Starting phenix.real_space_refine on Sun Sep 13 01:04:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x9r_22108/09_2026/6x9r_22108.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x9r_22108/09_2026/6x9r_22108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x9r_22108/09_2026/6x9r_22108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x9r_22108/09_2026/6x9r_22108.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6x9r_22108/09_2026/6x9r_22108.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x9r_22108/09_2026/6x9r_22108.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x9r_22108/09_2026/6x9r_22108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x9r_22108/09_2026/6x9r_22108.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 12258 2.51 5 N 3273 2.21 5 O 3933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 4 Time building chain proxies: 3.51, per 1000 atoms: 0.18 Number of scatterers: 19590 At special positions: 0 Unit cell: (122.57, 126.69, 149.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 3933 8.00 N 3273 7.00 C 12258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.17 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.15 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.06 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.17 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.15 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 119 " - pdb=" SG CYS S 205 " distance=2.06 Simple disulfide: pdb=" SG CYS S 126 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS S 131 " - pdb=" SG CYS S 157 " distance=2.02 Simple disulfide: pdb=" SG CYS S 218 " - pdb=" SG CYS S 247 " distance=2.04 Simple disulfide: pdb=" SG CYS S 228 " - pdb=" SG CYS S 239 " distance=2.16 Simple disulfide: pdb=" SG CYS S 296 " - pdb=" SG CYS S 331 " distance=2.03 Simple disulfide: pdb=" SG CYS S 378 " - pdb=" SG CYS S 445 " distance=2.02 Simple disulfide: pdb=" SG CYS S 385 " - pdb=" SG CYS S 418 " distance=2.02 Simple disulfide: pdb=" SG CYS S 501 " - pdb=" SG CYS T 605 " distance=2.15 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.02 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.04 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG 0 1 " - " ASN S 448 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 606 " - " ASN A 160 " " NAG A 609 " - " ASN A 234 " " NAG A 614 " - " ASN A 276 " " NAG A 615 " - " ASN A 295 " " NAG A 616 " - " ASN A 301 " " NAG A 617 " - " ASN A 332 " " NAG A 618 " - " ASN A 339 " " NAG A 619 " - " ASN A 355 " " NAG A 620 " - " ASN A 363 " " NAG A 623 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG C 1 " - " ASN A 156 " " NAG D 1 " - " ASN A 197 " " NAG E 1 " - " ASN A 262 " " NAG F 1 " - " ASN A 386 " " NAG G 1 " - " ASN A 448 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 137 " " NAG I 606 " - " ASN I 160 " " NAG I 609 " - " ASN I 234 " " NAG I 614 " - " ASN I 276 " " NAG I 615 " - " ASN I 295 " " NAG I 616 " - " ASN I 301 " " NAG I 617 " - " ASN I 332 " " NAG I 618 " - " ASN I 339 " " NAG I 619 " - " ASN I 355 " " NAG I 620 " - " ASN I 363 " " NAG I 623 " - " ASN I 392 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG J 703 " - " ASN J 625 " " NAG J 704 " - " ASN J 637 " " NAG N 1 " - " ASN I 156 " " NAG O 1 " - " ASN I 197 " " NAG P 1 " - " ASN I 262 " " NAG Q 1 " - " ASN I 386 " " NAG R 1 " - " ASN I 448 " " NAG S 601 " - " ASN S 88 " " NAG S 602 " - " ASN S 133 " " NAG S 603 " - " ASN S 137 " " NAG S 606 " - " ASN S 160 " " NAG S 609 " - " ASN S 234 " " NAG S 614 " - " ASN S 276 " " NAG S 615 " - " ASN S 295 " " NAG S 616 " - " ASN S 301 " " NAG S 617 " - " ASN S 332 " " NAG S 618 " - " ASN S 339 " " NAG S 619 " - " ASN S 355 " " NAG S 620 " - " ASN S 363 " " NAG S 623 " - " ASN S 392 " " NAG T 701 " - " ASN T 611 " " NAG T 702 " - " ASN T 618 " " NAG T 703 " - " ASN T 625 " " NAG T 704 " - " ASN T 637 " " NAG W 1 " - " ASN S 156 " " NAG X 1 " - " ASN S 197 " " NAG Y 1 " - " ASN S 262 " " NAG Z 1 " - " ASN S 386 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 778.8 milliseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 20.6% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.134A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.048A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.756A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.519A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 660 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'I' and resid 98 through 115 removed outlier: 4.135A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 4.048A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 476 through 484 removed outlier: 3.755A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.520A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 660 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'S' and resid 98 through 115 removed outlier: 4.134A pdb=" N GLU S 102 " --> pdb=" O ASN S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 126 Processing helix chain 'S' and resid 139 through 151 Processing helix chain 'S' and resid 195 through 198 Processing helix chain 'S' and resid 334 through 354 removed outlier: 4.048A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS S 352 " --> pdb=" O GLN S 348 " (cutoff:3.500A) Processing helix chain 'S' and resid 368 through 373 Processing helix chain 'S' and resid 476 through 484 removed outlier: 3.756A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 removed outlier: 3.519A pdb=" N GLN T 540 " --> pdb=" O THR T 536 " (cutoff:3.500A) Processing helix chain 'T' and resid 569 through 596 Processing helix chain 'T' and resid 618 through 625 Processing helix chain 'T' and resid 627 through 635 Processing helix chain 'T' and resid 638 through 660 Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 Processing sheet with id=1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.868A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.450A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 393 through 394 removed outlier: 6.424A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.552A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=10, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.234A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=12, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.060A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=14, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=17, first strand: chain 'I' and resid 494 through 498 Processing sheet with id=18, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.868A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=20, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=21, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=22, first strand: chain 'I' and resid 200 through 203 removed outlier: 6.451A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'I' and resid 393 through 394 removed outlier: 6.423A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N VAL I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N CYS I 296 " --> pdb=" O VAL I 442 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.552A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'I' and resid 271 through 274 Processing sheet with id=26, first strand: chain 'I' and resid 315 through 323A removed outlier: 6.234A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE I 323 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN I 301 " --> pdb=" O ILE I 323 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'K' and resid 3 through 8 Processing sheet with id=28, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.059A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=30, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=33, first strand: chain 'S' and resid 494 through 498 Processing sheet with id=34, first strand: chain 'S' and resid 45 through 47 removed outlier: 3.869A pdb=" N ILE S 225 " --> pdb=" O VAL S 245 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL S 242 " --> pdb=" O LEU S 86 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'S' and resid 75 through 76 Processing sheet with id=36, first strand: chain 'S' and resid 91 through 94 Processing sheet with id=37, first strand: chain 'S' and resid 169 through 177 Processing sheet with id=38, first strand: chain 'S' and resid 200 through 203 removed outlier: 6.450A pdb=" N ALA S 200 " --> pdb=" O ALA S 433 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR S 435 " --> pdb=" O ALA S 200 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR S 202 " --> pdb=" O TYR S 435 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'S' and resid 393 through 394 removed outlier: 6.424A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N VAL S 442 " --> pdb=" O CYS S 296 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N CYS S 296 " --> pdb=" O VAL S 442 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N ARG S 444 " --> pdb=" O ILE S 294 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE S 294 " --> pdb=" O ARG S 444 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL S 446 " --> pdb=" O VAL S 292 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL S 292 " --> pdb=" O VAL S 446 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN S 448 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR S 290 " --> pdb=" O ASN S 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR S 450 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE S 382 " --> pdb=" O LYS S 421 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'S' and resid 259 through 261 removed outlier: 6.552A pdb=" N LEU S 260 " --> pdb=" O THR S 450 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'S' and resid 271 through 274 Processing sheet with id=42, first strand: chain 'S' and resid 315 through 323A removed outlier: 6.233A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR S 303 " --> pdb=" O GLY S 321 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE S 323 " --> pdb=" O ASN S 301 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN S 301 " --> pdb=" O ILE S 323 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'U' and resid 3 through 8 Processing sheet with id=44, first strand: chain 'U' and resid 11 through 12 removed outlier: 6.060A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'U' and resid 11 through 12 Processing sheet with id=46, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP V 35 " --> pdb=" O MET V 47 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'V' and resid 19 through 24 756 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.04 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3667 1.31 - 1.44: 5373 1.44 - 1.57: 10723 1.57 - 1.69: 40 1.69 - 1.82: 171 Bond restraints: 19974 Sorted by residual: bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C1 NAG I 603 " pdb=" O5 NAG I 603 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C1 NAG S 603 " pdb=" O5 NAG S 603 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 24188 2.67 - 5.33: 2592 5.33 - 8.00: 283 8.00 - 10.67: 24 10.67 - 13.33: 6 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 124.03 -13.33 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N PRO M 7 " pdb=" CA PRO M 7 " pdb=" C PRO M 7 " ideal model delta sigma weight residual 110.70 124.02 -13.32 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 123.99 -13.29 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N GLY M 100 " pdb=" CA GLY M 100 " pdb=" C GLY M 100 " ideal model delta sigma weight residual 112.85 100.34 12.51 1.61e+00 3.86e-01 6.04e+01 angle pdb=" C ASP M 50 " pdb=" N VAL M 51 " pdb=" CA VAL M 51 " ideal model delta sigma weight residual 123.16 114.93 8.23 1.06e+00 8.90e-01 6.03e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 10810 17.58 - 35.15: 287 35.15 - 52.73: 87 52.73 - 70.31: 30 70.31 - 87.88: 9 Dihedral angle restraints: 11223 sinusoidal: 4476 harmonic: 6747 Sorted by residual: dihedral pdb=" CB CYS S 228 " pdb=" SG CYS S 228 " pdb=" SG CYS S 239 " pdb=" CB CYS S 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.97 -68.97 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS I 228 " pdb=" SG CYS I 228 " pdb=" SG CYS I 239 " pdb=" CB CYS I 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.95 -68.95 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.95 -68.95 1 1.00e+01 1.00e-02 6.15e+01 ... (remaining 11220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2322 0.098 - 0.196: 769 0.196 - 0.294: 164 0.294 - 0.392: 18 0.392 - 0.491: 6 Chirality restraints: 3279 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.50e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " 0.222 2.00e-02 2.50e+03 1.84e-01 4.21e+02 pdb=" C7 NAG T 702 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.222 2.00e-02 2.50e+03 1.83e-01 4.20e+02 pdb=" C7 NAG B 702 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " -0.221 2.00e-02 2.50e+03 1.83e-01 4.20e+02 pdb=" C7 NAG J 702 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " -0.158 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " 0.300 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.019 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4131 2.76 - 3.30: 16799 3.30 - 3.83: 32207 3.83 - 4.37: 38497 4.37 - 4.90: 65141 Nonbonded interactions: 156775 Sorted by model distance: nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR S 37 " pdb=" OG1 THR S 499 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.229 3.040 nonbonded pdb=" N ASN A 355 " pdb=" OD1 ASN A 355 " model vdw 2.283 3.120 nonbonded pdb=" N ASN S 355 " pdb=" OD1 ASN S 355 " model vdw 2.283 3.120 ... (remaining 156770 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.550 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.150 20097 Z= 1.300 Angle : 1.748 13.332 27426 Z= 1.126 Chirality : 0.100 0.491 3279 Planarity : 0.011 0.184 3339 Dihedral : 9.808 87.884 6783 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.30 % Favored : 96.35 % Rotamer: Outliers : 0.44 % Allowed : 0.15 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.17), residues: 2304 helix: -0.32 (0.24), residues: 393 sheet: 0.83 (0.20), residues: 630 loop : 0.48 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 66 TYR 0.047 0.007 TYR V 36 PHE 0.035 0.006 PHE S 383 TRP 0.069 0.012 TRP A 427 HIS 0.008 0.002 HIS U 82A Details of bonding type rmsd/Z covalent geometry : bond 0.02494 / 1.29 (19974) covalent geometry : angle 1.71874 / 1.12 (27093) SS BOND : bond 0.05245 / 3.74 ( 36) SS BOND : angle 2.91409 / 2.04 ( 72) hydrogen bonds : bond 0.16093 / 10.53 ( 735) hydrogen bonds : angle 7.02831 / 4.80 ( 1935) link_ALPHA1-3 : bond 0.04240 / 2.12 ( 3) link_ALPHA1-3 : angle 2.95194 / 1.99 ( 9) link_BETA1-4 : bond 0.03047 / 1.74 ( 18) link_BETA1-4 : angle 3.84126 / 2.86 ( 54) link_NAG-ASN : bond 0.03219 / 1.89 ( 66) link_NAG-ASN : angle 3.37105 / 2.43 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 495 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8724 (mmtp) cc_final: 0.8520 (mmtp) REVERT: A 150 MET cc_start: 0.8053 (mmm) cc_final: 0.7750 (mmm) REVERT: A 318 TYR cc_start: 0.8763 (m-80) cc_final: 0.8518 (m-80) REVERT: A 492 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8420 (mt-10) REVERT: A 502 LYS cc_start: 0.6886 (mmtp) cc_final: 0.6563 (mmtt) REVERT: L 94 ARG cc_start: 0.5936 (mmt180) cc_final: 0.4520 (mmt180) REVERT: I 150 MET cc_start: 0.7869 (mmm) cc_final: 0.7138 (mmt) REVERT: I 502 LYS cc_start: 0.6375 (mmtp) cc_final: 0.5552 (mmtm) REVERT: J 624 ASP cc_start: 0.8293 (m-30) cc_final: 0.8039 (m-30) REVERT: M 94 ARG cc_start: 0.6375 (mmt180) cc_final: 0.4691 (mtp180) REVERT: S 46 LYS cc_start: 0.8803 (mmtp) cc_final: 0.8562 (mmtp) REVERT: S 502 LYS cc_start: 0.6176 (mmtp) cc_final: 0.5682 (mmtp) REVERT: V 47 MET cc_start: 0.8170 (mmm) cc_final: 0.7801 (mmt) REVERT: V 94 ARG cc_start: 0.6002 (mmt180) cc_final: 0.5111 (mmt180) outliers start: 9 outliers final: 7 residues processed: 500 average time/residue: 0.1563 time to fit residues: 114.2538 Evaluate side-chains 279 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 272 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN J 607 ASN S 103 GLN T 607 ASN U 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.101214 restraints weight = 26711.994| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.59 r_work: 0.2940 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20097 Z= 0.164 Angle : 0.722 8.587 27426 Z= 0.372 Chirality : 0.046 0.273 3279 Planarity : 0.004 0.038 3339 Dihedral : 5.912 59.582 2534 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.47 % Favored : 96.27 % Rotamer: Outliers : 1.96 % Allowed : 5.96 % Favored : 92.08 % 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: 0.57 (0.17), residues: 2304 helix: 1.60 (0.28), residues: 384 sheet: 0.41 (0.20), residues: 660 loop : 0.07 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 542 TYR 0.015 0.001 TYR L 96 PHE 0.018 0.002 PHE I 383 TRP 0.015 0.001 TRP I 479 HIS 0.004 0.001 HIS H 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (19974) covalent geometry : angle 0.68353 / 0.37 (27093) SS BOND : bond 0.00376 / 0.20 ( 36) SS BOND : angle 0.87933 / 0.61 ( 72) hydrogen bonds : bond 0.05379 / 3.57 ( 735) hydrogen bonds : angle 5.63861 / 3.86 ( 1935) link_ALPHA1-3 : bond 0.00511 / 0.26 ( 3) link_ALPHA1-3 : angle 1.81148 / 1.14 ( 9) link_BETA1-4 : bond 0.00493 / 0.27 ( 18) link_BETA1-4 : angle 2.28548 / 1.62 ( 54) link_NAG-ASN : bond 0.00327 / 0.19 ( 66) link_NAG-ASN : angle 2.52277 / 1.88 ( 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 384 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 344 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9500 (ptm) cc_final: 0.9191 (ptm) REVERT: A 117 LYS cc_start: 0.7767 (mtpt) cc_final: 0.7174 (mttp) REVERT: A 150 MET cc_start: 0.8314 (mmm) cc_final: 0.8069 (mmm) REVERT: A 213 ILE cc_start: 0.8259 (mm) cc_final: 0.8039 (mt) REVERT: A 322 ASP cc_start: 0.8025 (m-30) cc_final: 0.7701 (p0) REVERT: A 371 VAL cc_start: 0.9013 (t) cc_final: 0.8675 (m) REVERT: A 502 LYS cc_start: 0.6970 (mmtp) cc_final: 0.5492 (mmtm) REVERT: B 657 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8317 (tt0) REVERT: H 6 GLU cc_start: 0.8505 (mp0) cc_final: 0.8050 (mp0) REVERT: L 79 GLN cc_start: 0.6306 (mt0) cc_final: 0.6085 (mt0) REVERT: I 121 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8344 (mmtp) REVERT: I 161 MET cc_start: 0.9307 (tpp) cc_final: 0.9090 (tpp) REVERT: I 426 MET cc_start: 0.9136 (mmt) cc_final: 0.8810 (tpt) REVERT: I 502 LYS cc_start: 0.6681 (mmtp) cc_final: 0.5477 (mmtt) REVERT: J 624 ASP cc_start: 0.8759 (m-30) cc_final: 0.8387 (m-30) REVERT: M 45 LYS cc_start: 0.8988 (tttm) cc_final: 0.8627 (tttm) REVERT: M 94 ARG cc_start: 0.6436 (mmt180) cc_final: 0.4369 (mmt180) REVERT: S 322 ASP cc_start: 0.8217 (m-30) cc_final: 0.7988 (p0) REVERT: S 502 LYS cc_start: 0.6554 (mmtp) cc_final: 0.5911 (mmtp) REVERT: T 575 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7339 (tt0) REVERT: U 6 GLU cc_start: 0.8520 (mp0) cc_final: 0.8179 (mp0) REVERT: U 43 LYS cc_start: 0.8216 (mmtm) cc_final: 0.7871 (mmmm) REVERT: V 47 MET cc_start: 0.9062 (mmm) cc_final: 0.8795 (mmt) REVERT: V 94 ARG cc_start: 0.6071 (mmt180) cc_final: 0.3806 (mtp180) outliers start: 40 outliers final: 27 residues processed: 370 average time/residue: 0.1535 time to fit residues: 83.9267 Evaluate side-chains 307 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 607 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 125 optimal weight: 0.0870 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 67 ASN I 377 ASN J 651 ASN S 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.125779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.093021 restraints weight = 27461.835| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.81 r_work: 0.2857 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20097 Z= 0.124 Angle : 0.627 12.450 27426 Z= 0.318 Chirality : 0.045 0.389 3279 Planarity : 0.004 0.048 3339 Dihedral : 5.530 52.133 2532 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.95 % Favored : 95.92 % Rotamer: Outliers : 2.10 % Allowed : 7.43 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.17), residues: 2304 helix: 1.70 (0.28), residues: 405 sheet: 0.61 (0.20), residues: 645 loop : -0.12 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 444 TYR 0.009 0.001 TYR B 643 PHE 0.015 0.002 PHE S 53 TRP 0.011 0.001 TRP I 479 HIS 0.005 0.001 HIS S 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (19974) covalent geometry : angle 0.59229 / 0.31 (27093) SS BOND : bond 0.00212 / 0.13 ( 36) SS BOND : angle 0.86921 / 0.61 ( 72) hydrogen bonds : bond 0.04550 / 3.02 ( 735) hydrogen bonds : angle 5.20862 / 3.57 ( 1935) link_ALPHA1-3 : bond 0.00698 / 0.35 ( 3) link_ALPHA1-3 : angle 1.27069 / 0.78 ( 9) link_BETA1-4 : bond 0.00470 / 0.24 ( 18) link_BETA1-4 : angle 1.63107 / 1.14 ( 54) link_NAG-ASN : bond 0.00495 / 0.33 ( 66) link_NAG-ASN : angle 2.30752 / 1.69 ( 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 350 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 307 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8805 (mmtm) cc_final: 0.8549 (mmtt) REVERT: A 117 LYS cc_start: 0.7788 (mtpt) cc_final: 0.7197 (mttp) REVERT: A 150 MET cc_start: 0.8325 (mmm) cc_final: 0.8111 (mmm) REVERT: A 322 ASP cc_start: 0.8044 (m-30) cc_final: 0.7548 (p0) REVERT: A 327 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7202 (mmm-85) REVERT: A 502 LYS cc_start: 0.6914 (mmtp) cc_final: 0.5466 (mmtm) REVERT: H 6 GLU cc_start: 0.8452 (mp0) cc_final: 0.8103 (mp0) REVERT: H 25 SER cc_start: 0.8581 (p) cc_final: 0.8181 (m) REVERT: H 105 GLN cc_start: 0.8324 (pm20) cc_final: 0.7993 (pm20) REVERT: L 104 LEU cc_start: 0.8493 (tp) cc_final: 0.8149 (tt) REVERT: I 138 ILE cc_start: 0.8130 (tp) cc_final: 0.7920 (tp) REVERT: I 161 MET cc_start: 0.9371 (tpp) cc_final: 0.9095 (tpp) REVERT: I 426 MET cc_start: 0.9143 (mmt) cc_final: 0.8879 (tpt) REVERT: I 502 LYS cc_start: 0.6670 (mmtp) cc_final: 0.5267 (mmtm) REVERT: J 657 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8288 (tt0) REVERT: M 79 GLN cc_start: 0.7025 (mp10) cc_final: 0.6796 (mp10) REVERT: M 94 ARG cc_start: 0.6386 (mmt180) cc_final: 0.4138 (mmt180) REVERT: S 46 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8228 (mmtp) REVERT: S 67 ASN cc_start: 0.8509 (m-40) cc_final: 0.8051 (m-40) REVERT: S 322 ASP cc_start: 0.8171 (m-30) cc_final: 0.7936 (p0) REVERT: S 395 TRP cc_start: 0.6801 (m-10) cc_final: 0.6424 (m-10) REVERT: S 502 LYS cc_start: 0.6565 (mmtp) cc_final: 0.5961 (mmtp) REVERT: T 585 ARG cc_start: 0.9020 (mtp180) cc_final: 0.8743 (mtp180) REVERT: T 657 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8284 (tt0) REVERT: U 25 SER cc_start: 0.8645 (p) cc_final: 0.8210 (m) REVERT: U 75 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8445 (mttm) REVERT: U 105 GLN cc_start: 0.8126 (pm20) cc_final: 0.7808 (pm20) REVERT: V 45 LYS cc_start: 0.8695 (tttt) cc_final: 0.8382 (tttt) REVERT: V 47 MET cc_start: 0.9025 (mmm) cc_final: 0.8687 (mmt) REVERT: V 94 ARG cc_start: 0.5979 (mmt180) cc_final: 0.3693 (mtp180) outliers start: 43 outliers final: 32 residues processed: 327 average time/residue: 0.1732 time to fit residues: 83.2088 Evaluate side-chains 305 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 273 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain I residue 67 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 159 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 192 optimal weight: 0.6980 chunk 182 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN J 651 ASN S 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.085933 restraints weight = 27486.571| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.81 r_work: 0.2720 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20097 Z= 0.247 Angle : 0.719 12.790 27426 Z= 0.363 Chirality : 0.048 0.430 3279 Planarity : 0.005 0.057 3339 Dihedral : 5.532 45.550 2532 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.64 % Favored : 95.23 % Rotamer: Outliers : 2.69 % Allowed : 8.55 % Favored : 88.76 % Cbeta Deviations : 0.05 % 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: 0.33 (0.17), residues: 2304 helix: 1.65 (0.27), residues: 387 sheet: 0.48 (0.19), residues: 687 loop : -0.35 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 480 TYR 0.023 0.002 TYR L 49 PHE 0.022 0.002 PHE I 383 TRP 0.015 0.002 TRP S 427 HIS 0.007 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.25 (19974) covalent geometry : angle 0.67694 / 0.35 (27093) SS BOND : bond 0.00402 / 0.26 ( 36) SS BOND : angle 1.44690 / 1.03 ( 72) hydrogen bonds : bond 0.05496 / 3.64 ( 735) hydrogen bonds : angle 5.10096 / 3.51 ( 1935) link_ALPHA1-3 : bond 0.00867 / 0.44 ( 3) link_ALPHA1-3 : angle 1.12289 / 0.68 ( 9) link_BETA1-4 : bond 0.00322 / 0.16 ( 18) link_BETA1-4 : angle 1.64177 / 1.16 ( 54) link_NAG-ASN : bond 0.00449 / 0.25 ( 66) link_NAG-ASN : angle 2.70683 / 1.94 ( 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 337 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 282 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7205 (mttp) REVERT: A 150 MET cc_start: 0.8382 (mmm) cc_final: 0.8113 (mmm) REVERT: A 322 ASP cc_start: 0.7950 (m-30) cc_final: 0.7501 (p0) REVERT: A 371 VAL cc_start: 0.9022 (t) cc_final: 0.8638 (m) REVERT: A 502 LYS cc_start: 0.7053 (mmtp) cc_final: 0.5408 (mmtp) REVERT: H 6 GLU cc_start: 0.8352 (mp0) cc_final: 0.8148 (mp0) REVERT: H 25 SER cc_start: 0.8770 (p) cc_final: 0.8424 (m) REVERT: H 105 GLN cc_start: 0.8342 (pm20) cc_final: 0.8101 (pm20) REVERT: L 45 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8397 (tttm) REVERT: L 103 ARG cc_start: 0.8666 (mmm160) cc_final: 0.8190 (mmt180) REVERT: L 104 LEU cc_start: 0.8440 (tp) cc_final: 0.8087 (tt) REVERT: I 67 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8269 (t0) REVERT: I 502 LYS cc_start: 0.6827 (mmtp) cc_final: 0.5400 (mmtm) REVERT: J 624 ASP cc_start: 0.8645 (m-30) cc_final: 0.8360 (m-30) REVERT: K 3 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7566 (mt0) REVERT: M 94 ARG cc_start: 0.6046 (mmt180) cc_final: 0.4407 (mmt180) REVERT: S 46 LYS cc_start: 0.8504 (mmtp) cc_final: 0.8241 (mmtp) REVERT: S 322 ASP cc_start: 0.8121 (m-30) cc_final: 0.7880 (p0) REVERT: S 395 TRP cc_start: 0.6900 (m-10) cc_final: 0.6566 (m-10) REVERT: S 502 LYS cc_start: 0.6908 (mmtp) cc_final: 0.5622 (mmtt) REVERT: T 632 ASP cc_start: 0.8598 (t70) cc_final: 0.8289 (t0) REVERT: U 6 GLU cc_start: 0.8368 (mp0) cc_final: 0.8157 (mp0) REVERT: U 25 SER cc_start: 0.8950 (p) cc_final: 0.8605 (m) REVERT: U 105 GLN cc_start: 0.8029 (pm20) cc_final: 0.7794 (pm20) REVERT: V 45 LYS cc_start: 0.8788 (tttt) cc_final: 0.8457 (tttt) REVERT: V 47 MET cc_start: 0.8854 (mmm) cc_final: 0.8483 (mmt) REVERT: V 94 ARG cc_start: 0.6034 (mmt180) cc_final: 0.4552 (mmt180) outliers start: 55 outliers final: 39 residues processed: 310 average time/residue: 0.1682 time to fit residues: 77.2997 Evaluate side-chains 307 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 267 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain I residue 67 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 95 MET Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 377 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 94 THR 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: 2.9990 chunk 184 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 651 ASN L 79 GLN ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 607 ASN J 651 ASN M 17 GLN M 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.086072 restraints weight = 27477.101| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.58 r_work: 0.2712 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 20097 Z= 0.270 Angle : 0.703 8.275 27426 Z= 0.357 Chirality : 0.049 0.430 3279 Planarity : 0.005 0.058 3339 Dihedral : 5.609 42.156 2532 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.21 % Favored : 94.66 % Rotamer: Outliers : 2.98 % Allowed : 9.14 % Favored : 87.88 % 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: 0.08 (0.17), residues: 2304 helix: 1.23 (0.27), residues: 405 sheet: 0.34 (0.19), residues: 687 loop : -0.48 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 480 TYR 0.023 0.002 TYR M 49 PHE 0.024 0.002 PHE S 383 TRP 0.015 0.002 TRP S 427 HIS 0.007 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.27 (19974) covalent geometry : angle 0.67549 / 0.35 (27093) SS BOND : bond 0.00427 / 0.27 ( 36) SS BOND : angle 1.32689 / 0.94 ( 72) hydrogen bonds : bond 0.05595 / 3.71 ( 735) hydrogen bonds : angle 5.11627 / 3.53 ( 1935) link_ALPHA1-3 : bond 0.00817 / 0.41 ( 3) link_ALPHA1-3 : angle 1.14543 / 0.70 ( 9) link_BETA1-4 : bond 0.00314 / 0.15 ( 18) link_BETA1-4 : angle 1.48501 / 1.05 ( 54) link_NAG-ASN : bond 0.00490 / 0.31 ( 66) link_NAG-ASN : angle 2.18423 / 1.59 ( 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 335 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 274 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8500 (mmtt) REVERT: A 117 LYS cc_start: 0.7907 (mtpt) cc_final: 0.7258 (mmmt) REVERT: A 150 MET cc_start: 0.8534 (mmm) cc_final: 0.8199 (mmm) REVERT: A 322 ASP cc_start: 0.8142 (m-30) cc_final: 0.7538 (p0) REVERT: A 502 LYS cc_start: 0.7369 (mmtp) cc_final: 0.6483 (mmtt) REVERT: B 601 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9228 (mtpm) REVERT: H 6 GLU cc_start: 0.8384 (mp0) cc_final: 0.8163 (mp0) REVERT: H 25 SER cc_start: 0.9014 (p) cc_final: 0.8665 (m) REVERT: H 100 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9215 (mt) REVERT: H 105 GLN cc_start: 0.8402 (pm20) cc_final: 0.8120 (pm20) REVERT: L 104 LEU cc_start: 0.8531 (tp) cc_final: 0.8129 (tt) REVERT: I 117 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7843 (mtpt) REVERT: I 502 LYS cc_start: 0.7109 (mmtp) cc_final: 0.5800 (mmtt) REVERT: K 3 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7731 (mt0) REVERT: S 46 LYS cc_start: 0.8659 (mmtp) cc_final: 0.8448 (mmtp) REVERT: S 322 ASP cc_start: 0.8343 (m-30) cc_final: 0.7964 (p0) REVERT: S 395 TRP cc_start: 0.7138 (m-10) cc_final: 0.6865 (m-10) REVERT: S 502 LYS cc_start: 0.7170 (mmtp) cc_final: 0.5629 (mmtm) REVERT: T 575 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7409 (tt0) REVERT: T 632 ASP cc_start: 0.8927 (t70) cc_final: 0.8604 (t0) REVERT: T 657 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8413 (tt0) REVERT: U 6 GLU cc_start: 0.8382 (mp0) cc_final: 0.8131 (mp0) REVERT: U 25 SER cc_start: 0.9104 (p) cc_final: 0.8774 (m) REVERT: U 105 GLN cc_start: 0.8150 (pm20) cc_final: 0.7885 (pm20) REVERT: V 47 MET cc_start: 0.9017 (mmm) cc_final: 0.8778 (mmt) outliers start: 61 outliers final: 46 residues processed: 309 average time/residue: 0.1692 time to fit residues: 77.6019 Evaluate side-chains 308 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 260 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 95 MET Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 38 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 201 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 197 optimal weight: 0.0020 chunk 153 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 651 ASN ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 ASN M 17 GLN S 377 ASN V 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.089262 restraints weight = 27281.387| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.69 r_work: 0.2783 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20097 Z= 0.109 Angle : 0.580 11.736 27426 Z= 0.293 Chirality : 0.045 0.563 3279 Planarity : 0.004 0.053 3339 Dihedral : 5.159 38.775 2532 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 2.20 % Allowed : 10.12 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2304 helix: 1.88 (0.27), residues: 402 sheet: 0.50 (0.19), residues: 729 loop : -0.40 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 166 TYR 0.019 0.001 TYR M 49 PHE 0.015 0.001 PHE S 53 TRP 0.010 0.001 TRP B 623 HIS 0.003 0.001 HIS S 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (19974) covalent geometry : angle 0.54980 / 0.29 (27093) SS BOND : bond 0.00232 / 0.14 ( 36) SS BOND : angle 0.59894 / 0.42 ( 72) hydrogen bonds : bond 0.04075 / 2.68 ( 735) hydrogen bonds : angle 4.86826 / 3.35 ( 1935) link_ALPHA1-3 : bond 0.00535 / 0.27 ( 3) link_ALPHA1-3 : angle 1.39791 / 0.85 ( 9) link_BETA1-4 : bond 0.00412 / 0.21 ( 18) link_BETA1-4 : angle 1.20399 / 0.87 ( 54) link_NAG-ASN : bond 0.00505 / 0.36 ( 66) link_NAG-ASN : angle 2.14717 / 1.60 ( 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 328 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 283 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7235 (mmmt) REVERT: A 141 ASP cc_start: 0.7638 (m-30) cc_final: 0.7090 (p0) REVERT: A 150 MET cc_start: 0.8480 (mmm) cc_final: 0.8041 (mmm) REVERT: A 322 ASP cc_start: 0.8061 (m-30) cc_final: 0.7538 (p0) REVERT: A 327 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7343 (mmm-85) REVERT: A 502 LYS cc_start: 0.7145 (mmtp) cc_final: 0.5407 (mmtm) REVERT: H 105 GLN cc_start: 0.8373 (pm20) cc_final: 0.7998 (pm20) REVERT: L 45 LYS cc_start: 0.8950 (tttt) cc_final: 0.8592 (tttm) REVERT: L 103 ARG cc_start: 0.8620 (mmm160) cc_final: 0.8123 (mmt180) REVERT: L 104 LEU cc_start: 0.8478 (tp) cc_final: 0.8078 (tt) REVERT: I 117 LYS cc_start: 0.7992 (mtpt) cc_final: 0.7760 (mtpt) REVERT: I 502 LYS cc_start: 0.6850 (mmtp) cc_final: 0.5105 (mmtp) REVERT: J 657 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8391 (tt0) REVERT: K 3 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7652 (mt0) REVERT: K 46 GLU cc_start: 0.8960 (tt0) cc_final: 0.8685 (tt0) REVERT: K 100 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9061 (mp) REVERT: M 79 GLN cc_start: 0.7212 (mp10) cc_final: 0.6785 (mp10) REVERT: S 322 ASP cc_start: 0.8244 (m-30) cc_final: 0.7841 (p0) REVERT: S 395 TRP cc_start: 0.7033 (m-10) cc_final: 0.6520 (m-10) REVERT: S 502 LYS cc_start: 0.7021 (mmtp) cc_final: 0.5804 (mmtm) REVERT: T 632 ASP cc_start: 0.8861 (t70) cc_final: 0.8501 (t0) REVERT: T 657 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8355 (tt0) REVERT: U 3 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7840 (mt0) REVERT: U 43 LYS cc_start: 0.8527 (mmtm) cc_final: 0.8277 (mmmm) REVERT: V 47 MET cc_start: 0.8945 (mmm) cc_final: 0.8704 (mmt) outliers start: 45 outliers final: 31 residues processed: 309 average time/residue: 0.1631 time to fit residues: 74.2050 Evaluate side-chains 297 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 265 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 99 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.089092 restraints weight = 27466.751| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.71 r_work: 0.2752 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20097 Z= 0.126 Angle : 0.616 29.379 27426 Z= 0.302 Chirality : 0.044 0.321 3279 Planarity : 0.004 0.055 3339 Dihedral : 5.062 37.445 2532 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.90 % Favored : 94.97 % Rotamer: Outliers : 2.15 % Allowed : 10.80 % Favored : 87.05 % 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: 0.46 (0.18), residues: 2304 helix: 2.02 (0.27), residues: 402 sheet: 0.51 (0.19), residues: 723 loop : -0.40 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 585 TYR 0.024 0.001 TYR M 49 PHE 0.014 0.001 PHE S 53 TRP 0.010 0.001 TRP A 96 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (19974) covalent geometry : angle 0.55523 / 0.29 (27093) SS BOND : bond 0.00253 / 0.15 ( 36) SS BOND : angle 0.74178 / 0.53 ( 72) hydrogen bonds : bond 0.04173 / 2.75 ( 735) hydrogen bonds : angle 4.75620 / 3.26 ( 1935) link_ALPHA1-3 : bond 0.00629 / 0.32 ( 3) link_ALPHA1-3 : angle 1.29745 / 0.79 ( 9) link_BETA1-4 : bond 0.00391 / 0.20 ( 18) link_BETA1-4 : angle 1.24677 / 0.90 ( 54) link_NAG-ASN : bond 0.00317 / 0.21 ( 66) link_NAG-ASN : angle 3.09980 / 2.51 ( 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: 44 poor density : 271 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7242 (mmmt) REVERT: A 150 MET cc_start: 0.8447 (mmm) cc_final: 0.8164 (mmm) REVERT: A 322 ASP cc_start: 0.7851 (m-30) cc_final: 0.7483 (p0) REVERT: A 327 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7343 (mmm-85) REVERT: A 502 LYS cc_start: 0.6942 (mmtp) cc_final: 0.5268 (mmtm) REVERT: H 43 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8319 (mmmm) REVERT: H 105 GLN cc_start: 0.8297 (pm20) cc_final: 0.8095 (pm20) REVERT: L 45 LYS cc_start: 0.8886 (tttt) cc_final: 0.8424 (tttm) REVERT: L 103 ARG cc_start: 0.8562 (mmm160) cc_final: 0.8089 (mmt180) REVERT: I 117 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7730 (mtpt) REVERT: I 502 LYS cc_start: 0.6726 (mmtp) cc_final: 0.5011 (mmtp) REVERT: J 657 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8197 (tt0) REVERT: K 3 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7637 (mt0) REVERT: K 46 GLU cc_start: 0.8897 (tt0) cc_final: 0.8596 (tt0) REVERT: K 82 MET cc_start: 0.9124 (mtm) cc_final: 0.8802 (mtm) REVERT: K 100 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9023 (mp) REVERT: M 79 GLN cc_start: 0.7326 (mp10) cc_final: 0.6887 (mp10) REVERT: S 322 ASP cc_start: 0.8061 (m-30) cc_final: 0.7745 (p0) REVERT: S 395 TRP cc_start: 0.7009 (m-10) cc_final: 0.6542 (m-10) REVERT: S 502 LYS cc_start: 0.6868 (mmtp) cc_final: 0.5622 (mmtm) REVERT: T 632 ASP cc_start: 0.8580 (t70) cc_final: 0.8289 (t0) REVERT: U 3 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7777 (mt0) REVERT: U 46 GLU cc_start: 0.8816 (tt0) cc_final: 0.8595 (tt0) REVERT: V 47 MET cc_start: 0.8791 (mmm) cc_final: 0.8550 (mmt) outliers start: 44 outliers final: 35 residues processed: 295 average time/residue: 0.1641 time to fit residues: 72.1402 Evaluate side-chains 303 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 267 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 188 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 31 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.086233 restraints weight = 27543.670| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.69 r_work: 0.2712 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20097 Z= 0.204 Angle : 0.646 13.998 27426 Z= 0.325 Chirality : 0.047 0.391 3279 Planarity : 0.004 0.057 3339 Dihedral : 5.241 36.143 2532 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.49 % Rotamer: Outliers : 2.15 % Allowed : 10.65 % Favored : 87.19 % 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: 0.19 (0.18), residues: 2304 helix: 1.78 (0.27), residues: 405 sheet: 0.27 (0.19), residues: 744 loop : -0.52 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 480 TYR 0.028 0.002 TYR M 49 PHE 0.019 0.002 PHE S 383 TRP 0.014 0.001 TRP S 427 HIS 0.005 0.001 HIS S 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (19974) covalent geometry : angle 0.61828 / 0.32 (27093) SS BOND : bond 0.00368 / 0.23 ( 36) SS BOND : angle 1.09361 / 0.78 ( 72) hydrogen bonds : bond 0.04989 / 3.29 ( 735) hydrogen bonds : angle 4.90124 / 3.38 ( 1935) link_ALPHA1-3 : bond 0.00707 / 0.35 ( 3) link_ALPHA1-3 : angle 1.22869 / 0.75 ( 9) link_BETA1-4 : bond 0.00322 / 0.16 ( 18) link_BETA1-4 : angle 1.32042 / 0.96 ( 54) link_NAG-ASN : bond 0.00324 / 0.19 ( 66) link_NAG-ASN : angle 2.13039 / 1.59 ( 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 308 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 264 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7277 (mmmt) REVERT: A 141 ASP cc_start: 0.7775 (m-30) cc_final: 0.7189 (p0) REVERT: A 150 MET cc_start: 0.8531 (mmm) cc_final: 0.8085 (mmm) REVERT: A 322 ASP cc_start: 0.8118 (m-30) cc_final: 0.7572 (p0) REVERT: A 327 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7386 (mmm-85) REVERT: A 502 LYS cc_start: 0.7229 (mmtp) cc_final: 0.5564 (mmtm) REVERT: H 6 GLU cc_start: 0.8260 (mp0) cc_final: 0.7950 (mp0) REVERT: H 25 SER cc_start: 0.9086 (p) cc_final: 0.8808 (m) REVERT: H 43 LYS cc_start: 0.8847 (mmtm) cc_final: 0.8271 (mmmm) REVERT: I 117 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7762 (mtpt) REVERT: I 502 LYS cc_start: 0.7134 (mmtp) cc_final: 0.5263 (mmtp) REVERT: J 657 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8376 (tt0) REVERT: K 3 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7713 (mt0) REVERT: K 82 MET cc_start: 0.9181 (mtm) cc_final: 0.8936 (mtm) REVERT: K 100 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9057 (mp) REVERT: M 45 LYS cc_start: 0.8973 (tttt) cc_final: 0.8626 (tttm) REVERT: M 79 GLN cc_start: 0.7272 (mp10) cc_final: 0.6377 (mp10) REVERT: S 46 LYS cc_start: 0.8650 (mmtp) cc_final: 0.8435 (mmtp) REVERT: S 322 ASP cc_start: 0.8291 (m-30) cc_final: 0.7823 (p0) REVERT: S 356 ASN cc_start: 0.8077 (p0) cc_final: 0.7728 (m-40) REVERT: S 395 TRP cc_start: 0.7183 (m-10) cc_final: 0.6701 (m-10) REVERT: S 502 LYS cc_start: 0.7124 (mmtp) cc_final: 0.5435 (mmtm) REVERT: T 632 ASP cc_start: 0.8852 (t70) cc_final: 0.8485 (t0) REVERT: U 3 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7840 (mt0) REVERT: U 43 LYS cc_start: 0.8570 (mmtm) cc_final: 0.8313 (mmmm) REVERT: V 47 MET cc_start: 0.8953 (mmm) cc_final: 0.8716 (mmt) outliers start: 44 outliers final: 33 residues processed: 294 average time/residue: 0.1615 time to fit residues: 70.4092 Evaluate side-chains 291 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 174 optimal weight: 0.2980 chunk 147 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 246 GLN V 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.087939 restraints weight = 27314.968| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.69 r_work: 0.2732 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20097 Z= 0.150 Angle : 0.585 10.517 27426 Z= 0.295 Chirality : 0.045 0.369 3279 Planarity : 0.004 0.057 3339 Dihedral : 4.986 34.915 2528 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.38 % Favored : 94.53 % Rotamer: Outliers : 2.20 % Allowed : 10.75 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 2304 helix: 1.95 (0.27), residues: 402 sheet: 0.41 (0.19), residues: 726 loop : -0.45 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 585 TYR 0.026 0.001 TYR M 49 PHE 0.014 0.001 PHE A 53 TRP 0.012 0.001 TRP S 427 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (19974) covalent geometry : angle 0.55724 / 0.29 (27093) SS BOND : bond 0.00295 / 0.18 ( 36) SS BOND : angle 0.82571 / 0.59 ( 72) hydrogen bonds : bond 0.04449 / 2.93 ( 735) hydrogen bonds : angle 4.83280 / 3.33 ( 1935) link_ALPHA1-3 : bond 0.00648 / 0.32 ( 3) link_ALPHA1-3 : angle 1.30166 / 0.79 ( 9) link_BETA1-4 : bond 0.00358 / 0.18 ( 18) link_BETA1-4 : angle 1.21921 / 0.89 ( 54) link_NAG-ASN : bond 0.00397 / 0.27 ( 66) link_NAG-ASN : angle 2.04261 / 1.48 ( 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 309 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7288 (mmmt) REVERT: A 150 MET cc_start: 0.8510 (mmm) cc_final: 0.8180 (mmm) REVERT: A 322 ASP cc_start: 0.7899 (m-30) cc_final: 0.7516 (p0) REVERT: A 327 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7347 (mmm-85) REVERT: A 502 LYS cc_start: 0.6961 (mmtp) cc_final: 0.5821 (mmtt) REVERT: H 43 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8229 (mmmm) REVERT: H 105 GLN cc_start: 0.8084 (pm20) cc_final: 0.7718 (pm20) REVERT: I 502 LYS cc_start: 0.6815 (mmtp) cc_final: 0.5096 (mmtp) REVERT: J 657 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8103 (tt0) REVERT: K 3 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7701 (mt0) REVERT: K 46 GLU cc_start: 0.8839 (tt0) cc_final: 0.8565 (tt0) REVERT: K 100 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9062 (mp) REVERT: M 61 ARG cc_start: 0.7669 (mtm110) cc_final: 0.6918 (mtm110) REVERT: M 79 GLN cc_start: 0.7323 (mp10) cc_final: 0.6374 (mp10) REVERT: S 322 ASP cc_start: 0.8068 (m-30) cc_final: 0.7736 (p0) REVERT: S 356 ASN cc_start: 0.8002 (p0) cc_final: 0.7774 (m-40) REVERT: S 395 TRP cc_start: 0.7044 (m-10) cc_final: 0.6594 (m-10) REVERT: S 502 LYS cc_start: 0.6893 (mmtp) cc_final: 0.5973 (mmtp) REVERT: T 632 ASP cc_start: 0.8583 (t70) cc_final: 0.8228 (t0) REVERT: U 3 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7815 (mt0) REVERT: U 43 LYS cc_start: 0.8399 (mmtm) cc_final: 0.8132 (mmmm) REVERT: V 47 MET cc_start: 0.8760 (mmm) cc_final: 0.8528 (mmt) outliers start: 45 outliers final: 41 residues processed: 296 average time/residue: 0.1562 time to fit residues: 68.9288 Evaluate side-chains 303 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 95 MET Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 226 optimal weight: 0.0470 chunk 91 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 218 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.090137 restraints weight = 27558.040| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.51 r_work: 0.2771 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20097 Z= 0.116 Angle : 0.567 12.775 27426 Z= 0.287 Chirality : 0.044 0.237 3279 Planarity : 0.004 0.056 3339 Dihedral : 4.881 33.592 2528 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.16 % Favored : 94.79 % Rotamer: Outliers : 2.00 % Allowed : 11.24 % Favored : 86.75 % 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: 0.44 (0.18), residues: 2304 helix: 2.16 (0.27), residues: 402 sheet: 0.42 (0.19), residues: 720 loop : -0.40 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 585 TYR 0.025 0.001 TYR M 49 PHE 0.014 0.001 PHE A 53 TRP 0.011 0.001 TRP S 427 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (19974) covalent geometry : angle 0.53875 / 0.28 (27093) SS BOND : bond 0.00241 / 0.15 ( 36) SS BOND : angle 0.66082 / 0.47 ( 72) hydrogen bonds : bond 0.04094 / 2.70 ( 735) hydrogen bonds : angle 4.70661 / 3.23 ( 1935) link_ALPHA1-3 : bond 0.00555 / 0.28 ( 3) link_ALPHA1-3 : angle 1.33320 / 0.81 ( 9) link_BETA1-4 : bond 0.00384 / 0.20 ( 18) link_BETA1-4 : angle 1.17493 / 0.86 ( 54) link_NAG-ASN : bond 0.00232 / 0.14 ( 66) link_NAG-ASN : angle 2.04730 / 1.49 ( 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 307 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8775 (mtm) REVERT: A 117 LYS cc_start: 0.7883 (mtpt) cc_final: 0.7313 (mmmt) REVERT: A 150 MET cc_start: 0.8591 (mmm) cc_final: 0.8227 (mmm) REVERT: A 267 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8340 (mp0) REVERT: A 322 ASP cc_start: 0.8055 (m-30) cc_final: 0.7641 (p0) REVERT: A 327 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7394 (mmm-85) REVERT: A 502 LYS cc_start: 0.7171 (mmtp) cc_final: 0.5919 (mmtt) REVERT: H 43 LYS cc_start: 0.8750 (mmtm) cc_final: 0.8173 (mmmm) REVERT: H 105 GLN cc_start: 0.8191 (pm20) cc_final: 0.7926 (pm20) REVERT: I 117 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7634 (mttp) REVERT: I 502 LYS cc_start: 0.7032 (mmtp) cc_final: 0.5212 (mmtp) REVERT: J 657 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8467 (tt0) REVERT: K 3 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7781 (mt0) REVERT: K 46 GLU cc_start: 0.8957 (tt0) cc_final: 0.8683 (tt0) REVERT: K 100 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9163 (mp) REVERT: M 45 LYS cc_start: 0.8988 (tttt) cc_final: 0.8734 (tttm) REVERT: M 61 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7272 (mtm110) REVERT: M 79 GLN cc_start: 0.7363 (mp10) cc_final: 0.6927 (mp10) REVERT: S 322 ASP cc_start: 0.8112 (m-30) cc_final: 0.7817 (p0) REVERT: S 356 ASN cc_start: 0.8029 (p0) cc_final: 0.7786 (m-40) REVERT: S 395 TRP cc_start: 0.7108 (m-10) cc_final: 0.6674 (m-10) REVERT: S 502 LYS cc_start: 0.7051 (mmtp) cc_final: 0.5530 (mmtm) REVERT: U 3 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7894 (mt0) REVERT: U 43 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8241 (mmmm) REVERT: V 47 MET cc_start: 0.8953 (mmm) cc_final: 0.8747 (mmt) outliers start: 41 outliers final: 36 residues processed: 292 average time/residue: 0.1652 time to fit residues: 71.8080 Evaluate side-chains 295 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 27 optimal weight: 0.4980 chunk 223 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 0.0030 chunk 206 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 191 optimal weight: 0.0030 chunk 75 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 79 GLN I 246 GLN V 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.089530 restraints weight = 27457.414| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.63 r_work: 0.2762 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 20097 Z= 0.119 Angle : 0.556 8.474 27426 Z= 0.281 Chirality : 0.044 0.254 3279 Planarity : 0.004 0.056 3339 Dihedral : 4.794 32.635 2528 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.16 % Favored : 94.79 % Rotamer: Outliers : 1.96 % Allowed : 11.39 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 2304 helix: 2.60 (0.27), residues: 384 sheet: 0.45 (0.19), residues: 726 loop : -0.43 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 585 TYR 0.026 0.001 TYR M 49 PHE 0.014 0.001 PHE A 53 TRP 0.010 0.001 TRP A 96 HIS 0.003 0.001 HIS S 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (19974) covalent geometry : angle 0.53101 / 0.28 (27093) SS BOND : bond 0.00251 / 0.15 ( 36) SS BOND : angle 0.69966 / 0.50 ( 72) hydrogen bonds : bond 0.04000 / 2.64 ( 735) hydrogen bonds : angle 4.71110 / 3.24 ( 1935) link_ALPHA1-3 : bond 0.00610 / 0.31 ( 3) link_ALPHA1-3 : angle 1.32523 / 0.80 ( 9) link_BETA1-4 : bond 0.00388 / 0.20 ( 18) link_BETA1-4 : angle 1.18029 / 0.86 ( 54) link_NAG-ASN : bond 0.00219 / 0.14 ( 66) link_NAG-ASN : angle 1.89108 / 1.43 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4919.85 seconds wall clock time: 85 minutes 7.88 seconds (5107.88 seconds total)