Starting phenix.real_space_refine on Thu Mar 5 06:13:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x9v_22112/03_2026/6x9v_22112.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x9v_22112/03_2026/6x9v_22112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x9v_22112/03_2026/6x9v_22112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x9v_22112/03_2026/6x9v_22112.map" model { file = "/net/cci-nas-00/data/ceres_data/6x9v_22112/03_2026/6x9v_22112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x9v_22112/03_2026/6x9v_22112.cif" } resolution = 3.5 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 1 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: 4.51, per 1000 atoms: 0.23 Number of scatterers: 19590 At special positions: 0 Unit cell: (123.05, 125.35, 148.35, 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=2.07 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.13 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=2.08 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 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=2.07 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=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.13 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=2.08 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 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=2.07 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=2.03 Simple disulfide: pdb=" SG CYS S 228 " - pdb=" SG CYS S 239 " distance=2.13 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=2.08 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.03 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: 1.38 Conformation dependent library (CDL) restraints added in 681.6 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, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.059A 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 334 through 354 removed outlier: 3.932A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.086A 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 387 through 390 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.693A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 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: 4.059A 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 334 through 354 removed outlier: 3.932A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.086A 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 387 through 390 Processing helix chain 'I' and resid 476 through 484 removed outlier: 3.694A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 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: 4.058A 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 334 through 354 removed outlier: 3.933A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.086A 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 387 through 390 Processing helix chain 'S' and resid 476 through 484 removed outlier: 3.693A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 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: 3.727A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (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: 6.356A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.598A 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: 6.318A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.993A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.284A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.320A 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 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: 6.293A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.471A 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: 6.004A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.555A 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: 6.589A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.499A 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: 6.589A 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: 3.727A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (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: 6.356A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.598A 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: 6.318A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.994A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.285A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.320A 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 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: 6.292A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE I 323 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.471A 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: 6.004A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.554A 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: 6.589A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.499A 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: 6.589A 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: 3.727A pdb=" N ILE S 225 " --> pdb=" O VAL S 245 " (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: 6.357A pdb=" N ALA S 200 " --> pdb=" O ALA S 433 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR S 435 " --> pdb=" O ALA S 200 " (cutoff:3.500A) removed outlier: 6.598A 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: 6.318A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY S 441 " --> pdb=" O ASN S 300 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASN S 300 " --> pdb=" O GLY S 441 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY S 451 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR S 290 " --> pdb=" O GLY S 451 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N ILE S 453 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 11.993A pdb=" N PHE S 288 " --> pdb=" O ILE S 453 " (cutoff:3.500A) removed outlier: 10.861A pdb=" N THR S 455 " --> pdb=" O VAL S 286 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N VAL S 286 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N ASP S 457 " --> pdb=" O ILE S 284 " (cutoff:3.500A) removed outlier: 12.284A pdb=" N ILE S 284 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.320A 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 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: 6.293A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR S 303 " --> pdb=" O GLY S 321 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE S 323 " --> pdb=" O ASN S 301 " (cutoff:3.500A) removed outlier: 6.471A 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: 6.005A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.554A 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: 6.590A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.498A 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: 6.590A 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 24 768 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 1.89 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: 3620 1.31 - 1.44: 5414 1.44 - 1.56: 10680 1.56 - 1.69: 86 1.69 - 1.82: 174 Bond restraints: 19974 Sorted by residual: bond pdb=" CD ARG U 71 " pdb=" NE ARG U 71 " ideal model delta sigma weight residual 1.458 1.358 0.100 1.40e-02 5.10e+03 5.10e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" CD ARG K 71 " pdb=" NE ARG K 71 " ideal model delta sigma weight residual 1.458 1.358 0.100 1.40e-02 5.10e+03 5.08e+01 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.07e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 23161 2.38 - 4.76: 3413 4.76 - 7.13: 462 7.13 - 9.51: 45 9.51 - 11.89: 12 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N PRO M 7 " pdb=" CA PRO M 7 " pdb=" C PRO M 7 " ideal model delta sigma weight residual 110.70 122.59 -11.89 1.22e+00 6.72e-01 9.50e+01 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 122.58 -11.88 1.22e+00 6.72e-01 9.47e+01 angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 122.57 -11.87 1.22e+00 6.72e-01 9.46e+01 angle pdb=" C CYS I 239 " pdb=" N PRO I 240 " pdb=" CA PRO I 240 " ideal model delta sigma weight residual 120.98 129.17 -8.19 1.07e+00 8.73e-01 5.85e+01 angle pdb=" C CYS S 239 " pdb=" N PRO S 240 " pdb=" CA PRO S 240 " ideal model delta sigma weight residual 120.98 129.16 -8.18 1.07e+00 8.73e-01 5.85e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 12615 21.78 - 43.55: 297 43.55 - 65.33: 84 65.33 - 87.11: 30 87.11 - 108.89: 12 Dihedral angle restraints: 13038 sinusoidal: 6291 harmonic: 6747 Sorted by residual: 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 93.00 163.47 -70.47 1 1.00e+01 1.00e-02 6.39e+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 93.00 163.46 -70.46 1 1.00e+01 1.00e-02 6.39e+01 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 93.00 163.46 -70.46 1 1.00e+01 1.00e-02 6.39e+01 ... (remaining 13035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2434 0.108 - 0.215: 724 0.215 - 0.323: 105 0.323 - 0.430: 13 0.430 - 0.538: 3 Chirality restraints: 3279 Sorted by residual: 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 -2.62 0.22 2.00e-02 2.50e+03 1.17e+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 -2.61 0.21 2.00e-02 2.50e+03 1.13e+02 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 -2.61 0.21 2.00e-02 2.50e+03 1.13e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.237 2.00e-02 2.50e+03 1.96e-01 4.79e+02 pdb=" C7 NAG B 702 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.321 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " -0.237 2.00e-02 2.50e+03 1.96e-01 4.78e+02 pdb=" C7 NAG J 702 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " 0.321 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " 0.237 2.00e-02 2.50e+03 1.95e-01 4.78e+02 pdb=" C7 NAG T 702 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " -0.320 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.018 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4611 2.77 - 3.30: 17084 3.30 - 3.83: 32577 3.83 - 4.37: 38969 4.37 - 4.90: 64839 Nonbonded interactions: 158080 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR S 37 " pdb=" OG1 THR S 499 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.234 3.040 nonbonded pdb=" N ASP K 84 " pdb=" OD1 ASP K 84 " model vdw 2.327 3.120 nonbonded pdb=" N ASP H 84 " pdb=" OD1 ASP H 84 " model vdw 2.327 3.120 ... (remaining 158075 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: 0.04 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.030 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.026 0.148 20097 Z= 1.393 Angle : 1.761 11.889 27426 Z= 1.132 Chirality : 0.101 0.538 3279 Planarity : 0.011 0.196 3339 Dihedral : 11.128 108.886 8598 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.39 % Favored : 96.35 % Rotamer: Outliers : 0.29 % Allowed : 0.44 % Favored : 99.27 % 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: 0.76 (0.17), residues: 2304 helix: 0.06 (0.25), residues: 378 sheet: 0.89 (0.19), residues: 690 loop : 0.59 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 66 TYR 0.058 0.008 TYR S 40 PHE 0.032 0.006 PHE A 383 TRP 0.065 0.012 TRP I 427 HIS 0.011 0.002 HIS U 82A Details of bonding type rmsd covalent geometry : bond 0.02628 (19974) covalent geometry : angle 1.73468 (27093) SS BOND : bond 0.03398 ( 36) SS BOND : angle 2.44054 ( 72) hydrogen bonds : bond 0.15826 ( 747) hydrogen bonds : angle 7.33218 ( 1980) link_ALPHA1-3 : bond 0.03731 ( 3) link_ALPHA1-3 : angle 3.08002 ( 9) link_BETA1-4 : bond 0.02806 ( 18) link_BETA1-4 : angle 3.75036 ( 54) link_NAG-ASN : bond 0.03681 ( 66) link_NAG-ASN : angle 3.36431 ( 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: 6 poor density : 498 time to evaluate : 0.615 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 46 LYS cc_start: 0.8454 (mmtp) cc_final: 0.8219 (mmtp) REVERT: A 108 ILE cc_start: 0.8727 (pp) cc_final: 0.8437 (mm) REVERT: A 492 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7926 (mt-10) REVERT: B 625 ASN cc_start: 0.7934 (m110) cc_final: 0.7707 (m-40) REVERT: L 45 LYS cc_start: 0.8776 (tttt) cc_final: 0.8489 (ttmm) REVERT: L 60 ASP cc_start: 0.8345 (p0) cc_final: 0.8074 (t0) REVERT: L 105 THR cc_start: 0.7867 (m) cc_final: 0.7656 (p) REVERT: J 625 ASN cc_start: 0.7995 (m110) cc_final: 0.7729 (m-40) REVERT: K 72 ASP cc_start: 0.7636 (t0) cc_final: 0.7288 (t70) REVERT: M 45 LYS cc_start: 0.8166 (tttt) cc_final: 0.7868 (ttmm) REVERT: M 94 ARG cc_start: 0.6206 (mmt180) cc_final: 0.5071 (ttm-80) REVERT: M 95 THR cc_start: 0.7841 (m) cc_final: 0.7546 (p) REVERT: S 161 MET cc_start: 0.8423 (tpp) cc_final: 0.7998 (tpp) REVERT: V 45 LYS cc_start: 0.8913 (tttt) cc_final: 0.8551 (ttmm) REVERT: V 94 ARG cc_start: 0.5748 (mmt180) cc_final: 0.5334 (mmt-90) outliers start: 6 outliers final: 3 residues processed: 503 average time/residue: 0.1532 time to fit residues: 114.0102 Evaluate side-chains 261 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 258 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain S residue 355 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 432 GLN J 653 GLN M 6 GLN ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 GLN S 432 GLN T 630 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.093609 restraints weight = 34907.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096602 restraints weight = 20706.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098596 restraints weight = 14643.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099923 restraints weight = 11518.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100807 restraints weight = 9731.905| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20097 Z= 0.180 Angle : 0.764 12.926 27426 Z= 0.390 Chirality : 0.048 0.264 3279 Planarity : 0.004 0.058 3339 Dihedral : 7.580 60.209 4341 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.08 % Favored : 96.66 % Rotamer: Outliers : 2.05 % Allowed : 7.92 % Favored : 90.03 % 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: 0.69 (0.17), residues: 2304 helix: 1.57 (0.27), residues: 387 sheet: 0.47 (0.20), residues: 627 loop : 0.21 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 151 TYR 0.018 0.002 TYR M 96 PHE 0.025 0.002 PHE U 102 TRP 0.025 0.002 TRP A 479 HIS 0.007 0.001 HIS I 72 Details of bonding type rmsd covalent geometry : bond 0.00389 (19974) covalent geometry : angle 0.71386 (27093) SS BOND : bond 0.00317 ( 36) SS BOND : angle 1.07211 ( 72) hydrogen bonds : bond 0.05179 ( 747) hydrogen bonds : angle 5.87812 ( 1980) link_ALPHA1-3 : bond 0.00539 ( 3) link_ALPHA1-3 : angle 3.01802 ( 9) link_BETA1-4 : bond 0.00447 ( 18) link_BETA1-4 : angle 2.34559 ( 54) link_NAG-ASN : bond 0.00464 ( 66) link_NAG-ASN : angle 2.95734 ( 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 381 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 339 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 601 LYS cc_start: 0.9017 (mttp) cc_final: 0.8811 (mttt) REVERT: H 72 ASP cc_start: 0.7613 (t70) cc_final: 0.7353 (t70) REVERT: H 111 VAL cc_start: 0.8496 (t) cc_final: 0.8065 (m) REVERT: L 45 LYS cc_start: 0.8487 (tttt) cc_final: 0.8020 (ttmm) REVERT: I 271 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7317 (mtp) REVERT: I 323 ILE cc_start: 0.8502 (mt) cc_final: 0.8291 (mt) REVERT: J 648 GLU cc_start: 0.8126 (tp30) cc_final: 0.7754 (tt0) REVERT: K 23 ARG cc_start: 0.7667 (mmm160) cc_final: 0.7447 (mmm160) REVERT: K 28 THR cc_start: 0.8540 (m) cc_final: 0.8228 (p) REVERT: K 70 SER cc_start: 0.8527 (t) cc_final: 0.8230 (m) REVERT: K 72 ASP cc_start: 0.7485 (t0) cc_final: 0.6821 (t0) REVERT: M 45 LYS cc_start: 0.8072 (tttt) cc_final: 0.7624 (ttmm) REVERT: M 94 ARG cc_start: 0.5154 (mmt180) cc_final: 0.4466 (mmt-90) REVERT: S 161 MET cc_start: 0.8274 (tpp) cc_final: 0.7827 (tpt) REVERT: T 625 ASN cc_start: 0.6310 (m110) cc_final: 0.6032 (m-40) REVERT: T 633 LYS cc_start: 0.8671 (mttt) cc_final: 0.8383 (mttp) REVERT: U 72 ASP cc_start: 0.7594 (t70) cc_final: 0.7350 (t70) REVERT: V 45 LYS cc_start: 0.8367 (tttt) cc_final: 0.7864 (ttmm) REVERT: V 78 LEU cc_start: 0.7555 (tt) cc_final: 0.7334 (tt) REVERT: V 94 ARG cc_start: 0.5235 (mmt180) cc_final: 0.4839 (mtt-85) outliers start: 42 outliers final: 28 residues processed: 365 average time/residue: 0.1345 time to fit residues: 76.0498 Evaluate side-chains 294 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain S residue 140 ASP Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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** S 352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.092175 restraints weight = 34939.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.095126 restraints weight = 20668.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097081 restraints weight = 14614.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098363 restraints weight = 11513.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099146 restraints weight = 9762.684| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20097 Z= 0.156 Angle : 0.644 9.547 27426 Z= 0.328 Chirality : 0.045 0.257 3279 Planarity : 0.004 0.048 3339 Dihedral : 5.962 48.254 4335 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.08 % Favored : 96.66 % Rotamer: Outliers : 2.30 % Allowed : 9.92 % Favored : 87.78 % 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: 0.57 (0.17), residues: 2304 helix: 1.78 (0.27), residues: 387 sheet: 0.28 (0.19), residues: 675 loop : 0.08 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 151 TYR 0.016 0.001 TYR L 49 PHE 0.016 0.002 PHE I 468 TRP 0.018 0.001 TRP S 112 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00349 (19974) covalent geometry : angle 0.60885 (27093) SS BOND : bond 0.00359 ( 36) SS BOND : angle 1.02886 ( 72) hydrogen bonds : bond 0.04315 ( 747) hydrogen bonds : angle 5.44824 ( 1980) link_ALPHA1-3 : bond 0.01075 ( 3) link_ALPHA1-3 : angle 1.59499 ( 9) link_BETA1-4 : bond 0.00471 ( 18) link_BETA1-4 : angle 1.66784 ( 54) link_NAG-ASN : bond 0.00571 ( 66) link_NAG-ASN : angle 2.31875 ( 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 330 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 283 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8101 (mmtp) cc_final: 0.7300 (mmtt) REVERT: A 161 MET cc_start: 0.8570 (tpt) cc_final: 0.8098 (tpt) REVERT: A 492 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7493 (mt-10) REVERT: H 72 ASP cc_start: 0.7577 (t70) cc_final: 0.7317 (t70) REVERT: L 45 LYS cc_start: 0.8510 (tttt) cc_final: 0.8070 (ttmm) REVERT: I 161 MET cc_start: 0.8420 (tpp) cc_final: 0.7815 (tpp) REVERT: I 271 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7489 (mtp) REVERT: J 648 GLU cc_start: 0.8114 (tp30) cc_final: 0.7732 (tt0) REVERT: K 70 SER cc_start: 0.8619 (t) cc_final: 0.8281 (m) REVERT: K 72 ASP cc_start: 0.7702 (t0) cc_final: 0.7146 (t0) REVERT: M 45 LYS cc_start: 0.8224 (tttt) cc_final: 0.7871 (ttmm) REVERT: M 94 ARG cc_start: 0.5109 (mmt180) cc_final: 0.4492 (tpp-160) REVERT: S 161 MET cc_start: 0.8344 (tpp) cc_final: 0.7818 (tpt) REVERT: S 271 MET cc_start: 0.7218 (mtp) cc_final: 0.6895 (tpt) REVERT: T 542 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.7451 (mtm-85) REVERT: T 625 ASN cc_start: 0.6608 (m110) cc_final: 0.6343 (m-40) REVERT: V 45 LYS cc_start: 0.8360 (tttt) cc_final: 0.7798 (ttmm) REVERT: V 94 ARG cc_start: 0.5542 (mmt180) cc_final: 0.5201 (mmt-90) outliers start: 47 outliers final: 34 residues processed: 306 average time/residue: 0.1446 time to fit residues: 67.4730 Evaluate side-chains 286 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain S residue 69 TRP Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain V residue 52 THR 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: 8.9990 chunk 108 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 145 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS I 352 HIS V 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.106565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.087028 restraints weight = 35175.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.089868 restraints weight = 20840.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.091743 restraints weight = 14811.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092989 restraints weight = 11772.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.093817 restraints weight = 10034.750| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20097 Z= 0.195 Angle : 0.646 8.845 27426 Z= 0.328 Chirality : 0.046 0.288 3279 Planarity : 0.004 0.064 3339 Dihedral : 5.180 49.926 4335 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.86 % Favored : 95.88 % Rotamer: Outliers : 3.08 % Allowed : 10.02 % 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: 0.41 (0.18), residues: 2304 helix: 1.83 (0.27), residues: 384 sheet: 0.10 (0.19), residues: 696 loop : -0.04 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 103 TYR 0.016 0.001 TYR V 86 PHE 0.020 0.002 PHE I 468 TRP 0.014 0.002 TRP S 112 HIS 0.005 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00447 (19974) covalent geometry : angle 0.61478 (27093) SS BOND : bond 0.00382 ( 36) SS BOND : angle 1.06736 ( 72) hydrogen bonds : bond 0.04228 ( 747) hydrogen bonds : angle 5.25541 ( 1980) link_ALPHA1-3 : bond 0.01047 ( 3) link_ALPHA1-3 : angle 1.93983 ( 9) link_BETA1-4 : bond 0.00414 ( 18) link_BETA1-4 : angle 1.57608 ( 54) link_NAG-ASN : bond 0.00619 ( 66) link_NAG-ASN : angle 2.21528 ( 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: 63 poor density : 264 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8153 (mmtp) cc_final: 0.7390 (mmtt) REVERT: A 102 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: A 150 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7968 (mmm) REVERT: A 161 MET cc_start: 0.8549 (tpt) cc_final: 0.7975 (tpt) REVERT: A 492 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7427 (mt-10) REVERT: B 624 ASP cc_start: 0.8214 (m-30) cc_final: 0.7970 (m-30) REVERT: L 45 LYS cc_start: 0.8567 (tttt) cc_final: 0.8202 (ttmm) REVERT: L 91 TYR cc_start: 0.8857 (t80) cc_final: 0.8652 (t80) REVERT: I 161 MET cc_start: 0.8378 (tpp) cc_final: 0.7751 (tpp) REVERT: I 271 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7609 (mtp) REVERT: I 318 TYR cc_start: 0.8489 (m-80) cc_final: 0.8257 (m-80) REVERT: J 624 ASP cc_start: 0.8232 (m-30) cc_final: 0.7820 (m-30) REVERT: J 648 GLU cc_start: 0.8054 (tp30) cc_final: 0.7832 (tt0) REVERT: K 70 SER cc_start: 0.8730 (t) cc_final: 0.8405 (m) REVERT: M 45 LYS cc_start: 0.8493 (tttt) cc_final: 0.8009 (ttmm) REVERT: M 94 ARG cc_start: 0.5183 (mmt180) cc_final: 0.4691 (mmt-90) REVERT: S 140 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6886 (p0) REVERT: S 161 MET cc_start: 0.8232 (tpp) cc_final: 0.7629 (tpt) REVERT: T 625 ASN cc_start: 0.6983 (m110) cc_final: 0.6719 (m-40) REVERT: U 72 ASP cc_start: 0.7639 (t70) cc_final: 0.7200 (t70) REVERT: V 45 LYS cc_start: 0.8490 (tttt) cc_final: 0.7999 (ttmm) REVERT: V 94 ARG cc_start: 0.5504 (mmt180) cc_final: 0.5106 (mmt-90) REVERT: V 95 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8620 (pm20) outliers start: 63 outliers final: 42 residues processed: 302 average time/residue: 0.1382 time to fit residues: 65.1491 Evaluate side-chains 290 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 185 ASN Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain J residue 621 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain S residue 140 ASP Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 95 GLN 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: 0.5980 chunk 184 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 HIS ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 103 GLN S 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.102853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.082829 restraints weight = 35568.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.085646 restraints weight = 21310.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.087471 restraints weight = 15259.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.088644 restraints weight = 12217.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.089479 restraints weight = 10523.170| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4434 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= 0.278 Angle : 0.710 11.687 27426 Z= 0.357 Chirality : 0.048 0.304 3279 Planarity : 0.004 0.049 3339 Dihedral : 5.489 50.473 4335 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.60 % Favored : 95.18 % Rotamer: Outliers : 3.81 % Allowed : 10.31 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.17), residues: 2304 helix: 1.77 (0.26), residues: 378 sheet: -0.10 (0.20), residues: 684 loop : -0.42 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 83 TYR 0.015 0.002 TYR M 96 PHE 0.023 0.002 PHE I 468 TRP 0.014 0.002 TRP S 112 HIS 0.006 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00648 (19974) covalent geometry : angle 0.67835 (27093) SS BOND : bond 0.00618 ( 36) SS BOND : angle 1.35950 ( 72) hydrogen bonds : bond 0.04556 ( 747) hydrogen bonds : angle 5.35985 ( 1980) link_ALPHA1-3 : bond 0.00859 ( 3) link_ALPHA1-3 : angle 1.64660 ( 9) link_BETA1-4 : bond 0.00452 ( 18) link_BETA1-4 : angle 1.56640 ( 54) link_NAG-ASN : bond 0.00540 ( 66) link_NAG-ASN : angle 2.33119 ( 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 332 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 254 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8161 (mmtp) cc_final: 0.7224 (mmtt) REVERT: A 102 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: A 428 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7279 (mm110) REVERT: A 492 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7301 (mt-10) REVERT: B 624 ASP cc_start: 0.8349 (m-30) cc_final: 0.8099 (m-30) REVERT: B 648 GLU cc_start: 0.7981 (tp30) cc_final: 0.7733 (tp30) REVERT: H 72 ASP cc_start: 0.7536 (t70) cc_final: 0.7290 (t70) REVERT: L 45 LYS cc_start: 0.8569 (tttt) cc_final: 0.8165 (ttmm) REVERT: I 161 MET cc_start: 0.8239 (tpp) cc_final: 0.7635 (tpp) REVERT: I 271 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7535 (mmp) REVERT: I 318 TYR cc_start: 0.8611 (m-80) cc_final: 0.8382 (m-80) REVERT: I 475 MET cc_start: 0.7707 (tpp) cc_final: 0.7395 (mpp) REVERT: K 70 SER cc_start: 0.8867 (t) cc_final: 0.8635 (m) REVERT: M 45 LYS cc_start: 0.8787 (tttt) cc_final: 0.8327 (ttmm) REVERT: S 102 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: S 161 MET cc_start: 0.8139 (tpp) cc_final: 0.7606 (tpt) REVERT: S 217 TYR cc_start: 0.8673 (m-80) cc_final: 0.8373 (m-80) REVERT: T 625 ASN cc_start: 0.7006 (m110) cc_final: 0.6736 (m-40) REVERT: U 72 ASP cc_start: 0.7724 (t70) cc_final: 0.7319 (t70) REVERT: V 45 LYS cc_start: 0.8598 (tttt) cc_final: 0.8156 (ttmm) REVERT: V 70 THR cc_start: 0.8354 (m) cc_final: 0.7845 (p) REVERT: V 94 ARG cc_start: 0.5673 (mmt180) cc_final: 0.5137 (mmt-90) REVERT: V 95 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8563 (pm20) outliers start: 78 outliers final: 50 residues processed: 303 average time/residue: 0.1351 time to fit residues: 64.1944 Evaluate side-chains 285 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 230 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 185 ASN Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 225 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 439 ILE Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain V residue 95 GLN Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 38 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** S 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.105510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.085617 restraints weight = 35037.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.088485 restraints weight = 20794.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.090364 restraints weight = 14854.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.091611 restraints weight = 11829.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.092451 restraints weight = 10110.714| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20097 Z= 0.153 Angle : 0.627 12.512 27426 Z= 0.316 Chirality : 0.045 0.322 3279 Planarity : 0.004 0.050 3339 Dihedral : 5.168 48.397 4335 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.43 % Favored : 95.36 % Rotamer: Outliers : 2.59 % Allowed : 12.27 % Favored : 85.14 % 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: 2.36 (0.26), residues: 366 sheet: -0.03 (0.20), residues: 696 loop : -0.42 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 500 TYR 0.011 0.001 TYR U 100G PHE 0.013 0.001 PHE S 383 TRP 0.016 0.001 TRP S 112 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00353 (19974) covalent geometry : angle 0.59299 (27093) SS BOND : bond 0.00531 ( 36) SS BOND : angle 1.92696 ( 72) hydrogen bonds : bond 0.03935 ( 747) hydrogen bonds : angle 5.18395 ( 1980) link_ALPHA1-3 : bond 0.00849 ( 3) link_ALPHA1-3 : angle 1.54495 ( 9) link_BETA1-4 : bond 0.00351 ( 18) link_BETA1-4 : angle 1.42409 ( 54) link_NAG-ASN : bond 0.00338 ( 66) link_NAG-ASN : angle 2.08213 ( 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 308 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 255 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8173 (mmtp) cc_final: 0.7137 (mmtt) REVERT: A 102 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: A 161 MET cc_start: 0.8459 (tpt) cc_final: 0.7850 (tpt) REVERT: A 428 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7219 (mm110) REVERT: A 492 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7329 (mt-10) REVERT: B 624 ASP cc_start: 0.8299 (m-30) cc_final: 0.8043 (m-30) REVERT: L 45 LYS cc_start: 0.8500 (tttt) cc_final: 0.8034 (ttmm) REVERT: L 87 TYR cc_start: 0.8882 (m-80) cc_final: 0.8590 (m-80) REVERT: I 150 MET cc_start: 0.8278 (ttm) cc_final: 0.8043 (tpp) REVERT: I 161 MET cc_start: 0.8228 (tpp) cc_final: 0.7609 (tpp) REVERT: I 271 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7585 (mmp) REVERT: I 318 TYR cc_start: 0.8564 (m-80) cc_final: 0.8238 (m-80) REVERT: K 100 TYR cc_start: 0.9220 (m-80) cc_final: 0.8938 (m-80) REVERT: M 45 LYS cc_start: 0.8756 (tttt) cc_final: 0.8316 (ttmm) REVERT: S 102 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: S 161 MET cc_start: 0.8100 (tpp) cc_final: 0.7636 (tpt) REVERT: T 625 ASN cc_start: 0.6969 (m110) cc_final: 0.6743 (m-40) REVERT: T 635 ILE cc_start: 0.8847 (tt) cc_final: 0.8598 (tt) REVERT: U 72 ASP cc_start: 0.7684 (t70) cc_final: 0.7340 (t70) REVERT: U 101 ASP cc_start: 0.8244 (m-30) cc_final: 0.8031 (m-30) REVERT: U 105 GLN cc_start: 0.8193 (mp10) cc_final: 0.7924 (mp10) REVERT: V 45 LYS cc_start: 0.8557 (tttt) cc_final: 0.8058 (ttmm) REVERT: V 70 THR cc_start: 0.8266 (m) cc_final: 0.7807 (p) REVERT: V 94 ARG cc_start: 0.5558 (mmt180) cc_final: 0.4887 (mmt-90) outliers start: 53 outliers final: 36 residues processed: 289 average time/residue: 0.1374 time to fit residues: 62.1746 Evaluate side-chains 281 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain S residue 69 TRP Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 225 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain T residue 599 SER Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.104421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.084465 restraints weight = 35350.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.087324 restraints weight = 21067.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089225 restraints weight = 14999.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090440 restraints weight = 11946.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.091213 restraints weight = 10225.775| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20097 Z= 0.208 Angle : 0.654 9.402 27426 Z= 0.330 Chirality : 0.046 0.332 3279 Planarity : 0.004 0.050 3339 Dihedral : 5.173 48.758 4335 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.95 % Favored : 94.84 % Rotamer: Outliers : 2.59 % Allowed : 13.05 % Favored : 84.36 % 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: 0.10 (0.18), residues: 2304 helix: 2.13 (0.26), residues: 375 sheet: 0.12 (0.20), residues: 669 loop : -0.57 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 151 TYR 0.011 0.001 TYR K 100G PHE 0.017 0.002 PHE I 468 TRP 0.018 0.001 TRP I 112 HIS 0.005 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00486 (19974) covalent geometry : angle 0.62246 (27093) SS BOND : bond 0.00525 ( 36) SS BOND : angle 1.65978 ( 72) hydrogen bonds : bond 0.04096 ( 747) hydrogen bonds : angle 5.15800 ( 1980) link_ALPHA1-3 : bond 0.00790 ( 3) link_ALPHA1-3 : angle 1.51259 ( 9) link_BETA1-4 : bond 0.00393 ( 18) link_BETA1-4 : angle 1.44057 ( 54) link_NAG-ASN : bond 0.00406 ( 66) link_NAG-ASN : angle 2.11747 ( 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 315 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 262 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8193 (mmtp) cc_final: 0.7075 (mmtt) REVERT: A 102 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: A 161 MET cc_start: 0.8517 (tpt) cc_final: 0.7931 (tpt) REVERT: A 428 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7376 (mm110) REVERT: A 492 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7309 (mt-10) REVERT: B 624 ASP cc_start: 0.8348 (m-30) cc_final: 0.8082 (m-30) REVERT: L 45 LYS cc_start: 0.8623 (tttt) cc_final: 0.8162 (ttmm) REVERT: L 87 TYR cc_start: 0.8881 (m-80) cc_final: 0.8598 (m-80) REVERT: I 217 TYR cc_start: 0.8423 (m-80) cc_final: 0.8110 (m-80) REVERT: I 271 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7634 (mmp) REVERT: I 318 TYR cc_start: 0.8592 (m-80) cc_final: 0.8249 (m-80) REVERT: K 100 TYR cc_start: 0.9233 (m-80) cc_final: 0.8974 (m-80) REVERT: K 105 GLN cc_start: 0.7606 (mp10) cc_final: 0.7358 (mp10) REVERT: M 45 LYS cc_start: 0.8796 (tttt) cc_final: 0.8359 (ttmm) REVERT: S 102 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7250 (mm-30) REVERT: S 104 MET cc_start: 0.8553 (ttt) cc_final: 0.8312 (ttt) REVERT: T 625 ASN cc_start: 0.7255 (m110) cc_final: 0.7012 (m-40) REVERT: T 635 ILE cc_start: 0.8902 (tt) cc_final: 0.8696 (tt) REVERT: U 72 ASP cc_start: 0.7723 (t70) cc_final: 0.7201 (t70) REVERT: U 101 ASP cc_start: 0.8303 (m-30) cc_final: 0.8081 (m-30) REVERT: V 45 LYS cc_start: 0.8491 (tttt) cc_final: 0.8011 (ttmm) REVERT: V 70 THR cc_start: 0.8274 (m) cc_final: 0.7913 (p) REVERT: V 94 ARG cc_start: 0.5579 (mmt180) cc_final: 0.4924 (mmt-90) outliers start: 53 outliers final: 40 residues processed: 297 average time/residue: 0.1312 time to fit residues: 61.6494 Evaluate side-chains 291 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 225 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 377 ASN Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 188 optimal weight: 0.0170 chunk 13 optimal weight: 0.4980 chunk 173 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- 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 185 ASN K 73 ASN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.087413 restraints weight = 34752.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.090278 restraints weight = 20478.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.092214 restraints weight = 14608.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.093434 restraints weight = 11523.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094316 restraints weight = 9851.434| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20097 Z= 0.115 Angle : 0.578 9.201 27426 Z= 0.295 Chirality : 0.044 0.350 3279 Planarity : 0.004 0.049 3339 Dihedral : 4.851 46.523 4335 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.12 % Favored : 95.75 % Rotamer: Outliers : 2.05 % Allowed : 13.59 % Favored : 84.36 % 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: 0.30 (0.18), residues: 2304 helix: 2.28 (0.27), residues: 384 sheet: 0.28 (0.20), residues: 669 loop : -0.48 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 151 TYR 0.010 0.001 TYR A 484 PHE 0.012 0.001 PHE S 383 TRP 0.017 0.001 TRP T 571 HIS 0.003 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00259 (19974) covalent geometry : angle 0.55163 (27093) SS BOND : bond 0.00420 ( 36) SS BOND : angle 1.25042 ( 72) hydrogen bonds : bond 0.03526 ( 747) hydrogen bonds : angle 5.00922 ( 1980) link_ALPHA1-3 : bond 0.00805 ( 3) link_ALPHA1-3 : angle 1.35795 ( 9) link_BETA1-4 : bond 0.00364 ( 18) link_BETA1-4 : angle 1.30370 ( 54) link_NAG-ASN : bond 0.00291 ( 66) link_NAG-ASN : angle 1.88353 ( 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 306 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8222 (mmtp) cc_final: 0.7210 (mmtt) REVERT: A 102 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7199 (mm-30) REVERT: A 161 MET cc_start: 0.8512 (tpt) cc_final: 0.7929 (tpt) REVERT: A 428 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7399 (mm110) REVERT: A 492 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7658 (mt-10) REVERT: B 624 ASP cc_start: 0.8277 (m-30) cc_final: 0.8043 (m-30) REVERT: B 655 LYS cc_start: 0.8583 (tptp) cc_final: 0.8259 (tptt) REVERT: L 42 LYS cc_start: 0.8295 (mtmt) cc_final: 0.8047 (mtmm) REVERT: L 45 LYS cc_start: 0.8550 (tttt) cc_final: 0.8123 (ttmm) REVERT: L 87 TYR cc_start: 0.8841 (m-80) cc_final: 0.8580 (m-80) REVERT: I 217 TYR cc_start: 0.8323 (m-80) cc_final: 0.8018 (m-80) REVERT: I 271 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7682 (mmp) REVERT: I 318 TYR cc_start: 0.8524 (m-80) cc_final: 0.8125 (m-80) REVERT: K 100 TYR cc_start: 0.9098 (m-80) cc_final: 0.8766 (m-80) REVERT: K 105 GLN cc_start: 0.7530 (mp10) cc_final: 0.7223 (mp10) REVERT: M 45 LYS cc_start: 0.8727 (tttt) cc_final: 0.8324 (ttmm) REVERT: S 102 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7146 (mm-30) REVERT: S 104 MET cc_start: 0.8493 (ttt) cc_final: 0.8239 (ttt) REVERT: S 161 MET cc_start: 0.8196 (tpt) cc_final: 0.7435 (tpt) REVERT: T 625 ASN cc_start: 0.7286 (m110) cc_final: 0.7048 (m-40) REVERT: T 635 ILE cc_start: 0.8810 (tt) cc_final: 0.8577 (tt) REVERT: T 636 SER cc_start: 0.9117 (t) cc_final: 0.8839 (p) REVERT: U 72 ASP cc_start: 0.7611 (t70) cc_final: 0.7064 (t70) REVERT: V 45 LYS cc_start: 0.8439 (tttt) cc_final: 0.7963 (ttmm) REVERT: V 70 THR cc_start: 0.8214 (m) cc_final: 0.7867 (p) REVERT: V 94 ARG cc_start: 0.5464 (mmt180) cc_final: 0.4986 (mmt180) outliers start: 42 outliers final: 28 residues processed: 293 average time/residue: 0.1343 time to fit residues: 61.6046 Evaluate side-chains 291 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 259 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 377 ASN Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 203 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 185 ASN ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.112611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.093162 restraints weight = 34172.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096456 restraints weight = 18838.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098576 restraints weight = 12879.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.099951 restraints weight = 9964.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.100837 restraints weight = 8331.398| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5067 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= 0.173 Angle : 0.608 9.068 27426 Z= 0.308 Chirality : 0.045 0.355 3279 Planarity : 0.004 0.051 3339 Dihedral : 4.891 48.094 4335 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.30 % Favored : 95.57 % Rotamer: Outliers : 1.96 % Allowed : 13.64 % Favored : 84.41 % 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: 0.28 (0.18), residues: 2304 helix: 2.52 (0.26), residues: 366 sheet: 0.27 (0.20), residues: 669 loop : -0.53 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 476 TYR 0.011 0.001 TYR K 100G PHE 0.015 0.001 PHE I 468 TRP 0.017 0.001 TRP T 571 HIS 0.006 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00403 (19974) covalent geometry : angle 0.57984 (27093) SS BOND : bond 0.00458 ( 36) SS BOND : angle 1.40598 ( 72) hydrogen bonds : bond 0.03800 ( 747) hydrogen bonds : angle 5.01002 ( 1980) link_ALPHA1-3 : bond 0.00654 ( 3) link_ALPHA1-3 : angle 1.37174 ( 9) link_BETA1-4 : bond 0.00388 ( 18) link_BETA1-4 : angle 1.37202 ( 54) link_NAG-ASN : bond 0.00343 ( 66) link_NAG-ASN : angle 1.95924 ( 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 296 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8181 (mmtp) cc_final: 0.7144 (mmtt) REVERT: A 102 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: A 428 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7371 (mm110) REVERT: A 492 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7614 (mt-10) REVERT: B 624 ASP cc_start: 0.8310 (m-30) cc_final: 0.8049 (m-30) REVERT: B 655 LYS cc_start: 0.8646 (tptp) cc_final: 0.8331 (tptt) REVERT: L 42 LYS cc_start: 0.8331 (mtmt) cc_final: 0.8113 (mtmm) REVERT: L 45 LYS cc_start: 0.8600 (tttt) cc_final: 0.8200 (ttmm) REVERT: L 87 TYR cc_start: 0.8819 (m-80) cc_final: 0.8555 (m-80) REVERT: I 217 TYR cc_start: 0.8352 (m-80) cc_final: 0.8075 (m-80) REVERT: I 271 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7712 (mmp) REVERT: I 318 TYR cc_start: 0.8544 (m-80) cc_final: 0.8164 (m-80) REVERT: J 651 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8513 (m-40) REVERT: M 45 LYS cc_start: 0.8765 (tttt) cc_final: 0.8390 (ttmm) REVERT: S 102 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7210 (mm-30) REVERT: S 104 MET cc_start: 0.8510 (ttt) cc_final: 0.8275 (ttt) REVERT: S 161 MET cc_start: 0.8153 (tpt) cc_final: 0.7431 (tpt) REVERT: T 635 ILE cc_start: 0.8896 (tt) cc_final: 0.8675 (tt) REVERT: U 72 ASP cc_start: 0.7527 (t70) cc_final: 0.7257 (t70) REVERT: V 45 LYS cc_start: 0.8485 (tttt) cc_final: 0.8040 (ttmm) REVERT: V 70 THR cc_start: 0.8191 (m) cc_final: 0.7839 (p) REVERT: V 94 ARG cc_start: 0.5678 (mmt180) cc_final: 0.5178 (mmt180) outliers start: 40 outliers final: 30 residues processed: 283 average time/residue: 0.1349 time to fit residues: 59.8150 Evaluate side-chains 283 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 377 ASN Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 226 optimal weight: 0.0670 chunk 91 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 GLN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.113991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094891 restraints weight = 34388.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098153 restraints weight = 18971.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100247 restraints weight = 12943.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101609 restraints weight = 10011.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102501 restraints weight = 8371.265| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20097 Z= 0.115 Angle : 0.576 9.436 27426 Z= 0.292 Chirality : 0.044 0.368 3279 Planarity : 0.004 0.049 3339 Dihedral : 4.770 46.847 4335 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.99 % Favored : 95.88 % Rotamer: Outliers : 1.81 % Allowed : 14.22 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2304 helix: 2.29 (0.27), residues: 384 sheet: 0.36 (0.21), residues: 651 loop : -0.48 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 151 TYR 0.009 0.001 TYR A 484 PHE 0.012 0.001 PHE S 383 TRP 0.016 0.001 TRP I 112 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00258 (19974) covalent geometry : angle 0.54869 (27093) SS BOND : bond 0.00411 ( 36) SS BOND : angle 1.22702 ( 72) hydrogen bonds : bond 0.03464 ( 747) hydrogen bonds : angle 4.91670 ( 1980) link_ALPHA1-3 : bond 0.00705 ( 3) link_ALPHA1-3 : angle 1.31847 ( 9) link_BETA1-4 : bond 0.00361 ( 18) link_BETA1-4 : angle 1.29630 ( 54) link_NAG-ASN : bond 0.00439 ( 66) link_NAG-ASN : angle 1.92735 ( 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 298 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8226 (mmtp) cc_final: 0.7198 (mmtt) REVERT: A 102 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: A 492 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7572 (mt-10) REVERT: B 624 ASP cc_start: 0.8259 (m-30) cc_final: 0.8012 (m-30) REVERT: B 655 LYS cc_start: 0.8573 (tptp) cc_final: 0.8257 (tptt) REVERT: L 42 LYS cc_start: 0.8315 (mtmt) cc_final: 0.8113 (mtmm) REVERT: L 45 LYS cc_start: 0.8574 (tttt) cc_final: 0.8218 (ttmm) REVERT: L 87 TYR cc_start: 0.8813 (m-80) cc_final: 0.8568 (m-80) REVERT: I 217 TYR cc_start: 0.8241 (m-80) cc_final: 0.7970 (m-80) REVERT: I 271 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7818 (mmp) REVERT: I 318 TYR cc_start: 0.8493 (m-80) cc_final: 0.8116 (m-80) REVERT: K 105 GLN cc_start: 0.7556 (mp10) cc_final: 0.7293 (mp10) REVERT: M 45 LYS cc_start: 0.8742 (tttt) cc_final: 0.8375 (ttmm) REVERT: S 102 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7125 (mm-30) REVERT: S 104 MET cc_start: 0.8436 (ttt) cc_final: 0.8169 (ttt) REVERT: S 161 MET cc_start: 0.8165 (tpt) cc_final: 0.7450 (tpt) REVERT: T 636 SER cc_start: 0.9041 (t) cc_final: 0.8827 (p) REVERT: V 45 LYS cc_start: 0.8527 (tttt) cc_final: 0.8084 (ttmm) REVERT: V 79 GLN cc_start: 0.8619 (mt0) cc_final: 0.7920 (mp10) outliers start: 37 outliers final: 31 residues processed: 286 average time/residue: 0.1308 time to fit residues: 58.9858 Evaluate side-chains 282 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 377 ASN Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 27 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 206 optimal weight: 0.2980 chunk 175 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.114054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.094928 restraints weight = 34272.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098181 restraints weight = 19039.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100258 restraints weight = 13037.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101607 restraints weight = 10105.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102481 restraints weight = 8456.794| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5252 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= 0.121 Angle : 0.571 11.452 27426 Z= 0.290 Chirality : 0.044 0.366 3279 Planarity : 0.004 0.050 3339 Dihedral : 4.644 46.860 4335 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.99 % Favored : 95.88 % Rotamer: Outliers : 1.81 % Allowed : 14.32 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2304 helix: 2.66 (0.26), residues: 366 sheet: 0.43 (0.21), residues: 648 loop : -0.47 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 151 TYR 0.010 0.001 TYR K 100G PHE 0.012 0.001 PHE I 468 TRP 0.015 0.001 TRP T 571 HIS 0.003 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00275 (19974) covalent geometry : angle 0.54549 (27093) SS BOND : bond 0.00403 ( 36) SS BOND : angle 1.18504 ( 72) hydrogen bonds : bond 0.03449 ( 747) hydrogen bonds : angle 4.88308 ( 1980) link_ALPHA1-3 : bond 0.00665 ( 3) link_ALPHA1-3 : angle 1.32734 ( 9) link_BETA1-4 : bond 0.00364 ( 18) link_BETA1-4 : angle 1.28708 ( 54) link_NAG-ASN : bond 0.00417 ( 66) link_NAG-ASN : angle 1.86159 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2925.72 seconds wall clock time: 51 minutes 54.79 seconds (3114.79 seconds total)