': 955} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7658 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 37, 'TRANS': 955} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.35, per 1000 atoms: 0.26 Number of scatterers: 24192 At special positions: 0 Unit cell: (135.66, 144.84, 168.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 4842 8.00 N 3960 7.00 C 15264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS A 160 " distance=2.02 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 120 " distance=2.02 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS A 381 " - pdb=" SG CYS A 395 " distance=2.01 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS A 491 " distance=2.04 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 610 " - pdb=" SG CYS A 632 " distance=2.04 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 621 " distance=2.03 Simple disulfide: pdb=" SG CYS A 715 " - pdb=" SG CYS A 728 " distance=2.03 Simple disulfide: pdb=" SG CYS A 905 " - pdb=" SG CYS A 916 " distance=2.05 Simple disulfide: pdb=" SG CYS A 955 " - pdb=" SG CYS A1006 " distance=2.04 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 160 " distance=2.02 Simple disulfide: pdb=" SG CYS B 114 " - pdb=" SG CYS B 120 " distance=2.02 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 395 " distance=2.01 Simple disulfide: pdb=" SG CYS B 431 " - pdb=" SG CYS B 491 " distance=2.04 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 555 " distance=2.03 Simple disulfide: pdb=" SG CYS B 610 " - pdb=" SG CYS B 632 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 621 " distance=2.03 Simple disulfide: pdb=" SG CYS B 715 " - pdb=" SG CYS B 728 " distance=2.03 Simple disulfide: pdb=" SG CYS B 905 " - pdb=" SG CYS B 916 " distance=2.05 Simple disulfide: pdb=" SG CYS B 955 " - pdb=" SG CYS B1006 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 160 " distance=2.02 Simple disulfide: pdb=" SG CYS C 114 " - pdb=" SG CYS C 120 " distance=2.02 Simple disulfide: pdb=" SG CYS C 221 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 369 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 381 " - pdb=" SG CYS C 395 " distance=2.01 Simple disulfide: pdb=" SG CYS C 431 " - pdb=" SG CYS C 491 " distance=2.04 Simple disulfide: pdb=" SG CYS C 546 " - pdb=" SG CYS C 555 " distance=2.03 Simple disulfide: pdb=" SG CYS C 610 " - pdb=" SG CYS C 632 " distance=2.04 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 621 " distance=2.03 Simple disulfide: pdb=" SG CYS C 715 " - pdb=" SG CYS C 728 " distance=2.03 Simple disulfide: pdb=" SG CYS C 905 " - pdb=" SG CYS C 916 " distance=2.05 Simple disulfide: pdb=" SG CYS C 955 " - pdb=" SG CYS C1006 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " NAG H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " NAG I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " NAG O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " NAG P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " NAG V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " NAG W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1201 " - " ASN A 676 " " NAG A1202 " - " ASN A 714 " " NAG A1203 " - " ASN A 669 " " NAG A1204 " - " ASN A 591 " " NAG A1207 " - " ASN A 947 " " NAG A1212 " - " ASN A 178 " " NAG A1213 " - " ASN A 163 " " NAG A1216 " - " ASN A 51 " " NAG A1217 " - " ASN A 247 " " NAG A1218 " - " ASN A 271 " " NAG A1219 " - " ASN A 306 " " NAG A1226 " - " ASN A 513 " " NAG A1229 " - " ASN A 77 " " NAG B1201 " - " ASN B 676 " " NAG B1202 " - " ASN B 714 " " NAG B1203 " - " ASN B 669 " " NAG B1204 " - " ASN B 591 " " NAG B1207 " - " ASN B 947 " " NAG B1212 " - " ASN B 178 " " NAG B1213 " - " ASN B 163 " " NAG B1216 " - " ASN B 51 " " NAG B1217 " - " ASN B 247 " " NAG B1218 " - " ASN B 271 " " NAG B1219 " - " ASN B 306 " " NAG B1226 " - " ASN B 513 " " NAG B1229 " - " ASN B 77 " " NAG C1201 " - " ASN C 676 " " NAG C1202 " - " ASN C 714 " " NAG C1203 " - " ASN C 669 " " NAG C1204 " - " ASN C 591 " " NAG C1207 " - " ASN C 947 " " NAG C1212 " - " ASN C 178 " " NAG C1213 " - " ASN C 163 " " NAG C1216 " - " ASN C 51 " " NAG C1217 " - " ASN C 247 " " NAG C1218 " - " ASN C 271 " " NAG C1219 " - " ASN C 306 " " NAG C1226 " - " ASN C 513 " " NAG C1229 " - " ASN C 77 " " NAG D 1 " - " ASN A 579 " " NAG E 1 " - " ASN A 237 " " NAG F 1 " - " ASN A 212 " " NAG G 1 " - " ASN A 144 " " NAG H 1 " - " ASN A 276 " " NAG I 1 " - " ASN A 447 " " NAG J 1 " - " ASN A 103 " " NAG K 1 " - " ASN B 579 " " NAG L 1 " - " ASN B 237 " " NAG M 1 " - " ASN B 212 " " NAG N 1 " - " ASN B 144 " " NAG O 1 " - " ASN B 276 " " NAG P 1 " - " ASN B 447 " " NAG Q 1 " - " ASN B 103 " " NAG R 1 " - " ASN C 579 " " NAG S 1 " - " ASN C 237 " " NAG T 1 " - " ASN C 212 " " NAG U 1 " - " ASN C 144 " " NAG V 1 " - " ASN C 276 " " NAG W 1 " - " ASN C 447 " " NAG X 1 " - " ASN C 103 " Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.3 seconds 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 42 sheets defined 20.1% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 224 through 234 removed outlier: 4.407A pdb=" N LEU A 229 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 removed outlier: 3.978A pdb=" N ILE A 336 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 removed outlier: 3.551A pdb=" N GLN A 360 " --> pdb=" O GLY A 356 " (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 609 through 615 removed outlier: 3.687A pdb=" N CYS A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 628 through 658 removed outlier: 4.024A pdb=" N CYS A 632 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 638 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 651 " --> pdb=" O ASP A 647 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 657 " --> pdb=" O PHE A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 726 through 732 Processing helix chain 'A' and resid 749 through 761 Processing helix chain 'A' and resid 771 through 780 removed outlier: 3.652A pdb=" N LEU A 775 " --> pdb=" O PHE A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 811 removed outlier: 3.675A pdb=" N ALA A 797 " --> pdb=" O GLN A 793 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 833 removed outlier: 3.946A pdb=" N GLN A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 832 " --> pdb=" O GLN A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 906 removed outlier: 3.830A pdb=" N ASN A 863 " --> pdb=" O ALA A 859 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ALA A 864 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 906 " --> pdb=" O ILE A 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 224 through 234 removed outlier: 4.407A pdb=" N LEU B 229 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 removed outlier: 3.978A pdb=" N ILE B 336 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 362 removed outlier: 3.550A pdb=" N GLN B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 470 No H-bonds generated for 'chain 'B' and resid 468 through 470' Processing helix chain 'B' and resid 609 through 615 removed outlier: 3.686A pdb=" N CYS B 615 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 628 through 658 removed outlier: 4.024A pdb=" N CYS B 632 " --> pdb=" O TYR B 628 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 638 " --> pdb=" O ASN B 634 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 639 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 651 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 657 " --> pdb=" O PHE B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 699 Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 726 through 732 Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'B' and resid 771 through 780 removed outlier: 3.653A pdb=" N LEU B 775 " --> pdb=" O PHE B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 811 removed outlier: 3.675A pdb=" N ALA B 797 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 833 removed outlier: 3.946A pdb=" N GLN B 820 " --> pdb=" O LEU B 816 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 832 " --> pdb=" O GLN B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 906 removed outlier: 3.830A pdb=" N ASN B 863 " --> pdb=" O ALA B 859 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA B 864 " --> pdb=" O ILE B 860 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 906 " --> pdb=" O ILE B 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 224 through 234 removed outlier: 4.407A pdb=" N LEU C 229 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.977A pdb=" N ILE C 336 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 removed outlier: 3.551A pdb=" N GLN C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 470 No H-bonds generated for 'chain 'C' and resid 468 through 470' Processing helix chain 'C' and resid 609 through 615 removed outlier: 3.686A pdb=" N CYS C 615 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 628 through 658 removed outlier: 4.024A pdb=" N CYS C 632 " --> pdb=" O TYR C 628 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL C 638 " --> pdb=" O ASN C 634 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL C 639 " --> pdb=" O ILE C 635 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU C 649 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 651 " --> pdb=" O ASP C 647 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C 657 " --> pdb=" O PHE C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 699 Processing helix chain 'C' and resid 723 through 725 No H-bonds generated for 'chain 'C' and resid 723 through 725' Processing helix chain 'C' and resid 726 through 732 Processing helix chain 'C' and resid 749 through 761 Processing helix chain 'C' and resid 771 through 780 removed outlier: 3.652A pdb=" N LEU C 775 " --> pdb=" O PHE C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 811 removed outlier: 3.675A pdb=" N ALA C 797 " --> pdb=" O GLN C 793 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 833 removed outlier: 3.946A pdb=" N GLN C 820 " --> pdb=" O LEU C 816 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU C 832 " --> pdb=" O GLN C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 906 removed outlier: 3.830A pdb=" N ASN C 863 " --> pdb=" O ALA C 859 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA C 864 " --> pdb=" O ILE C 860 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN C 865 " --> pdb=" O GLN C 861 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL C 906 " --> pdb=" O ILE C 902 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 45 removed outlier: 3.702A pdb=" N GLY A 39 " --> pdb=" O PHE A 210 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 210 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS A 41 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 206 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP A 217 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A 211 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 5.030A pdb=" N ASN A 51 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 200 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 78 removed outlier: 3.787A pdb=" N THR A 184 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 185 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 109 " --> pdb=" O CYS A 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 133 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 145 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 135 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR A 143 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 241 through 245 removed outlier: 3.633A pdb=" N TYR A 243 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A 496 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 507 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER A 501 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 518 " --> pdb=" O TYR A 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 255 through 257 removed outlier: 6.728A pdb=" N PHE A 255 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 434 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 436 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS A 487 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 484 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 477 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP A 473 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 465 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 273 removed outlier: 6.456A pdb=" N HIS A 270 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASN A 306 " --> pdb=" O HIS A 270 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE A 272 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY A 301 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLY A 406 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER A 344 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE A 342 " --> pdb=" O ARG A 408 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN A 410 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 340 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA8, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 556 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 587 removed outlier: 3.589A pdb=" N VAL A 948 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 586 " --> pdb=" O VAL A 946 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 594 through 600 removed outlier: 3.813A pdb=" N GLU A 597 " --> pdb=" O PHE A 935 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 599 " --> pdb=" O ILE A 933 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 933 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 605 through 608 removed outlier: 4.650A pdb=" N LYS A 605 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 736 " --> pdb=" O GLN A 607 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 965 through 966 removed outlier: 3.583A pdb=" N LEU A1003 " --> pdb=" O ALA A 965 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 975 through 978 removed outlier: 3.718A pdb=" N VAL A 978 " --> pdb=" O SER A 981 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 39 through 45 removed outlier: 3.701A pdb=" N GLY B 39 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 210 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS B 41 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 206 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP B 217 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 211 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 55 removed outlier: 5.030A pdb=" N ASN B 51 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL B 200 " --> pdb=" O ASN B 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 74 through 78 removed outlier: 3.786A pdb=" N THR B 184 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER B 185 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 109 " --> pdb=" O CYS B 102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 133 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 145 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA B 135 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR B 143 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 241 through 245 removed outlier: 3.634A pdb=" N TYR B 243 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN B 496 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 507 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER B 501 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN B 518 " --> pdb=" O TYR B 525 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 255 through 257 removed outlier: 6.727A pdb=" N PHE B 255 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 434 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE B 436 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 487 " --> pdb=" O THR B 446 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 484 " --> pdb=" O VAL B 477 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 477 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP B 473 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 465 " --> pdb=" O ASP B 473 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 270 through 273 removed outlier: 6.457A pdb=" N HIS B 270 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ASN B 306 " --> pdb=" O HIS B 270 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE B 272 " --> pdb=" O ASN B 306 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY B 301 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLY B 406 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER B 344 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE B 342 " --> pdb=" O ARG B 408 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN B 410 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 340 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 314 through 315 Processing sheet with id=AC4, first strand: chain 'B' and resid 347 through 350 Processing sheet with id=AC5, first strand: chain 'B' and resid 554 through 556 Processing sheet with id=AC6, first strand: chain 'B' and resid 584 through 587 removed outlier: 3.590A pdb=" N VAL B 948 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE B 586 " --> pdb=" O VAL B 946 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 594 through 600 removed outlier: 3.812A pdb=" N GLU B 597 " --> pdb=" O PHE B 935 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 599 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 933 " --> pdb=" O ILE B 599 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 605 through 608 removed outlier: 4.649A pdb=" N LYS B 605 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 736 " --> pdb=" O GLN B 607 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 965 through 966 removed outlier: 3.583A pdb=" N LEU B1003 " --> pdb=" O ALA B 965 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 975 through 978 removed outlier: 3.717A pdb=" N VAL B 978 " --> pdb=" O SER B 981 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 39 through 45 removed outlier: 3.701A pdb=" N GLY C 39 " --> pdb=" O PHE C 210 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE C 210 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS C 41 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 206 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP C 217 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C 211 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ALA C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 50 through 55 removed outlier: 5.029A pdb=" N ASN C 51 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL C 200 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 74 through 78 removed outlier: 3.786A pdb=" N THR C 184 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER C 185 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 109 " --> pdb=" O CYS C 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 133 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 145 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C 135 " --> pdb=" O TYR C 143 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR C 143 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 241 through 245 removed outlier: 3.633A pdb=" N TYR C 243 " --> pdb=" O PHE C 498 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN C 496 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 507 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER C 501 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN C 518 " --> pdb=" O TYR C 525 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.728A pdb=" N PHE C 255 " --> pdb=" O ASN C 435 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR C 434 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE C 436 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS C 487 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 484 " --> pdb=" O VAL C 477 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL C 477 " --> pdb=" O THR C 484 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP C 473 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE C 465 " --> pdb=" O ASP C 473 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 270 through 273 removed outlier: 6.458A pdb=" N HIS C 270 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ASN C 306 " --> pdb=" O HIS C 270 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE C 272 " --> pdb=" O ASN C 306 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY C 301 " --> pdb=" O GLN C 410 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLY C 406 " --> pdb=" O SER C 344 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER C 344 " --> pdb=" O GLY C 406 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE C 342 " --> pdb=" O ARG C 408 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN C 410 " --> pdb=" O LEU C 340 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU C 340 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 314 through 315 Processing sheet with id=AD9, first strand: chain 'C' and resid 347 through 350 Processing sheet with id=AE1, first strand: chain 'C' and resid 554 through 556 Processing sheet with id=AE2, first strand: chain 'C' and resid 584 through 587 removed outlier: 3.589A pdb=" N VAL C 948 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE C 586 " --> pdb=" O VAL C 946 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 594 through 600 removed outlier: 3.812A pdb=" N GLU C 597 " --> pdb=" O PHE C 935 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 599 " --> pdb=" O ILE C 933 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 933 " --> pdb=" O ILE C 599 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 605 through 608 removed outlier: 4.649A pdb=" N LYS C 605 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 736 " --> pdb=" O GLN C 607 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 965 through 966 removed outlier: 3.583A pdb=" N LEU C1003 " --> pdb=" O ALA C 965 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 975 through 978 removed outlier: 3.717A pdb=" N VAL C 978 " --> pdb=" O SER C 981 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1638 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: 5.04 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7550 1.34 - 1.46: 6133 1.46 - 1.58: 10836 1.58 - 1.71: 0 1.71 - 1.83: 168 Bond restraints: 24687 Sorted by residual: bond pdb=" C1 NAG A1213 " pdb=" O5 NAG A1213 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.88e+00 bond pdb=" CA LEU B 169 " pdb=" C LEU B 169 " ideal model delta sigma weight residual 1.524 1.558 -0.035 1.26e-02 6.30e+03 7.66e+00 bond pdb=" CA LEU C 169 " pdb=" C LEU C 169 " ideal model delta sigma weight residual 1.524 1.558 -0.034 1.26e-02 6.30e+03 7.25e+00 bond pdb=" CA LEU A 169 " pdb=" C LEU A 169 " ideal model delta sigma weight residual 1.524 1.557 -0.034 1.26e-02 6.30e+03 7.23e+00 bond pdb=" N ASN A 170 " pdb=" CA ASN A 170 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.08e+00 ... (remaining 24682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 32033 2.33 - 4.65: 1330 4.65 - 6.98: 133 6.98 - 9.30: 46 9.30 - 11.63: 28 Bond angle restraints: 33570 Sorted by residual: angle pdb=" N LEU B 169 " pdb=" CA LEU B 169 " pdb=" C LEU B 169 " ideal model delta sigma weight residual 110.23 98.60 11.63 1.45e+00 4.76e-01 6.43e+01 angle pdb=" N LEU A 169 " pdb=" CA LEU A 169 " pdb=" C LEU A 169 " ideal model delta sigma weight residual 110.23 98.61 11.62 1.45e+00 4.76e-01 6.42e+01 angle pdb=" N LEU C 169 " pdb=" CA LEU C 169 " pdb=" C LEU C 169 " ideal model delta sigma weight residual 110.23 98.67 11.56 1.45e+00 4.76e-01 6.36e+01 angle pdb=" N MET B 746 " pdb=" CA MET B 746 " pdb=" C MET B 746 " ideal model delta sigma weight residual 114.75 106.43 8.32 1.26e+00 6.30e-01 4.36e+01 angle pdb=" N MET C 746 " pdb=" CA MET C 746 " pdb=" C MET C 746 " ideal model delta sigma weight residual 114.75 106.47 8.28 1.26e+00 6.30e-01 4.31e+01 ... (remaining 33565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 14529 16.66 - 33.31: 901 33.31 - 49.97: 277 49.97 - 66.63: 43 66.63 - 83.29: 42 Dihedral angle restraints: 15792 sinusoidal: 7143 harmonic: 8649 Sorted by residual: dihedral pdb=" CB CYS A 715 " pdb=" SG CYS A 715 " pdb=" SG CYS A 728 " pdb=" CB CYS A 728 " ideal model delta sinusoidal sigma weight residual 93.00 176.29 -83.29 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS B 715 " pdb=" SG CYS B 715 " pdb=" SG CYS B 728 " pdb=" CB CYS B 728 " ideal model delta sinusoidal sigma weight residual 93.00 176.28 -83.28 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS C 715 " pdb=" SG CYS C 715 " pdb=" SG CYS C 728 " pdb=" CB CYS C 728 " ideal model delta sinusoidal sigma weight residual 93.00 176.26 -83.26 1 1.00e+01 1.00e-02 8.47e+01 ... (remaining 15789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 3839 0.126 - 0.252: 201 0.252 - 0.378: 15 0.378 - 0.504: 3 0.504 - 0.630: 4 Chirality restraints: 4062 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.91e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 103 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.70e+00 chirality pdb=" C1 NAG C1213 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG C1213 " pdb=" O5 NAG C1213 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.85e+00 ... (remaining 4059 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 163 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ASN A 163 " 0.058 2.00e-02 2.50e+03 pdb=" O ASN A 163 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU A 164 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 163 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ASN B 163 " 0.057 2.00e-02 2.50e+03 pdb=" O ASN B 163 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU B 164 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 163 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C ASN C 163 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN C 163 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU C 164 " 0.018 2.00e-02 2.50e+03 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 977 2.70 - 3.25: 22494 3.25 - 3.80: 35779 3.80 - 4.35: 41708 4.35 - 4.90: 70315 Nonbonded interactions: 171273 Sorted by model distance: nonbonded pdb=" CD1 TYR A 28 " pdb=" N TYR A 29 " model vdw 2.150 3.420 nonbonded pdb=" CD1 TYR C 28 " pdb=" N TYR C 29 " model vdw 2.151 3.420 nonbonded pdb=" CD1 TYR B 28 " pdb=" N TYR B 29 " model vdw 2.155 3.420 nonbonded pdb=" OD1 ASN B 276 " pdb=" OH TYR B 351 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASN C 276 " pdb=" OH TYR C 351 " model vdw 2.256 3.040 ... (remaining 171268 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'O' selection = chain 'P' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.170 Find NCS groups from input model: 0.760 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 24816 Z= 0.316 Angle : 1.153 19.757 33915 Z= 0.604 Chirality : 0.068 0.630 4062 Planarity : 0.007 0.072 4227 Dihedral : 12.099 76.297 10158 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.31 % Favored : 86.48 % Rotamer: Outliers : 0.51 % Allowed : 6.95 % Favored : 92.54 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.95 (0.12), residues: 2967 helix: -2.43 (0.16), residues: 534 sheet: -3.73 (0.16), residues: 462 loop : -3.66 (0.11), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 890 TYR 0.029 0.002 TYR C 29 PHE 0.035 0.004 PHE A 975 TRP 0.015 0.002 TRP B 40 HIS 0.013 0.003 HIS B 823 Details of bonding type rmsd covalent geometry : bond 0.00661 (24687) covalent geometry : angle 1.09499 (33570) SS BOND : bond 0.00872 ( 42) SS BOND : angle 1.88808 ( 84) hydrogen bonds : bond 0.21484 ( 594) hydrogen bonds : angle 8.24469 ( 1638) link_BETA1-4 : bond 0.00994 ( 27) link_BETA1-4 : angle 2.54102 ( 81) link_NAG-ASN : bond 0.01085 ( 60) link_NAG-ASN : angle 4.73438 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 596 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 THR cc_start: 0.8166 (p) cc_final: 0.7950 (p) REVERT: A 440 THR cc_start: 0.9165 (m) cc_final: 0.8892 (p) REVERT: A 493 ASP cc_start: 0.7564 (p0) cc_final: 0.7260 (p0) REVERT: A 508 ILE cc_start: 0.9507 (mp) cc_final: 0.9273 (mt) REVERT: A 732 TYR cc_start: 0.7460 (m-10) cc_final: 0.7231 (m-10) REVERT: A 941 THR cc_start: 0.8818 (m) cc_final: 0.8560 (p) REVERT: A 949 THR cc_start: 0.8392 (p) cc_final: 0.8076 (p) REVERT: A 974 ILE cc_start: 0.7882 (tp) cc_final: 0.7564 (mp) REVERT: B 184 THR cc_start: 0.8118 (t) cc_final: 0.7861 (m) REVERT: B 235 THR cc_start: 0.9432 (t) cc_final: 0.9154 (m) REVERT: B 371 TYR cc_start: 0.8550 (m-10) cc_final: 0.7854 (m-80) REVERT: B 440 THR cc_start: 0.9186 (m) cc_final: 0.8983 (p) REVERT: B 508 ILE cc_start: 0.9495 (mp) cc_final: 0.9190 (mt) REVERT: B 634 ASN cc_start: 0.8619 (t0) cc_final: 0.8238 (t0) REVERT: B 732 TYR cc_start: 0.7458 (m-10) cc_final: 0.7237 (m-10) REVERT: B 828 GLN cc_start: 0.7698 (mm110) cc_final: 0.7466 (tm-30) REVERT: B 941 THR cc_start: 0.8772 (m) cc_final: 0.8490 (p) REVERT: B 974 ILE cc_start: 0.7934 (tp) cc_final: 0.7640 (mp) REVERT: C 184 THR cc_start: 0.8003 (t) cc_final: 0.7737 (m) REVERT: C 201 MET cc_start: 0.7949 (ptp) cc_final: 0.7370 (ptt) REVERT: C 249 SER cc_start: 0.6832 (p) cc_final: 0.6571 (t) REVERT: C 253 GLN cc_start: 0.8089 (mt0) cc_final: 0.6925 (pm20) REVERT: C 440 THR cc_start: 0.9095 (m) cc_final: 0.8813 (p) REVERT: C 828 GLN cc_start: 0.7739 (mm110) cc_final: 0.7093 (tm-30) REVERT: C 846 ILE cc_start: 0.8861 (tp) cc_final: 0.8619 (tp) REVERT: C 887 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 941 THR cc_start: 0.8879 (m) cc_final: 0.8516 (p) REVERT: C 974 ILE cc_start: 0.7877 (tp) cc_final: 0.7583 (mp) REVERT: C 991 MET cc_start: 0.8288 (ttt) cc_final: 0.7959 (tpp) outliers start: 13 outliers final: 0 residues processed: 606 average time/residue: 0.1709 time to fit residues: 162.3515 Evaluate side-chains 347 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN A 129 ASN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 HIS A 355 GLN A 523 GLN A 774 GLN A 776 GLN A 822 GLN A 888 HIS ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 GLN A 963 GLN ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 41 HIS B 96 GLN B 129 ASN B 216 GLN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS B 355 GLN B 523 GLN B 774 GLN B 776 GLN B 822 GLN B 888 HIS B 900 GLN B 963 GLN ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 HIS C 43 HIS C 96 GLN C 129 ASN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 HIS C 523 GLN C 774 GLN C 822 GLN C 888 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 900 GLN C 963 GLN C 979 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130177 restraints weight = 35593.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129276 restraints weight = 40140.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129848 restraints weight = 38488.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130191 restraints weight = 34529.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.130304 restraints weight = 31892.480| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24816 Z= 0.163 Angle : 0.806 15.675 33915 Z= 0.404 Chirality : 0.050 0.515 4062 Planarity : 0.005 0.058 4227 Dihedral : 8.427 59.980 5070 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 3.42 % Allowed : 13.00 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.99 (0.13), residues: 2967 helix: -0.31 (0.23), residues: 504 sheet: -2.86 (0.19), residues: 477 loop : -3.48 (0.11), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 689 TYR 0.022 0.001 TYR C 29 PHE 0.021 0.002 PHE A 210 TRP 0.003 0.001 TRP B 341 HIS 0.005 0.001 HIS B 921 Details of bonding type rmsd covalent geometry : bond 0.00355 (24687) covalent geometry : angle 0.75846 (33570) SS BOND : bond 0.00428 ( 42) SS BOND : angle 1.38284 ( 84) hydrogen bonds : bond 0.05877 ( 594) hydrogen bonds : angle 6.03626 ( 1638) link_BETA1-4 : bond 0.00565 ( 27) link_BETA1-4 : angle 1.45587 ( 81) link_NAG-ASN : bond 0.00767 ( 60) link_NAG-ASN : angle 3.63429 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 384 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8134 (mpp) cc_final: 0.7886 (mtt) REVERT: A 113 HIS cc_start: 0.7445 (t-90) cc_final: 0.6735 (p90) REVERT: A 184 THR cc_start: 0.7847 (t) cc_final: 0.7516 (m) REVERT: A 189 TYR cc_start: 0.6110 (m-10) cc_final: 0.5900 (m-10) REVERT: A 253 GLN cc_start: 0.8236 (mt0) cc_final: 0.7012 (pm20) REVERT: A 508 ILE cc_start: 0.9497 (mp) cc_final: 0.9270 (mt) REVERT: A 512 ARG cc_start: 0.8016 (ptt90) cc_final: 0.7680 (ttp80) REVERT: A 677 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7464 (pp) REVERT: A 742 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8416 (pp) REVERT: A 746 MET cc_start: 0.8498 (tpp) cc_final: 0.7893 (ttp) REVERT: A 758 MET cc_start: 0.8976 (tmm) cc_final: 0.8727 (tmm) REVERT: A 784 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7845 (pt) REVERT: A 814 THR cc_start: 0.8093 (t) cc_final: 0.7734 (m) REVERT: A 846 ILE cc_start: 0.8956 (tp) cc_final: 0.8687 (tp) REVERT: A 974 ILE cc_start: 0.7930 (tp) cc_final: 0.7700 (mp) REVERT: B 113 HIS cc_start: 0.7633 (t-90) cc_final: 0.6826 (p-80) REVERT: B 184 THR cc_start: 0.8084 (t) cc_final: 0.7841 (m) REVERT: B 508 ILE cc_start: 0.9476 (mp) cc_final: 0.9206 (mt) REVERT: B 512 ARG cc_start: 0.8321 (ptt180) cc_final: 0.7651 (ttp80) REVERT: B 611 LEU cc_start: 0.9161 (tm) cc_final: 0.8759 (tp) REVERT: B 634 ASN cc_start: 0.8685 (t0) cc_final: 0.8248 (t0) REVERT: B 732 TYR cc_start: 0.7414 (m-10) cc_final: 0.7200 (m-10) REVERT: B 742 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8482 (pp) REVERT: B 746 MET cc_start: 0.8595 (tpp) cc_final: 0.7698 (ttp) REVERT: B 784 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7987 (pt) REVERT: B 814 THR cc_start: 0.7869 (t) cc_final: 0.7552 (m) REVERT: B 828 GLN cc_start: 0.7851 (mm110) cc_final: 0.7639 (tm-30) REVERT: B 860 ILE cc_start: 0.7735 (pp) cc_final: 0.7412 (pt) REVERT: B 902 ILE cc_start: 0.8980 (mm) cc_final: 0.8735 (mt) REVERT: B 974 ILE cc_start: 0.7983 (tp) cc_final: 0.7679 (mp) REVERT: C 83 MET cc_start: 0.8216 (mpp) cc_final: 0.7824 (mtt) REVERT: C 184 THR cc_start: 0.8050 (t) cc_final: 0.7701 (m) REVERT: C 201 MET cc_start: 0.7929 (ptp) cc_final: 0.7586 (ptt) REVERT: C 253 GLN cc_start: 0.8167 (mt0) cc_final: 0.7040 (pm20) REVERT: C 389 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7289 (pp) REVERT: C 512 ARG cc_start: 0.8060 (ptt90) cc_final: 0.7602 (ttp80) REVERT: C 648 MET cc_start: 0.6778 (tmm) cc_final: 0.6501 (tmm) REVERT: C 677 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7590 (pp) REVERT: C 726 LEU cc_start: 0.8088 (mm) cc_final: 0.7632 (tp) REVERT: C 746 MET cc_start: 0.8649 (tpp) cc_final: 0.7734 (ttp) REVERT: C 784 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7950 (pt) REVERT: C 814 THR cc_start: 0.7887 (t) cc_final: 0.7536 (m) REVERT: C 828 GLN cc_start: 0.7846 (mm110) cc_final: 0.7590 (tm-30) REVERT: C 846 ILE cc_start: 0.9025 (tp) cc_final: 0.8711 (tp) REVERT: C 941 THR cc_start: 0.8686 (m) cc_final: 0.8483 (p) outliers start: 87 outliers final: 34 residues processed: 447 average time/residue: 0.1485 time to fit residues: 109.9297 Evaluate side-chains 349 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 307 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 1018 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 84 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 150 optimal weight: 0.0050 chunk 252 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 41 HIS ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN C 979 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.140697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.123647 restraints weight = 36314.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121744 restraints weight = 37808.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121919 restraints weight = 41068.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122171 restraints weight = 40215.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.122219 restraints weight = 35924.450| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24816 Z= 0.146 Angle : 0.744 15.490 33915 Z= 0.371 Chirality : 0.049 0.574 4062 Planarity : 0.005 0.050 4227 Dihedral : 7.359 58.472 5070 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 3.14 % Allowed : 16.69 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.14), residues: 2967 helix: 0.31 (0.23), residues: 534 sheet: -2.29 (0.22), residues: 456 loop : -3.37 (0.11), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 895 TYR 0.021 0.001 TYR A 598 PHE 0.020 0.002 PHE A 210 TRP 0.003 0.001 TRP B 341 HIS 0.004 0.001 HIS B 921 Details of bonding type rmsd covalent geometry : bond 0.00325 (24687) covalent geometry : angle 0.69918 (33570) SS BOND : bond 0.00411 ( 42) SS BOND : angle 1.00153 ( 84) hydrogen bonds : bond 0.05127 ( 594) hydrogen bonds : angle 5.51456 ( 1638) link_BETA1-4 : bond 0.00488 ( 27) link_BETA1-4 : angle 1.29133 ( 81) link_NAG-ASN : bond 0.00930 ( 60) link_NAG-ASN : angle 3.43490 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 330 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8116 (mpp) cc_final: 0.7793 (mtt) REVERT: A 184 THR cc_start: 0.8107 (t) cc_final: 0.7789 (m) REVERT: A 253 GLN cc_start: 0.8216 (mt0) cc_final: 0.7054 (pm20) REVERT: A 371 TYR cc_start: 0.8721 (m-80) cc_final: 0.8457 (m-80) REVERT: A 512 ARG cc_start: 0.7990 (ptt90) cc_final: 0.7704 (ttp80) REVERT: A 677 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7591 (pp) REVERT: A 758 MET cc_start: 0.9051 (tmm) cc_final: 0.8663 (tmm) REVERT: A 784 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8107 (pt) REVERT: A 846 ILE cc_start: 0.8961 (tp) cc_final: 0.8705 (tp) REVERT: A 857 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8421 (pp) REVERT: A 858 ASP cc_start: 0.6853 (t0) cc_final: 0.6580 (t0) REVERT: A 974 ILE cc_start: 0.7872 (tp) cc_final: 0.7583 (mp) REVERT: B 184 THR cc_start: 0.8259 (t) cc_final: 0.7996 (m) REVERT: B 261 ASN cc_start: 0.6282 (t0) cc_final: 0.5986 (t0) REVERT: B 371 TYR cc_start: 0.8706 (m-10) cc_final: 0.8151 (m-80) REVERT: B 508 ILE cc_start: 0.9463 (mp) cc_final: 0.9183 (mt) REVERT: B 512 ARG cc_start: 0.8263 (ptt180) cc_final: 0.7712 (ttp80) REVERT: B 611 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8688 (tp) REVERT: B 634 ASN cc_start: 0.8549 (t0) cc_final: 0.8051 (t0) REVERT: B 732 TYR cc_start: 0.7470 (m-10) cc_final: 0.7240 (m-10) REVERT: B 784 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8161 (pt) REVERT: B 902 ILE cc_start: 0.9002 (mm) cc_final: 0.8742 (mt) REVERT: B 974 ILE cc_start: 0.8069 (tp) cc_final: 0.7644 (mp) REVERT: C 83 MET cc_start: 0.8159 (mpp) cc_final: 0.7841 (mtt) REVERT: C 184 THR cc_start: 0.8145 (t) cc_final: 0.7804 (m) REVERT: C 201 MET cc_start: 0.7881 (ptp) cc_final: 0.7505 (ptt) REVERT: C 253 GLN cc_start: 0.8211 (mt0) cc_final: 0.7137 (pm20) REVERT: C 512 ARG cc_start: 0.8038 (ptt90) cc_final: 0.7614 (ttp80) REVERT: C 648 MET cc_start: 0.6743 (tmm) cc_final: 0.6435 (tmm) REVERT: C 677 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7583 (pp) REVERT: C 726 LEU cc_start: 0.8186 (mm) cc_final: 0.7670 (tp) REVERT: C 746 MET cc_start: 0.8602 (tpp) cc_final: 0.7651 (ttp) REVERT: C 784 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8032 (pt) REVERT: C 828 GLN cc_start: 0.7768 (mm110) cc_final: 0.7556 (tm-30) REVERT: C 846 ILE cc_start: 0.9019 (tp) cc_final: 0.8689 (tp) outliers start: 80 outliers final: 39 residues processed: 387 average time/residue: 0.1438 time to fit residues: 93.4157 Evaluate side-chains 336 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 290 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 949 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 13 optimal weight: 0.0570 chunk 77 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 295 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 96 GLN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 ASN A 894 GLN ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN B 863 ASN B 921 HIS ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN C 232 GLN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 863 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120422 restraints weight = 36384.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119181 restraints weight = 49935.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119958 restraints weight = 48780.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120013 restraints weight = 40317.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120126 restraints weight = 36549.220| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24816 Z= 0.173 Angle : 0.741 15.459 33915 Z= 0.372 Chirality : 0.050 0.534 4062 Planarity : 0.004 0.048 4227 Dihedral : 6.823 59.686 5070 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 4.16 % Allowed : 17.59 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.14), residues: 2967 helix: 0.81 (0.24), residues: 513 sheet: -1.99 (0.21), residues: 561 loop : -3.43 (0.12), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 895 TYR 0.024 0.001 TYR C 29 PHE 0.028 0.002 PHE C 210 TRP 0.002 0.001 TRP C 341 HIS 0.005 0.001 HIS B 937 Details of bonding type rmsd covalent geometry : bond 0.00400 (24687) covalent geometry : angle 0.69891 (33570) SS BOND : bond 0.00469 ( 42) SS BOND : angle 0.94700 ( 84) hydrogen bonds : bond 0.05175 ( 594) hydrogen bonds : angle 5.32520 ( 1638) link_BETA1-4 : bond 0.00474 ( 27) link_BETA1-4 : angle 1.23727 ( 81) link_NAG-ASN : bond 0.00816 ( 60) link_NAG-ASN : angle 3.34739 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 305 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8055 (mpp) cc_final: 0.7808 (mtt) REVERT: A 184 THR cc_start: 0.8273 (t) cc_final: 0.7977 (m) REVERT: A 253 GLN cc_start: 0.8223 (mt0) cc_final: 0.7102 (pm20) REVERT: A 371 TYR cc_start: 0.8726 (m-80) cc_final: 0.8421 (m-80) REVERT: A 512 ARG cc_start: 0.8043 (ptt90) cc_final: 0.7599 (ttp80) REVERT: A 677 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7548 (pp) REVERT: A 784 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8229 (pt) REVERT: A 836 MET cc_start: 0.8395 (tpp) cc_final: 0.8111 (tpp) REVERT: A 846 ILE cc_start: 0.8975 (tp) cc_final: 0.8711 (tp) REVERT: A 857 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8412 (pp) REVERT: A 858 ASP cc_start: 0.6835 (t0) cc_final: 0.6579 (t0) REVERT: A 974 ILE cc_start: 0.7852 (tp) cc_final: 0.7624 (mp) REVERT: B 184 THR cc_start: 0.8427 (t) cc_final: 0.8154 (m) REVERT: B 201 MET cc_start: 0.7806 (ptt) cc_final: 0.7513 (ptt) REVERT: B 253 GLN cc_start: 0.8103 (mt0) cc_final: 0.7123 (pm20) REVERT: B 430 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.8911 (m) REVERT: B 508 ILE cc_start: 0.9478 (mp) cc_final: 0.9222 (mt) REVERT: B 512 ARG cc_start: 0.8232 (ptt180) cc_final: 0.7624 (ttp80) REVERT: B 611 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8863 (tp) REVERT: B 634 ASN cc_start: 0.8590 (t0) cc_final: 0.8210 (t0) REVERT: B 649 GLU cc_start: 0.8260 (pp20) cc_final: 0.7919 (pp20) REVERT: B 732 TYR cc_start: 0.7591 (m-10) cc_final: 0.7370 (m-10) REVERT: B 784 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8225 (pt) REVERT: B 902 ILE cc_start: 0.9009 (mm) cc_final: 0.8743 (mt) REVERT: B 974 ILE cc_start: 0.8053 (tp) cc_final: 0.7686 (mp) REVERT: C 83 MET cc_start: 0.8115 (mpp) cc_final: 0.7865 (mtt) REVERT: C 184 THR cc_start: 0.8158 (t) cc_final: 0.7799 (m) REVERT: C 201 MET cc_start: 0.8013 (ptp) cc_final: 0.7728 (ptt) REVERT: C 253 GLN cc_start: 0.8208 (mt0) cc_final: 0.7195 (pm20) REVERT: C 430 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8817 (m) REVERT: C 512 ARG cc_start: 0.8008 (ptt90) cc_final: 0.7625 (ttp80) REVERT: C 648 MET cc_start: 0.6722 (tmm) cc_final: 0.6415 (tmm) REVERT: C 677 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7633 (pp) REVERT: C 726 LEU cc_start: 0.8233 (mm) cc_final: 0.7725 (tp) REVERT: C 784 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8176 (pt) outliers start: 106 outliers final: 62 residues processed: 384 average time/residue: 0.1408 time to fit residues: 91.1864 Evaluate side-chains 349 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 278 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 985 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 195 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 172 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 0.0570 chunk 43 optimal weight: 4.9990 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** 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 = 0.3640 r_free = 0.3640 target = 0.142342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124841 restraints weight = 36149.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.123553 restraints weight = 34231.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123609 restraints weight = 34799.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123698 restraints weight = 33521.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.123794 restraints weight = 32640.876| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24816 Z= 0.189 Angle : 0.755 15.497 33915 Z= 0.375 Chirality : 0.050 0.532 4062 Planarity : 0.004 0.047 4227 Dihedral : 6.650 57.997 5070 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 4.67 % Allowed : 17.63 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.14), residues: 2967 helix: 1.03 (0.24), residues: 525 sheet: -1.83 (0.22), residues: 546 loop : -3.42 (0.12), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 920 TYR 0.016 0.002 TYR C 28 PHE 0.030 0.002 PHE C 210 TRP 0.002 0.001 TRP B 40 HIS 0.013 0.001 HIS B 921 Details of bonding type rmsd covalent geometry : bond 0.00443 (24687) covalent geometry : angle 0.70971 (33570) SS BOND : bond 0.00590 ( 42) SS BOND : angle 0.94094 ( 84) hydrogen bonds : bond 0.05250 ( 594) hydrogen bonds : angle 5.27708 ( 1638) link_BETA1-4 : bond 0.00494 ( 27) link_BETA1-4 : angle 1.23069 ( 81) link_NAG-ASN : bond 0.00820 ( 60) link_NAG-ASN : angle 3.50360 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 291 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8157 (mpp) cc_final: 0.7899 (mtt) REVERT: A 172 ASP cc_start: 0.8704 (p0) cc_final: 0.8423 (p0) REVERT: A 184 THR cc_start: 0.8354 (t) cc_final: 0.8074 (m) REVERT: A 253 GLN cc_start: 0.8286 (mt0) cc_final: 0.7021 (pm20) REVERT: A 371 TYR cc_start: 0.8763 (m-80) cc_final: 0.8455 (m-80) REVERT: A 430 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8900 (m) REVERT: A 512 ARG cc_start: 0.8036 (ptt90) cc_final: 0.7478 (ttp80) REVERT: A 677 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7708 (pp) REVERT: A 784 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8292 (pt) REVERT: A 857 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8407 (pp) REVERT: A 858 ASP cc_start: 0.6994 (t0) cc_final: 0.6673 (t0) REVERT: A 974 ILE cc_start: 0.7796 (tp) cc_final: 0.7544 (mp) REVERT: B 184 THR cc_start: 0.8510 (t) cc_final: 0.8246 (m) REVERT: B 253 GLN cc_start: 0.8218 (mt0) cc_final: 0.7037 (pm20) REVERT: B 321 MET cc_start: 0.8056 (mmm) cc_final: 0.7849 (tpt) REVERT: B 330 ASN cc_start: 0.8227 (m-40) cc_final: 0.7797 (m-40) REVERT: B 430 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.8927 (m) REVERT: B 463 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8389 (mm) REVERT: B 498 PHE cc_start: 0.8580 (p90) cc_final: 0.8325 (p90) REVERT: B 508 ILE cc_start: 0.9501 (mp) cc_final: 0.9247 (mt) REVERT: B 512 ARG cc_start: 0.8227 (ptt180) cc_final: 0.7546 (ttp80) REVERT: B 611 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8915 (tp) REVERT: B 634 ASN cc_start: 0.8701 (t0) cc_final: 0.8395 (t0) REVERT: B 732 TYR cc_start: 0.7655 (m-10) cc_final: 0.7439 (m-10) REVERT: B 784 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8231 (pt) REVERT: B 846 ILE cc_start: 0.8910 (tp) cc_final: 0.8366 (mt) REVERT: B 974 ILE cc_start: 0.7956 (tp) cc_final: 0.7592 (mp) REVERT: C 83 MET cc_start: 0.8148 (mpp) cc_final: 0.7819 (mtt) REVERT: C 184 THR cc_start: 0.8157 (t) cc_final: 0.7833 (m) REVERT: C 201 MET cc_start: 0.8146 (ptp) cc_final: 0.7902 (ptt) REVERT: C 253 GLN cc_start: 0.8336 (mt0) cc_final: 0.7122 (pm20) REVERT: C 269 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8094 (pp) REVERT: C 430 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8843 (m) REVERT: C 512 ARG cc_start: 0.8094 (ptt90) cc_final: 0.7548 (ttp80) REVERT: C 635 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8636 (tp) REVERT: C 648 MET cc_start: 0.6605 (tmm) cc_final: 0.6294 (tmm) REVERT: C 677 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7703 (pp) REVERT: C 726 LEU cc_start: 0.8225 (mm) cc_final: 0.7764 (tp) REVERT: C 746 MET cc_start: 0.8668 (tpp) cc_final: 0.7888 (ttp) REVERT: C 784 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8283 (pt) REVERT: C 846 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8349 (tp) outliers start: 119 outliers final: 70 residues processed: 375 average time/residue: 0.1404 time to fit residues: 88.7012 Evaluate side-chains 359 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 275 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 985 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 83 optimal weight: 0.7980 chunk 236 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 254 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN ** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 822 GLN ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** 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 = 0.3598 r_free = 0.3598 target = 0.139819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131426 restraints weight = 36739.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.130098 restraints weight = 74326.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122700 restraints weight = 81568.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122324 restraints weight = 69312.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122479 restraints weight = 71386.208| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 24816 Z= 0.263 Angle : 0.832 15.978 33915 Z= 0.416 Chirality : 0.053 0.541 4062 Planarity : 0.005 0.052 4227 Dihedral : 6.918 45.931 5070 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.68 % Favored : 86.32 % Rotamer: Outliers : 5.14 % Allowed : 18.53 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.14), residues: 2967 helix: 1.28 (0.24), residues: 513 sheet: -1.93 (0.22), residues: 543 loop : -3.49 (0.12), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 920 TYR 0.022 0.002 TYR A 373 PHE 0.047 0.003 PHE A 210 TRP 0.003 0.001 TRP C 92 HIS 0.009 0.002 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00631 (24687) covalent geometry : angle 0.79125 (33570) SS BOND : bond 0.00727 ( 42) SS BOND : angle 1.10132 ( 84) hydrogen bonds : bond 0.05992 ( 594) hydrogen bonds : angle 5.44519 ( 1638) link_BETA1-4 : bond 0.00492 ( 27) link_BETA1-4 : angle 1.31914 ( 81) link_NAG-ASN : bond 0.00866 ( 60) link_NAG-ASN : angle 3.52504 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 271 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8153 (mpp) cc_final: 0.7938 (mtt) REVERT: A 184 THR cc_start: 0.8517 (t) cc_final: 0.8203 (m) REVERT: A 253 GLN cc_start: 0.8274 (mt0) cc_final: 0.7178 (pm20) REVERT: A 430 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8910 (m) REVERT: A 512 ARG cc_start: 0.8004 (ptt90) cc_final: 0.7588 (ttp-170) REVERT: A 677 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7822 (pp) REVERT: A 784 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8174 (pt) REVERT: A 857 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8680 (pp) REVERT: A 911 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7104 (tp) REVERT: A 974 ILE cc_start: 0.7949 (tp) cc_final: 0.7711 (mp) REVERT: B 184 THR cc_start: 0.8630 (t) cc_final: 0.8331 (m) REVERT: B 321 MET cc_start: 0.7933 (mmm) cc_final: 0.7541 (tpt) REVERT: B 385 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.6713 (t80) REVERT: B 430 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.8862 (m) REVERT: B 463 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8402 (mm) REVERT: B 512 ARG cc_start: 0.8228 (ptt180) cc_final: 0.7657 (ttp80) REVERT: B 611 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8946 (tp) REVERT: B 634 ASN cc_start: 0.8725 (t0) cc_final: 0.8471 (t0) REVERT: B 677 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7949 (pp) REVERT: B 784 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8192 (pt) REVERT: B 846 ILE cc_start: 0.8708 (tp) cc_final: 0.8136 (tp) REVERT: B 911 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7285 (tp) REVERT: B 974 ILE cc_start: 0.7866 (tp) cc_final: 0.7548 (mp) REVERT: C 83 MET cc_start: 0.8072 (mpp) cc_final: 0.7870 (mtt) REVERT: C 184 THR cc_start: 0.8303 (t) cc_final: 0.7925 (m) REVERT: C 253 GLN cc_start: 0.8453 (mt0) cc_final: 0.7325 (pm20) REVERT: C 269 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8230 (pp) REVERT: C 430 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8826 (m) REVERT: C 512 ARG cc_start: 0.8090 (ptt90) cc_final: 0.7632 (ttp80) REVERT: C 635 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8768 (tp) REVERT: C 648 MET cc_start: 0.6672 (tmm) cc_final: 0.6394 (tmm) REVERT: C 677 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7805 (pp) REVERT: C 726 LEU cc_start: 0.8353 (mm) cc_final: 0.7971 (tp) REVERT: C 784 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8270 (pt) REVERT: C 846 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8025 (tp) outliers start: 131 outliers final: 85 residues processed: 367 average time/residue: 0.1372 time to fit residues: 85.0478 Evaluate side-chains 352 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 249 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 934 VAL Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 1013 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 169 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 264 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 979 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 HIS ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125245 restraints weight = 36234.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124193 restraints weight = 37464.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124533 restraints weight = 37078.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124693 restraints weight = 35750.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124803 restraints weight = 33206.595| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24816 Z= 0.133 Angle : 0.735 15.056 33915 Z= 0.363 Chirality : 0.049 0.578 4062 Planarity : 0.004 0.046 4227 Dihedral : 6.213 37.699 5070 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 3.81 % Allowed : 20.38 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.15), residues: 2967 helix: 1.82 (0.24), residues: 504 sheet: -1.77 (0.22), residues: 549 loop : -3.35 (0.12), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 332 TYR 0.022 0.001 TYR B 26 PHE 0.022 0.001 PHE A 210 TRP 0.002 0.000 TRP B 40 HIS 0.005 0.001 HIS B 823 Details of bonding type rmsd covalent geometry : bond 0.00291 (24687) covalent geometry : angle 0.69159 (33570) SS BOND : bond 0.00376 ( 42) SS BOND : angle 1.13997 ( 84) hydrogen bonds : bond 0.04834 ( 594) hydrogen bonds : angle 5.17535 ( 1638) link_BETA1-4 : bond 0.00479 ( 27) link_BETA1-4 : angle 1.19650 ( 81) link_NAG-ASN : bond 0.00912 ( 60) link_NAG-ASN : angle 3.36301 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 290 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 THR cc_start: 0.8246 (t) cc_final: 0.7963 (m) REVERT: A 253 GLN cc_start: 0.8216 (mt0) cc_final: 0.6955 (pm20) REVERT: A 371 TYR cc_start: 0.8677 (m-80) cc_final: 0.8432 (m-80) REVERT: A 430 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8929 (m) REVERT: A 512 ARG cc_start: 0.8007 (ptt90) cc_final: 0.7355 (ttp-110) REVERT: A 651 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8692 (tp) REVERT: A 677 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7595 (pp) REVERT: A 846 ILE cc_start: 0.8864 (tp) cc_final: 0.8183 (tp) REVERT: A 857 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8532 (pp) REVERT: A 858 ASP cc_start: 0.6867 (t0) cc_final: 0.6664 (t0) REVERT: A 974 ILE cc_start: 0.7828 (tp) cc_final: 0.7553 (mp) REVERT: B 184 THR cc_start: 0.8453 (t) cc_final: 0.8180 (m) REVERT: B 321 MET cc_start: 0.8046 (mmm) cc_final: 0.7679 (tpt) REVERT: B 359 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7634 (tmtt) REVERT: B 371 TYR cc_start: 0.8618 (m-80) cc_final: 0.8355 (m-80) REVERT: B 385 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.6899 (t80) REVERT: B 430 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.8886 (m) REVERT: B 498 PHE cc_start: 0.8639 (p90) cc_final: 0.8420 (p90) REVERT: B 512 ARG cc_start: 0.8339 (ptt180) cc_final: 0.7796 (ttp-170) REVERT: B 611 LEU cc_start: 0.9167 (tm) cc_final: 0.8960 (tp) REVERT: B 634 ASN cc_start: 0.8744 (t0) cc_final: 0.8498 (t0) REVERT: B 649 GLU cc_start: 0.8226 (pp20) cc_final: 0.7980 (pp20) REVERT: B 677 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7790 (pp) REVERT: B 974 ILE cc_start: 0.7793 (tp) cc_final: 0.7496 (mp) REVERT: C 83 MET cc_start: 0.8021 (mpp) cc_final: 0.7806 (mtt) REVERT: C 184 THR cc_start: 0.8075 (t) cc_final: 0.7768 (m) REVERT: C 269 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8145 (pp) REVERT: C 430 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8790 (m) REVERT: C 512 ARG cc_start: 0.8056 (ptt90) cc_final: 0.7827 (ttp-170) REVERT: C 635 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8656 (tp) REVERT: C 649 GLU cc_start: 0.8278 (pp20) cc_final: 0.7898 (pp20) REVERT: C 677 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7654 (pp) REVERT: C 726 LEU cc_start: 0.8180 (mm) cc_final: 0.7707 (tp) REVERT: C 746 MET cc_start: 0.8660 (tpp) cc_final: 0.7659 (ttp) REVERT: C 846 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8664 (tp) outliers start: 97 outliers final: 60 residues processed: 366 average time/residue: 0.1430 time to fit residues: 88.6460 Evaluate side-chains 326 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 253 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 921 HIS Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 985 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 150 optimal weight: 0.3980 chunk 226 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 234 ASN A 264 ASN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 921 HIS B 927 GLN C 264 ASN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123641 restraints weight = 36320.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122472 restraints weight = 40972.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123053 restraints weight = 39393.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123191 restraints weight = 37212.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123294 restraints weight = 34660.971| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24816 Z= 0.169 Angle : 0.750 15.225 33915 Z= 0.373 Chirality : 0.050 0.576 4062 Planarity : 0.004 0.048 4227 Dihedral : 6.147 37.321 5070 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 4.16 % Allowed : 20.69 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.15), residues: 2967 helix: 1.89 (0.24), residues: 507 sheet: -1.82 (0.22), residues: 552 loop : -3.39 (0.12), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 920 TYR 0.016 0.001 TYR C 28 PHE 0.032 0.002 PHE C 320 TRP 0.002 0.001 TRP A 40 HIS 0.011 0.001 HIS B 921 Details of bonding type rmsd covalent geometry : bond 0.00394 (24687) covalent geometry : angle 0.70859 (33570) SS BOND : bond 0.00496 ( 42) SS BOND : angle 1.20562 ( 84) hydrogen bonds : bond 0.04970 ( 594) hydrogen bonds : angle 5.14331 ( 1638) link_BETA1-4 : bond 0.00492 ( 27) link_BETA1-4 : angle 1.19653 ( 81) link_NAG-ASN : bond 0.00872 ( 60) link_NAG-ASN : angle 3.32568 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 264 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.8772 (p0) cc_final: 0.8568 (p0) REVERT: A 184 THR cc_start: 0.8282 (t) cc_final: 0.8036 (m) REVERT: A 253 GLN cc_start: 0.8272 (mt0) cc_final: 0.7022 (pm20) REVERT: A 371 TYR cc_start: 0.8661 (m-80) cc_final: 0.8454 (m-80) REVERT: A 430 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8942 (m) REVERT: A 512 ARG cc_start: 0.8031 (ptt90) cc_final: 0.7308 (ttp-110) REVERT: A 677 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7678 (pp) REVERT: A 857 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8587 (pp) REVERT: A 974 ILE cc_start: 0.7819 (tp) cc_final: 0.7570 (mp) REVERT: B 184 THR cc_start: 0.8463 (t) cc_final: 0.8173 (m) REVERT: B 321 MET cc_start: 0.8090 (mmm) cc_final: 0.7716 (tpt) REVERT: B 371 TYR cc_start: 0.8598 (m-80) cc_final: 0.8330 (m-80) REVERT: B 385 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.6868 (t80) REVERT: B 430 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.8887 (m) REVERT: B 463 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8352 (mm) REVERT: B 498 PHE cc_start: 0.8715 (p90) cc_final: 0.8484 (p90) REVERT: B 512 ARG cc_start: 0.8317 (ptt180) cc_final: 0.7332 (ttp-110) REVERT: B 514 GLU cc_start: 0.4852 (tp30) cc_final: 0.4568 (tp30) REVERT: B 611 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8991 (tp) REVERT: B 649 GLU cc_start: 0.8276 (pp20) cc_final: 0.7972 (pp20) REVERT: B 677 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7828 (pp) REVERT: B 836 MET cc_start: 0.8590 (tpp) cc_final: 0.8375 (tpp) REVERT: B 974 ILE cc_start: 0.7700 (tp) cc_final: 0.7411 (mp) REVERT: C 83 MET cc_start: 0.8084 (mpp) cc_final: 0.7812 (mtt) REVERT: C 184 THR cc_start: 0.8155 (t) cc_final: 0.7840 (m) REVERT: C 269 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8217 (pp) REVERT: C 430 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8785 (m) REVERT: C 512 ARG cc_start: 0.8120 (ptt90) cc_final: 0.7607 (ttp-170) REVERT: C 635 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8685 (tp) REVERT: C 649 GLU cc_start: 0.8324 (pp20) cc_final: 0.7925 (pp20) REVERT: C 677 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7687 (pp) REVERT: C 726 LEU cc_start: 0.8221 (mm) cc_final: 0.7788 (tp) REVERT: C 746 MET cc_start: 0.8680 (tpp) cc_final: 0.7748 (ttp) outliers start: 106 outliers final: 72 residues processed: 345 average time/residue: 0.1451 time to fit residues: 84.0366 Evaluate side-chains 337 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 253 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 908 SER Chi-restraints excluded: chain C residue 934 VAL Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 985 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 50 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 249 optimal weight: 0.0670 chunk 86 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 271 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 216 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 234 ASN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 ASN ** C 283 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 = 0.3667 r_free = 0.3667 target = 0.144571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126142 restraints weight = 36324.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.125003 restraints weight = 33979.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125222 restraints weight = 34221.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125375 restraints weight = 33535.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125632 restraints weight = 31586.629| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24816 Z= 0.133 Angle : 0.724 14.812 33915 Z= 0.357 Chirality : 0.049 0.554 4062 Planarity : 0.004 0.045 4227 Dihedral : 5.757 35.124 5070 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 3.77 % Allowed : 21.01 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.15), residues: 2967 helix: 2.08 (0.24), residues: 507 sheet: -1.77 (0.22), residues: 561 loop : -3.34 (0.12), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 332 TYR 0.015 0.001 TYR C 28 PHE 0.033 0.001 PHE C 320 TRP 0.003 0.001 TRP B 40 HIS 0.005 0.001 HIS C 937 Details of bonding type rmsd covalent geometry : bond 0.00295 (24687) covalent geometry : angle 0.68352 (33570) SS BOND : bond 0.00294 ( 42) SS BOND : angle 0.98103 ( 84) hydrogen bonds : bond 0.04474 ( 594) hydrogen bonds : angle 5.06912 ( 1638) link_BETA1-4 : bond 0.00447 ( 27) link_BETA1-4 : angle 1.14089 ( 81) link_NAG-ASN : bond 0.00898 ( 60) link_NAG-ASN : angle 3.24992 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 282 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 THR cc_start: 0.8087 (t) cc_final: 0.7804 (m) REVERT: A 191 LYS cc_start: 0.6532 (tptt) cc_final: 0.5851 (tppt) REVERT: A 253 GLN cc_start: 0.8208 (mt0) cc_final: 0.6932 (pm20) REVERT: A 385 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.6920 (t80) REVERT: A 512 ARG cc_start: 0.8004 (ptt90) cc_final: 0.7373 (ttp-110) REVERT: A 677 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7546 (pp) REVERT: A 857 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8618 (pp) REVERT: A 974 ILE cc_start: 0.7780 (tp) cc_final: 0.7534 (mp) REVERT: B 184 THR cc_start: 0.8391 (t) cc_final: 0.8108 (m) REVERT: B 321 MET cc_start: 0.8055 (mmm) cc_final: 0.7666 (tpt) REVERT: B 371 TYR cc_start: 0.8594 (m-80) cc_final: 0.8371 (m-80) REVERT: B 385 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.6792 (t80) REVERT: B 430 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8923 (m) REVERT: B 498 PHE cc_start: 0.8596 (p90) cc_final: 0.8388 (p90) REVERT: B 512 ARG cc_start: 0.8271 (ptt180) cc_final: 0.7543 (ttp80) REVERT: B 611 LEU cc_start: 0.9168 (tm) cc_final: 0.8963 (tp) REVERT: B 677 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7751 (pp) REVERT: B 836 MET cc_start: 0.8530 (tpp) cc_final: 0.8300 (tpp) REVERT: B 846 ILE cc_start: 0.8684 (tp) cc_final: 0.8378 (pt) REVERT: B 974 ILE cc_start: 0.7756 (tp) cc_final: 0.7519 (mp) REVERT: C 83 MET cc_start: 0.8092 (mpp) cc_final: 0.7841 (mtt) REVERT: C 184 THR cc_start: 0.8011 (t) cc_final: 0.7697 (m) REVERT: C 430 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8800 (m) REVERT: C 512 ARG cc_start: 0.8080 (ptt90) cc_final: 0.7499 (ttp80) REVERT: C 635 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8617 (tp) REVERT: C 677 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7575 (pp) REVERT: C 726 LEU cc_start: 0.8165 (mm) cc_final: 0.7715 (tp) REVERT: C 746 MET cc_start: 0.8657 (tpp) cc_final: 0.7660 (ttp) outliers start: 96 outliers final: 71 residues processed: 351 average time/residue: 0.1420 time to fit residues: 84.3083 Evaluate side-chains 340 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 260 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 934 VAL Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 984 ILE Chi-restraints excluded: chain C residue 985 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 265 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 259 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 52 optimal weight: 0.8980 chunk 250 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.145155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.126680 restraints weight = 36262.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125718 restraints weight = 39858.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126188 restraints weight = 39120.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126404 restraints weight = 37219.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126766 restraints weight = 33911.721| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24816 Z= 0.132 Angle : 0.727 14.701 33915 Z= 0.359 Chirality : 0.049 0.551 4062 Planarity : 0.004 0.045 4227 Dihedral : 5.597 34.084 5070 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 3.34 % Allowed : 21.48 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.15), residues: 2967 helix: 2.10 (0.24), residues: 507 sheet: -1.68 (0.22), residues: 561 loop : -3.29 (0.12), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 895 TYR 0.027 0.001 TYR B 598 PHE 0.030 0.001 PHE C 320 TRP 0.003 0.001 TRP B 40 HIS 0.004 0.001 HIS C 823 Details of bonding type rmsd covalent geometry : bond 0.00293 (24687) covalent geometry : angle 0.68833 (33570) SS BOND : bond 0.00363 ( 42) SS BOND : angle 0.92076 ( 84) hydrogen bonds : bond 0.04419 ( 594) hydrogen bonds : angle 5.05288 ( 1638) link_BETA1-4 : bond 0.00443 ( 27) link_BETA1-4 : angle 1.13169 ( 81) link_NAG-ASN : bond 0.00884 ( 60) link_NAG-ASN : angle 3.22189 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 268 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 THR cc_start: 0.8029 (t) cc_final: 0.7797 (m) REVERT: A 191 LYS cc_start: 0.6603 (tptt) cc_final: 0.5865 (tppt) REVERT: A 253 GLN cc_start: 0.8243 (mt0) cc_final: 0.6910 (pm20) REVERT: A 512 ARG cc_start: 0.7984 (ptt90) cc_final: 0.7287 (ttp-110) REVERT: A 677 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7497 (pp) REVERT: A 857 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8529 (pp) REVERT: A 974 ILE cc_start: 0.7739 (tp) cc_final: 0.7523 (mp) REVERT: B 184 THR cc_start: 0.8279 (t) cc_final: 0.7999 (m) REVERT: B 321 MET cc_start: 0.8090 (mmm) cc_final: 0.7745 (tpt) REVERT: B 371 TYR cc_start: 0.8521 (m-80) cc_final: 0.8288 (m-80) REVERT: B 385 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.6749 (t80) REVERT: B 430 THR cc_start: 0.9265 (OUTLIER) cc_final: 0.8925 (m) REVERT: B 498 PHE cc_start: 0.8606 (p90) cc_final: 0.8396 (p90) REVERT: B 512 ARG cc_start: 0.8280 (ptt180) cc_final: 0.7491 (ttp80) REVERT: B 611 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8968 (tp) REVERT: B 677 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7716 (pp) REVERT: B 836 MET cc_start: 0.8545 (tpp) cc_final: 0.8319 (tpp) REVERT: B 846 ILE cc_start: 0.8736 (tp) cc_final: 0.8444 (pt) REVERT: B 974 ILE cc_start: 0.7737 (tp) cc_final: 0.7514 (mp) REVERT: C 83 MET cc_start: 0.8114 (mpp) cc_final: 0.7846 (mtt) REVERT: C 184 THR cc_start: 0.8030 (t) cc_final: 0.7734 (m) REVERT: C 253 GLN cc_start: 0.8296 (mt0) cc_final: 0.6984 (pm20) REVERT: C 430 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8886 (m) REVERT: C 512 ARG cc_start: 0.8061 (ptt90) cc_final: 0.7385 (ttp80) REVERT: C 635 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8575 (tp) REVERT: C 677 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7531 (pp) REVERT: C 726 LEU cc_start: 0.8149 (mm) cc_final: 0.7610 (tp) REVERT: C 746 MET cc_start: 0.8700 (tpp) cc_final: 0.7741 (ttp) REVERT: C 846 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8496 (tp) REVERT: C 904 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7171 (tm-30) outliers start: 85 outliers final: 69 residues processed: 326 average time/residue: 0.1425 time to fit residues: 78.6205 Evaluate side-chains 335 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 256 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 921 HIS Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 677 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 840 ASN Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 934 VAL Chi-restraints excluded: chain C residue 949 THR Chi-restraints excluded: chain C residue 984 ILE Chi-restraints excluded: chain C residue 985 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 245 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 170 optimal weight: 0.0010 chunk 281 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 chunk 294 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127898 restraints weight = 36185.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127166 restraints weight = 36513.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.127807 restraints weight = 35753.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128057 restraints weight = 32287.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128168 restraints weight = 30099.838| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24816 Z= 0.125 Angle : 0.709 14.580 33915 Z= 0.350 Chirality : 0.048 0.532 4062 Planarity : 0.004 0.043 4227 Dihedral : 5.365 32.195 5070 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 3.06 % Allowed : 21.83 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.15), residues: 2967 helix: 2.22 (0.24), residues: 507 sheet: -1.63 (0.22), residues: 579 loop : -3.22 (0.12), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 895 TYR 0.024 0.001 TYR B 598 PHE 0.023 0.001 PHE C 320 TRP 0.003 0.001 TRP B 40 HIS 0.004 0.001 HIS C 823 Details of bonding type rmsd covalent geometry : bond 0.00275 (24687) covalent geometry : angle 0.67028 (33570) SS BOND : bond 0.00361 ( 42) SS BOND : angle 0.85692 ( 84) hydrogen bonds : bond 0.04092 ( 594) hydrogen bonds : angle 4.93815 ( 1638) link_BETA1-4 : bond 0.00467 ( 27) link_BETA1-4 : angle 1.09829 ( 81) link_NAG-ASN : bond 0.00888 ( 60) link_NAG-ASN : angle 3.16725 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3451.03 seconds wall clock time: 60 minutes 51.59 seconds (3651.59 seconds total)