Starting phenix.real_space_refine on Thu Mar 5 05:54:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x9r_22108/03_2026/6x9r_22108.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x9r_22108/03_2026/6x9r_22108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x9r_22108/03_2026/6x9r_22108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x9r_22108/03_2026/6x9r_22108.map" model { file = "/net/cci-nas-00/data/ceres_data/6x9r_22108/03_2026/6x9r_22108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x9r_22108/03_2026/6x9r_22108.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 12258 2.51 5 N 3273 2.21 5 O 3933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19590 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "J" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "M" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "T" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "U" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "V" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "T" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.55, per 1000 atoms: 0.23 Number of scatterers: 19590 At special positions: 0 Unit cell: (122.57, 126.69, 149.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 3933 8.00 N 3273 7.00 C 12258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.17 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=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.15 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.06 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.17 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.15 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 119 " - pdb=" SG CYS S 205 " distance=2.06 Simple disulfide: pdb=" SG CYS S 126 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS S 131 " - pdb=" SG CYS S 157 " distance=2.02 Simple disulfide: pdb=" SG CYS S 218 " - pdb=" SG CYS S 247 " distance=2.04 Simple disulfide: pdb=" SG CYS S 228 " - pdb=" SG CYS S 239 " distance=2.16 Simple disulfide: pdb=" SG CYS S 296 " - pdb=" SG CYS S 331 " distance=2.03 Simple disulfide: pdb=" SG CYS S 378 " - pdb=" SG CYS S 445 " distance=2.02 Simple disulfide: pdb=" SG CYS S 385 " - pdb=" SG CYS S 418 " distance=2.02 Simple disulfide: pdb=" SG CYS S 501 " - pdb=" SG CYS T 605 " distance=2.15 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.02 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.04 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG 0 1 " - " ASN S 448 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 606 " - " ASN A 160 " " NAG A 609 " - " ASN A 234 " " NAG A 614 " - " ASN A 276 " " NAG A 615 " - " ASN A 295 " " NAG A 616 " - " ASN A 301 " " NAG A 617 " - " ASN A 332 " " NAG A 618 " - " ASN A 339 " " NAG A 619 " - " ASN A 355 " " NAG A 620 " - " ASN A 363 " " NAG A 623 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG C 1 " - " ASN A 156 " " NAG D 1 " - " ASN A 197 " " NAG E 1 " - " ASN A 262 " " NAG F 1 " - " ASN A 386 " " NAG G 1 " - " ASN A 448 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 137 " " NAG I 606 " - " ASN I 160 " " NAG I 609 " - " ASN I 234 " " NAG I 614 " - " ASN I 276 " " NAG I 615 " - " ASN I 295 " " NAG I 616 " - " ASN I 301 " " NAG I 617 " - " ASN I 332 " " NAG I 618 " - " ASN I 339 " " NAG I 619 " - " ASN I 355 " " NAG I 620 " - " ASN I 363 " " NAG I 623 " - " ASN I 392 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG J 703 " - " ASN J 625 " " NAG J 704 " - " ASN J 637 " " NAG N 1 " - " ASN I 156 " " NAG O 1 " - " ASN I 197 " " NAG P 1 " - " ASN I 262 " " NAG Q 1 " - " ASN I 386 " " NAG R 1 " - " ASN I 448 " " NAG S 601 " - " ASN S 88 " " NAG S 602 " - " ASN S 133 " " NAG S 603 " - " ASN S 137 " " NAG S 606 " - " ASN S 160 " " NAG S 609 " - " ASN S 234 " " NAG S 614 " - " ASN S 276 " " NAG S 615 " - " ASN S 295 " " NAG S 616 " - " ASN S 301 " " NAG S 617 " - " ASN S 332 " " NAG S 618 " - " ASN S 339 " " NAG S 619 " - " ASN S 355 " " NAG S 620 " - " ASN S 363 " " NAG S 623 " - " ASN S 392 " " NAG T 701 " - " ASN T 611 " " NAG T 702 " - " ASN T 618 " " NAG T 703 " - " ASN T 625 " " NAG T 704 " - " ASN T 637 " " NAG W 1 " - " ASN S 156 " " NAG X 1 " - " ASN S 197 " " NAG Y 1 " - " ASN S 262 " " NAG Z 1 " - " ASN S 386 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 715.3 milliseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 20.6% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.134A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.048A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.756A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.519A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 660 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'I' and resid 98 through 115 removed outlier: 4.135A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 4.048A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 476 through 484 removed outlier: 3.755A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.520A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 660 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'S' and resid 98 through 115 removed outlier: 4.134A pdb=" N GLU S 102 " --> pdb=" O ASN S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 126 Processing helix chain 'S' and resid 139 through 151 Processing helix chain 'S' and resid 195 through 198 Processing helix chain 'S' and resid 334 through 354 removed outlier: 4.048A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS S 352 " --> pdb=" O GLN S 348 " (cutoff:3.500A) Processing helix chain 'S' and resid 368 through 373 Processing helix chain 'S' and resid 476 through 484 removed outlier: 3.756A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 removed outlier: 3.519A pdb=" N GLN T 540 " --> pdb=" O THR T 536 " (cutoff:3.500A) Processing helix chain 'T' and resid 569 through 596 Processing helix chain 'T' and resid 618 through 625 Processing helix chain 'T' and resid 627 through 635 Processing helix chain 'T' and resid 638 through 660 Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 Processing sheet with id=1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.868A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.450A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 393 through 394 removed outlier: 6.424A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.552A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=10, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.234A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=12, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.060A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=14, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=17, first strand: chain 'I' and resid 494 through 498 Processing sheet with id=18, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.868A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=20, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=21, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=22, first strand: chain 'I' and resid 200 through 203 removed outlier: 6.451A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'I' and resid 393 through 394 removed outlier: 6.423A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N VAL I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N CYS I 296 " --> pdb=" O VAL I 442 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.552A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'I' and resid 271 through 274 Processing sheet with id=26, first strand: chain 'I' and resid 315 through 323A removed outlier: 6.234A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE I 323 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN I 301 " --> pdb=" O ILE I 323 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'K' and resid 3 through 8 Processing sheet with id=28, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.059A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=30, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=33, first strand: chain 'S' and resid 494 through 498 Processing sheet with id=34, first strand: chain 'S' and resid 45 through 47 removed outlier: 3.869A pdb=" N ILE S 225 " --> pdb=" O VAL S 245 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL S 242 " --> pdb=" O LEU S 86 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'S' and resid 75 through 76 Processing sheet with id=36, first strand: chain 'S' and resid 91 through 94 Processing sheet with id=37, first strand: chain 'S' and resid 169 through 177 Processing sheet with id=38, first strand: chain 'S' and resid 200 through 203 removed outlier: 6.450A pdb=" N ALA S 200 " --> pdb=" O ALA S 433 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR S 435 " --> pdb=" O ALA S 200 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR S 202 " --> pdb=" O TYR S 435 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'S' and resid 393 through 394 removed outlier: 6.424A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N VAL S 442 " --> pdb=" O CYS S 296 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N CYS S 296 " --> pdb=" O VAL S 442 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N ARG S 444 " --> pdb=" O ILE S 294 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE S 294 " --> pdb=" O ARG S 444 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL S 446 " --> pdb=" O VAL S 292 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL S 292 " --> pdb=" O VAL S 446 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN S 448 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR S 290 " --> pdb=" O ASN S 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR S 450 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE S 382 " --> pdb=" O LYS S 421 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'S' and resid 259 through 261 removed outlier: 6.552A pdb=" N LEU S 260 " --> pdb=" O THR S 450 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'S' and resid 271 through 274 Processing sheet with id=42, first strand: chain 'S' and resid 315 through 323A removed outlier: 6.233A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR S 303 " --> pdb=" O GLY S 321 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE S 323 " --> pdb=" O ASN S 301 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN S 301 " --> pdb=" O ILE S 323 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'U' and resid 3 through 8 Processing sheet with id=44, first strand: chain 'U' and resid 11 through 12 removed outlier: 6.060A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'U' and resid 11 through 12 Processing sheet with id=46, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP V 35 " --> pdb=" O MET V 47 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'V' and resid 19 through 24 756 hydrogen bonds defined for protein. 1935 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: 4.08 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3667 1.31 - 1.44: 5373 1.44 - 1.57: 10723 1.57 - 1.69: 40 1.69 - 1.82: 171 Bond restraints: 19974 Sorted by residual: bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C1 NAG I 603 " pdb=" O5 NAG I 603 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C1 NAG S 603 " pdb=" O5 NAG S 603 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 24188 2.67 - 5.33: 2592 5.33 - 8.00: 283 8.00 - 10.67: 24 10.67 - 13.33: 6 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 124.03 -13.33 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N PRO M 7 " pdb=" CA PRO M 7 " pdb=" C PRO M 7 " ideal model delta sigma weight residual 110.70 124.02 -13.32 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 123.99 -13.29 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N GLY M 100 " pdb=" CA GLY M 100 " pdb=" C GLY M 100 " ideal model delta sigma weight residual 112.85 100.34 12.51 1.61e+00 3.86e-01 6.04e+01 angle pdb=" C ASP M 50 " pdb=" N VAL M 51 " pdb=" CA VAL M 51 " ideal model delta sigma weight residual 123.16 114.93 8.23 1.06e+00 8.90e-01 6.03e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 12574 21.78 - 43.55: 329 43.55 - 65.33: 93 65.33 - 87.11: 27 87.11 - 108.88: 15 Dihedral angle restraints: 13038 sinusoidal: 6291 harmonic: 6747 Sorted by residual: dihedral pdb=" CB CYS S 228 " pdb=" SG CYS S 228 " pdb=" SG CYS S 239 " pdb=" CB CYS S 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.97 -68.97 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS I 228 " pdb=" SG CYS I 228 " pdb=" SG CYS I 239 " pdb=" CB CYS I 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.95 -68.95 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.95 -68.95 1 1.00e+01 1.00e-02 6.15e+01 ... (remaining 13035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2322 0.098 - 0.196: 769 0.196 - 0.294: 164 0.294 - 0.392: 18 0.392 - 0.491: 6 Chirality restraints: 3279 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 -2.65 0.25 2.00e-02 2.50e+03 1.50e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 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 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " 0.222 2.00e-02 2.50e+03 1.84e-01 4.21e+02 pdb=" C7 NAG T 702 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.222 2.00e-02 2.50e+03 1.83e-01 4.20e+02 pdb=" C7 NAG B 702 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " -0.221 2.00e-02 2.50e+03 1.83e-01 4.20e+02 pdb=" C7 NAG J 702 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " -0.158 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " 0.300 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.019 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4131 2.76 - 3.30: 16799 3.30 - 3.83: 32207 3.83 - 4.37: 38497 4.37 - 4.90: 65141 Nonbonded interactions: 156775 Sorted by model distance: nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR S 37 " pdb=" OG1 THR S 499 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.229 3.040 nonbonded pdb=" N ASN A 355 " pdb=" OD1 ASN A 355 " model vdw 2.283 3.120 nonbonded pdb=" N ASN S 355 " pdb=" OD1 ASN S 355 " model vdw 2.283 3.120 ... (remaining 156770 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: 0.05 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'V' } 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 individual isotropic 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.540 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 : 0.025 0.150 20097 Z= 1.300 Angle : 1.748 13.332 27426 Z= 1.126 Chirality : 0.100 0.491 3279 Planarity : 0.011 0.184 3339 Dihedral : 11.452 108.883 8598 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.30 % Favored : 96.35 % Rotamer: Outliers : 0.44 % Allowed : 0.15 % Favored : 99.41 % 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: 0.53 (0.17), residues: 2304 helix: -0.32 (0.24), residues: 393 sheet: 0.83 (0.20), residues: 630 loop : 0.48 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 66 TYR 0.047 0.007 TYR V 36 PHE 0.035 0.006 PHE S 383 TRP 0.069 0.012 TRP A 427 HIS 0.008 0.002 HIS U 82A Details of bonding type rmsd covalent geometry : bond 0.02494 (19974) covalent geometry : angle 1.71874 (27093) SS BOND : bond 0.05245 ( 36) SS BOND : angle 2.91409 ( 72) hydrogen bonds : bond 0.16093 ( 735) hydrogen bonds : angle 7.02831 ( 1935) link_ALPHA1-3 : bond 0.04240 ( 3) link_ALPHA1-3 : angle 2.95194 ( 9) link_BETA1-4 : bond 0.03047 ( 18) link_BETA1-4 : angle 3.84126 ( 54) link_NAG-ASN : bond 0.03219 ( 66) link_NAG-ASN : angle 3.37105 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 495 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8724 (mmtp) cc_final: 0.8520 (mmtp) REVERT: A 150 MET cc_start: 0.8053 (mmm) cc_final: 0.7750 (mmm) REVERT: A 318 TYR cc_start: 0.8763 (m-80) cc_final: 0.8518 (m-80) REVERT: A 492 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8420 (mt-10) REVERT: A 502 LYS cc_start: 0.6886 (mmtp) cc_final: 0.6563 (mmtt) REVERT: L 94 ARG cc_start: 0.5936 (mmt180) cc_final: 0.4520 (mmt180) REVERT: I 150 MET cc_start: 0.7869 (mmm) cc_final: 0.7138 (mmt) REVERT: I 502 LYS cc_start: 0.6375 (mmtp) cc_final: 0.5552 (mmtm) REVERT: J 624 ASP cc_start: 0.8293 (m-30) cc_final: 0.8039 (m-30) REVERT: M 94 ARG cc_start: 0.6375 (mmt180) cc_final: 0.4691 (mtp180) REVERT: S 46 LYS cc_start: 0.8803 (mmtp) cc_final: 0.8562 (mmtp) REVERT: S 502 LYS cc_start: 0.6176 (mmtp) cc_final: 0.5682 (mmtp) REVERT: V 47 MET cc_start: 0.8170 (mmm) cc_final: 0.7801 (mmt) REVERT: V 94 ARG cc_start: 0.6002 (mmt180) cc_final: 0.5111 (mmt180) outliers start: 9 outliers final: 7 residues processed: 500 average time/residue: 0.1551 time to fit residues: 111.8422 Evaluate side-chains 279 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 272 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN J 607 ASN S 103 GLN T 607 ASN U 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.097313 restraints weight = 26927.718| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.69 r_work: 0.2871 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20097 Z= 0.168 Angle : 0.735 8.921 27426 Z= 0.378 Chirality : 0.046 0.241 3279 Planarity : 0.004 0.036 3339 Dihedral : 8.727 65.446 4349 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.43 % Favored : 96.31 % Rotamer: Outliers : 1.91 % Allowed : 6.06 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.17), residues: 2304 helix: 1.63 (0.28), residues: 384 sheet: 0.42 (0.20), residues: 660 loop : 0.10 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 542 TYR 0.014 0.001 TYR L 96 PHE 0.019 0.002 PHE I 383 TRP 0.016 0.002 TRP I 479 HIS 0.004 0.001 HIS H 82A Details of bonding type rmsd covalent geometry : bond 0.00374 (19974) covalent geometry : angle 0.69250 (27093) SS BOND : bond 0.00291 ( 36) SS BOND : angle 1.03316 ( 72) hydrogen bonds : bond 0.05487 ( 735) hydrogen bonds : angle 5.65295 ( 1935) link_ALPHA1-3 : bond 0.00721 ( 3) link_ALPHA1-3 : angle 2.57861 ( 9) link_BETA1-4 : bond 0.00427 ( 18) link_BETA1-4 : angle 2.52690 ( 54) link_NAG-ASN : bond 0.00307 ( 66) link_NAG-ASN : angle 2.59966 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 346 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9497 (ptm) cc_final: 0.9178 (ptm) REVERT: A 117 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7167 (mttp) REVERT: A 150 MET cc_start: 0.8300 (mmm) cc_final: 0.8069 (mmm) REVERT: A 213 ILE cc_start: 0.8282 (mm) cc_final: 0.8061 (mt) REVERT: A 271 MET cc_start: 0.9033 (mtp) cc_final: 0.8730 (mtp) REVERT: A 322 ASP cc_start: 0.8067 (m-30) cc_final: 0.7704 (p0) REVERT: A 333 VAL cc_start: 0.9280 (t) cc_final: 0.9077 (p) REVERT: A 502 LYS cc_start: 0.6993 (mmtp) cc_final: 0.5506 (mmtm) REVERT: B 657 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8338 (tt0) REVERT: H 6 GLU cc_start: 0.8502 (mp0) cc_final: 0.8035 (mp0) REVERT: L 79 GLN cc_start: 0.6248 (mt0) cc_final: 0.5973 (mt0) REVERT: I 121 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8350 (mmtp) REVERT: I 161 MET cc_start: 0.9335 (tpp) cc_final: 0.9087 (tpp) REVERT: I 426 MET cc_start: 0.9143 (mmt) cc_final: 0.8814 (tpt) REVERT: I 502 LYS cc_start: 0.6735 (mmtp) cc_final: 0.5436 (mmtm) REVERT: J 624 ASP cc_start: 0.8721 (m-30) cc_final: 0.8360 (m-30) REVERT: K 82 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6755 (mt) REVERT: M 45 LYS cc_start: 0.8998 (tttm) cc_final: 0.8635 (tttm) REVERT: M 94 ARG cc_start: 0.6526 (mmt180) cc_final: 0.4472 (mmt180) REVERT: S 46 LYS cc_start: 0.8681 (mmtp) cc_final: 0.8239 (mmtp) REVERT: S 162 THR cc_start: 0.9132 (m) cc_final: 0.8918 (p) REVERT: S 322 ASP cc_start: 0.8228 (m-30) cc_final: 0.7990 (p0) REVERT: S 502 LYS cc_start: 0.6571 (mmtp) cc_final: 0.5923 (mmtp) REVERT: U 6 GLU cc_start: 0.8540 (mp0) cc_final: 0.8177 (mp0) REVERT: U 43 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7851 (mmmm) REVERT: V 45 LYS cc_start: 0.8760 (tttt) cc_final: 0.8416 (tttt) REVERT: V 47 MET cc_start: 0.9069 (mmm) cc_final: 0.8748 (mmt) REVERT: V 94 ARG cc_start: 0.6136 (mmt180) cc_final: 0.3809 (mtp180) outliers start: 39 outliers final: 26 residues processed: 372 average time/residue: 0.1492 time to fit residues: 81.6856 Evaluate side-chains 309 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 282 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 607 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 0.0470 chunk 155 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 0.0020 chunk 91 optimal weight: 4.9990 chunk 116 optimal weight: 0.0670 chunk 192 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN J 651 ASN S 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.095581 restraints weight = 27453.545| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.66 r_work: 0.2936 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20097 Z= 0.116 Angle : 0.619 11.360 27426 Z= 0.314 Chirality : 0.046 0.380 3279 Planarity : 0.004 0.047 3339 Dihedral : 7.593 58.628 4347 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.91 % Favored : 95.96 % Rotamer: Outliers : 1.91 % Allowed : 7.77 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.63 (0.17), residues: 2304 helix: 1.79 (0.28), residues: 402 sheet: 0.61 (0.20), residues: 651 loop : -0.07 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 542 TYR 0.009 0.001 TYR B 643 PHE 0.015 0.002 PHE S 53 TRP 0.011 0.001 TRP I 479 HIS 0.004 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00238 (19974) covalent geometry : angle 0.58309 (27093) SS BOND : bond 0.00238 ( 36) SS BOND : angle 0.93323 ( 72) hydrogen bonds : bond 0.04385 ( 735) hydrogen bonds : angle 5.21512 ( 1935) link_ALPHA1-3 : bond 0.01051 ( 3) link_ALPHA1-3 : angle 1.37735 ( 9) link_BETA1-4 : bond 0.00488 ( 18) link_BETA1-4 : angle 1.75189 ( 54) link_NAG-ASN : bond 0.00297 ( 66) link_NAG-ASN : angle 2.31870 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 320 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8584 (mmtt) REVERT: A 117 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7261 (mttp) REVERT: A 150 MET cc_start: 0.8348 (mmm) cc_final: 0.8108 (mmm) REVERT: A 217 TYR cc_start: 0.9085 (m-80) cc_final: 0.8799 (m-80) REVERT: A 322 ASP cc_start: 0.7912 (m-30) cc_final: 0.7583 (p0) REVERT: A 327 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7296 (mmm-85) REVERT: A 492 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8731 (mt-10) REVERT: A 502 LYS cc_start: 0.6871 (mmtp) cc_final: 0.5496 (mmtm) REVERT: H 6 GLU cc_start: 0.8499 (mp0) cc_final: 0.8268 (mp0) REVERT: H 25 SER cc_start: 0.8587 (p) cc_final: 0.8179 (m) REVERT: H 105 GLN cc_start: 0.8306 (pm20) cc_final: 0.8040 (pm20) REVERT: L 103 ARG cc_start: 0.8345 (mmt180) cc_final: 0.8085 (mmt180) REVERT: I 161 MET cc_start: 0.9312 (tpp) cc_final: 0.9072 (tpp) REVERT: I 213 ILE cc_start: 0.8183 (mm) cc_final: 0.7960 (mt) REVERT: I 426 MET cc_start: 0.9156 (mmt) cc_final: 0.8903 (tpt) REVERT: I 502 LYS cc_start: 0.6686 (mmtp) cc_final: 0.5346 (mmtm) REVERT: J 657 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8303 (tt0) REVERT: K 82 LEU cc_start: 0.7387 (mm) cc_final: 0.7109 (mt) REVERT: M 45 LYS cc_start: 0.9030 (tttm) cc_final: 0.8693 (tttm) REVERT: M 79 GLN cc_start: 0.7154 (mp10) cc_final: 0.6936 (mp10) REVERT: M 94 ARG cc_start: 0.6365 (mmt180) cc_final: 0.4234 (mmt180) REVERT: S 46 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8214 (mmtp) REVERT: S 67 ASN cc_start: 0.8449 (m-40) cc_final: 0.8025 (m-40) REVERT: S 117 LYS cc_start: 0.7589 (tttt) cc_final: 0.7238 (mttp) REVERT: S 395 TRP cc_start: 0.6789 (m-10) cc_final: 0.6448 (m-10) REVERT: S 502 LYS cc_start: 0.6518 (mmtp) cc_final: 0.5261 (mmtm) REVERT: T 585 ARG cc_start: 0.9042 (mtp180) cc_final: 0.8753 (mtp180) REVERT: T 651 ASN cc_start: 0.8918 (m110) cc_final: 0.8523 (m110) REVERT: U 25 SER cc_start: 0.8634 (p) cc_final: 0.8201 (m) REVERT: U 75 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8426 (mttm) REVERT: V 45 LYS cc_start: 0.8770 (tttt) cc_final: 0.8436 (tttt) REVERT: V 47 MET cc_start: 0.9004 (mmm) cc_final: 0.8662 (mmt) REVERT: V 94 ARG cc_start: 0.5903 (mmt180) cc_final: 0.3770 (mtp180) outliers start: 39 outliers final: 28 residues processed: 341 average time/residue: 0.1489 time to fit residues: 74.4320 Evaluate side-chains 308 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 159 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN J 651 ASN S 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.088102 restraints weight = 27488.852| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.53 r_work: 0.2759 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20097 Z= 0.227 Angle : 0.697 10.949 27426 Z= 0.352 Chirality : 0.048 0.375 3279 Planarity : 0.005 0.056 3339 Dihedral : 6.791 56.933 4347 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.64 % Favored : 95.23 % Rotamer: Outliers : 2.44 % Allowed : 8.70 % Favored : 88.86 % 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 (0.17), residues: 2304 helix: 1.76 (0.27), residues: 387 sheet: 0.51 (0.20), residues: 687 loop : -0.32 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 542 TYR 0.022 0.002 TYR L 49 PHE 0.024 0.002 PHE I 383 TRP 0.015 0.002 TRP S 427 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00543 (19974) covalent geometry : angle 0.65990 (27093) SS BOND : bond 0.00405 ( 36) SS BOND : angle 1.47222 ( 72) hydrogen bonds : bond 0.05415 ( 735) hydrogen bonds : angle 5.09755 ( 1935) link_ALPHA1-3 : bond 0.01333 ( 3) link_ALPHA1-3 : angle 1.37964 ( 9) link_BETA1-4 : bond 0.00379 ( 18) link_BETA1-4 : angle 1.76777 ( 54) link_NAG-ASN : bond 0.00444 ( 66) link_NAG-ASN : angle 2.43080 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 277 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7266 (mttp) REVERT: A 150 MET cc_start: 0.8477 (mmm) cc_final: 0.8157 (mmm) REVERT: A 322 ASP cc_start: 0.8121 (m-30) cc_final: 0.7605 (p0) REVERT: A 502 LYS cc_start: 0.7324 (mmtp) cc_final: 0.5836 (mmtm) REVERT: H 25 SER cc_start: 0.8808 (p) cc_final: 0.8479 (m) REVERT: H 82 LEU cc_start: 0.7855 (mm) cc_final: 0.7599 (mt) REVERT: H 105 GLN cc_start: 0.8412 (pm20) cc_final: 0.8082 (pm20) REVERT: L 42 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8126 (mmmm) REVERT: L 45 LYS cc_start: 0.8855 (ttpt) cc_final: 0.8517 (tttm) REVERT: I 502 LYS cc_start: 0.7051 (mmtp) cc_final: 0.5505 (mmtp) REVERT: J 624 ASP cc_start: 0.9021 (m-30) cc_final: 0.8596 (m-30) REVERT: K 43 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8262 (mmmm) REVERT: M 45 LYS cc_start: 0.9065 (tttm) cc_final: 0.8702 (tttm) REVERT: M 94 ARG cc_start: 0.6449 (mmt180) cc_final: 0.4660 (mmt180) REVERT: S 395 TRP cc_start: 0.7001 (m-10) cc_final: 0.6681 (m-10) REVERT: S 502 LYS cc_start: 0.7162 (mmtp) cc_final: 0.5833 (mmtt) REVERT: T 632 ASP cc_start: 0.8797 (t70) cc_final: 0.8495 (t0) REVERT: U 25 SER cc_start: 0.8990 (p) cc_final: 0.8648 (m) REVERT: V 47 MET cc_start: 0.9044 (mmm) cc_final: 0.8752 (mmt) REVERT: V 94 ARG cc_start: 0.6425 (mmt180) cc_final: 0.4855 (mmt180) outliers start: 50 outliers final: 38 residues processed: 304 average time/residue: 0.1530 time to fit residues: 68.5236 Evaluate side-chains 302 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 95 MET Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 377 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 99 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 135 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 180 optimal weight: 0.5980 chunk 228 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN L 79 GLN I 67 ASN I 377 ASN J 651 ASN M 17 GLN S 377 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.088146 restraints weight = 27364.125| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.56 r_work: 0.2724 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 20097 Z= 0.247 Angle : 0.685 9.481 27426 Z= 0.345 Chirality : 0.048 0.365 3279 Planarity : 0.004 0.058 3339 Dihedral : 7.217 110.323 4347 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.21 % Favored : 94.66 % Rotamer: Outliers : 2.88 % Allowed : 9.29 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.20 (0.17), residues: 2304 helix: 1.61 (0.27), residues: 387 sheet: 0.39 (0.19), residues: 687 loop : -0.46 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG T 542 TYR 0.024 0.002 TYR M 49 PHE 0.022 0.002 PHE S 383 TRP 0.014 0.002 TRP A 427 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00599 (19974) covalent geometry : angle 0.65172 (27093) SS BOND : bond 0.00399 ( 36) SS BOND : angle 1.21510 ( 72) hydrogen bonds : bond 0.05366 ( 735) hydrogen bonds : angle 5.08945 ( 1935) link_ALPHA1-3 : bond 0.01304 ( 3) link_ALPHA1-3 : angle 1.38795 ( 9) link_BETA1-4 : bond 0.00360 ( 18) link_BETA1-4 : angle 1.61865 ( 54) link_NAG-ASN : bond 0.00515 ( 66) link_NAG-ASN : angle 2.34902 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 265 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7901 (mtpt) cc_final: 0.7293 (mttp) REVERT: A 141 ASP cc_start: 0.7597 (m-30) cc_final: 0.7111 (p0) REVERT: A 150 MET cc_start: 0.8518 (mmm) cc_final: 0.8078 (mmm) REVERT: A 322 ASP cc_start: 0.8119 (m-30) cc_final: 0.7558 (p0) REVERT: A 502 LYS cc_start: 0.7308 (mmtp) cc_final: 0.5634 (mmtt) REVERT: B 601 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9262 (mtpm) REVERT: H 6 GLU cc_start: 0.8406 (mp0) cc_final: 0.8174 (mp0) REVERT: H 25 SER cc_start: 0.8975 (p) cc_final: 0.8645 (m) REVERT: H 105 GLN cc_start: 0.8407 (pm20) cc_final: 0.8060 (pm20) REVERT: L 42 LYS cc_start: 0.8403 (mmmm) cc_final: 0.8110 (mmmm) REVERT: I 117 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7844 (mtpt) REVERT: I 502 LYS cc_start: 0.7062 (mmtp) cc_final: 0.5375 (mmtm) REVERT: J 601 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9138 (mttm) REVERT: J 624 ASP cc_start: 0.8906 (m-30) cc_final: 0.8533 (m-30) REVERT: K 3 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7743 (mt0) REVERT: K 43 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8275 (mmmm) REVERT: M 79 GLN cc_start: 0.7418 (mp10) cc_final: 0.6627 (mp10) REVERT: S 395 TRP cc_start: 0.7120 (m-10) cc_final: 0.6856 (m-10) REVERT: S 502 LYS cc_start: 0.7201 (mmtp) cc_final: 0.6266 (mmtp) REVERT: T 632 ASP cc_start: 0.8832 (t70) cc_final: 0.8558 (t0) REVERT: U 25 SER cc_start: 0.9084 (p) cc_final: 0.8751 (m) REVERT: V 47 MET cc_start: 0.9023 (mmm) cc_final: 0.8791 (mmt) REVERT: V 94 ARG cc_start: 0.6520 (mmt180) cc_final: 0.3822 (mtp180) outliers start: 59 outliers final: 45 residues processed: 302 average time/residue: 0.1585 time to fit residues: 69.6394 Evaluate side-chains 305 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 258 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 601 LYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 95 MET Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 38 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 153 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN J 651 ASN V 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.089314 restraints weight = 27264.254| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.59 r_work: 0.2763 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20097 Z= 0.153 Angle : 0.607 13.850 27426 Z= 0.306 Chirality : 0.047 0.680 3279 Planarity : 0.004 0.055 3339 Dihedral : 6.674 107.738 4347 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.99 % Favored : 94.88 % Rotamer: Outliers : 2.69 % Allowed : 9.53 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.32 (0.18), residues: 2304 helix: 1.72 (0.27), residues: 402 sheet: 0.40 (0.19), residues: 735 loop : -0.40 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 542 TYR 0.021 0.001 TYR M 49 PHE 0.014 0.002 PHE I 383 TRP 0.012 0.001 TRP S 427 HIS 0.004 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00358 (19974) covalent geometry : angle 0.57489 (27093) SS BOND : bond 0.00282 ( 36) SS BOND : angle 0.84860 ( 72) hydrogen bonds : bond 0.04531 ( 735) hydrogen bonds : angle 4.93533 ( 1935) link_ALPHA1-3 : bond 0.01087 ( 3) link_ALPHA1-3 : angle 1.46513 ( 9) link_BETA1-4 : bond 0.00393 ( 18) link_BETA1-4 : angle 1.47557 ( 54) link_NAG-ASN : bond 0.00355 ( 66) link_NAG-ASN : angle 2.21081 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7339 (mmmt) REVERT: A 150 MET cc_start: 0.8535 (mmm) cc_final: 0.8194 (mmm) REVERT: A 322 ASP cc_start: 0.8063 (m-30) cc_final: 0.7593 (p0) REVERT: A 327 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7433 (mmm-85) REVERT: A 492 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8835 (mt-10) REVERT: A 502 LYS cc_start: 0.7265 (mmtp) cc_final: 0.5651 (mmtm) REVERT: B 601 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.9299 (mtpm) REVERT: H 25 SER cc_start: 0.9024 (p) cc_final: 0.8711 (m) REVERT: H 100 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9252 (mt) REVERT: H 105 GLN cc_start: 0.8384 (pm20) cc_final: 0.8002 (pm20) REVERT: L 42 LYS cc_start: 0.8437 (mmmm) cc_final: 0.8149 (mmmm) REVERT: L 45 LYS cc_start: 0.8991 (tttt) cc_final: 0.8660 (tttm) REVERT: I 117 LYS cc_start: 0.8045 (mtpt) cc_final: 0.7814 (mtpt) REVERT: I 502 LYS cc_start: 0.7081 (mmtp) cc_final: 0.5170 (mmtp) REVERT: J 601 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9122 (mttm) REVERT: J 624 ASP cc_start: 0.8694 (m-30) cc_final: 0.8484 (m-30) REVERT: J 657 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8444 (tt0) REVERT: K 3 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7754 (mt0) REVERT: K 100 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.8980 (mp) REVERT: M 79 GLN cc_start: 0.7409 (mp10) cc_final: 0.6527 (mp10) REVERT: S 395 TRP cc_start: 0.7146 (m-10) cc_final: 0.6619 (m-10) REVERT: S 502 LYS cc_start: 0.7186 (mmtp) cc_final: 0.6008 (mmtp) REVERT: T 626 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.9072 (mmt) REVERT: T 632 ASP cc_start: 0.8792 (t70) cc_final: 0.8519 (t0) REVERT: U 25 SER cc_start: 0.9106 (p) cc_final: 0.8784 (m) REVERT: U 82 MET cc_start: 0.8703 (mtt) cc_final: 0.8154 (mtt) REVERT: V 47 MET cc_start: 0.9005 (mmm) cc_final: 0.8741 (mmt) outliers start: 55 outliers final: 38 residues processed: 296 average time/residue: 0.1502 time to fit residues: 65.4491 Evaluate side-chains 297 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 601 LYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN I 67 ASN J 607 ASN J 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.085586 restraints weight = 27621.072| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.68 r_work: 0.2674 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 20097 Z= 0.256 Angle : 0.677 8.509 27426 Z= 0.342 Chirality : 0.048 0.387 3279 Planarity : 0.005 0.058 3339 Dihedral : 6.940 112.870 4347 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.51 % Favored : 94.40 % Rotamer: Outliers : 3.08 % Allowed : 9.78 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.01 (0.17), residues: 2304 helix: 1.40 (0.26), residues: 405 sheet: 0.20 (0.19), residues: 717 loop : -0.59 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 480 TYR 0.020 0.002 TYR M 49 PHE 0.021 0.002 PHE S 383 TRP 0.016 0.002 TRP A 427 HIS 0.006 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00623 (19974) covalent geometry : angle 0.64877 (27093) SS BOND : bond 0.00457 ( 36) SS BOND : angle 1.29983 ( 72) hydrogen bonds : bond 0.05424 ( 735) hydrogen bonds : angle 5.03318 ( 1935) link_ALPHA1-3 : bond 0.01252 ( 3) link_ALPHA1-3 : angle 1.22860 ( 9) link_BETA1-4 : bond 0.00374 ( 18) link_BETA1-4 : angle 1.57803 ( 54) link_NAG-ASN : bond 0.00517 ( 66) link_NAG-ASN : angle 2.12844 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 270 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7336 (mmmt) REVERT: A 141 ASP cc_start: 0.7575 (m-30) cc_final: 0.7096 (p0) REVERT: A 150 MET cc_start: 0.8460 (mmm) cc_final: 0.8040 (mmm) REVERT: A 322 ASP cc_start: 0.7988 (m-30) cc_final: 0.7543 (p0) REVERT: A 502 LYS cc_start: 0.7053 (mmtp) cc_final: 0.5399 (mmtp) REVERT: B 601 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9210 (mtpm) REVERT: H 25 SER cc_start: 0.9074 (p) cc_final: 0.8804 (m) REVERT: H 100 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9268 (mt) REVERT: H 105 GLN cc_start: 0.8358 (pm20) cc_final: 0.7859 (pm20) REVERT: L 45 LYS cc_start: 0.8930 (tttt) cc_final: 0.8471 (tttm) REVERT: I 117 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7762 (mtpt) REVERT: I 502 LYS cc_start: 0.6854 (mmtp) cc_final: 0.5886 (mmtt) REVERT: J 601 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9076 (mttm) REVERT: J 624 ASP cc_start: 0.8800 (m-30) cc_final: 0.8535 (m-30) REVERT: K 3 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7690 (mt0) REVERT: K 100 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9009 (mp) REVERT: S 178 ARG cc_start: 0.8416 (tpt90) cc_final: 0.8195 (tpt90) REVERT: S 395 TRP cc_start: 0.7151 (m-10) cc_final: 0.6630 (m-10) REVERT: S 502 LYS cc_start: 0.7004 (mmtp) cc_final: 0.5507 (mmtm) REVERT: T 632 ASP cc_start: 0.8633 (t70) cc_final: 0.8332 (t0) REVERT: U 3 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7828 (mt0) outliers start: 63 outliers final: 51 residues processed: 309 average time/residue: 0.1486 time to fit residues: 67.5594 Evaluate side-chains 316 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 601 LYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 20 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 188 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 185 optimal weight: 20.0000 chunk 125 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN J 651 ASN M 17 GLN V 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.088901 restraints weight = 27346.420| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.62 r_work: 0.2785 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20097 Z= 0.132 Angle : 0.604 21.684 27426 Z= 0.300 Chirality : 0.048 1.028 3279 Planarity : 0.004 0.056 3339 Dihedral : 6.626 112.288 4347 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.84 % Rotamer: Outliers : 2.35 % Allowed : 10.75 % Favored : 86.90 % 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: 0.19 (0.18), residues: 2304 helix: 1.86 (0.27), residues: 402 sheet: 0.26 (0.19), residues: 750 loop : -0.54 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 542 TYR 0.019 0.001 TYR M 49 PHE 0.014 0.001 PHE S 53 TRP 0.013 0.001 TRP S 427 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00300 (19974) covalent geometry : angle 0.56421 (27093) SS BOND : bond 0.00263 ( 36) SS BOND : angle 0.71277 ( 72) hydrogen bonds : bond 0.04348 ( 735) hydrogen bonds : angle 4.85134 ( 1935) link_ALPHA1-3 : bond 0.01069 ( 3) link_ALPHA1-3 : angle 1.50467 ( 9) link_BETA1-4 : bond 0.00364 ( 18) link_BETA1-4 : angle 1.38395 ( 54) link_NAG-ASN : bond 0.00323 ( 66) link_NAG-ASN : angle 2.47849 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7401 (mmmt) REVERT: A 141 ASP cc_start: 0.7469 (m-30) cc_final: 0.7066 (p0) REVERT: A 150 MET cc_start: 0.8530 (mmm) cc_final: 0.8067 (mmm) REVERT: A 322 ASP cc_start: 0.7837 (m-30) cc_final: 0.7544 (p0) REVERT: A 327 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7465 (mmm-85) REVERT: A 502 LYS cc_start: 0.7049 (mmtp) cc_final: 0.5471 (mmtp) REVERT: H 25 SER cc_start: 0.9107 (p) cc_final: 0.8815 (m) REVERT: H 43 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8317 (mmmm) REVERT: H 105 GLN cc_start: 0.8301 (pm20) cc_final: 0.7830 (pm20) REVERT: L 42 LYS cc_start: 0.8522 (mmmm) cc_final: 0.8208 (mmmm) REVERT: I 502 LYS cc_start: 0.6831 (mmtp) cc_final: 0.5205 (mmtp) REVERT: J 601 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9059 (mttm) REVERT: J 624 ASP cc_start: 0.8147 (m-30) cc_final: 0.7945 (t0) REVERT: J 657 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8208 (tt0) REVERT: K 3 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7812 (mt0) REVERT: K 19 LYS cc_start: 0.8861 (tptm) cc_final: 0.8651 (tptm) REVERT: K 46 GLU cc_start: 0.8790 (tt0) cc_final: 0.8525 (tt0) REVERT: K 100 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9102 (mp) REVERT: M 79 GLN cc_start: 0.7430 (mp10) cc_final: 0.7008 (mp10) REVERT: S 46 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8370 (mmtp) REVERT: S 356 ASN cc_start: 0.7938 (p0) cc_final: 0.7681 (m-40) REVERT: S 395 TRP cc_start: 0.7044 (m-10) cc_final: 0.6578 (m-10) REVERT: S 502 LYS cc_start: 0.6934 (mmtp) cc_final: 0.6040 (mmtp) REVERT: T 626 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.9002 (mmt) REVERT: T 632 ASP cc_start: 0.8505 (t70) cc_final: 0.8176 (t0) REVERT: U 3 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7904 (mt0) REVERT: U 82 MET cc_start: 0.8559 (mtt) cc_final: 0.8014 (mtt) outliers start: 48 outliers final: 39 residues processed: 294 average time/residue: 0.1541 time to fit residues: 66.9594 Evaluate side-chains 301 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 601 LYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 203 optimal weight: 0.0570 chunk 163 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN J 651 ASN V 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.089766 restraints weight = 27161.601| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.62 r_work: 0.2798 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20097 Z= 0.136 Angle : 0.602 25.380 27426 Z= 0.298 Chirality : 0.046 0.675 3279 Planarity : 0.004 0.055 3339 Dihedral : 6.468 112.322 4347 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.12 % Favored : 94.79 % Rotamer: Outliers : 2.54 % Allowed : 10.51 % Favored : 86.95 % 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: 0.37 (0.18), residues: 2304 helix: 1.99 (0.27), residues: 402 sheet: 0.43 (0.19), residues: 726 loop : -0.45 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 585 TYR 0.019 0.001 TYR M 49 PHE 0.013 0.001 PHE A 53 TRP 0.012 0.001 TRP S 427 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00317 (19974) covalent geometry : angle 0.55023 (27093) SS BOND : bond 0.00263 ( 36) SS BOND : angle 0.81165 ( 72) hydrogen bonds : bond 0.04270 ( 735) hydrogen bonds : angle 4.80991 ( 1935) link_ALPHA1-3 : bond 0.01121 ( 3) link_ALPHA1-3 : angle 1.41381 ( 9) link_BETA1-4 : bond 0.00381 ( 18) link_BETA1-4 : angle 1.38264 ( 54) link_NAG-ASN : bond 0.00269 ( 66) link_NAG-ASN : angle 2.82442 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7358 (mmmt) REVERT: A 150 MET cc_start: 0.8595 (mmm) cc_final: 0.8235 (mmm) REVERT: A 267 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8333 (mp0) REVERT: A 322 ASP cc_start: 0.8032 (m-30) cc_final: 0.7591 (p0) REVERT: A 327 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7449 (mmm-85) REVERT: A 502 LYS cc_start: 0.7236 (mmtp) cc_final: 0.5999 (mmtt) REVERT: H 25 SER cc_start: 0.9111 (p) cc_final: 0.8841 (m) REVERT: H 43 LYS cc_start: 0.8838 (mmtm) cc_final: 0.8311 (mmmm) REVERT: H 82 MET cc_start: 0.9015 (mtm) cc_final: 0.8762 (mtt) REVERT: L 45 LYS cc_start: 0.8966 (tttt) cc_final: 0.8623 (tttm) REVERT: I 117 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7710 (mttm) REVERT: I 502 LYS cc_start: 0.7009 (mmtp) cc_final: 0.5210 (mmtp) REVERT: J 601 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9114 (mttm) REVERT: J 657 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8440 (tt0) REVERT: K 3 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7815 (mt0) REVERT: K 46 GLU cc_start: 0.8935 (tt0) cc_final: 0.8688 (tt0) REVERT: K 100 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9129 (mp) REVERT: M 61 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7263 (mtm110) REVERT: M 79 GLN cc_start: 0.7426 (mp10) cc_final: 0.6986 (mp10) REVERT: S 356 ASN cc_start: 0.7998 (p0) cc_final: 0.7673 (m-40) REVERT: S 395 TRP cc_start: 0.7140 (m-10) cc_final: 0.6686 (m-10) REVERT: S 502 LYS cc_start: 0.7109 (mmtp) cc_final: 0.5809 (mmtm) REVERT: T 632 ASP cc_start: 0.8762 (t70) cc_final: 0.8440 (t0) REVERT: U 3 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7917 (mt0) REVERT: U 82 MET cc_start: 0.8720 (mtt) cc_final: 0.8255 (mtt) outliers start: 52 outliers final: 43 residues processed: 297 average time/residue: 0.1484 time to fit residues: 64.7547 Evaluate side-chains 305 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 601 LYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 226 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN S 246 GLN V 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.089921 restraints weight = 27528.491| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.60 r_work: 0.2761 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20097 Z= 0.160 Angle : 0.616 17.429 27426 Z= 0.306 Chirality : 0.045 0.246 3279 Planarity : 0.004 0.055 3339 Dihedral : 6.925 111.286 4343 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 2.30 % Allowed : 10.95 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.18), residues: 2304 helix: 1.96 (0.27), residues: 402 sheet: 0.40 (0.19), residues: 726 loop : -0.46 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 585 TYR 0.018 0.001 TYR M 49 PHE 0.014 0.001 PHE S 383 TRP 0.012 0.001 TRP S 427 HIS 0.004 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00379 (19974) covalent geometry : angle 0.57568 (27093) SS BOND : bond 0.00299 ( 36) SS BOND : angle 0.96061 ( 72) hydrogen bonds : bond 0.04449 ( 735) hydrogen bonds : angle 4.76437 ( 1935) link_ALPHA1-3 : bond 0.01038 ( 3) link_ALPHA1-3 : angle 1.31169 ( 9) link_BETA1-4 : bond 0.00376 ( 18) link_BETA1-4 : angle 1.39848 ( 54) link_NAG-ASN : bond 0.00281 ( 66) link_NAG-ASN : angle 2.49225 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7370 (mmmt) REVERT: A 150 MET cc_start: 0.8595 (mmm) cc_final: 0.8252 (mmm) REVERT: A 178 ARG cc_start: 0.8575 (tpt170) cc_final: 0.8342 (tpt170) REVERT: A 267 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8325 (mp0) REVERT: A 322 ASP cc_start: 0.8060 (m-30) cc_final: 0.7658 (p0) REVERT: A 327 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7430 (mmm-85) REVERT: A 502 LYS cc_start: 0.7276 (mmtp) cc_final: 0.5629 (mmtm) REVERT: H 25 SER cc_start: 0.9138 (p) cc_final: 0.8866 (m) REVERT: H 43 LYS cc_start: 0.8784 (mmtm) cc_final: 0.8267 (mmmm) REVERT: H 82 MET cc_start: 0.9014 (mtm) cc_final: 0.8755 (mtt) REVERT: H 105 GLN cc_start: 0.8205 (pm20) cc_final: 0.7832 (pm20) REVERT: I 117 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7746 (mttm) REVERT: I 502 LYS cc_start: 0.7037 (mmtp) cc_final: 0.5229 (mmtp) REVERT: J 601 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9110 (mttm) REVERT: J 657 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8406 (tt0) REVERT: K 3 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7816 (mt0) REVERT: K 46 GLU cc_start: 0.8954 (tt0) cc_final: 0.8684 (tt0) REVERT: K 100 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9080 (mp) REVERT: M 61 ARG cc_start: 0.7695 (mtm110) cc_final: 0.6972 (mtm110) REVERT: M 79 GLN cc_start: 0.7379 (mp10) cc_final: 0.6470 (mp10) REVERT: S 46 LYS cc_start: 0.8778 (mmtp) cc_final: 0.8552 (mmtp) REVERT: S 356 ASN cc_start: 0.8034 (p0) cc_final: 0.7780 (m-40) REVERT: S 395 TRP cc_start: 0.7157 (m-10) cc_final: 0.6710 (m-10) REVERT: S 502 LYS cc_start: 0.7144 (mmtp) cc_final: 0.6181 (mmtp) REVERT: T 632 ASP cc_start: 0.8788 (t70) cc_final: 0.8415 (t0) REVERT: U 3 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7885 (mt0) REVERT: U 82 MET cc_start: 0.8705 (mtt) cc_final: 0.8251 (mtt) REVERT: V 61 ARG cc_start: 0.7902 (mtm110) cc_final: 0.7238 (mtm110) outliers start: 47 outliers final: 43 residues processed: 294 average time/residue: 0.1526 time to fit residues: 66.3455 Evaluate side-chains 308 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 263 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 601 LYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 27 optimal weight: 0.7980 chunk 223 optimal weight: 6.9990 chunk 16 optimal weight: 0.0060 chunk 68 optimal weight: 0.0770 chunk 206 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN I 246 GLN V 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.093500 restraints weight = 27162.292| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.53 r_work: 0.2817 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20097 Z= 0.135 Angle : 0.582 11.868 27426 Z= 0.292 Chirality : 0.045 0.451 3279 Planarity : 0.004 0.055 3339 Dihedral : 7.106 111.504 4343 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.21 % Favored : 94.75 % Rotamer: Outliers : 2.30 % Allowed : 11.14 % Favored : 86.56 % 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: 0.43 (0.18), residues: 2304 helix: 2.38 (0.27), residues: 384 sheet: 0.43 (0.19), residues: 726 loop : -0.48 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 585 TYR 0.019 0.001 TYR M 49 PHE 0.013 0.001 PHE A 53 TRP 0.011 0.001 TRP A 427 HIS 0.004 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00315 (19974) covalent geometry : angle 0.54970 (27093) SS BOND : bond 0.00273 ( 36) SS BOND : angle 0.84878 ( 72) hydrogen bonds : bond 0.04193 ( 735) hydrogen bonds : angle 4.76047 ( 1935) link_ALPHA1-3 : bond 0.01024 ( 3) link_ALPHA1-3 : angle 1.35295 ( 9) link_BETA1-4 : bond 0.00368 ( 18) link_BETA1-4 : angle 1.35032 ( 54) link_NAG-ASN : bond 0.00407 ( 66) link_NAG-ASN : angle 2.15667 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4607.64 seconds wall clock time: 80 minutes 8.68 seconds (4808.68 seconds total)