Starting phenix.real_space_refine on Wed Mar 4 20:19:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mdt_23779/03_2026/7mdt_23779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mdt_23779/03_2026/7mdt_23779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mdt_23779/03_2026/7mdt_23779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mdt_23779/03_2026/7mdt_23779.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mdt_23779/03_2026/7mdt_23779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mdt_23779/03_2026/7mdt_23779.map" } resolution = 3.6 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= 0.003 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 111 5.16 5 C 9973 2.51 5 N 2678 2.21 5 O 3194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15956 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3469 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 894 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "C" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3393 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 22, 'TRANS': 405} Chain breaks: 4 Chain: "E" Number of atoms: 3428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3428 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "D" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "F" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" 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: "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: "Y" 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: "Z" 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 3.91, per 1000 atoms: 0.25 Number of scatterers: 15956 At special positions: 0 Unit cell: (138.02, 126.69, 144.2, 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 111 16.00 O 3194 8.00 N 2678 7.00 C 9973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.11 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.09 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 4 " " BMA a 3 " - " MAN a 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA 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 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A 601 " - " ASN A 392 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 462 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 339 " " NAG A 610 " - " ASN A 363 " " NAG C 601 " - " ASN C 137 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 363 " " NAG C 604 " - " ASN C 392 " " NAG C 605 " - " ASN C 88 " " NAG C 606 " - " ASN C 234 " " NAG C 607 " - " ASN C 276 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 355 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 448 " " NAG C 612 " - " ASN C 339 " " NAG E 601 " - " ASN E 137 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 363 " " NAG E 604 " - " ASN E 88 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 301 " " NAG E 609 " - " ASN E 160 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 137 " " NAG J 1 " - " ASN A 133 " " NAG K 1 " - " ASN A 332 " " NAG M 1 " - " ASN A 197 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 448 " " NAG R 1 " - " ASN C 156 " " NAG S 1 " - " ASN C 332 " " NAG T 1 " - " ASN C 386 " " NAG U 1 " - " ASN C 160 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN E 156 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN E 197 " " NAG Z 1 " - " ASN E 386 " " NAG a 1 " - " ASN E 262 " " NAG b 1 " - " ASN E 448 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 751.5 milliseconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3522 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 38 sheets defined 25.2% alpha, 53.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 139 through 151 removed outlier: 3.732A pdb=" N ARG A 151 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.906A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.423A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.067A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 67 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.977A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 350 removed outlier: 5.163A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLY C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.949A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.089A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.935A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.252A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 570 through 596 Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.299A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.261A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.436A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.038A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.567A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.516A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.642A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.772A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.642A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.516A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.505A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.491A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.574A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY L 95B" --> pdb=" O ASP L 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.574A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.556A pdb=" N LEU H 101 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU H 96 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TRP H 103 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ARG H 94 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLN H 105 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS H 92 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 18 through 22 Processing sheet with id=AB6, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.378A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.890A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC2, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.954A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.649A pdb=" N SER C 375 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 315 through 323 removed outlier: 6.461A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 375 " --> pdb=" O THR C 257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.649A pdb=" N SER C 375 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 360 through 361 removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 375 " --> pdb=" O THR C 257 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.556A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 315 through 323 removed outlier: 6.461A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.556A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.871A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 360 through 361 removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.311A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AD5, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.452A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD8, first strand: chain 'E' and resid 200 through 203 removed outlier: 5.923A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 256 through 257 removed outlier: 3.539A pdb=" N SER E 375 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.289A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.034A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.583A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.552A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.583A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.034A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.289A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 302 current: chain 'E' and resid 358 through 361 Processing sheet with id=AE2, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.860A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 1926 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: 3.36 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3514 1.32 - 1.46: 5065 1.46 - 1.59: 7472 1.59 - 1.73: 60 1.73 - 1.87: 146 Bond restraints: 16257 Sorted by residual: bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.415 -0.089 1.10e-02 8.26e+03 6.50e+01 bond pdb=" CA THR E 132 " pdb=" C THR E 132 " ideal model delta sigma weight residual 1.520 1.555 -0.036 4.80e-03 4.34e+04 5.56e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.649 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" CB LEU D 663 " pdb=" CG LEU D 663 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" CB ILE C 396 " pdb=" CG1 ILE C 396 " ideal model delta sigma weight residual 1.530 1.647 -0.117 2.00e-02 2.50e+03 3.42e+01 ... (remaining 16252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.67: 22022 7.67 - 15.34: 35 15.34 - 23.01: 0 23.01 - 30.68: 0 30.68 - 38.35: 4 Bond angle restraints: 22061 Sorted by residual: angle pdb=" C2 NAG C 606 " pdb=" N2 NAG C 606 " pdb=" C7 NAG C 606 " ideal model delta sigma weight residual 124.56 162.91 -38.35 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C2 NAG V 1 " pdb=" N2 NAG V 1 " pdb=" C7 NAG V 1 " ideal model delta sigma weight residual 124.56 161.82 -37.26 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C2 NAG I 2 " pdb=" N2 NAG I 2 " pdb=" C7 NAG I 2 " ideal model delta sigma weight residual 124.56 161.68 -37.12 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " pdb=" C7 NAG P 1 " ideal model delta sigma weight residual 124.56 160.64 -36.08 3.00e+00 1.11e-01 1.45e+02 angle pdb=" N GLN L 79 " pdb=" CA GLN L 79 " pdb=" C GLN L 79 " ideal model delta sigma weight residual 110.52 98.94 11.58 1.48e+00 4.57e-01 6.12e+01 ... (remaining 22056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 10421 21.72 - 43.43: 233 43.43 - 65.15: 82 65.15 - 86.87: 33 86.87 - 108.59: 16 Dihedral angle restraints: 10785 sinusoidal: 5341 harmonic: 5444 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 156.03 -63.03 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.63 -61.63 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.50 -57.50 1 1.00e+01 1.00e-02 4.44e+01 ... (remaining 10782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1785 0.107 - 0.213: 568 0.213 - 0.320: 211 0.320 - 0.427: 102 0.427 - 0.533: 45 Chirality restraints: 2711 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.84e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.74e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 ... (remaining 2708 not shown) Planarity restraints: 2757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 339 " 0.077 2.00e-02 2.50e+03 8.02e-02 8.05e+01 pdb=" CG ASN C 339 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN C 339 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 339 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG C 612 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " 0.072 2.00e-02 2.50e+03 7.42e-02 6.88e+01 pdb=" CG ASN E 234 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " -0.113 2.00e-02 2.50e+03 pdb=" C1 NAG E 605 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 88 " -0.068 2.00e-02 2.50e+03 7.18e-02 6.44e+01 pdb=" CG ASN E 88 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN E 88 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN E 88 " 0.112 2.00e-02 2.50e+03 pdb=" C1 NAG E 604 " -0.087 2.00e-02 2.50e+03 ... (remaining 2754 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5685 2.88 - 3.39: 14100 3.39 - 3.89: 26158 3.89 - 4.40: 30245 4.40 - 4.90: 48013 Nonbonded interactions: 124201 Sorted by model distance: nonbonded pdb=" N GLN L 79 " pdb=" O GLN L 79 " model vdw 2.380 2.496 nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.403 3.120 nonbonded pdb=" N LEU D 544 " pdb=" O LEU D 544 " model vdw 2.415 2.496 nonbonded pdb=" OD1 ASP E 474 " pdb=" N MET E 475 " model vdw 2.429 3.120 nonbonded pdb=" OD1 ASP H 72 " pdb=" NZ LYS H 75 " model vdw 2.434 3.120 ... (remaining 124196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 57 or resid 66 through 457 or resid 466 through \ 503 or resid 601 through 609)) selection = (chain 'C' and (resid 34 through 503 or resid 603 through 611)) selection = (chain 'E' and (resid 34 through 57 or resid 66 through 457 or resid 466 through \ 503 or resid 601 through 609)) } ncs_group { reference = (chain 'B' and resid 521 through 663) selection = (chain 'D' and (resid 521 through 546 or resid 569 through 663)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' } ncs_group { reference = chain 'P' selection = chain 'V' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.800 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.023 0.134 16370 Z= 1.226 Angle : 1.849 38.348 22365 Z= 1.144 Chirality : 0.146 0.533 2711 Planarity : 0.008 0.044 2706 Dihedral : 11.861 108.585 7158 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.12 % Allowed : 0.48 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 1848 helix: 0.22 (0.25), residues: 379 sheet: 0.82 (0.23), residues: 481 loop : 0.49 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 166 TYR 0.051 0.007 TYR L 36 PHE 0.032 0.006 PHE C 383 TRP 0.056 0.010 TRP H 103 HIS 0.009 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.02284 (16257) covalent geometry : angle 1.80829 (22061) SS BOND : bond 0.01871 ( 35) SS BOND : angle 3.54349 ( 70) hydrogen bonds : bond 0.16771 ( 589) hydrogen bonds : angle 7.43966 ( 1926) link_ALPHA1-3 : bond 0.07936 ( 3) link_ALPHA1-3 : angle 4.16524 ( 9) link_BETA1-4 : bond 0.07711 ( 24) link_BETA1-4 : angle 5.61316 ( 72) link_NAG-ASN : bond 0.07785 ( 51) link_NAG-ASN : angle 2.55146 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 450 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8997 (m-80) cc_final: 0.8446 (m-80) REVERT: A 279 ASN cc_start: 0.8205 (t0) cc_final: 0.7892 (t0) REVERT: A 315 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8082 (mt0) REVERT: A 485 LYS cc_start: 0.8817 (mttt) cc_final: 0.8561 (mtmt) REVERT: B 599 SER cc_start: 0.8856 (t) cc_final: 0.8570 (p) REVERT: B 652 GLN cc_start: 0.8051 (mt0) cc_final: 0.7512 (mt0) REVERT: L 69 THR cc_start: 0.8660 (p) cc_final: 0.8420 (t) REVERT: H 31 ARG cc_start: 0.8229 (mtp85) cc_final: 0.8012 (mtt-85) REVERT: H 81 GLN cc_start: 0.7872 (tp40) cc_final: 0.7576 (mm110) REVERT: C 207 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8445 (ptmt) REVERT: E 125 LEU cc_start: 0.8821 (mt) cc_final: 0.8562 (mt) REVERT: E 239 CYS cc_start: 0.7422 (t) cc_final: 0.7018 (t) REVERT: E 486 TYR cc_start: 0.9415 (m-80) cc_final: 0.9179 (m-80) REVERT: D 625 ASN cc_start: 0.8402 (t0) cc_final: 0.8196 (t0) REVERT: D 640 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7879 (tp40) REVERT: F 575 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7740 (tt0) REVERT: F 635 ILE cc_start: 0.8722 (pt) cc_final: 0.8370 (pt) outliers start: 2 outliers final: 0 residues processed: 452 average time/residue: 0.1483 time to fit residues: 95.6347 Evaluate side-chains 276 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 302 ASN A 428 GLN A 478 ASN B 625 ASN B 630 GLN L 51 ASN L 94 ASN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82AASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS C 374 HIS C 432 GLN E 103 GLN E 374 HIS E 478 ASN D 540 GLN D 543 ASN F 653 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102029 restraints weight = 26203.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.105414 restraints weight = 13829.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107675 restraints weight = 9076.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109190 restraints weight = 6760.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110231 restraints weight = 5476.599| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16370 Z= 0.164 Angle : 0.766 12.379 22365 Z= 0.380 Chirality : 0.051 0.317 2711 Planarity : 0.004 0.054 2706 Dihedral : 9.174 71.224 3633 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.27 % Favored : 97.67 % Rotamer: Outliers : 2.58 % Allowed : 8.58 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1848 helix: 1.74 (0.27), residues: 382 sheet: 0.76 (0.23), residues: 492 loop : 0.17 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 308 TYR 0.019 0.002 TYR L 50 PHE 0.027 0.002 PHE C 53 TRP 0.016 0.002 TRP E 69 HIS 0.007 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00352 (16257) covalent geometry : angle 0.70755 (22061) SS BOND : bond 0.00276 ( 35) SS BOND : angle 1.11249 ( 70) hydrogen bonds : bond 0.06081 ( 589) hydrogen bonds : angle 5.34166 ( 1926) link_ALPHA1-3 : bond 0.00889 ( 3) link_ALPHA1-3 : angle 2.78838 ( 9) link_BETA1-4 : bond 0.00886 ( 24) link_BETA1-4 : angle 3.30477 ( 72) link_NAG-ASN : bond 0.00513 ( 51) link_NAG-ASN : angle 2.71525 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 322 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7989 (mt0) REVERT: A 485 LYS cc_start: 0.8403 (mttt) cc_final: 0.8120 (mtpp) REVERT: B 618 ASN cc_start: 0.7460 (m110) cc_final: 0.7182 (m110) REVERT: B 626 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7563 (ttm) REVERT: L 69 THR cc_start: 0.8836 (p) cc_final: 0.8451 (t) REVERT: H 82 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8257 (mtp) REVERT: C 35 TRP cc_start: 0.8720 (m100) cc_final: 0.8427 (m100) REVERT: C 207 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8251 (ptmt) REVERT: D 625 ASN cc_start: 0.8081 (t0) cc_final: 0.7872 (t0) REVERT: F 626 MET cc_start: 0.7835 (ttp) cc_final: 0.7508 (ttp) outliers start: 43 outliers final: 15 residues processed: 347 average time/residue: 0.1189 time to fit residues: 61.5101 Evaluate side-chains 263 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 246 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 181 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 156 optimal weight: 0.0070 chunk 168 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 185 ASN L 94 ASN C 85 HIS C 99 ASN C 195 ASN E 478 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.100263 restraints weight = 26475.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.103631 restraints weight = 14018.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105881 restraints weight = 9229.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.107366 restraints weight = 6913.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108427 restraints weight = 5621.611| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16370 Z= 0.140 Angle : 0.650 11.048 22365 Z= 0.325 Chirality : 0.048 0.336 2711 Planarity : 0.004 0.038 2706 Dihedral : 7.733 59.586 3633 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.10 % Allowed : 10.98 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1848 helix: 1.95 (0.28), residues: 387 sheet: 0.75 (0.23), residues: 494 loop : -0.14 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 192 TYR 0.018 0.001 TYR E 484 PHE 0.027 0.002 PHE C 53 TRP 0.011 0.001 TRP C 69 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00310 (16257) covalent geometry : angle 0.59987 (22061) SS BOND : bond 0.00258 ( 35) SS BOND : angle 0.87740 ( 70) hydrogen bonds : bond 0.05065 ( 589) hydrogen bonds : angle 4.83510 ( 1926) link_ALPHA1-3 : bond 0.01140 ( 3) link_ALPHA1-3 : angle 1.52642 ( 9) link_BETA1-4 : bond 0.00889 ( 24) link_BETA1-4 : angle 2.91519 ( 72) link_NAG-ASN : bond 0.00389 ( 51) link_NAG-ASN : angle 2.31763 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 315 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7984 (mt0) REVERT: B 542 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7860 (ttp-170) REVERT: B 626 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7274 (ttm) REVERT: L 50 TYR cc_start: 0.8381 (t80) cc_final: 0.8171 (t80) REVERT: L 79 GLN cc_start: 0.7932 (mp10) cc_final: 0.6762 (mt0) REVERT: H 46 GLU cc_start: 0.8475 (tt0) cc_final: 0.8264 (tt0) REVERT: H 58 TYR cc_start: 0.8692 (m-80) cc_final: 0.8460 (m-80) REVERT: C 35 TRP cc_start: 0.8758 (m100) cc_final: 0.8443 (m100) REVERT: C 207 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8275 (ptmt) REVERT: C 246 GLN cc_start: 0.6748 (mt0) cc_final: 0.6491 (mp10) REVERT: E 421 LYS cc_start: 0.8810 (tttt) cc_final: 0.8417 (ttpt) REVERT: E 486 TYR cc_start: 0.9237 (m-80) cc_final: 0.8797 (m-80) REVERT: D 545 LEU cc_start: 0.9095 (tp) cc_final: 0.8868 (tp) REVERT: D 621 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: F 655 LYS cc_start: 0.8592 (tptp) cc_final: 0.8348 (tptp) outliers start: 35 outliers final: 20 residues processed: 289 average time/residue: 0.1250 time to fit residues: 55.1652 Evaluate side-chains 266 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 244 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 185 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 37 optimal weight: 0.0270 chunk 101 optimal weight: 2.9990 overall best weight: 1.0840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 478 ASN D 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.098757 restraints weight = 26495.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.102035 restraints weight = 14218.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.104229 restraints weight = 9462.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105714 restraints weight = 7136.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.106744 restraints weight = 5827.046| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16370 Z= 0.153 Angle : 0.633 10.315 22365 Z= 0.314 Chirality : 0.047 0.254 2711 Planarity : 0.004 0.032 2706 Dihedral : 6.835 59.994 3633 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.10 % Allowed : 12.36 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 1848 helix: 2.06 (0.28), residues: 393 sheet: 0.75 (0.23), residues: 495 loop : -0.31 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 542 TYR 0.012 0.001 TYR C 173 PHE 0.024 0.002 PHE C 53 TRP 0.017 0.001 TRP C 427 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00349 (16257) covalent geometry : angle 0.58768 (22061) SS BOND : bond 0.00292 ( 35) SS BOND : angle 0.86676 ( 70) hydrogen bonds : bond 0.04633 ( 589) hydrogen bonds : angle 4.64358 ( 1926) link_ALPHA1-3 : bond 0.01109 ( 3) link_ALPHA1-3 : angle 1.90293 ( 9) link_BETA1-4 : bond 0.00779 ( 24) link_BETA1-4 : angle 2.65875 ( 72) link_NAG-ASN : bond 0.00664 ( 51) link_NAG-ASN : angle 2.22230 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 GLN cc_start: 0.8474 (mm-40) cc_final: 0.7947 (mt0) REVERT: B 542 ARG cc_start: 0.8209 (ttp-110) cc_final: 0.7928 (ttp-170) REVERT: B 543 ASN cc_start: 0.8529 (m-40) cc_final: 0.8127 (t0) REVERT: L 50 TYR cc_start: 0.8204 (t80) cc_final: 0.7923 (t80) REVERT: H 34 MET cc_start: 0.8688 (mmm) cc_final: 0.8481 (mmt) REVERT: C 35 TRP cc_start: 0.8784 (m100) cc_final: 0.8496 (m100) REVERT: C 246 GLN cc_start: 0.6448 (mt0) cc_final: 0.6156 (mp10) REVERT: E 271 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8324 (mtp) REVERT: E 421 LYS cc_start: 0.8764 (tttt) cc_final: 0.8439 (ttpt) REVERT: E 486 TYR cc_start: 0.9237 (m-80) cc_final: 0.8661 (m-80) REVERT: D 647 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7398 (mt-10) REVERT: F 571 TRP cc_start: 0.7645 (m100) cc_final: 0.7336 (m100) REVERT: F 655 LYS cc_start: 0.8704 (tptp) cc_final: 0.8473 (tptp) outliers start: 35 outliers final: 20 residues processed: 279 average time/residue: 0.1229 time to fit residues: 52.4501 Evaluate side-chains 260 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 31 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN L 94 ASN H 73 ASN C 425 ASN E 478 ASN D 625 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.097151 restraints weight = 26584.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.100370 restraints weight = 14280.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.102531 restraints weight = 9513.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.103978 restraints weight = 7173.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104980 restraints weight = 5871.783| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16370 Z= 0.178 Angle : 0.631 9.042 22365 Z= 0.314 Chirality : 0.048 0.557 2711 Planarity : 0.004 0.037 2706 Dihedral : 6.619 58.872 3633 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.52 % Allowed : 12.91 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1848 helix: 2.04 (0.28), residues: 394 sheet: 0.68 (0.23), residues: 504 loop : -0.42 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 542 TYR 0.019 0.001 TYR E 484 PHE 0.021 0.002 PHE C 53 TRP 0.013 0.001 TRP C 427 HIS 0.008 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00421 (16257) covalent geometry : angle 0.58981 (22061) SS BOND : bond 0.00330 ( 35) SS BOND : angle 0.82162 ( 70) hydrogen bonds : bond 0.04638 ( 589) hydrogen bonds : angle 4.62400 ( 1926) link_ALPHA1-3 : bond 0.01137 ( 3) link_ALPHA1-3 : angle 1.73115 ( 9) link_BETA1-4 : bond 0.00780 ( 24) link_BETA1-4 : angle 2.60295 ( 72) link_NAG-ASN : bond 0.00358 ( 51) link_NAG-ASN : angle 2.10960 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7945 (ttp-170) REVERT: B 543 ASN cc_start: 0.8528 (m-40) cc_final: 0.8170 (t0) REVERT: B 626 MET cc_start: 0.7931 (ttm) cc_final: 0.7290 (ttm) REVERT: L 27 ASN cc_start: 0.8425 (p0) cc_final: 0.8224 (p0) REVERT: H 34 MET cc_start: 0.8712 (mmm) cc_final: 0.8467 (mmt) REVERT: C 35 TRP cc_start: 0.8842 (m100) cc_final: 0.8533 (m100) REVERT: C 99 ASN cc_start: 0.8515 (m-40) cc_final: 0.8121 (t0) REVERT: E 271 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8316 (mtp) REVERT: E 486 TYR cc_start: 0.9264 (m-80) cc_final: 0.8751 (m-80) REVERT: F 571 TRP cc_start: 0.7725 (m100) cc_final: 0.7454 (m100) REVERT: F 654 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8172 (tp30) outliers start: 42 outliers final: 27 residues processed: 265 average time/residue: 0.1239 time to fit residues: 50.3278 Evaluate side-chains 259 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 648 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 133 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 128 optimal weight: 0.0270 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN E 478 ASN D 625 ASN F 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.098635 restraints weight = 26417.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.101912 restraints weight = 14202.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.104071 restraints weight = 9441.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.105527 restraints weight = 7128.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106506 restraints weight = 5831.166| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16370 Z= 0.122 Angle : 0.590 12.075 22365 Z= 0.294 Chirality : 0.047 0.465 2711 Planarity : 0.003 0.033 2706 Dihedral : 6.362 58.785 3633 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.10 % Allowed : 13.99 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.20), residues: 1848 helix: 2.18 (0.28), residues: 394 sheet: 0.73 (0.23), residues: 500 loop : -0.42 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 192 TYR 0.013 0.001 TYR C 173 PHE 0.020 0.001 PHE C 53 TRP 0.013 0.001 TRP A 427 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00270 (16257) covalent geometry : angle 0.54759 (22061) SS BOND : bond 0.00226 ( 35) SS BOND : angle 0.82734 ( 70) hydrogen bonds : bond 0.04191 ( 589) hydrogen bonds : angle 4.45634 ( 1926) link_ALPHA1-3 : bond 0.01098 ( 3) link_ALPHA1-3 : angle 1.52019 ( 9) link_BETA1-4 : bond 0.00778 ( 24) link_BETA1-4 : angle 2.40129 ( 72) link_NAG-ASN : bond 0.00383 ( 51) link_NAG-ASN : angle 2.13340 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8433 (t-100) cc_final: 0.7961 (t-100) REVERT: B 542 ARG cc_start: 0.8219 (ttp-110) cc_final: 0.7999 (ttp-170) REVERT: B 543 ASN cc_start: 0.8429 (m-40) cc_final: 0.8181 (t0) REVERT: B 626 MET cc_start: 0.7864 (ttm) cc_final: 0.7174 (ttm) REVERT: L 79 GLN cc_start: 0.8078 (mp10) cc_final: 0.7175 (pt0) REVERT: C 35 TRP cc_start: 0.8825 (m100) cc_final: 0.8513 (m100) REVERT: C 99 ASN cc_start: 0.8425 (m-40) cc_final: 0.8033 (t0) REVERT: C 161 MET cc_start: 0.8792 (tpt) cc_final: 0.8498 (tpt) REVERT: C 486 TYR cc_start: 0.9282 (m-80) cc_final: 0.9032 (m-80) REVERT: E 271 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8379 (mtp) REVERT: E 421 LYS cc_start: 0.8753 (tttt) cc_final: 0.8381 (ttpt) REVERT: E 486 TYR cc_start: 0.9231 (m-80) cc_final: 0.8641 (m-80) REVERT: D 647 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7538 (mt-10) REVERT: F 652 GLN cc_start: 0.8350 (tt0) cc_final: 0.8147 (tm-30) REVERT: F 654 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8137 (tp30) outliers start: 35 outliers final: 22 residues processed: 276 average time/residue: 0.1244 time to fit residues: 52.3974 Evaluate side-chains 257 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 11 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN E 85 HIS E 478 ASN D 625 ASN F 653 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.097960 restraints weight = 26479.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.101198 restraints weight = 14286.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.103342 restraints weight = 9548.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.104774 restraints weight = 7230.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105795 restraints weight = 5924.877| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16370 Z= 0.139 Angle : 0.593 11.075 22365 Z= 0.296 Chirality : 0.047 0.450 2711 Planarity : 0.003 0.035 2706 Dihedral : 6.264 56.918 3633 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.04 % Allowed : 15.07 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1848 helix: 2.15 (0.28), residues: 395 sheet: 0.75 (0.24), residues: 494 loop : -0.51 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 542 TYR 0.020 0.001 TYR E 484 PHE 0.020 0.002 PHE C 53 TRP 0.014 0.001 TRP A 427 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00321 (16257) covalent geometry : angle 0.55571 (22061) SS BOND : bond 0.00261 ( 35) SS BOND : angle 0.84299 ( 70) hydrogen bonds : bond 0.04221 ( 589) hydrogen bonds : angle 4.42490 ( 1926) link_ALPHA1-3 : bond 0.01085 ( 3) link_ALPHA1-3 : angle 1.47136 ( 9) link_BETA1-4 : bond 0.00784 ( 24) link_BETA1-4 : angle 2.37769 ( 72) link_NAG-ASN : bond 0.00359 ( 51) link_NAG-ASN : angle 1.94745 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8439 (t-100) cc_final: 0.7976 (t-100) REVERT: B 542 ARG cc_start: 0.8234 (ttp-110) cc_final: 0.8031 (ttp-170) REVERT: B 626 MET cc_start: 0.7873 (ttm) cc_final: 0.7216 (ttm) REVERT: L 79 GLN cc_start: 0.8100 (mp10) cc_final: 0.7275 (pt0) REVERT: H 81 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7530 (tp40) REVERT: C 35 TRP cc_start: 0.8857 (m100) cc_final: 0.8532 (m100) REVERT: C 99 ASN cc_start: 0.8448 (m-40) cc_final: 0.8052 (t0) REVERT: C 100 MET cc_start: 0.8823 (mtp) cc_final: 0.8536 (mtm) REVERT: C 161 MET cc_start: 0.8754 (tpt) cc_final: 0.8451 (tpt) REVERT: E 271 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8369 (mtp) REVERT: E 421 LYS cc_start: 0.8758 (tttt) cc_final: 0.8434 (ttpt) REVERT: E 486 TYR cc_start: 0.9230 (m-80) cc_final: 0.8628 (m-80) REVERT: D 647 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7602 (mt-10) REVERT: F 631 TRP cc_start: 0.8279 (t-100) cc_final: 0.7973 (t-100) REVERT: F 654 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8066 (tp30) outliers start: 34 outliers final: 25 residues processed: 266 average time/residue: 0.1299 time to fit residues: 51.9665 Evaluate side-chains 259 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 648 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 144 optimal weight: 2.9990 chunk 179 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN E 478 ASN D 625 ASN F 652 GLN F 653 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098070 restraints weight = 26727.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101314 restraints weight = 14355.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.103492 restraints weight = 9565.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104954 restraints weight = 7205.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105959 restraints weight = 5887.017| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16370 Z= 0.136 Angle : 0.587 11.130 22365 Z= 0.293 Chirality : 0.046 0.436 2711 Planarity : 0.003 0.034 2706 Dihedral : 6.206 56.400 3633 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.16 % Allowed : 14.95 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1848 helix: 2.25 (0.27), residues: 394 sheet: 0.71 (0.24), residues: 481 loop : -0.53 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 542 TYR 0.017 0.001 TYR H 58 PHE 0.020 0.001 PHE C 53 TRP 0.013 0.001 TRP A 427 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00317 (16257) covalent geometry : angle 0.55189 (22061) SS BOND : bond 0.00253 ( 35) SS BOND : angle 0.78330 ( 70) hydrogen bonds : bond 0.04083 ( 589) hydrogen bonds : angle 4.37639 ( 1926) link_ALPHA1-3 : bond 0.00959 ( 3) link_ALPHA1-3 : angle 1.35970 ( 9) link_BETA1-4 : bond 0.00758 ( 24) link_BETA1-4 : angle 2.30224 ( 72) link_NAG-ASN : bond 0.00338 ( 51) link_NAG-ASN : angle 1.87620 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8226 (ttp-110) cc_final: 0.7982 (ttp-170) REVERT: B 626 MET cc_start: 0.7887 (ttm) cc_final: 0.7219 (ttm) REVERT: L 79 GLN cc_start: 0.8125 (mp10) cc_final: 0.7215 (pt0) REVERT: H 81 GLN cc_start: 0.7931 (tp-100) cc_final: 0.7565 (tp40) REVERT: C 35 TRP cc_start: 0.8788 (m100) cc_final: 0.8469 (m100) REVERT: C 99 ASN cc_start: 0.8511 (m-40) cc_final: 0.8073 (t0) REVERT: C 161 MET cc_start: 0.8755 (tpt) cc_final: 0.8462 (tpt) REVERT: C 213 ILE cc_start: 0.8879 (mt) cc_final: 0.8654 (pt) REVERT: C 486 TYR cc_start: 0.9296 (m-80) cc_final: 0.9042 (m-80) REVERT: E 271 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8332 (mtp) REVERT: E 421 LYS cc_start: 0.8762 (tttt) cc_final: 0.8432 (ttpt) REVERT: E 486 TYR cc_start: 0.9215 (m-80) cc_final: 0.8522 (m-80) REVERT: F 631 TRP cc_start: 0.8323 (t-100) cc_final: 0.7951 (t-100) REVERT: F 654 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7915 (tp30) outliers start: 36 outliers final: 28 residues processed: 266 average time/residue: 0.1263 time to fit residues: 51.1462 Evaluate side-chains 261 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 648 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 74 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 93 optimal weight: 0.0000 chunk 56 optimal weight: 9.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 478 ASN D 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.099203 restraints weight = 26452.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.102456 restraints weight = 14208.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.104608 restraints weight = 9451.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.106064 restraints weight = 7129.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107094 restraints weight = 5822.447| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16370 Z= 0.123 Angle : 0.581 10.428 22365 Z= 0.293 Chirality : 0.046 0.427 2711 Planarity : 0.003 0.032 2706 Dihedral : 6.083 56.416 3633 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.92 % Allowed : 15.61 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1848 helix: 2.34 (0.27), residues: 395 sheet: 0.72 (0.24), residues: 489 loop : -0.59 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 542 TYR 0.020 0.001 TYR E 484 PHE 0.019 0.001 PHE C 53 TRP 0.013 0.001 TRP E 69 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00277 (16257) covalent geometry : angle 0.54830 (22061) SS BOND : bond 0.00236 ( 35) SS BOND : angle 0.79295 ( 70) hydrogen bonds : bond 0.03885 ( 589) hydrogen bonds : angle 4.30031 ( 1926) link_ALPHA1-3 : bond 0.00903 ( 3) link_ALPHA1-3 : angle 1.30459 ( 9) link_BETA1-4 : bond 0.00752 ( 24) link_BETA1-4 : angle 2.22273 ( 72) link_NAG-ASN : bond 0.00351 ( 51) link_NAG-ASN : angle 1.79516 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8419 (t-100) cc_final: 0.8013 (t-100) REVERT: B 626 MET cc_start: 0.7807 (ttm) cc_final: 0.7165 (ttm) REVERT: L 79 GLN cc_start: 0.8108 (mp10) cc_final: 0.7232 (pt0) REVERT: H 81 GLN cc_start: 0.7928 (tp-100) cc_final: 0.7585 (tp40) REVERT: C 35 TRP cc_start: 0.8767 (m100) cc_final: 0.8462 (m100) REVERT: C 99 ASN cc_start: 0.8499 (m-40) cc_final: 0.8230 (m-40) REVERT: C 161 MET cc_start: 0.8712 (tpt) cc_final: 0.8417 (tpt) REVERT: C 213 ILE cc_start: 0.8878 (mt) cc_final: 0.8663 (pt) REVERT: C 486 TYR cc_start: 0.9288 (m-80) cc_final: 0.9054 (m-80) REVERT: E 271 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8334 (mtp) REVERT: E 421 LYS cc_start: 0.8715 (tttt) cc_final: 0.8353 (ttpt) REVERT: F 631 TRP cc_start: 0.8249 (t-100) cc_final: 0.7935 (t-100) REVERT: F 654 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7859 (tp30) outliers start: 32 outliers final: 23 residues processed: 259 average time/residue: 0.1233 time to fit residues: 48.7438 Evaluate side-chains 259 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 84 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 128 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN E 195 ASN D 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.099729 restraints weight = 26432.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102997 restraints weight = 14205.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105173 restraints weight = 9462.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106635 restraints weight = 7123.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107611 restraints weight = 5812.793| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16370 Z= 0.116 Angle : 0.580 10.570 22365 Z= 0.293 Chirality : 0.045 0.424 2711 Planarity : 0.004 0.043 2706 Dihedral : 5.980 56.223 3633 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.92 % Allowed : 15.43 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1848 helix: 2.37 (0.27), residues: 395 sheet: 0.73 (0.25), residues: 468 loop : -0.58 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 542 TYR 0.026 0.001 TYR A 191 PHE 0.019 0.001 PHE C 53 TRP 0.024 0.001 TRP A 96 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00257 (16257) covalent geometry : angle 0.54925 (22061) SS BOND : bond 0.00233 ( 35) SS BOND : angle 0.77809 ( 70) hydrogen bonds : bond 0.03780 ( 589) hydrogen bonds : angle 4.25707 ( 1926) link_ALPHA1-3 : bond 0.00863 ( 3) link_ALPHA1-3 : angle 1.28440 ( 9) link_BETA1-4 : bond 0.00755 ( 24) link_BETA1-4 : angle 2.16641 ( 72) link_NAG-ASN : bond 0.00368 ( 51) link_NAG-ASN : angle 1.77036 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.7823 (ttm) cc_final: 0.7178 (ttm) REVERT: L 79 GLN cc_start: 0.8139 (mp10) cc_final: 0.7210 (pt0) REVERT: H 81 GLN cc_start: 0.7969 (tp-100) cc_final: 0.7659 (tp40) REVERT: C 35 TRP cc_start: 0.8758 (m100) cc_final: 0.8414 (m100) REVERT: C 99 ASN cc_start: 0.8418 (m-40) cc_final: 0.8159 (m-40) REVERT: C 161 MET cc_start: 0.8713 (tpt) cc_final: 0.8424 (tpt) REVERT: C 475 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6288 (ptt) REVERT: C 486 TYR cc_start: 0.9273 (m-80) cc_final: 0.8949 (m-80) REVERT: E 271 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8252 (mtp) REVERT: E 421 LYS cc_start: 0.8692 (tttt) cc_final: 0.8336 (ttpt) REVERT: F 631 TRP cc_start: 0.8196 (t-100) cc_final: 0.7867 (t-100) REVERT: F 654 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7832 (tp30) outliers start: 32 outliers final: 25 residues processed: 261 average time/residue: 0.1270 time to fit residues: 50.5362 Evaluate side-chains 263 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 34 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN D 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.099166 restraints weight = 26257.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102387 restraints weight = 14172.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.104530 restraints weight = 9445.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105969 restraints weight = 7129.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106981 restraints weight = 5832.460| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16370 Z= 0.130 Angle : 0.586 10.113 22365 Z= 0.294 Chirality : 0.046 0.416 2711 Planarity : 0.003 0.037 2706 Dihedral : 5.987 56.182 3633 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.80 % Allowed : 15.91 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1848 helix: 2.36 (0.27), residues: 396 sheet: 0.70 (0.24), residues: 478 loop : -0.62 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 542 TYR 0.023 0.001 TYR E 484 PHE 0.019 0.001 PHE C 53 TRP 0.014 0.001 TRP A 96 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00297 (16257) covalent geometry : angle 0.55552 (22061) SS BOND : bond 0.00260 ( 35) SS BOND : angle 0.80163 ( 70) hydrogen bonds : bond 0.03846 ( 589) hydrogen bonds : angle 4.25617 ( 1926) link_ALPHA1-3 : bond 0.00839 ( 3) link_ALPHA1-3 : angle 1.28986 ( 9) link_BETA1-4 : bond 0.00739 ( 24) link_BETA1-4 : angle 2.18494 ( 72) link_NAG-ASN : bond 0.00330 ( 51) link_NAG-ASN : angle 1.75982 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2581.05 seconds wall clock time: 45 minutes 30.39 seconds (2730.39 seconds total)