Starting phenix.real_space_refine on Fri Jul 3 20:43:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mdt_23779/07_2026/7mdt_23779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mdt_23779/07_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_23779/07_2026/7mdt_23779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mdt_23779/07_2026/7mdt_23779.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mdt_23779/07_2026/7mdt_23779.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mdt_23779/07_2026/7mdt_23779.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mdt_23779/07_2026/7mdt_23779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mdt_23779/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 9 Time building chain proxies: 4.03, 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: 1.63 Conformation dependent library (CDL) restraints added in 828.0 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: 0.74 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: 3.30 Time building geometry restraints manager: 2.08 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 - 16.71: 8794 16.71 - 33.41: 248 33.41 - 50.12: 71 50.12 - 66.82: 37 66.82 - 83.53: 11 Dihedral angle restraints: 9161 sinusoidal: 3717 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 9158 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: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.120 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 : 9.995 83.529 5534 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/Z covalent geometry : bond 0.02284 / 1.20 (16257) covalent geometry : angle 1.80829 / 1.14 (22061) SS BOND : bond 0.01871 / 1.31 ( 35) SS BOND : angle 3.54349 / 2.51 ( 70) hydrogen bonds : bond 0.16771 / 10.88 ( 589) hydrogen bonds : angle 7.43966 / 5.27 ( 1926) link_ALPHA1-3 : bond 0.07936 / 3.98 ( 3) link_ALPHA1-3 : angle 4.16524 / 2.66 ( 9) link_BETA1-4 : bond 0.07711 / 4.63 ( 24) link_BETA1-4 : angle 5.61316 / 3.96 ( 72) link_NAG-ASN : bond 0.07785 / 5.06 ( 51) link_NAG-ASN : angle 2.55146 / 1.75 ( 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 : 0.735 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: 0.1460 time to fit residues: 94.6719 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 : 0.498 ------------------------------------------------------------------------------- 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... 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 = 0.119798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102013 restraints weight = 26216.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.105393 restraints weight = 13816.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107655 restraints weight = 9075.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109163 restraints weight = 6753.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110192 restraints weight = 5475.479| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16370 Z= 0.165 Angle : 0.756 12.167 22365 Z= 0.378 Chirality : 0.050 0.315 2711 Planarity : 0.004 0.054 2706 Dihedral : 5.086 21.808 2009 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 2.40 % Allowed : 8.82 % Favored : 88.78 % 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: 0.89 (0.20), residues: 1848 helix: 1.62 (0.27), residues: 388 sheet: 0.81 (0.23), residues: 502 loop : 0.12 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 308 TYR 0.018 0.002 TYR L 50 PHE 0.027 0.002 PHE C 53 TRP 0.014 0.002 TRP A 427 HIS 0.007 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (16257) covalent geometry : angle 0.70289 / 0.37 (22061) SS BOND : bond 0.00265 / 0.19 ( 35) SS BOND : angle 1.13677 / 0.80 ( 70) hydrogen bonds : bond 0.06087 / 4.07 ( 589) hydrogen bonds : angle 5.32709 / 3.75 ( 1926) link_ALPHA1-3 : bond 0.00653 / 0.33 ( 3) link_ALPHA1-3 : angle 1.71187 / 1.04 ( 9) link_BETA1-4 : bond 0.00805 / 0.50 ( 24) link_BETA1-4 : angle 3.08382 / 2.19 ( 72) link_NAG-ASN : bond 0.00511 / 0.34 ( 51) link_NAG-ASN : angle 2.64784 / 1.75 ( 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 361 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 321 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8015 (mt0) REVERT: A 485 LYS cc_start: 0.8408 (mttt) cc_final: 0.8136 (mtpp) REVERT: B 618 ASN cc_start: 0.7462 (m110) cc_final: 0.7197 (m110) REVERT: B 626 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7502 (ttm) REVERT: L 69 THR cc_start: 0.8836 (p) cc_final: 0.8451 (t) REVERT: H 82 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8258 (mtp) REVERT: H 105 GLN cc_start: 0.7720 (mm-40) cc_final: 0.6077 (mp10) REVERT: C 35 TRP cc_start: 0.8738 (m100) cc_final: 0.8425 (m100) REVERT: C 207 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8249 (ptmt) REVERT: D 625 ASN cc_start: 0.8077 (t0) cc_final: 0.7867 (t0) REVERT: D 661 LEU cc_start: 0.9313 (mm) cc_final: 0.9110 (mp) outliers start: 40 outliers final: 15 residues processed: 345 average time/residue: 0.1273 time to fit residues: 65.7927 Evaluate side-chains 265 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 248 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 199 SER Chi-restraints excluded: chain C residue 340 GLU 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 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: 0.9990 chunk 90 optimal weight: 0.0980 chunk 64 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN L 94 ASN H 81 GLN C 72 HIS C 85 HIS 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 = 0.3380 r_free = 0.3380 target = 0.116315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.098454 restraints weight = 26657.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.101688 restraints weight = 14135.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.103900 restraints weight = 9377.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.105371 restraints weight = 7051.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106400 restraints weight = 5747.309| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16370 Z= 0.171 Angle : 0.668 10.364 22365 Z= 0.335 Chirality : 0.048 0.261 2711 Planarity : 0.004 0.038 2706 Dihedral : 4.790 22.279 2009 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.10 % Allowed : 11.16 % Favored : 86.73 % 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: 0.74 (0.20), residues: 1848 helix: 1.97 (0.28), residues: 387 sheet: 0.77 (0.23), residues: 512 loop : -0.25 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 542 TYR 0.018 0.002 TYR E 484 PHE 0.028 0.002 PHE C 53 TRP 0.015 0.002 TRP C 69 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (16257) covalent geometry : angle 0.62216 / 0.33 (22061) SS BOND : bond 0.00323 / 0.23 ( 35) SS BOND : angle 0.95378 / 0.67 ( 70) hydrogen bonds : bond 0.05202 / 3.46 ( 589) hydrogen bonds : angle 4.85008 / 3.39 ( 1926) link_ALPHA1-3 : bond 0.00723 / 0.36 ( 3) link_ALPHA1-3 : angle 1.48422 / 1.00 ( 9) link_BETA1-4 : bond 0.00865 / 0.53 ( 24) link_BETA1-4 : angle 2.75564 / 1.94 ( 72) link_NAG-ASN : bond 0.00481 / 0.32 ( 51) link_NAG-ASN : angle 2.28498 / 1.55 ( 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 299 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 315 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7956 (mt0) REVERT: B 542 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7919 (ttp-170) REVERT: B 626 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7263 (ttm) REVERT: L 27 ASN cc_start: 0.8151 (p0) cc_final: 0.7929 (p0) REVERT: L 79 GLN cc_start: 0.8032 (mp10) cc_final: 0.6918 (mt0) REVERT: H 46 GLU cc_start: 0.8420 (tt0) cc_final: 0.8213 (tt0) REVERT: H 105 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7941 (mp10) REVERT: C 35 TRP cc_start: 0.8810 (m100) cc_final: 0.8523 (m100) REVERT: C 99 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7580 (t0) REVERT: C 207 LYS cc_start: 0.8484 (mmtt) cc_final: 0.8258 (ptmt) REVERT: E 486 TYR cc_start: 0.9259 (m-80) cc_final: 0.8950 (m-80) REVERT: D 647 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7430 (mt-10) outliers start: 35 outliers final: 16 residues processed: 286 average time/residue: 0.1057 time to fit residues: 46.4039 Evaluate side-chains 256 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 237 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 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 B residue 651 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 340 GLU 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 E residue 434 MET Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 185 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 94 ASN E 195 ASN E 478 ASN D 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.096443 restraints weight = 26772.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.099648 restraints weight = 14340.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.101783 restraints weight = 9567.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.103228 restraints weight = 7236.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.104230 restraints weight = 5927.015| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16370 Z= 0.187 Angle : 0.660 10.300 22365 Z= 0.326 Chirality : 0.048 0.561 2711 Planarity : 0.004 0.036 2706 Dihedral : 4.682 20.803 2009 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.58 % Allowed : 12.55 % Favored : 84.87 % 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: 0.59 (0.20), residues: 1848 helix: 2.06 (0.28), residues: 387 sheet: 0.65 (0.23), residues: 493 loop : -0.42 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 192 TYR 0.017 0.001 TYR H 58 PHE 0.024 0.002 PHE C 53 TRP 0.014 0.001 TRP C 427 HIS 0.007 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (16257) covalent geometry : angle 0.61527 / 0.32 (22061) SS BOND : bond 0.00352 / 0.25 ( 35) SS BOND : angle 0.96582 / 0.65 ( 70) hydrogen bonds : bond 0.04897 / 3.25 ( 589) hydrogen bonds : angle 4.75775 / 3.32 ( 1926) link_ALPHA1-3 : bond 0.00706 / 0.35 ( 3) link_ALPHA1-3 : angle 1.56155 / 1.00 ( 9) link_BETA1-4 : bond 0.00745 / 0.46 ( 24) link_BETA1-4 : angle 2.57898 / 1.80 ( 72) link_NAG-ASN : bond 0.00674 / 0.53 ( 51) link_NAG-ASN : angle 2.31019 / 1.59 ( 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 295 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 GLN cc_start: 0.8512 (mm-40) cc_final: 0.7959 (mt0) REVERT: B 542 ARG cc_start: 0.8262 (ttp-110) cc_final: 0.7814 (ttp-170) REVERT: B 543 ASN cc_start: 0.8591 (m-40) cc_final: 0.8164 (t0) REVERT: L 27 ASN cc_start: 0.8207 (p0) cc_final: 0.7965 (p0) REVERT: H 105 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7751 (mp10) REVERT: C 35 TRP cc_start: 0.8859 (m100) cc_final: 0.8580 (m100) REVERT: C 100 MET cc_start: 0.8943 (mtp) cc_final: 0.8738 (mtp) REVERT: C 246 GLN cc_start: 0.6627 (mt0) cc_final: 0.6288 (mp10) REVERT: E 271 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8380 (mtp) REVERT: E 486 TYR cc_start: 0.9255 (m-80) cc_final: 0.8740 (m-80) REVERT: D 647 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7364 (mt-10) REVERT: F 571 TRP cc_start: 0.7657 (m100) cc_final: 0.7341 (m100) outliers start: 43 outliers final: 27 residues processed: 280 average time/residue: 0.1179 time to fit residues: 50.5274 Evaluate side-chains 265 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 184 ILE 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 B residue 540 GLN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 339 ASN 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 373 THR 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: 4.9990 chunk 145 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN L 94 ASN E 85 HIS E 478 ASN D 625 ASN F 575 GLN F 653 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094651 restraints weight = 26919.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.097762 restraints weight = 14526.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.099846 restraints weight = 9732.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101256 restraints weight = 7379.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.102206 restraints weight = 6061.062| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16370 Z= 0.243 Angle : 0.709 10.984 22365 Z= 0.352 Chirality : 0.050 0.525 2711 Planarity : 0.004 0.043 2706 Dihedral : 4.819 20.949 2009 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.24 % Allowed : 12.91 % Favored : 83.85 % 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: 0.25 (0.20), residues: 1848 helix: 1.82 (0.28), residues: 395 sheet: 0.47 (0.23), residues: 506 loop : -0.72 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 542 TYR 0.021 0.002 TYR E 484 PHE 0.022 0.002 PHE C 53 TRP 0.017 0.002 TRP A 427 HIS 0.011 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.24 (16257) covalent geometry : angle 0.67036 / 0.34 (22061) SS BOND : bond 0.00461 / 0.31 ( 35) SS BOND : angle 0.95098 / 0.67 ( 70) hydrogen bonds : bond 0.05264 / 3.50 ( 589) hydrogen bonds : angle 4.85469 / 3.39 ( 1926) link_ALPHA1-3 : bond 0.00678 / 0.34 ( 3) link_ALPHA1-3 : angle 1.44928 / 0.91 ( 9) link_BETA1-4 : bond 0.00700 / 0.43 ( 24) link_BETA1-4 : angle 2.65263 / 1.84 ( 72) link_NAG-ASN : bond 0.00408 / 0.27 ( 51) link_NAG-ASN : angle 2.20155 / 1.55 ( 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 301 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 247 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.7862 (ttp-170) REVERT: L 27 ASN cc_start: 0.8372 (p0) cc_final: 0.8060 (p0) REVERT: L 79 GLN cc_start: 0.8166 (mp10) cc_final: 0.7366 (pt0) REVERT: H 105 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7892 (mp10) REVERT: C 100 MET cc_start: 0.9040 (mtp) cc_final: 0.8832 (mtp) REVERT: C 178 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7405 (ttt-90) REVERT: C 213 ILE cc_start: 0.8900 (mt) cc_final: 0.8663 (pt) REVERT: E 271 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8391 (mtp) REVERT: E 486 TYR cc_start: 0.9295 (m-80) cc_final: 0.8911 (m-80) REVERT: D 647 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: F 571 TRP cc_start: 0.7828 (m100) cc_final: 0.7521 (m100) REVERT: F 654 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8254 (tp30) REVERT: F 659 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7654 (m-30) outliers start: 54 outliers final: 34 residues processed: 283 average time/residue: 0.1149 time to fit residues: 49.5160 Evaluate side-chains 267 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 154 LEU 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 375 SER Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 133 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 128 optimal weight: 0.0370 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 122 optimal weight: 0.0020 chunk 145 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 overall best weight: 0.5266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3368 r_free = 0.3368 target = 0.115532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.097671 restraints weight = 26578.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.100911 restraints weight = 14272.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.103055 restraints weight = 9501.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.104511 restraints weight = 7184.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105524 restraints weight = 5877.080| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4247 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= 0.118 Angle : 0.596 11.962 22365 Z= 0.296 Chirality : 0.046 0.434 2711 Planarity : 0.004 0.033 2706 Dihedral : 4.493 17.659 2009 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.28 % Allowed : 14.65 % Favored : 83.07 % 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: 0.39 (0.20), residues: 1848 helix: 2.11 (0.28), residues: 394 sheet: 0.49 (0.23), residues: 507 loop : -0.66 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 166 TYR 0.014 0.001 TYR H 58 PHE 0.021 0.001 PHE C 53 TRP 0.010 0.001 TRP A 427 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (16257) covalent geometry : angle 0.55312 / 0.29 (22061) SS BOND : bond 0.00259 / 0.19 ( 35) SS BOND : angle 0.98040 / 0.72 ( 70) hydrogen bonds : bond 0.04286 / 2.85 ( 589) hydrogen bonds : angle 4.53685 / 3.15 ( 1926) link_ALPHA1-3 : bond 0.00613 / 0.31 ( 3) link_ALPHA1-3 : angle 1.42486 / 0.98 ( 9) link_BETA1-4 : bond 0.00767 / 0.48 ( 24) link_BETA1-4 : angle 2.26416 / 1.59 ( 72) link_NAG-ASN : bond 0.00397 / 0.26 ( 51) link_NAG-ASN : angle 2.19818 / 1.56 ( 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 288 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8230 (ttp-110) cc_final: 0.7789 (ttp-170) REVERT: B 626 MET cc_start: 0.7820 (ttm) cc_final: 0.7013 (ttm) REVERT: L 27 ASN cc_start: 0.8277 (p0) cc_final: 0.7903 (p0) REVERT: L 79 GLN cc_start: 0.8264 (mp10) cc_final: 0.7497 (pt0) REVERT: H 105 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7991 (mp10) REVERT: C 35 TRP cc_start: 0.8869 (m100) cc_final: 0.8538 (m100) REVERT: C 161 MET cc_start: 0.8849 (tpt) cc_final: 0.8542 (tpt) REVERT: C 213 ILE cc_start: 0.8917 (mt) cc_final: 0.8703 (pt) REVERT: E 271 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8412 (mtp) REVERT: E 421 LYS cc_start: 0.8737 (tttt) cc_final: 0.8430 (ttpt) REVERT: E 486 TYR cc_start: 0.9260 (m-80) cc_final: 0.8706 (m-80) REVERT: D 647 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: F 654 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8116 (tp30) outliers start: 38 outliers final: 22 residues processed: 274 average time/residue: 0.1213 time to fit residues: 50.9196 Evaluate side-chains 261 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain H residue 79 SER 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 376 PHE Chi-restraints excluded: chain C residue 416 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 440 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS A 136 ASN L 51 ASN H 81 GLN 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 = 0.3356 r_free = 0.3356 target = 0.114826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.096979 restraints weight = 26517.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.100156 restraints weight = 14309.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.102290 restraints weight = 9589.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.103713 restraints weight = 7271.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.104706 restraints weight = 5977.276| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16370 Z= 0.138 Angle : 0.597 10.340 22365 Z= 0.295 Chirality : 0.046 0.444 2711 Planarity : 0.004 0.037 2706 Dihedral : 4.390 18.833 2009 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.22 % Allowed : 14.89 % 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: 0.39 (0.20), residues: 1848 helix: 2.12 (0.28), residues: 395 sheet: 0.56 (0.23), residues: 499 loop : -0.72 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 617 TYR 0.021 0.001 TYR E 484 PHE 0.020 0.002 PHE C 53 TRP 0.010 0.001 TRP C 427 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (16257) covalent geometry : angle 0.55944 / 0.29 (22061) SS BOND : bond 0.00276 / 0.19 ( 35) SS BOND : angle 0.96199 / 0.68 ( 70) hydrogen bonds : bond 0.04259 / 2.83 ( 589) hydrogen bonds : angle 4.49307 / 3.12 ( 1926) link_ALPHA1-3 : bond 0.00602 / 0.30 ( 3) link_ALPHA1-3 : angle 1.36389 / 0.90 ( 9) link_BETA1-4 : bond 0.00677 / 0.42 ( 24) link_BETA1-4 : angle 2.27317 / 1.59 ( 72) link_NAG-ASN : bond 0.00379 / 0.25 ( 51) link_NAG-ASN : angle 1.98348 / 1.39 ( 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 281 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8310 (ttp-110) cc_final: 0.7979 (ttp-170) REVERT: L 27 ASN cc_start: 0.8313 (p0) cc_final: 0.7983 (p0) REVERT: L 50 TYR cc_start: 0.7623 (t80) cc_final: 0.7072 (m-80) REVERT: L 79 GLN cc_start: 0.8313 (mp10) cc_final: 0.7536 (pt0) REVERT: C 161 MET cc_start: 0.8838 (tpt) cc_final: 0.8607 (tpt) REVERT: C 213 ILE cc_start: 0.8910 (mt) cc_final: 0.8708 (pt) REVERT: E 271 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8396 (mtp) REVERT: E 486 TYR cc_start: 0.9254 (m-80) cc_final: 0.8710 (m-80) REVERT: D 647 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7466 (mt-10) REVERT: F 654 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8118 (tp30) outliers start: 37 outliers final: 25 residues processed: 263 average time/residue: 0.1280 time to fit residues: 51.2932 Evaluate side-chains 258 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 213 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 375 SER Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain L residue 69 THR 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 376 PHE 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 612 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 661 LEU 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: 1.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3357 r_free = 0.3357 target = 0.114854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.096850 restraints weight = 26821.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.100061 restraints weight = 14445.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.102235 restraints weight = 9652.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.103647 restraints weight = 7293.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.104656 restraints weight = 6004.892| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16370 Z= 0.143 Angle : 0.596 9.226 22365 Z= 0.296 Chirality : 0.046 0.432 2711 Planarity : 0.004 0.035 2706 Dihedral : 4.350 18.090 2009 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.22 % Allowed : 14.83 % Favored : 82.95 % 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: 0.35 (0.20), residues: 1848 helix: 2.13 (0.28), residues: 395 sheet: 0.51 (0.24), residues: 502 loop : -0.74 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 166 TYR 0.020 0.001 TYR A 191 PHE 0.020 0.002 PHE C 376 TRP 0.009 0.001 TRP A 427 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (16257) covalent geometry : angle 0.56203 / 0.29 (22061) SS BOND : bond 0.00283 / 0.18 ( 35) SS BOND : angle 0.88929 / 0.63 ( 70) hydrogen bonds : bond 0.04221 / 2.80 ( 589) hydrogen bonds : angle 4.46547 / 3.10 ( 1926) link_ALPHA1-3 : bond 0.00603 / 0.30 ( 3) link_ALPHA1-3 : angle 1.37983 / 0.92 ( 9) link_BETA1-4 : bond 0.00722 / 0.44 ( 24) link_BETA1-4 : angle 2.24839 / 1.57 ( 72) link_NAG-ASN : bond 0.00363 / 0.24 ( 51) link_NAG-ASN : angle 1.90014 / 1.33 ( 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 277 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7947 (ttp-170) REVERT: L 27 ASN cc_start: 0.8320 (p0) cc_final: 0.7988 (p0) REVERT: L 50 TYR cc_start: 0.7657 (t80) cc_final: 0.7099 (m-80) REVERT: L 79 GLN cc_start: 0.8287 (mp10) cc_final: 0.7440 (pt0) REVERT: C 100 MET cc_start: 0.8893 (mtp) cc_final: 0.8476 (mtp) REVERT: C 161 MET cc_start: 0.8833 (tpt) cc_final: 0.8593 (tpt) REVERT: E 268 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7027 (mm-30) REVERT: E 271 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8361 (mtp) REVERT: E 486 TYR cc_start: 0.9240 (m-80) cc_final: 0.8608 (m-80) REVERT: D 647 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7480 (mt-10) REVERT: F 654 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8055 (tp30) outliers start: 37 outliers final: 27 residues processed: 264 average time/residue: 0.1034 time to fit residues: 41.9804 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 : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 213 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 A residue 439 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain L residue 69 THR 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 339 ASN Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 416 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 D residue 612 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 74 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 128 optimal weight: 0.0270 chunk 123 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 195 ASN E 478 ASN D 625 ASN F 653 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.095556 restraints weight = 26099.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.098828 restraints weight = 14025.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.101018 restraints weight = 9357.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102524 restraints weight = 7084.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103551 restraints weight = 5798.200| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16370 Z= 0.139 Angle : 0.594 8.762 22365 Z= 0.295 Chirality : 0.046 0.423 2711 Planarity : 0.004 0.035 2706 Dihedral : 4.300 18.542 2009 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.46 % Allowed : 14.77 % Favored : 82.77 % 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: 0.34 (0.20), residues: 1848 helix: 2.19 (0.27), residues: 395 sheet: 0.44 (0.24), residues: 487 loop : -0.73 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 166 TYR 0.021 0.001 TYR E 484 PHE 0.020 0.002 PHE C 376 TRP 0.012 0.001 TRP E 69 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (16257) covalent geometry : angle 0.56022 / 0.29 (22061) SS BOND : bond 0.00273 / 0.18 ( 35) SS BOND : angle 0.88289 / 0.63 ( 70) hydrogen bonds : bond 0.04142 / 2.75 ( 589) hydrogen bonds : angle 4.43216 / 3.08 ( 1926) link_ALPHA1-3 : bond 0.00592 / 0.30 ( 3) link_ALPHA1-3 : angle 1.36766 / 0.91 ( 9) link_BETA1-4 : bond 0.00727 / 0.45 ( 24) link_BETA1-4 : angle 2.21122 / 1.54 ( 72) link_NAG-ASN : bond 0.00372 / 0.24 ( 51) link_NAG-ASN : angle 1.86952 / 1.31 ( 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 279 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.9124 (m100) cc_final: 0.8914 (m100) REVERT: A 191 TYR cc_start: 0.9089 (m-80) cc_final: 0.8801 (m-80) REVERT: B 542 ARG cc_start: 0.8335 (ttp-110) cc_final: 0.7980 (ttp-170) REVERT: L 27 ASN cc_start: 0.8320 (p0) cc_final: 0.7946 (p0) REVERT: L 50 TYR cc_start: 0.7746 (t80) cc_final: 0.7115 (m-80) REVERT: L 79 GLN cc_start: 0.8273 (mp10) cc_final: 0.7377 (pt0) REVERT: C 100 MET cc_start: 0.8903 (mtp) cc_final: 0.8461 (mtp) REVERT: C 161 MET cc_start: 0.8823 (tpt) cc_final: 0.8564 (tpt) REVERT: C 475 MET cc_start: 0.6389 (ptt) cc_final: 0.6098 (ptt) REVERT: E 195 ASN cc_start: 0.8459 (m-40) cc_final: 0.8203 (m-40) REVERT: E 268 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7142 (mm-30) REVERT: E 271 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8371 (mtp) REVERT: E 486 TYR cc_start: 0.9189 (m-80) cc_final: 0.8553 (m-80) REVERT: D 647 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7543 (mt-10) REVERT: F 654 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8009 (tp30) outliers start: 41 outliers final: 32 residues processed: 265 average time/residue: 0.1109 time to fit residues: 44.9954 Evaluate side-chains 262 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 213 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 A residue 434 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain L residue 69 THR 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 213 ILE Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 215 ILE 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 612 SER 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: 0.0470 chunk 14 optimal weight: 0.0570 chunk 124 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 HIS D 625 ASN F 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.099216 restraints weight = 26356.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102460 restraints weight = 14143.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104657 restraints weight = 9426.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.106122 restraints weight = 7083.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107080 restraints weight = 5788.522| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16370 Z= 0.110 Angle : 0.582 10.725 22365 Z= 0.290 Chirality : 0.045 0.412 2711 Planarity : 0.004 0.044 2706 Dihedral : 4.207 18.448 2009 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.62 % Allowed : 15.49 % 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: 0.40 (0.20), residues: 1848 helix: 2.28 (0.27), residues: 395 sheet: 0.48 (0.24), residues: 485 loop : -0.71 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 542 TYR 0.016 0.001 TYR A 191 PHE 0.020 0.001 PHE C 53 TRP 0.012 0.001 TRP E 69 HIS 0.007 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (16257) covalent geometry : angle 0.55172 / 0.28 (22061) SS BOND : bond 0.00200 / 0.13 ( 35) SS BOND : angle 0.78444 / 0.56 ( 70) hydrogen bonds : bond 0.03817 / 2.54 ( 589) hydrogen bonds : angle 4.33010 / 3.00 ( 1926) link_ALPHA1-3 : bond 0.00584 / 0.29 ( 3) link_ALPHA1-3 : angle 1.37438 / 0.94 ( 9) link_BETA1-4 : bond 0.00734 / 0.45 ( 24) link_BETA1-4 : angle 2.09435 / 1.46 ( 72) link_NAG-ASN : bond 0.00397 / 0.25 ( 51) link_NAG-ASN : angle 1.78257 / 1.24 ( 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 278 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASN cc_start: 0.8850 (t0) cc_final: 0.8284 (t0) REVERT: A 191 TYR cc_start: 0.9003 (m-80) cc_final: 0.8782 (m-80) REVERT: B 542 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7905 (ttp-170) REVERT: L 27 ASN cc_start: 0.8278 (p0) cc_final: 0.7952 (p0) REVERT: L 50 TYR cc_start: 0.7625 (t80) cc_final: 0.7318 (m-80) REVERT: L 79 GLN cc_start: 0.8292 (mp10) cc_final: 0.7439 (pt0) REVERT: H 81 GLN cc_start: 0.7923 (tp-100) cc_final: 0.7527 (tp40) REVERT: C 35 TRP cc_start: 0.8795 (m100) cc_final: 0.8493 (m100) REVERT: C 100 MET cc_start: 0.8871 (mtp) cc_final: 0.8541 (mtp) REVERT: C 161 MET cc_start: 0.8788 (tpt) cc_final: 0.8452 (tpt) REVERT: C 199 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8749 (t) REVERT: C 475 MET cc_start: 0.6409 (ptt) cc_final: 0.6146 (ptt) REVERT: C 486 TYR cc_start: 0.9274 (m-80) cc_final: 0.9001 (m-80) REVERT: E 268 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6979 (mm-30) REVERT: E 271 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8339 (mtp) REVERT: E 421 LYS cc_start: 0.8730 (tttt) cc_final: 0.8417 (ttpt) REVERT: D 647 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7374 (mt-10) REVERT: F 652 GLN cc_start: 0.8326 (tm130) cc_final: 0.7788 (tm-30) REVERT: F 654 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7850 (tp30) outliers start: 27 outliers final: 23 residues processed: 269 average time/residue: 0.1092 time to fit residues: 44.7159 Evaluate side-chains 265 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 434 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain L residue 69 THR 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 339 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 194 ILE 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 34 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.096267 restraints weight = 25858.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.099587 restraints weight = 13812.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101845 restraints weight = 9169.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.103372 restraints weight = 6895.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104406 restraints weight = 5635.997| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16370 Z= 0.149 Angle : 0.609 11.827 22365 Z= 0.302 Chirality : 0.046 0.407 2711 Planarity : 0.004 0.035 2706 Dihedral : 4.270 20.365 2009 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.86 % Allowed : 15.67 % 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: 0.36 (0.20), residues: 1848 helix: 2.23 (0.27), residues: 395 sheet: 0.47 (0.24), residues: 486 loop : -0.74 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 542 TYR 0.022 0.001 TYR E 484 PHE 0.021 0.002 PHE C 376 TRP 0.024 0.001 TRP A 96 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (16257) covalent geometry : angle 0.57719 / 0.30 (22061) SS BOND : bond 0.00322 / 0.22 ( 35) SS BOND : angle 1.04378 / 0.77 ( 70) hydrogen bonds : bond 0.04073 / 2.71 ( 589) hydrogen bonds : angle 4.37505 / 3.04 ( 1926) link_ALPHA1-3 : bond 0.00588 / 0.30 ( 3) link_ALPHA1-3 : angle 1.36112 / 0.90 ( 9) link_BETA1-4 : bond 0.00720 / 0.45 ( 24) link_BETA1-4 : angle 2.17542 / 1.51 ( 72) link_NAG-ASN : bond 0.00346 / 0.22 ( 51) link_NAG-ASN : angle 1.81422 / 1.27 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2481.14 seconds wall clock time: 43 minutes 48.80 seconds (2628.80 seconds total)