Starting phenix.real_space_refine on Sun Sep 13 01:26:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x9v_22112/09_2026/6x9v_22112.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x9v_22112/09_2026/6x9v_22112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6x9v_22112/09_2026/6x9v_22112.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x9v_22112/09_2026/6x9v_22112.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x9v_22112/09_2026/6x9v_22112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x9v_22112/09_2026/6x9v_22112.map" model { file = "/net/cci-nas-00/data/ceres_data/6x9v_22112/09_2026/6x9v_22112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x9v_22112/09_2026/6x9v_22112.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 12258 2.51 5 N 3273 2.21 5 O 3933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-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: 4.37, per 1000 atoms: 0.22 Number of scatterers: 19590 At special positions: 0 Unit cell: (123.05, 125.35, 148.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 3933 8.00 N 3273 7.00 C 12258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.07 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.13 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.08 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.07 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.13 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.08 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 119 " - pdb=" SG CYS S 205 " distance=2.07 Simple disulfide: pdb=" SG CYS S 126 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS S 131 " - pdb=" SG CYS S 157 " distance=2.02 Simple disulfide: pdb=" SG CYS S 218 " - pdb=" SG CYS S 247 " distance=2.03 Simple disulfide: pdb=" SG CYS S 228 " - pdb=" SG CYS S 239 " distance=2.13 Simple disulfide: pdb=" SG CYS S 296 " - pdb=" SG CYS S 331 " distance=2.03 Simple disulfide: pdb=" SG CYS S 378 " - pdb=" SG CYS S 445 " distance=2.02 Simple disulfide: pdb=" SG CYS S 385 " - pdb=" SG CYS S 418 " distance=2.02 Simple disulfide: pdb=" SG CYS S 501 " - pdb=" SG CYS T 605 " distance=2.08 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.04 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG 0 1 " - " ASN S 448 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 606 " - " ASN A 160 " " NAG A 609 " - " ASN A 234 " " NAG A 614 " - " ASN A 276 " " NAG A 615 " - " ASN A 295 " " NAG A 616 " - " ASN A 301 " " NAG A 617 " - " ASN A 332 " " NAG A 618 " - " ASN A 339 " " NAG A 619 " - " ASN A 355 " " NAG A 620 " - " ASN A 363 " " NAG A 623 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG C 1 " - " ASN A 156 " " NAG D 1 " - " ASN A 197 " " NAG E 1 " - " ASN A 262 " " NAG F 1 " - " ASN A 386 " " NAG G 1 " - " ASN A 448 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 137 " " NAG I 606 " - " ASN I 160 " " NAG I 609 " - " ASN I 234 " " NAG I 614 " - " ASN I 276 " " NAG I 615 " - " ASN I 295 " " NAG I 616 " - " ASN I 301 " " NAG I 617 " - " ASN I 332 " " NAG I 618 " - " ASN I 339 " " NAG I 619 " - " ASN I 355 " " NAG I 620 " - " ASN I 363 " " NAG I 623 " - " ASN I 392 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG J 703 " - " ASN J 625 " " NAG J 704 " - " ASN J 637 " " NAG N 1 " - " ASN I 156 " " NAG O 1 " - " ASN I 197 " " NAG P 1 " - " ASN I 262 " " NAG Q 1 " - " ASN I 386 " " NAG R 1 " - " ASN I 448 " " NAG S 601 " - " ASN S 88 " " NAG S 602 " - " ASN S 133 " " NAG S 603 " - " ASN S 137 " " NAG S 606 " - " ASN S 160 " " NAG S 609 " - " ASN S 234 " " NAG S 614 " - " ASN S 276 " " NAG S 615 " - " ASN S 295 " " NAG S 616 " - " ASN S 301 " " NAG S 617 " - " ASN S 332 " " NAG S 618 " - " ASN S 339 " " NAG S 619 " - " ASN S 355 " " NAG S 620 " - " ASN S 363 " " NAG S 623 " - " ASN S 392 " " NAG T 701 " - " ASN T 611 " " NAG T 702 " - " ASN T 618 " " NAG T 703 " - " ASN T 625 " " NAG T 704 " - " ASN T 637 " " NAG W 1 " - " ASN S 156 " " NAG X 1 " - " ASN S 197 " " NAG Y 1 " - " ASN S 262 " " NAG Z 1 " - " ASN S 386 " Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 819.0 milliseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 20.6% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.059A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.932A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.693A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 660 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'I' and resid 98 through 115 removed outlier: 4.059A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 334 through 354 removed outlier: 3.932A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 390 Processing helix chain 'I' and resid 476 through 484 removed outlier: 3.694A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 660 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'S' and resid 98 through 115 removed outlier: 4.058A pdb=" N GLU S 102 " --> pdb=" O ASN S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 126 Processing helix chain 'S' and resid 139 through 151 Processing helix chain 'S' and resid 334 through 354 removed outlier: 3.933A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS S 352 " --> pdb=" O GLN S 348 " (cutoff:3.500A) Processing helix chain 'S' and resid 368 through 373 Processing helix chain 'S' and resid 387 through 390 Processing helix chain 'S' and resid 476 through 484 removed outlier: 3.693A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 Processing helix chain 'T' and resid 569 through 596 Processing helix chain 'T' and resid 618 through 625 Processing helix chain 'T' and resid 627 through 635 Processing helix chain 'T' and resid 638 through 660 Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 Processing sheet with id=1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.727A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.356A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 393 through 394 removed outlier: 6.318A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.993A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.284A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 259 through 261 Processing sheet with id=9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=10, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.293A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=12, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.004A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=14, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.589A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.589A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=17, first strand: chain 'I' and resid 494 through 498 Processing sheet with id=18, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.727A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=20, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=21, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=22, first strand: chain 'I' and resid 200 through 203 removed outlier: 6.356A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'I' and resid 393 through 394 removed outlier: 6.318A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.994A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.285A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'I' and resid 259 through 261 Processing sheet with id=25, first strand: chain 'I' and resid 271 through 274 Processing sheet with id=26, first strand: chain 'I' and resid 315 through 323A removed outlier: 6.292A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE I 323 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN I 301 " --> pdb=" O ILE I 323 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'K' and resid 3 through 8 Processing sheet with id=28, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.004A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=30, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.589A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.589A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=33, first strand: chain 'S' and resid 494 through 498 Processing sheet with id=34, first strand: chain 'S' and resid 45 through 47 removed outlier: 3.727A pdb=" N ILE S 225 " --> pdb=" O VAL S 245 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'S' and resid 75 through 76 Processing sheet with id=36, first strand: chain 'S' and resid 91 through 94 Processing sheet with id=37, first strand: chain 'S' and resid 169 through 177 Processing sheet with id=38, first strand: chain 'S' and resid 200 through 203 removed outlier: 6.357A pdb=" N ALA S 200 " --> pdb=" O ALA S 433 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR S 435 " --> pdb=" O ALA S 200 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR S 202 " --> pdb=" O TYR S 435 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'S' and resid 393 through 394 removed outlier: 6.318A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY S 441 " --> pdb=" O ASN S 300 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASN S 300 " --> pdb=" O GLY S 441 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY S 451 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR S 290 " --> pdb=" O GLY S 451 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N ILE S 453 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 11.993A pdb=" N PHE S 288 " --> pdb=" O ILE S 453 " (cutoff:3.500A) removed outlier: 10.861A pdb=" N THR S 455 " --> pdb=" O VAL S 286 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N VAL S 286 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N ASP S 457 " --> pdb=" O ILE S 284 " (cutoff:3.500A) removed outlier: 12.284A pdb=" N ILE S 284 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE S 382 " --> pdb=" O LYS S 421 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'S' and resid 259 through 261 Processing sheet with id=41, first strand: chain 'S' and resid 271 through 274 Processing sheet with id=42, first strand: chain 'S' and resid 315 through 323A removed outlier: 6.293A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR S 303 " --> pdb=" O GLY S 321 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE S 323 " --> pdb=" O ASN S 301 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASN S 301 " --> pdb=" O ILE S 323 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'U' and resid 3 through 8 Processing sheet with id=44, first strand: chain 'U' and resid 11 through 12 removed outlier: 6.005A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'U' and resid 11 through 12 Processing sheet with id=46, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.590A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP V 35 " --> pdb=" O MET V 47 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.590A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'V' and resid 19 through 24 768 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3620 1.31 - 1.44: 5414 1.44 - 1.56: 10680 1.56 - 1.69: 86 1.69 - 1.82: 174 Bond restraints: 19974 Sorted by residual: bond pdb=" CD ARG U 71 " pdb=" NE ARG U 71 " ideal model delta sigma weight residual 1.458 1.358 0.100 1.40e-02 5.10e+03 5.10e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" CD ARG K 71 " pdb=" NE ARG K 71 " ideal model delta sigma weight residual 1.458 1.358 0.100 1.40e-02 5.10e+03 5.08e+01 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.07e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 23161 2.38 - 4.76: 3413 4.76 - 7.13: 462 7.13 - 9.51: 45 9.51 - 11.89: 12 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N PRO M 7 " pdb=" CA PRO M 7 " pdb=" C PRO M 7 " ideal model delta sigma weight residual 110.70 122.59 -11.89 1.22e+00 6.72e-01 9.50e+01 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 122.58 -11.88 1.22e+00 6.72e-01 9.47e+01 angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 122.57 -11.87 1.22e+00 6.72e-01 9.46e+01 angle pdb=" C CYS I 239 " pdb=" N PRO I 240 " pdb=" CA PRO I 240 " ideal model delta sigma weight residual 120.98 129.17 -8.19 1.07e+00 8.73e-01 5.85e+01 angle pdb=" C CYS S 239 " pdb=" N PRO S 240 " pdb=" CA PRO S 240 " ideal model delta sigma weight residual 120.98 129.16 -8.18 1.07e+00 8.73e-01 5.85e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 10644 15.37 - 30.73: 438 30.73 - 46.10: 69 46.10 - 61.47: 54 61.47 - 76.83: 18 Dihedral angle restraints: 11223 sinusoidal: 4476 harmonic: 6747 Sorted by residual: dihedral pdb=" CB CYS I 228 " pdb=" SG CYS I 228 " pdb=" SG CYS I 239 " pdb=" CB CYS I 239 " ideal model delta sinusoidal sigma weight residual 93.00 163.47 -70.47 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 163.46 -70.46 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS S 228 " pdb=" SG CYS S 228 " pdb=" SG CYS S 239 " pdb=" CB CYS S 239 " ideal model delta sinusoidal sigma weight residual 93.00 163.46 -70.46 1 1.00e+01 1.00e-02 6.39e+01 ... (remaining 11220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2434 0.108 - 0.215: 724 0.215 - 0.323: 105 0.323 - 0.430: 13 0.430 - 0.538: 3 Chirality restraints: 3279 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.13e+02 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.13e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.237 2.00e-02 2.50e+03 1.96e-01 4.79e+02 pdb=" C7 NAG B 702 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.321 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " -0.237 2.00e-02 2.50e+03 1.96e-01 4.78e+02 pdb=" C7 NAG J 702 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " 0.321 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " 0.237 2.00e-02 2.50e+03 1.95e-01 4.78e+02 pdb=" C7 NAG T 702 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " -0.320 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.018 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4611 2.77 - 3.30: 17084 3.30 - 3.83: 32577 3.83 - 4.37: 38969 4.37 - 4.90: 64839 Nonbonded interactions: 158080 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR S 37 " pdb=" OG1 THR S 499 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.234 3.040 nonbonded pdb=" N ASP K 84 " pdb=" OD1 ASP K 84 " model vdw 2.327 3.120 nonbonded pdb=" N ASP H 84 " pdb=" OD1 ASP H 84 " model vdw 2.327 3.120 ... (remaining 158075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.100 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.026 0.148 20097 Z= 1.393 Angle : 1.761 11.889 27426 Z= 1.132 Chirality : 0.101 0.538 3279 Planarity : 0.011 0.196 3339 Dihedral : 9.782 76.832 6783 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.39 % Favored : 96.35 % Rotamer: Outliers : 0.29 % Allowed : 0.44 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.17), residues: 2304 helix: 0.06 (0.25), residues: 378 sheet: 0.89 (0.19), residues: 690 loop : 0.59 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 66 TYR 0.058 0.008 TYR S 40 PHE 0.032 0.006 PHE A 383 TRP 0.065 0.012 TRP I 427 HIS 0.011 0.002 HIS U 82A Details of bonding type rmsd/Z covalent geometry : bond 0.02628 / 1.39 (19974) covalent geometry : angle 1.73468 / 1.13 (27093) SS BOND : bond 0.03398 / 2.49 ( 36) SS BOND : angle 2.44054 / 1.72 ( 72) hydrogen bonds : bond 0.15826 / 10.71 ( 747) hydrogen bonds : angle 7.33218 / 5.15 ( 1980) link_ALPHA1-3 : bond 0.03731 / 1.87 ( 3) link_ALPHA1-3 : angle 3.08002 / 2.07 ( 9) link_BETA1-4 : bond 0.02806 / 1.69 ( 18) link_BETA1-4 : angle 3.75036 / 2.73 ( 54) link_NAG-ASN : bond 0.03681 / 2.21 ( 66) link_NAG-ASN : angle 3.36431 / 2.33 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 498 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8454 (mmtp) cc_final: 0.8219 (mmtp) REVERT: A 108 ILE cc_start: 0.8727 (pp) cc_final: 0.8437 (mm) REVERT: A 492 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7926 (mt-10) REVERT: B 625 ASN cc_start: 0.7934 (m110) cc_final: 0.7707 (m-40) REVERT: L 45 LYS cc_start: 0.8776 (tttt) cc_final: 0.8489 (ttmm) REVERT: L 60 ASP cc_start: 0.8345 (p0) cc_final: 0.8074 (t0) REVERT: L 105 THR cc_start: 0.7867 (m) cc_final: 0.7656 (p) REVERT: J 625 ASN cc_start: 0.7995 (m110) cc_final: 0.7729 (m-40) REVERT: K 72 ASP cc_start: 0.7636 (t0) cc_final: 0.7288 (t70) REVERT: M 45 LYS cc_start: 0.8166 (tttt) cc_final: 0.7868 (ttmm) REVERT: M 94 ARG cc_start: 0.6206 (mmt180) cc_final: 0.5071 (ttm-80) REVERT: M 95 THR cc_start: 0.7841 (m) cc_final: 0.7546 (p) REVERT: S 161 MET cc_start: 0.8423 (tpp) cc_final: 0.7998 (tpp) REVERT: V 45 LYS cc_start: 0.8913 (tttt) cc_final: 0.8551 (ttmm) REVERT: V 94 ARG cc_start: 0.5748 (mmt180) cc_final: 0.5334 (mmt-90) outliers start: 6 outliers final: 3 residues processed: 503 average time/residue: 0.1491 time to fit residues: 112.8158 Evaluate side-chains 261 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 258 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain S residue 355 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 432 GLN J 653 GLN M 6 GLN ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 GLN S 432 GLN T 630 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093550 restraints weight = 34920.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096555 restraints weight = 20763.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098502 restraints weight = 14660.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099856 restraints weight = 11572.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100766 restraints weight = 9758.922| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20097 Z= 0.180 Angle : 0.761 11.711 27426 Z= 0.391 Chirality : 0.047 0.257 3279 Planarity : 0.004 0.057 3339 Dihedral : 5.307 28.016 2526 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.04 % Favored : 96.70 % Rotamer: Outliers : 2.00 % Allowed : 8.11 % Favored : 89.88 % 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: 0.67 (0.17), residues: 2304 helix: 1.55 (0.27), residues: 387 sheet: 0.40 (0.20), residues: 645 loop : 0.23 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 151 TYR 0.018 0.002 TYR M 96 PHE 0.024 0.002 PHE U 102 TRP 0.025 0.002 TRP A 479 HIS 0.007 0.001 HIS I 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (19974) covalent geometry : angle 0.71361 / 0.38 (27093) SS BOND : bond 0.00305 / 0.20 ( 36) SS BOND : angle 1.14668 / 0.83 ( 72) hydrogen bonds : bond 0.05239 / 3.55 ( 747) hydrogen bonds : angle 5.87893 / 4.03 ( 1980) link_ALPHA1-3 : bond 0.00271 / 0.14 ( 3) link_ALPHA1-3 : angle 1.65497 / 1.04 ( 9) link_BETA1-4 : bond 0.00468 / 0.23 ( 18) link_BETA1-4 : angle 2.11019 / 1.56 ( 54) link_NAG-ASN : bond 0.00457 / 0.28 ( 66) link_NAG-ASN : angle 2.94671 / 1.96 ( 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 378 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 337 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 601 LYS cc_start: 0.9018 (mttp) cc_final: 0.8810 (mttt) REVERT: H 72 ASP cc_start: 0.7613 (t70) cc_final: 0.7354 (t70) REVERT: H 111 VAL cc_start: 0.8494 (t) cc_final: 0.8058 (m) REVERT: L 45 LYS cc_start: 0.8491 (tttt) cc_final: 0.8042 (ttmm) REVERT: I 271 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7322 (mtp) REVERT: J 648 GLU cc_start: 0.8131 (tp30) cc_final: 0.7757 (tt0) REVERT: K 23 ARG cc_start: 0.7666 (mmm160) cc_final: 0.7449 (mmm160) REVERT: K 28 THR cc_start: 0.8538 (m) cc_final: 0.8229 (p) REVERT: K 70 SER cc_start: 0.8531 (t) cc_final: 0.8237 (m) REVERT: K 72 ASP cc_start: 0.7491 (t0) cc_final: 0.6830 (t0) REVERT: M 45 LYS cc_start: 0.8065 (tttt) cc_final: 0.7633 (ttmm) REVERT: M 94 ARG cc_start: 0.5165 (mmt180) cc_final: 0.4854 (mtt-85) REVERT: S 161 MET cc_start: 0.8273 (tpp) cc_final: 0.7824 (tpt) REVERT: T 625 ASN cc_start: 0.6305 (m110) cc_final: 0.6035 (m-40) REVERT: T 633 LYS cc_start: 0.8672 (mttt) cc_final: 0.8386 (mttp) REVERT: U 72 ASP cc_start: 0.7596 (t70) cc_final: 0.7348 (t70) REVERT: V 45 LYS cc_start: 0.8373 (tttt) cc_final: 0.7871 (ttmm) REVERT: V 78 LEU cc_start: 0.7549 (tt) cc_final: 0.7313 (tt) REVERT: V 94 ARG cc_start: 0.5243 (mmt180) cc_final: 0.4840 (mtt-85) outliers start: 41 outliers final: 27 residues processed: 362 average time/residue: 0.1445 time to fit residues: 81.6325 Evaluate side-chains 292 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain S residue 140 ASP Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 116 optimal weight: 0.4980 chunk 192 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.111423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.091676 restraints weight = 34983.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094621 restraints weight = 20765.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096557 restraints weight = 14746.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.097846 restraints weight = 11674.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098699 restraints weight = 9922.526| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20097 Z= 0.160 Angle : 0.640 9.778 27426 Z= 0.327 Chirality : 0.045 0.277 3279 Planarity : 0.004 0.046 3339 Dihedral : 4.911 31.368 2520 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.12 % Favored : 96.61 % Rotamer: Outliers : 2.25 % Allowed : 10.02 % Favored : 87.73 % 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: 0.52 (0.17), residues: 2304 helix: 1.75 (0.27), residues: 387 sheet: 0.23 (0.19), residues: 675 loop : 0.06 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 151 TYR 0.017 0.001 TYR L 49 PHE 0.017 0.002 PHE I 468 TRP 0.018 0.001 TRP S 112 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (19974) covalent geometry : angle 0.60912 / 0.32 (27093) SS BOND : bond 0.00374 / 0.22 ( 36) SS BOND : angle 1.05253 / 0.74 ( 72) hydrogen bonds : bond 0.04267 / 2.89 ( 747) hydrogen bonds : angle 5.41107 / 3.71 ( 1980) link_ALPHA1-3 : bond 0.00665 / 0.33 ( 3) link_ALPHA1-3 : angle 1.22151 / 0.75 ( 9) link_BETA1-4 : bond 0.00474 / 0.23 ( 18) link_BETA1-4 : angle 1.43840 / 1.07 ( 54) link_NAG-ASN : bond 0.00429 / 0.25 ( 66) link_NAG-ASN : angle 2.22925 / 1.49 ( 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 334 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8136 (mmtp) cc_final: 0.7310 (mmtt) REVERT: A 161 MET cc_start: 0.8565 (tpt) cc_final: 0.8157 (tpt) REVERT: A 492 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7456 (mt-10) REVERT: B 624 ASP cc_start: 0.8192 (m-30) cc_final: 0.7970 (m-30) REVERT: H 72 ASP cc_start: 0.7578 (t70) cc_final: 0.7321 (t70) REVERT: L 45 LYS cc_start: 0.8482 (tttt) cc_final: 0.8104 (ttmm) REVERT: I 161 MET cc_start: 0.8368 (tpp) cc_final: 0.7792 (tpp) REVERT: I 271 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7501 (mtp) REVERT: J 589 ASP cc_start: 0.7987 (m-30) cc_final: 0.7780 (m-30) REVERT: J 648 GLU cc_start: 0.8107 (tp30) cc_final: 0.7709 (tt0) REVERT: K 70 SER cc_start: 0.8614 (t) cc_final: 0.8288 (m) REVERT: K 72 ASP cc_start: 0.7730 (t0) cc_final: 0.7181 (t0) REVERT: M 45 LYS cc_start: 0.8187 (tttt) cc_final: 0.7866 (ttmm) REVERT: S 46 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8139 (mmtt) REVERT: S 161 MET cc_start: 0.8306 (tpp) cc_final: 0.7843 (tpt) REVERT: S 271 MET cc_start: 0.7268 (mtp) cc_final: 0.7020 (tpt) REVERT: T 542 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7439 (mtm-85) REVERT: T 625 ASN cc_start: 0.6655 (m110) cc_final: 0.6401 (m-40) REVERT: U 72 ASP cc_start: 0.7562 (t70) cc_final: 0.7039 (t70) REVERT: V 45 LYS cc_start: 0.8378 (tttt) cc_final: 0.7825 (ttmm) REVERT: V 78 LEU cc_start: 0.7713 (tt) cc_final: 0.7477 (tt) REVERT: V 82 ASP cc_start: 0.7784 (m-30) cc_final: 0.7483 (m-30) outliers start: 46 outliers final: 31 residues processed: 312 average time/residue: 0.1499 time to fit residues: 71.6868 Evaluate side-chains 278 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain J residue 627 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 159 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 HIS L 39 HIS ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 352 HIS S 136 ASN V 17 GLN V 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.105398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.085825 restraints weight = 35373.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.088685 restraints weight = 21157.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.090529 restraints weight = 15027.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.091755 restraints weight = 11977.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.092396 restraints weight = 10224.254| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20097 Z= 0.230 Angle : 0.674 9.109 27426 Z= 0.341 Chirality : 0.047 0.276 3279 Planarity : 0.005 0.076 3339 Dihedral : 4.928 31.173 2520 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.91 % Favored : 95.88 % Rotamer: Outliers : 3.18 % Allowed : 9.97 % Favored : 86.85 % 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: 0.33 (0.17), residues: 2304 helix: 2.00 (0.26), residues: 366 sheet: 0.07 (0.20), residues: 678 loop : -0.16 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 83 TYR 0.017 0.002 TYR L 49 PHE 0.019 0.002 PHE I 468 TRP 0.015 0.002 TRP A 112 HIS 0.005 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (19974) covalent geometry : angle 0.64409 / 0.34 (27093) SS BOND : bond 0.00411 / 0.25 ( 36) SS BOND : angle 1.09354 / 0.77 ( 72) hydrogen bonds : bond 0.04399 / 2.99 ( 747) hydrogen bonds : angle 5.30221 / 3.66 ( 1980) link_ALPHA1-3 : bond 0.00442 / 0.22 ( 3) link_ALPHA1-3 : angle 1.26961 / 0.78 ( 9) link_BETA1-4 : bond 0.00378 / 0.20 ( 18) link_BETA1-4 : angle 1.39295 / 1.01 ( 54) link_NAG-ASN : bond 0.00445 / 0.28 ( 66) link_NAG-ASN : angle 2.26105 / 1.52 ( 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 334 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 269 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8163 (mmtp) cc_final: 0.7485 (mmtt) REVERT: A 102 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: A 150 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.8021 (mmm) REVERT: A 161 MET cc_start: 0.8512 (tpt) cc_final: 0.7909 (tpt) REVERT: A 492 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7385 (mt-10) REVERT: B 624 ASP cc_start: 0.8262 (m-30) cc_final: 0.8012 (m-30) REVERT: L 42 LYS cc_start: 0.8465 (mtpt) cc_final: 0.8261 (mtmt) REVERT: L 45 LYS cc_start: 0.8556 (tttt) cc_final: 0.8080 (ttmm) REVERT: I 161 MET cc_start: 0.8350 (tpp) cc_final: 0.7688 (tpp) REVERT: I 271 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7556 (mtp) REVERT: I 318 TYR cc_start: 0.8533 (m-80) cc_final: 0.8302 (m-80) REVERT: J 624 ASP cc_start: 0.8282 (m-30) cc_final: 0.7738 (m-30) REVERT: J 648 GLU cc_start: 0.8030 (tp30) cc_final: 0.7828 (tt0) REVERT: K 70 SER cc_start: 0.8762 (t) cc_final: 0.8465 (m) REVERT: M 45 LYS cc_start: 0.8602 (tttt) cc_final: 0.8144 (ttmm) REVERT: S 140 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6863 (p0) REVERT: S 161 MET cc_start: 0.8176 (tpp) cc_final: 0.7692 (tpt) REVERT: T 625 ASN cc_start: 0.6993 (m110) cc_final: 0.6739 (m-40) REVERT: U 101 ASP cc_start: 0.8327 (m-30) cc_final: 0.8071 (m-30) REVERT: V 45 LYS cc_start: 0.8486 (tttt) cc_final: 0.8044 (ttmm) outliers start: 65 outliers final: 42 residues processed: 309 average time/residue: 0.1386 time to fit residues: 66.9474 Evaluate side-chains 287 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 185 ASN Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 140 ASP Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 225 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 135 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.083487 restraints weight = 35432.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.086289 restraints weight = 21041.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.088128 restraints weight = 14988.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.089342 restraints weight = 11949.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.090074 restraints weight = 10227.476| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 20097 Z= 0.260 Angle : 0.690 9.412 27426 Z= 0.348 Chirality : 0.047 0.301 3279 Planarity : 0.004 0.050 3339 Dihedral : 5.067 29.886 2520 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.51 % Favored : 95.27 % Rotamer: Outliers : 3.47 % Allowed : 11.19 % Favored : 85.34 % 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: 0.07 (0.17), residues: 2304 helix: 1.94 (0.26), residues: 369 sheet: -0.07 (0.20), residues: 684 loop : -0.41 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 71 TYR 0.018 0.002 TYR L 49 PHE 0.022 0.002 PHE I 468 TRP 0.016 0.002 TRP S 112 HIS 0.006 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.26 (19974) covalent geometry : angle 0.65978 / 0.34 (27093) SS BOND : bond 0.00471 / 0.29 ( 36) SS BOND : angle 1.57310 / 1.16 ( 72) hydrogen bonds : bond 0.04395 / 2.98 ( 747) hydrogen bonds : angle 5.29028 / 3.67 ( 1980) link_ALPHA1-3 : bond 0.00513 / 0.26 ( 3) link_ALPHA1-3 : angle 1.34020 / 0.82 ( 9) link_BETA1-4 : bond 0.00383 / 0.19 ( 18) link_BETA1-4 : angle 1.31943 / 0.97 ( 54) link_NAG-ASN : bond 0.00505 / 0.31 ( 66) link_NAG-ASN : angle 2.21033 / 1.51 ( 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 328 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 257 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8192 (mmtp) cc_final: 0.7214 (mmtt) REVERT: A 102 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: A 161 MET cc_start: 0.8444 (tpt) cc_final: 0.7856 (tpt) REVERT: A 428 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7234 (mm110) REVERT: A 474 ASP cc_start: 0.7442 (t0) cc_final: 0.7166 (t0) REVERT: A 492 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7322 (mt-10) REVERT: B 624 ASP cc_start: 0.8337 (m-30) cc_final: 0.8085 (m-30) REVERT: H 72 ASP cc_start: 0.7542 (t70) cc_final: 0.7297 (t70) REVERT: L 45 LYS cc_start: 0.8563 (tttt) cc_final: 0.8151 (ttmm) REVERT: I 161 MET cc_start: 0.8234 (tpp) cc_final: 0.7632 (tpp) REVERT: I 271 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7510 (mmp) REVERT: I 318 TYR cc_start: 0.8587 (m-80) cc_final: 0.8360 (m-80) REVERT: I 475 MET cc_start: 0.7701 (tpp) cc_final: 0.7426 (mpp) REVERT: K 70 SER cc_start: 0.8783 (t) cc_final: 0.8555 (m) REVERT: M 45 LYS cc_start: 0.8783 (tttt) cc_final: 0.8344 (ttmm) REVERT: S 102 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: S 161 MET cc_start: 0.8140 (tpp) cc_final: 0.7594 (tpt) REVERT: S 217 TYR cc_start: 0.8666 (m-80) cc_final: 0.8308 (m-80) REVERT: V 45 LYS cc_start: 0.8548 (tttt) cc_final: 0.8040 (ttmm) REVERT: V 70 THR cc_start: 0.8354 (m) cc_final: 0.7846 (p) outliers start: 71 outliers final: 48 residues processed: 307 average time/residue: 0.1368 time to fit residues: 65.7691 Evaluate side-chains 290 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 238 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 53 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 225 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 439 ILE Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain V residue 102 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: 0.9980 chunk 21 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 197 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 185 ASN K 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.105413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.085711 restraints weight = 35073.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.088563 restraints weight = 20636.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.090444 restraints weight = 14654.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.091675 restraints weight = 11652.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.092532 restraints weight = 9941.290| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20097 Z= 0.148 Angle : 0.617 12.386 27426 Z= 0.310 Chirality : 0.045 0.320 3279 Planarity : 0.004 0.050 3339 Dihedral : 4.769 26.710 2520 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.17 % Favored : 95.62 % Rotamer: Outliers : 2.83 % Allowed : 12.51 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2304 helix: 2.03 (0.26), residues: 384 sheet: 0.03 (0.20), residues: 696 loop : -0.38 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 500 TYR 0.024 0.001 TYR L 91 PHE 0.013 0.001 PHE I 468 TRP 0.015 0.001 TRP S 112 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (19974) covalent geometry : angle 0.58805 / 0.30 (27093) SS BOND : bond 0.00511 / 0.31 ( 36) SS BOND : angle 1.61124 / 1.12 ( 72) hydrogen bonds : bond 0.03860 / 2.60 ( 747) hydrogen bonds : angle 5.14871 / 3.57 ( 1980) link_ALPHA1-3 : bond 0.00521 / 0.26 ( 3) link_ALPHA1-3 : angle 1.39728 / 0.85 ( 9) link_BETA1-4 : bond 0.00346 / 0.17 ( 18) link_BETA1-4 : angle 1.20262 / 0.89 ( 54) link_NAG-ASN : bond 0.00370 / 0.21 ( 66) link_NAG-ASN : angle 2.00034 / 1.35 ( 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 314 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 256 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7126 (mmtt) REVERT: A 102 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7219 (mm-30) REVERT: A 161 MET cc_start: 0.8503 (tpt) cc_final: 0.7935 (tpt) REVERT: A 428 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7179 (mm110) REVERT: A 492 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7347 (mt-10) REVERT: B 624 ASP cc_start: 0.8291 (m-30) cc_final: 0.8050 (m-30) REVERT: B 655 LYS cc_start: 0.8663 (tptp) cc_final: 0.8338 (tptt) REVERT: L 45 LYS cc_start: 0.8508 (tttt) cc_final: 0.8064 (ttmm) REVERT: L 87 TYR cc_start: 0.8875 (m-80) cc_final: 0.8595 (m-80) REVERT: I 217 TYR cc_start: 0.8461 (m-80) cc_final: 0.8224 (m-80) REVERT: I 271 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7555 (mmp) REVERT: K 100 TYR cc_start: 0.9216 (m-80) cc_final: 0.8924 (m-80) REVERT: M 45 LYS cc_start: 0.8766 (tttt) cc_final: 0.8336 (ttmm) REVERT: S 102 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7076 (mm-30) REVERT: S 161 MET cc_start: 0.8096 (tpp) cc_final: 0.7742 (tpt) REVERT: T 621 GLU cc_start: 0.7799 (tt0) cc_final: 0.7439 (tt0) REVERT: T 648 GLU cc_start: 0.8137 (tp30) cc_final: 0.7935 (tp30) REVERT: U 101 ASP cc_start: 0.8350 (m-30) cc_final: 0.8064 (m-30) REVERT: U 105 GLN cc_start: 0.8169 (mp10) cc_final: 0.7918 (mp10) REVERT: V 45 LYS cc_start: 0.8531 (tttt) cc_final: 0.7980 (ttmm) REVERT: V 70 THR cc_start: 0.8261 (m) cc_final: 0.7812 (p) outliers start: 58 outliers final: 44 residues processed: 295 average time/residue: 0.1309 time to fit residues: 60.7334 Evaluate side-chains 295 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 247 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain T residue 599 SER Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 164 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 ASN S 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.082867 restraints weight = 35531.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.085642 restraints weight = 21131.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087482 restraints weight = 15081.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.088702 restraints weight = 12008.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.089364 restraints weight = 10261.717| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 20097 Z= 0.261 Angle : 0.695 10.647 27426 Z= 0.349 Chirality : 0.047 0.326 3279 Planarity : 0.004 0.050 3339 Dihedral : 4.944 27.755 2520 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.12 % Favored : 94.66 % Rotamer: Outliers : 3.23 % Allowed : 12.71 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2304 helix: 1.92 (0.26), residues: 375 sheet: -0.03 (0.21), residues: 654 loop : -0.59 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 151 TYR 0.021 0.002 TYR L 91 PHE 0.019 0.002 PHE I 468 TRP 0.021 0.002 TRP T 571 HIS 0.005 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.26 (19974) covalent geometry : angle 0.66603 / 0.34 (27093) SS BOND : bond 0.00576 / 0.36 ( 36) SS BOND : angle 1.70702 / 1.18 ( 72) hydrogen bonds : bond 0.04339 / 2.93 ( 747) hydrogen bonds : angle 5.25166 / 3.65 ( 1980) link_ALPHA1-3 : bond 0.00528 / 0.26 ( 3) link_ALPHA1-3 : angle 1.36301 / 0.84 ( 9) link_BETA1-4 : bond 0.00409 / 0.20 ( 18) link_BETA1-4 : angle 1.29588 / 0.95 ( 54) link_NAG-ASN : bond 0.00490 / 0.30 ( 66) link_NAG-ASN : angle 2.15075 / 1.47 ( 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: 66 poor density : 249 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7385 (mm-30) REVERT: A 428 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7500 (mm110) REVERT: A 492 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7507 (mt-10) REVERT: B 624 ASP cc_start: 0.8396 (m-30) cc_final: 0.8137 (m-30) REVERT: L 24 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.8883 (p) REVERT: L 45 LYS cc_start: 0.8592 (tttt) cc_final: 0.8118 (ttmm) REVERT: L 87 TYR cc_start: 0.8878 (m-80) cc_final: 0.8575 (m-80) REVERT: I 217 TYR cc_start: 0.8475 (m-80) cc_final: 0.8170 (m-80) REVERT: I 271 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7605 (mmp) REVERT: K 100 TYR cc_start: 0.9256 (m-80) cc_final: 0.9017 (m-80) REVERT: K 105 GLN cc_start: 0.7592 (mp10) cc_final: 0.7381 (mp10) REVERT: M 45 LYS cc_start: 0.8806 (tttt) cc_final: 0.8356 (ttmm) REVERT: S 46 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7936 (mmtt) REVERT: S 102 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: S 103 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: S 161 MET cc_start: 0.8017 (tpp) cc_final: 0.7623 (tpt) REVERT: U 72 ASP cc_start: 0.7246 (t70) cc_final: 0.6902 (t70) REVERT: U 101 ASP cc_start: 0.8404 (m-30) cc_final: 0.8087 (m-30) REVERT: V 45 LYS cc_start: 0.8539 (tttt) cc_final: 0.8067 (ttmm) REVERT: V 70 THR cc_start: 0.8349 (m) cc_final: 0.7857 (p) outliers start: 66 outliers final: 53 residues processed: 291 average time/residue: 0.1346 time to fit residues: 61.9338 Evaluate side-chains 300 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 241 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 103 GLN Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 377 ASN Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 576 LEU Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain T residue 599 SER Chi-restraints excluded: chain T residue 605 CYS Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 188 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.085164 restraints weight = 35053.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.087941 restraints weight = 20894.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.089758 restraints weight = 14942.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.090982 restraints weight = 11915.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.091820 restraints weight = 10179.566| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20097 Z= 0.151 Angle : 0.614 9.603 27426 Z= 0.310 Chirality : 0.045 0.347 3279 Planarity : 0.004 0.047 3339 Dihedral : 4.721 25.621 2520 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.64 % Favored : 95.23 % Rotamer: Outliers : 2.83 % Allowed : 12.95 % Favored : 84.21 % 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: 0.11 (0.18), residues: 2304 helix: 2.05 (0.26), residues: 384 sheet: 0.15 (0.20), residues: 669 loop : -0.57 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 151 TYR 0.025 0.001 TYR L 91 PHE 0.012 0.001 PHE S 383 TRP 0.018 0.001 TRP I 112 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (19974) covalent geometry : angle 0.58798 / 0.30 (27093) SS BOND : bond 0.00482 / 0.28 ( 36) SS BOND : angle 1.41379 / 0.99 ( 72) hydrogen bonds : bond 0.03843 / 2.59 ( 747) hydrogen bonds : angle 5.14205 / 3.57 ( 1980) link_ALPHA1-3 : bond 0.00515 / 0.26 ( 3) link_ALPHA1-3 : angle 1.40574 / 0.86 ( 9) link_BETA1-4 : bond 0.00336 / 0.16 ( 18) link_BETA1-4 : angle 1.16259 / 0.86 ( 54) link_NAG-ASN : bond 0.00318 / 0.19 ( 66) link_NAG-ASN : angle 1.93327 / 1.31 ( 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 315 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 257 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: A 161 MET cc_start: 0.8401 (tpt) cc_final: 0.7800 (tpt) REVERT: A 428 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7394 (mm110) REVERT: B 624 ASP cc_start: 0.8311 (m-30) cc_final: 0.8058 (m-30) REVERT: L 24 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.8938 (p) REVERT: L 45 LYS cc_start: 0.8616 (tttt) cc_final: 0.8200 (ttmm) REVERT: L 87 TYR cc_start: 0.8833 (m-80) cc_final: 0.8553 (m-80) REVERT: I 217 TYR cc_start: 0.8399 (m-80) cc_final: 0.8131 (m-80) REVERT: I 271 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7657 (mmp) REVERT: I 318 TYR cc_start: 0.8534 (m-80) cc_final: 0.8139 (m-80) REVERT: M 45 LYS cc_start: 0.8775 (tttt) cc_final: 0.8375 (ttmm) REVERT: S 46 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7960 (mmtt) REVERT: S 102 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: S 161 MET cc_start: 0.7956 (tpp) cc_final: 0.7677 (tpt) REVERT: T 635 ILE cc_start: 0.8897 (tt) cc_final: 0.8673 (tt) REVERT: U 101 ASP cc_start: 0.8309 (m-30) cc_final: 0.8018 (m-30) REVERT: V 45 LYS cc_start: 0.8597 (tttt) cc_final: 0.8140 (ttmm) REVERT: V 70 THR cc_start: 0.8282 (m) cc_final: 0.7931 (p) outliers start: 58 outliers final: 48 residues processed: 294 average time/residue: 0.1272 time to fit residues: 59.6927 Evaluate side-chains 305 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 252 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 377 ASN Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 576 LEU Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain T residue 605 CYS Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 82 MET Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain V residue 107 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 174 optimal weight: 0.5980 chunk 147 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 156 optimal weight: 0.0770 chunk 148 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 114 GLN V 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.106610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.086857 restraints weight = 34765.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.089764 restraints weight = 20695.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.091670 restraints weight = 14682.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.092933 restraints weight = 11679.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.093731 restraints weight = 9955.127| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20097 Z= 0.112 Angle : 0.573 8.514 27426 Z= 0.291 Chirality : 0.044 0.373 3279 Planarity : 0.004 0.049 3339 Dihedral : 4.516 24.862 2520 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.34 % Favored : 95.53 % Rotamer: Outliers : 2.10 % Allowed : 13.64 % Favored : 84.26 % 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: 0.29 (0.18), residues: 2304 helix: 2.28 (0.27), residues: 384 sheet: 0.32 (0.20), residues: 648 loop : -0.51 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.024 0.001 TYR L 91 PHE 0.011 0.001 PHE S 383 TRP 0.016 0.001 TRP I 112 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (19974) covalent geometry : angle 0.54999 / 0.29 (27093) SS BOND : bond 0.00417 / 0.24 ( 36) SS BOND : angle 1.21882 / 0.85 ( 72) hydrogen bonds : bond 0.03486 / 2.34 ( 747) hydrogen bonds : angle 4.97980 / 3.46 ( 1980) link_ALPHA1-3 : bond 0.00426 / 0.21 ( 3) link_ALPHA1-3 : angle 1.35849 / 0.83 ( 9) link_BETA1-4 : bond 0.00358 / 0.17 ( 18) link_BETA1-4 : angle 1.10684 / 0.82 ( 54) link_NAG-ASN : bond 0.00324 / 0.18 ( 66) link_NAG-ASN : angle 1.78739 / 1.21 ( 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 310 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8379 (mmtt) cc_final: 0.7214 (mmtt) REVERT: A 102 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7212 (mm-30) REVERT: A 161 MET cc_start: 0.8383 (tpt) cc_final: 0.7786 (tpt) REVERT: A 428 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7545 (mm110) REVERT: B 624 ASP cc_start: 0.8292 (m-30) cc_final: 0.8035 (m-30) REVERT: B 655 LYS cc_start: 0.8609 (tptp) cc_final: 0.8285 (tptt) REVERT: L 42 LYS cc_start: 0.8327 (mtmt) cc_final: 0.8116 (mtmm) REVERT: L 45 LYS cc_start: 0.8564 (tttt) cc_final: 0.8151 (ttmm) REVERT: L 87 TYR cc_start: 0.8831 (m-80) cc_final: 0.8575 (m-80) REVERT: I 217 TYR cc_start: 0.8352 (m-80) cc_final: 0.8026 (m-80) REVERT: I 271 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7637 (mmp) REVERT: K 105 GLN cc_start: 0.7543 (mp10) cc_final: 0.7332 (mp10) REVERT: M 45 LYS cc_start: 0.8687 (tttt) cc_final: 0.8275 (ttmm) REVERT: S 46 LYS cc_start: 0.8261 (mmtt) cc_final: 0.8046 (mmtt) REVERT: S 102 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: T 621 GLU cc_start: 0.7653 (tt0) cc_final: 0.7339 (tt0) REVERT: T 635 ILE cc_start: 0.8864 (tt) cc_final: 0.8651 (tt) REVERT: T 636 SER cc_start: 0.9113 (t) cc_final: 0.8855 (p) REVERT: U 72 ASP cc_start: 0.7090 (t70) cc_final: 0.6765 (t70) REVERT: V 45 LYS cc_start: 0.8579 (tttt) cc_final: 0.8137 (ttmm) REVERT: V 70 THR cc_start: 0.8186 (m) cc_final: 0.7849 (p) outliers start: 43 outliers final: 35 residues processed: 297 average time/residue: 0.1333 time to fit residues: 63.2107 Evaluate side-chains 293 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 254 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 377 ASN Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 82 MET Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 226 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 59 optimal weight: 0.0470 chunk 218 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.086822 restraints weight = 35116.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.089740 restraints weight = 20544.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.091664 restraints weight = 14489.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.092935 restraints weight = 11423.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.093749 restraints weight = 9691.824| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20097 Z= 0.126 Angle : 0.580 10.224 27426 Z= 0.292 Chirality : 0.044 0.369 3279 Planarity : 0.004 0.048 3339 Dihedral : 4.471 24.799 2520 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.21 % Favored : 95.66 % Rotamer: Outliers : 2.00 % Allowed : 14.17 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 2304 helix: 2.30 (0.26), residues: 384 sheet: 0.39 (0.21), residues: 648 loop : -0.48 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 151 TYR 0.023 0.001 TYR L 91 PHE 0.018 0.001 PHE A 382 TRP 0.026 0.001 TRP T 571 HIS 0.003 0.001 HIS S 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (19974) covalent geometry : angle 0.55445 / 0.29 (27093) SS BOND : bond 0.00415 / 0.24 ( 36) SS BOND : angle 1.19029 / 0.83 ( 72) hydrogen bonds : bond 0.03521 / 2.38 ( 747) hydrogen bonds : angle 4.92015 / 3.41 ( 1980) link_ALPHA1-3 : bond 0.00493 / 0.25 ( 3) link_ALPHA1-3 : angle 1.37697 / 0.84 ( 9) link_BETA1-4 : bond 0.00365 / 0.18 ( 18) link_BETA1-4 : angle 1.11764 / 0.83 ( 54) link_NAG-ASN : bond 0.00295 / 0.17 ( 66) link_NAG-ASN : angle 1.90587 / 1.32 ( 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 301 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7581 (mmtt) REVERT: A 102 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: A 428 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7534 (mm110) REVERT: B 624 ASP cc_start: 0.8305 (m-30) cc_final: 0.8052 (m-30) REVERT: B 655 LYS cc_start: 0.8566 (tptp) cc_final: 0.8241 (tptt) REVERT: H 39 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: L 42 LYS cc_start: 0.8324 (mtmt) cc_final: 0.8118 (mtmm) REVERT: L 45 LYS cc_start: 0.8562 (tttt) cc_final: 0.8157 (ttmm) REVERT: L 87 TYR cc_start: 0.8842 (m-80) cc_final: 0.8542 (m-80) REVERT: I 217 TYR cc_start: 0.8299 (m-80) cc_final: 0.7967 (m-80) REVERT: I 271 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7742 (mmp) REVERT: K 105 GLN cc_start: 0.7610 (mp10) cc_final: 0.7373 (mp10) REVERT: M 45 LYS cc_start: 0.8697 (tttt) cc_final: 0.8292 (ttmm) REVERT: S 46 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7882 (mmtt) REVERT: S 102 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7104 (mm-30) REVERT: T 621 GLU cc_start: 0.7601 (tt0) cc_final: 0.7251 (tt0) REVERT: T 636 SER cc_start: 0.9109 (t) cc_final: 0.8848 (p) REVERT: V 45 LYS cc_start: 0.8632 (tttt) cc_final: 0.8196 (ttmm) outliers start: 41 outliers final: 35 residues processed: 288 average time/residue: 0.1365 time to fit residues: 62.8337 Evaluate side-chains 290 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 377 ASN Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain S residue 488 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain T residue 605 CYS Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 82 MET Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 27 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 191 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 17 GLN ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.085236 restraints weight = 35219.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088109 restraints weight = 20696.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.089991 restraints weight = 14633.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091239 restraints weight = 11608.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.092054 restraints weight = 9889.621| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20097 Z= 0.179 Angle : 0.618 10.965 27426 Z= 0.311 Chirality : 0.046 0.368 3279 Planarity : 0.004 0.048 3339 Dihedral : 4.562 25.243 2520 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.47 % Favored : 95.40 % Rotamer: Outliers : 2.15 % Allowed : 14.42 % Favored : 83.43 % 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: 0.23 (0.18), residues: 2304 helix: 2.17 (0.26), residues: 384 sheet: 0.30 (0.20), residues: 648 loop : -0.54 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 166 TYR 0.024 0.001 TYR L 91 PHE 0.015 0.001 PHE I 468 TRP 0.027 0.001 TRP T 571 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (19974) covalent geometry : angle 0.59095 / 0.31 (27093) SS BOND : bond 0.00449 / 0.26 ( 36) SS BOND : angle 1.27543 / 0.88 ( 72) hydrogen bonds : bond 0.03754 / 2.54 ( 747) hydrogen bonds : angle 4.95978 / 3.44 ( 1980) link_ALPHA1-3 : bond 0.00507 / 0.25 ( 3) link_ALPHA1-3 : angle 1.37496 / 0.84 ( 9) link_BETA1-4 : bond 0.00366 / 0.18 ( 18) link_BETA1-4 : angle 1.15767 / 0.86 ( 54) link_NAG-ASN : bond 0.00327 / 0.20 ( 66) link_NAG-ASN : angle 2.00441 / 1.40 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2991.62 seconds wall clock time: 52 minutes 50.18 seconds (3170.18 seconds total)