Starting phenix.real_space_refine on Sun Sep 13 01:11:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x9t_22110/09_2026/6x9t_22110.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x9t_22110/09_2026/6x9t_22110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x9t_22110/09_2026/6x9t_22110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x9t_22110/09_2026/6x9t_22110.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x9t_22110/09_2026/6x9t_22110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x9t_22110/09_2026/6x9t_22110.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6x9t_22110/09_2026/6x9t_22110.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x9t_22110/09_2026/6x9t_22110.cif" } resolution = 3.2 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 3 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: 3.96, per 1000 atoms: 0.20 Number of scatterers: 19590 At special positions: 0 Unit cell: (122.57, 125.66, 149.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 3933 8.00 N 3273 7.00 C 12258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.15 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=2.17 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=2.06 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.15 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=2.16 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=2.06 Simple disulfide: pdb=" SG CYS S 126 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS S 131 " - pdb=" SG CYS S 157 " distance=2.02 Simple disulfide: pdb=" SG CYS S 218 " - pdb=" SG CYS S 247 " distance=2.03 Simple disulfide: pdb=" SG CYS S 228 " - pdb=" SG CYS S 239 " distance=2.15 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=2.17 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.02 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.04 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG 0 1 " - " ASN S 448 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 606 " - " ASN A 160 " " NAG A 609 " - " ASN A 234 " " NAG A 614 " - " ASN A 276 " " NAG A 615 " - " ASN A 295 " " NAG A 616 " - " ASN A 301 " " NAG A 617 " - " ASN A 332 " " NAG A 618 " - " ASN A 339 " " NAG A 619 " - " ASN A 355 " " NAG A 620 " - " ASN A 363 " " NAG A 623 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG C 1 " - " ASN A 156 " " NAG D 1 " - " ASN A 197 " " NAG E 1 " - " ASN A 262 " " NAG F 1 " - " ASN A 386 " " NAG G 1 " - " ASN A 448 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 137 " " NAG I 606 " - " ASN I 160 " " NAG I 609 " - " ASN I 234 " " NAG I 614 " - " ASN I 276 " " NAG I 615 " - " ASN I 295 " " NAG I 616 " - " ASN I 301 " " NAG I 617 " - " ASN I 332 " " NAG I 618 " - " ASN I 339 " " NAG I 619 " - " ASN I 355 " " NAG I 620 " - " ASN I 363 " " NAG I 623 " - " ASN I 392 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG J 703 " - " ASN J 625 " " NAG J 704 " - " ASN J 637 " " NAG N 1 " - " ASN I 156 " " NAG O 1 " - " ASN I 197 " " NAG P 1 " - " ASN I 262 " " NAG Q 1 " - " ASN I 386 " " NAG R 1 " - " ASN I 448 " " NAG S 601 " - " ASN S 88 " " NAG S 602 " - " ASN S 133 " " NAG S 603 " - " ASN S 137 " " NAG S 606 " - " ASN S 160 " " NAG S 609 " - " ASN S 234 " " NAG S 614 " - " ASN S 276 " " NAG S 615 " - " ASN S 295 " " NAG S 616 " - " ASN S 301 " " NAG S 617 " - " ASN S 332 " " NAG S 618 " - " ASN S 339 " " NAG S 619 " - " ASN S 355 " " NAG S 620 " - " ASN S 363 " " NAG S 623 " - " ASN S 392 " " NAG T 701 " - " ASN T 611 " " NAG T 702 " - " ASN T 618 " " NAG T 703 " - " ASN T 625 " " NAG T 704 " - " ASN T 637 " " NAG W 1 " - " ASN S 156 " " NAG X 1 " - " ASN S 197 " " NAG Y 1 " - " ASN S 262 " " NAG Z 1 " - " ASN S 386 " Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 590.9 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: 51 helices and 48 sheets defined 21.4% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.141A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.070A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.752A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.390A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.558A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 660 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'I' and resid 98 through 115 removed outlier: 4.141A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 4.069A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 476 through 484 removed outlier: 3.752A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 removed outlier: 4.390A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.558A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 660 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'S' and resid 98 through 115 removed outlier: 4.142A pdb=" N GLU S 102 " --> pdb=" O ASN S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 126 Processing helix chain 'S' and resid 139 through 151 Processing helix chain 'S' and resid 195 through 198 Processing helix chain 'S' and resid 334 through 354 removed outlier: 4.070A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS S 352 " --> pdb=" O GLN S 348 " (cutoff:3.500A) Processing helix chain 'S' and resid 368 through 373 Processing helix chain 'S' and resid 476 through 484 removed outlier: 3.752A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 523 through 528 removed outlier: 4.391A pdb=" N GLY T 527 " --> pdb=" O GLY T 524 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 removed outlier: 3.557A pdb=" N GLN T 540 " --> pdb=" O THR T 536 " (cutoff:3.500A) Processing helix chain 'T' and resid 569 through 596 Processing helix chain 'T' and resid 618 through 625 Processing helix chain 'T' and resid 627 through 635 Processing helix chain 'T' and resid 638 through 660 Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 Processing sheet with id=1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.807A 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 removed outlier: 6.900A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) 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: 6.406A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.526A 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: 6.525A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.903A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.876A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.843A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.591A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=10, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.311A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.572A 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: 6.807A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (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: 6.650A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.481A 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: 6.650A 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: 3.808A 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 removed outlier: 6.900A pdb=" N CYS I 54 " --> pdb=" O VAL I 75 " (cutoff:3.500A) 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: 6.406A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.526A 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: 6.525A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR I 467 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.903A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.877A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.884A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.843A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.591A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'I' and resid 271 through 274 Processing sheet with id=26, first strand: chain 'I' and resid 315 through 323A removed outlier: 6.310A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE I 323 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.572A 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: 6.807A pdb=" N MET K 34 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (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: 6.649A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.482A 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: 6.649A 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: 3.807A 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 removed outlier: 6.899A pdb=" N CYS S 54 " --> pdb=" O VAL S 75 " (cutoff:3.500A) 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: 6.406A pdb=" N ALA S 200 " --> pdb=" O ALA S 433 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N TYR S 435 " --> pdb=" O ALA S 200 " (cutoff:3.500A) removed outlier: 6.526A 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: 6.526A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR S 467 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLY S 441 " --> pdb=" O ASN S 300 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASN S 300 " --> pdb=" O GLY S 441 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY S 451 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N THR S 290 " --> pdb=" O GLY S 451 " (cutoff:3.500A) removed outlier: 11.903A pdb=" N ILE S 453 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 11.876A pdb=" N PHE S 288 " --> pdb=" O ILE S 453 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N THR S 455 " --> pdb=" O VAL S 286 " (cutoff:3.500A) removed outlier: 10.843A pdb=" N VAL S 286 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N ASP S 457 " --> pdb=" O ILE S 284 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N ILE S 284 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE S 382 " --> pdb=" O LYS S 421 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'S' and resid 259 through 261 removed outlier: 6.591A pdb=" N LEU S 260 " --> pdb=" O THR S 450 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'S' and resid 271 through 274 Processing sheet with id=42, first strand: chain 'S' and resid 315 through 323A removed outlier: 6.311A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N THR S 303 " --> pdb=" O GLY S 321 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE S 323 " --> pdb=" O ASN S 301 " (cutoff:3.500A) removed outlier: 6.573A 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: 6.807A pdb=" N MET U 34 " --> pdb=" O LEU U 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (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: 6.650A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.481A 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: 6.650A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'V' and resid 19 through 24 756 hydrogen bonds defined for protein. 1944 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: 3.57 Time building geometry restraints manager: 1.81 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: 3489 1.31 - 1.44: 5380 1.44 - 1.56: 10846 1.56 - 1.69: 85 1.69 - 1.82: 174 Bond restraints: 19974 Sorted by residual: bond pdb=" C1 NAG Y 2 " pdb=" O5 NAG Y 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C1 NAG 0 2 " pdb=" O5 NAG 0 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 23524 2.44 - 4.89: 3113 4.89 - 7.33: 414 7.33 - 9.78: 36 9.78 - 12.22: 6 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 110.70 122.92 -12.22 1.22e+00 6.72e-01 1.00e+02 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 122.92 -12.22 1.22e+00 6.72e-01 1.00e+02 angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 122.88 -12.18 1.22e+00 6.72e-01 9.96e+01 angle pdb=" C ASP V 50 " pdb=" N VAL V 51 " pdb=" CA VAL V 51 " ideal model delta sigma weight residual 123.16 114.80 8.36 1.06e+00 8.90e-01 6.21e+01 angle pdb=" C ASP L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta sigma weight residual 123.16 114.83 8.33 1.06e+00 8.90e-01 6.18e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 10761 16.33 - 32.66: 321 32.66 - 49.00: 90 49.00 - 65.33: 36 65.33 - 81.66: 15 Dihedral angle restraints: 11223 sinusoidal: 4476 harmonic: 6747 Sorted by residual: 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 93.00 160.22 -67.22 1 1.00e+01 1.00e-02 5.88e+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 93.00 160.22 -67.22 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CB CYS I 228 " pdb=" SG CYS I 228 " pdb=" SG CYS I 239 " pdb=" CB CYS I 239 " ideal model delta sinusoidal sigma weight residual 93.00 160.20 -67.20 1 1.00e+01 1.00e-02 5.88e+01 ... (remaining 11220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2336 0.100 - 0.201: 787 0.201 - 0.301: 132 0.301 - 0.401: 21 0.401 - 0.502: 3 Chirality restraints: 3279 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.56e+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 -2.65 0.25 2.00e-02 2.50e+03 1.55e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.54e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.152 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" C7 NAG B 702 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.112 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.206 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " -0.152 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" C7 NAG J 702 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " -0.112 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " 0.205 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " 0.152 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" C7 NAG T 702 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " 0.112 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " -0.206 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.017 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4745 2.78 - 3.31: 16764 3.31 - 3.84: 31952 3.84 - 4.37: 38180 4.37 - 4.90: 64655 Nonbonded interactions: 156296 Sorted by model distance: nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR S 37 " pdb=" OG1 THR S 499 " model vdw 2.252 3.040 nonbonded pdb=" N ASN I 355 " pdb=" OD1 ASN I 355 " model vdw 2.272 3.120 nonbonded pdb=" N ASN A 355 " pdb=" OD1 ASN A 355 " model vdw 2.273 3.120 ... (remaining 156291 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.520 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.166 20097 Z= 1.293 Angle : 1.735 12.224 27426 Z= 1.116 Chirality : 0.101 0.502 3279 Planarity : 0.010 0.126 3339 Dihedral : 9.767 81.658 6783 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.26 % Favored : 96.35 % Rotamer: Outliers : 0.44 % Allowed : 0.15 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.17), residues: 2304 helix: -0.19 (0.24), residues: 384 sheet: 0.72 (0.20), residues: 666 loop : 0.35 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 66 TYR 0.054 0.007 TYR L 36 PHE 0.033 0.006 PHE I 383 TRP 0.058 0.010 TRP I 427 HIS 0.006 0.002 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.02488 / 1.29 (19974) covalent geometry : angle 1.70580 / 1.12 (27093) SS BOND : bond 0.05236 / 3.72 ( 36) SS BOND : angle 2.96302 / 2.08 ( 72) hydrogen bonds : bond 0.16313 / 11.06 ( 735) hydrogen bonds : angle 7.04151 / 4.89 ( 1944) link_ALPHA1-3 : bond 0.03610 / 1.81 ( 3) link_ALPHA1-3 : angle 2.82202 / 1.90 ( 9) link_BETA1-4 : bond 0.02594 / 1.49 ( 18) link_BETA1-4 : angle 4.05454 / 2.92 ( 54) link_NAG-ASN : bond 0.03225 / 1.91 ( 66) link_NAG-ASN : angle 3.25978 / 2.27 ( 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 498 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 489 time to evaluate : 0.712 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7783 (mm-30) REVERT: A 136 ASN cc_start: 0.7204 (m-40) cc_final: 0.6903 (p0) REVERT: A 502 LYS cc_start: 0.6423 (mmtp) cc_final: 0.6080 (mmtt) REVERT: B 632 ASP cc_start: 0.8593 (t70) cc_final: 0.8284 (t0) REVERT: L 54 ARG cc_start: 0.8602 (ptp90) cc_final: 0.8387 (ptp90) REVERT: L 94 ARG cc_start: 0.6210 (mmt180) cc_final: 0.5145 (ttm110) REVERT: I 136 ASN cc_start: 0.7035 (m-40) cc_final: 0.6819 (p0) REVERT: I 268 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7107 (mt-10) REVERT: I 502 LYS cc_start: 0.6416 (mmtp) cc_final: 0.5344 (mmtp) REVERT: J 616 ASN cc_start: 0.8275 (t0) cc_final: 0.7674 (p0) REVERT: J 633 LYS cc_start: 0.8670 (mttt) cc_final: 0.8469 (mtmm) REVERT: M 54 ARG cc_start: 0.8631 (ptp90) cc_final: 0.8421 (ptt-90) REVERT: M 94 ARG cc_start: 0.6113 (mmt180) cc_final: 0.4633 (mtp180) REVERT: S 49 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7917 (mm-30) REVERT: S 136 ASN cc_start: 0.7371 (m-40) cc_final: 0.6699 (p0) REVERT: S 207 LYS cc_start: 0.7673 (pttt) cc_final: 0.7442 (mmtm) REVERT: S 502 LYS cc_start: 0.6464 (mmtp) cc_final: 0.5548 (mmtm) REVERT: V 94 ARG cc_start: 0.6106 (mmt180) cc_final: 0.5129 (mmt180) outliers start: 9 outliers final: 8 residues processed: 497 average time/residue: 0.1545 time to fit residues: 113.3009 Evaluate side-chains 278 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 270 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain T residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN I 103 GLN M 38 GLN S 246 GLN ** S 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.100113 restraints weight = 25932.914| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.20 r_work: 0.2931 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20097 Z= 0.161 Angle : 0.707 10.569 27426 Z= 0.363 Chirality : 0.046 0.232 3279 Planarity : 0.004 0.054 3339 Dihedral : 5.584 33.923 2536 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.34 % Favored : 96.27 % Rotamer: Outliers : 1.42 % Allowed : 6.11 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2304 helix: 1.51 (0.27), residues: 399 sheet: 0.48 (0.20), residues: 684 loop : 0.15 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 444 TYR 0.022 0.002 TYR S 173 PHE 0.017 0.002 PHE I 383 TRP 0.019 0.002 TRP A 479 HIS 0.005 0.001 HIS U 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (19974) covalent geometry : angle 0.66537 / 0.36 (27093) SS BOND : bond 0.00273 / 0.17 ( 36) SS BOND : angle 1.06598 / 0.74 ( 72) hydrogen bonds : bond 0.05624 / 3.80 ( 735) hydrogen bonds : angle 5.51943 / 3.84 ( 1944) link_ALPHA1-3 : bond 0.00432 / 0.22 ( 3) link_ALPHA1-3 : angle 1.63741 / 1.02 ( 9) link_BETA1-4 : bond 0.00604 / 0.35 ( 18) link_BETA1-4 : angle 2.43914 / 1.72 ( 54) link_NAG-ASN : bond 0.00345 / 0.18 ( 66) link_NAG-ASN : angle 2.53723 / 1.75 ( 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 349 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 320 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7578 (mm-30) REVERT: A 136 ASN cc_start: 0.7361 (m-40) cc_final: 0.6400 (p0) REVERT: A 161 MET cc_start: 0.8848 (tpp) cc_final: 0.8636 (tpp) REVERT: A 207 LYS cc_start: 0.7902 (pttt) cc_final: 0.7184 (mmtt) REVERT: A 502 LYS cc_start: 0.6701 (mmtp) cc_final: 0.4943 (ttpt) REVERT: B 542 ARG cc_start: 0.8528 (mmm160) cc_final: 0.8154 (mtm110) REVERT: B 626 MET cc_start: 0.9249 (mtp) cc_final: 0.8993 (mtt) REVERT: B 632 ASP cc_start: 0.8582 (t70) cc_final: 0.8225 (t0) REVERT: L 27 ASP cc_start: 0.8122 (t0) cc_final: 0.7505 (m-30) REVERT: L 67 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8677 (m) REVERT: L 94 ARG cc_start: 0.6586 (mmt180) cc_final: 0.4596 (ttm110) REVERT: I 49 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8145 (mm-30) REVERT: I 136 ASN cc_start: 0.7146 (m-40) cc_final: 0.6347 (p0) REVERT: I 161 MET cc_start: 0.8777 (tpp) cc_final: 0.8532 (tpp) REVERT: I 268 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7663 (mt-10) REVERT: I 428 GLN cc_start: 0.7716 (mp10) cc_final: 0.7450 (mp10) REVERT: I 502 LYS cc_start: 0.6990 (mmtp) cc_final: 0.4948 (tttp) REVERT: J 616 ASN cc_start: 0.8375 (t0) cc_final: 0.7665 (p0) REVERT: M 27 ASP cc_start: 0.8145 (t0) cc_final: 0.7580 (m-30) REVERT: M 94 ARG cc_start: 0.6353 (mmt180) cc_final: 0.4255 (mtp180) REVERT: S 49 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8031 (mm-30) REVERT: S 136 ASN cc_start: 0.7353 (m-40) cc_final: 0.6176 (p0) REVERT: S 207 LYS cc_start: 0.7830 (pttt) cc_final: 0.7292 (mmtm) REVERT: S 502 LYS cc_start: 0.7097 (mmtp) cc_final: 0.5348 (mmtp) REVERT: V 27 ASP cc_start: 0.8010 (t0) cc_final: 0.7322 (m-30) REVERT: V 94 ARG cc_start: 0.6169 (mmt180) cc_final: 0.4863 (mmt180) outliers start: 29 outliers final: 17 residues processed: 342 average time/residue: 0.1537 time to fit residues: 77.8091 Evaluate side-chains 287 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 269 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain V residue 67 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 38 GLN I 103 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 82AHIS M 38 GLN S 67 ASN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.099068 restraints weight = 25806.866| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.98 r_work: 0.2904 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20097 Z= 0.211 Angle : 0.700 10.601 27426 Z= 0.353 Chirality : 0.047 0.272 3279 Planarity : 0.005 0.066 3339 Dihedral : 5.400 33.153 2528 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.17 % Favored : 95.57 % Rotamer: Outliers : 1.61 % Allowed : 7.92 % Favored : 90.47 % 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: 0.46 (0.18), residues: 2304 helix: 1.60 (0.28), residues: 396 sheet: 0.40 (0.20), residues: 669 loop : -0.11 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 71 TYR 0.024 0.002 TYR V 49 PHE 0.017 0.002 PHE S 383 TRP 0.018 0.002 TRP I 35 HIS 0.006 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (19974) covalent geometry : angle 0.66237 / 0.34 (27093) SS BOND : bond 0.00474 / 0.27 ( 36) SS BOND : angle 1.30017 / 0.94 ( 72) hydrogen bonds : bond 0.05506 / 3.73 ( 735) hydrogen bonds : angle 5.14649 / 3.58 ( 1944) link_ALPHA1-3 : bond 0.00506 / 0.25 ( 3) link_ALPHA1-3 : angle 1.22391 / 0.74 ( 9) link_BETA1-4 : bond 0.00461 / 0.26 ( 18) link_BETA1-4 : angle 1.90077 / 1.34 ( 54) link_NAG-ASN : bond 0.00446 / 0.27 ( 66) link_NAG-ASN : angle 2.48844 / 1.78 ( 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 314 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7862 (mm-30) REVERT: A 136 ASN cc_start: 0.7351 (m-40) cc_final: 0.6571 (p0) REVERT: A 161 MET cc_start: 0.8865 (tpp) cc_final: 0.8645 (tpt) REVERT: A 327 ARG cc_start: 0.6621 (mpp80) cc_final: 0.6041 (mpp80) REVERT: A 502 LYS cc_start: 0.7059 (mmtp) cc_final: 0.5770 (mmtp) REVERT: B 542 ARG cc_start: 0.8438 (mmm160) cc_final: 0.8151 (mtm110) REVERT: B 632 ASP cc_start: 0.8559 (t70) cc_final: 0.8192 (t0) REVERT: L 27 ASP cc_start: 0.8147 (t0) cc_final: 0.7619 (m-30) REVERT: L 42 LYS cc_start: 0.8150 (mppt) cc_final: 0.7638 (mptt) REVERT: L 67 SER cc_start: 0.9089 (OUTLIER) cc_final: 0.8735 (m) REVERT: L 94 ARG cc_start: 0.6577 (mmt180) cc_final: 0.4158 (mtp180) REVERT: I 49 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8116 (mm-30) REVERT: I 161 MET cc_start: 0.8822 (tpp) cc_final: 0.8439 (tpp) REVERT: I 268 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7630 (mt-10) REVERT: I 502 LYS cc_start: 0.6965 (mmtp) cc_final: 0.4917 (tttm) REVERT: M 17 GLN cc_start: 0.6891 (mt0) cc_final: 0.6558 (mt0) REVERT: M 27 ASP cc_start: 0.8081 (t0) cc_final: 0.7613 (m-30) REVERT: M 94 ARG cc_start: 0.6406 (mmt180) cc_final: 0.4156 (mtp180) REVERT: S 49 GLU cc_start: 0.8599 (mt-10) cc_final: 0.7987 (mm-30) REVERT: S 136 ASN cc_start: 0.7490 (m-40) cc_final: 0.6395 (p0) REVERT: S 207 LYS cc_start: 0.7835 (pttt) cc_final: 0.7297 (mmtm) REVERT: S 434 MET cc_start: 0.9326 (ttp) cc_final: 0.9111 (ttp) REVERT: S 502 LYS cc_start: 0.6885 (mmtp) cc_final: 0.6423 (mmtt) REVERT: V 27 ASP cc_start: 0.7971 (t0) cc_final: 0.7510 (m-30) REVERT: V 94 ARG cc_start: 0.6407 (mmt180) cc_final: 0.4119 (mtp180) outliers start: 33 outliers final: 26 residues processed: 297 average time/residue: 0.1541 time to fit residues: 67.9203 Evaluate side-chains 291 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 70 SER Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 159 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN I 67 ASN I 103 GLN I 246 GLN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.095255 restraints weight = 26035.382| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.19 r_work: 0.2852 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3061 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= 0.159 Angle : 0.617 10.025 27426 Z= 0.312 Chirality : 0.045 0.263 3279 Planarity : 0.004 0.051 3339 Dihedral : 5.085 32.837 2524 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.21 % Favored : 95.53 % Rotamer: Outliers : 1.91 % Allowed : 8.99 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2304 helix: 1.71 (0.28), residues: 396 sheet: 0.38 (0.19), residues: 675 loop : -0.17 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 327 TYR 0.017 0.001 TYR A 173 PHE 0.015 0.002 PHE K 29 TRP 0.011 0.001 TRP I 35 HIS 0.005 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (19974) covalent geometry : angle 0.58340 / 0.30 (27093) SS BOND : bond 0.00333 / 0.21 ( 36) SS BOND : angle 1.10728 / 0.79 ( 72) hydrogen bonds : bond 0.04765 / 3.21 ( 735) hydrogen bonds : angle 4.96858 / 3.46 ( 1944) link_ALPHA1-3 : bond 0.00485 / 0.24 ( 3) link_ALPHA1-3 : angle 1.35309 / 0.82 ( 9) link_BETA1-4 : bond 0.00436 / 0.26 ( 18) link_BETA1-4 : angle 1.66165 / 1.17 ( 54) link_NAG-ASN : bond 0.00380 / 0.24 ( 66) link_NAG-ASN : angle 2.20226 / 1.54 ( 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 314 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8663 (mt-10) cc_final: 0.7894 (mm-30) REVERT: A 136 ASN cc_start: 0.7355 (m-40) cc_final: 0.6495 (p0) REVERT: A 327 ARG cc_start: 0.6593 (mpp80) cc_final: 0.6224 (mpp80) REVERT: A 434 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.9072 (ttp) REVERT: A 502 LYS cc_start: 0.7086 (mmtp) cc_final: 0.5502 (mmtp) REVERT: B 542 ARG cc_start: 0.8555 (mmm160) cc_final: 0.8149 (mtm110) REVERT: B 632 ASP cc_start: 0.8713 (t70) cc_final: 0.8315 (t0) REVERT: H 39 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7899 (tp40) REVERT: L 17 GLN cc_start: 0.7016 (mt0) cc_final: 0.6648 (mt0) REVERT: L 27 ASP cc_start: 0.8218 (t0) cc_final: 0.7675 (m-30) REVERT: L 42 LYS cc_start: 0.8078 (mppt) cc_final: 0.7553 (mptt) REVERT: L 67 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8692 (m) REVERT: L 94 ARG cc_start: 0.6600 (mmt180) cc_final: 0.4090 (mtp180) REVERT: I 49 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8113 (mm-30) REVERT: I 161 MET cc_start: 0.8798 (tpp) cc_final: 0.8466 (tpp) REVERT: I 268 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7746 (mt-10) REVERT: I 502 LYS cc_start: 0.7021 (mmtp) cc_final: 0.4960 (tttm) REVERT: J 632 ASP cc_start: 0.8698 (t70) cc_final: 0.8247 (t0) REVERT: M 17 GLN cc_start: 0.7011 (mt0) cc_final: 0.6613 (mt0) REVERT: M 27 ASP cc_start: 0.8172 (t0) cc_final: 0.7680 (m-30) REVERT: M 94 ARG cc_start: 0.6482 (mmt180) cc_final: 0.4041 (mtp180) REVERT: S 49 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8042 (mm-30) REVERT: S 136 ASN cc_start: 0.7473 (m-40) cc_final: 0.6303 (p0) REVERT: S 207 LYS cc_start: 0.7930 (pttt) cc_final: 0.7334 (mmtm) REVERT: S 502 LYS cc_start: 0.6807 (mmtp) cc_final: 0.5839 (mmtt) REVERT: V 27 ASP cc_start: 0.7975 (t0) cc_final: 0.7529 (m-30) REVERT: V 94 ARG cc_start: 0.6474 (mmt180) cc_final: 0.4962 (mmt180) outliers start: 39 outliers final: 26 residues processed: 293 average time/residue: 0.1499 time to fit residues: 66.0905 Evaluate side-chains 289 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 260 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain I residue 67 ASN Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain S residue 67 ASN Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 70 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 135 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 180 optimal weight: 0.4980 chunk 228 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN I 103 GLN I 246 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN S 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.118464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.091347 restraints weight = 26145.404| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.19 r_work: 0.2796 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 20097 Z= 0.274 Angle : 0.712 9.984 27426 Z= 0.357 Chirality : 0.049 0.298 3279 Planarity : 0.005 0.044 3339 Dihedral : 5.383 33.310 2524 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.69 % Favored : 95.05 % Rotamer: Outliers : 2.39 % Allowed : 9.78 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 2304 helix: 1.39 (0.27), residues: 396 sheet: 0.16 (0.19), residues: 681 loop : -0.37 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 480 TYR 0.024 0.002 TYR M 49 PHE 0.022 0.002 PHE H 29 TRP 0.017 0.002 TRP I 35 HIS 0.005 0.002 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.27 (19974) covalent geometry : angle 0.68020 / 0.35 (27093) SS BOND : bond 0.00432 / 0.27 ( 36) SS BOND : angle 1.38266 / 0.97 ( 72) hydrogen bonds : bond 0.05698 / 3.86 ( 735) hydrogen bonds : angle 5.08389 / 3.56 ( 1944) link_ALPHA1-3 : bond 0.00499 / 0.25 ( 3) link_ALPHA1-3 : angle 1.25515 / 0.75 ( 9) link_BETA1-4 : bond 0.00530 / 0.34 ( 18) link_BETA1-4 : angle 1.91226 / 1.35 ( 54) link_NAG-ASN : bond 0.00495 / 0.28 ( 66) link_NAG-ASN : angle 2.25121 / 1.58 ( 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 329 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 280 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8628 (mt-10) cc_final: 0.7820 (mm-30) REVERT: A 103 GLN cc_start: 0.8318 (tt0) cc_final: 0.7902 (tt0) REVERT: A 107 ASP cc_start: 0.8485 (m-30) cc_final: 0.8281 (m-30) REVERT: A 136 ASN cc_start: 0.7352 (m-40) cc_final: 0.6474 (p0) REVERT: A 213 ILE cc_start: 0.8863 (tp) cc_final: 0.8532 (mm) REVERT: A 327 ARG cc_start: 0.6863 (mpp80) cc_final: 0.6510 (mpp80) REVERT: A 502 LYS cc_start: 0.7281 (mmtp) cc_final: 0.5772 (mmtp) REVERT: B 542 ARG cc_start: 0.8566 (mmm160) cc_final: 0.8141 (mtm110) REVERT: B 632 ASP cc_start: 0.8773 (t70) cc_final: 0.8330 (t0) REVERT: H 39 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7628 (tp40) REVERT: L 17 GLN cc_start: 0.7119 (mt0) cc_final: 0.6774 (mt0) REVERT: L 27 ASP cc_start: 0.8253 (t0) cc_final: 0.7710 (m-30) REVERT: L 42 LYS cc_start: 0.8191 (mppt) cc_final: 0.7485 (mptt) REVERT: L 67 SER cc_start: 0.9060 (OUTLIER) cc_final: 0.8729 (m) REVERT: L 94 ARG cc_start: 0.6816 (mmt180) cc_final: 0.4058 (mtp180) REVERT: I 136 ASN cc_start: 0.7237 (m-40) cc_final: 0.6176 (p0) REVERT: I 161 MET cc_start: 0.8895 (tpp) cc_final: 0.8513 (tpp) REVERT: I 268 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7889 (mt-10) REVERT: I 502 LYS cc_start: 0.7101 (mmtp) cc_final: 0.4760 (tttm) REVERT: J 616 ASN cc_start: 0.8540 (t0) cc_final: 0.7805 (p0) REVERT: J 632 ASP cc_start: 0.8856 (t70) cc_final: 0.8378 (t0) REVERT: K 6 GLU cc_start: 0.7910 (mp0) cc_final: 0.7673 (mp0) REVERT: M 17 GLN cc_start: 0.7207 (mt0) cc_final: 0.6819 (mt0) REVERT: M 27 ASP cc_start: 0.8166 (t0) cc_final: 0.7650 (m-30) REVERT: M 94 ARG cc_start: 0.6541 (mmt180) cc_final: 0.3913 (mtp180) REVERT: S 49 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8012 (mm-30) REVERT: S 136 ASN cc_start: 0.7596 (m-40) cc_final: 0.6385 (p0) REVERT: S 207 LYS cc_start: 0.7837 (pttt) cc_final: 0.7191 (mmtm) REVERT: S 308 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8431 (mtt90) REVERT: S 502 LYS cc_start: 0.7034 (mmtp) cc_final: 0.5764 (mmtm) REVERT: T 632 ASP cc_start: 0.8745 (t70) cc_final: 0.8494 (t0) REVERT: U 23 ARG cc_start: 0.8472 (tpt-90) cc_final: 0.8217 (tpp80) REVERT: V 27 ASP cc_start: 0.8095 (t0) cc_final: 0.7730 (m-30) REVERT: V 94 ARG cc_start: 0.6729 (mmt180) cc_final: 0.4166 (mtp180) outliers start: 49 outliers final: 38 residues processed: 304 average time/residue: 0.1589 time to fit residues: 71.8479 Evaluate side-chains 311 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 67 ASN Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain S residue 67 ASN Chi-restraints excluded: chain S residue 308 ARG Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR 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: 0.9980 chunk 178 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 197 optimal weight: 0.8980 chunk 153 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN I 67 ASN I 103 GLN T 607 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.099050 restraints weight = 25418.747| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.11 r_work: 0.2881 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20097 Z= 0.113 Angle : 0.570 9.841 27426 Z= 0.287 Chirality : 0.044 0.258 3279 Planarity : 0.004 0.044 3339 Dihedral : 4.861 32.683 2524 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.78 % Favored : 95.96 % Rotamer: Outliers : 2.05 % Allowed : 10.65 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2304 helix: 1.82 (0.27), residues: 396 sheet: 0.33 (0.20), residues: 681 loop : -0.28 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 444 TYR 0.019 0.001 TYR A 173 PHE 0.014 0.001 PHE S 53 TRP 0.015 0.001 TRP I 112 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (19974) covalent geometry : angle 0.53688 / 0.28 (27093) SS BOND : bond 0.00376 / 0.21 ( 36) SS BOND : angle 1.14067 / 0.79 ( 72) hydrogen bonds : bond 0.04111 / 2.77 ( 735) hydrogen bonds : angle 4.81303 / 3.35 ( 1944) link_ALPHA1-3 : bond 0.00450 / 0.22 ( 3) link_ALPHA1-3 : angle 1.40285 / 0.85 ( 9) link_BETA1-4 : bond 0.00419 / 0.24 ( 18) link_BETA1-4 : angle 1.43021 / 1.01 ( 54) link_NAG-ASN : bond 0.00362 / 0.20 ( 66) link_NAG-ASN : angle 2.11012 / 1.47 ( 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 320 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 278 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8599 (mt-10) cc_final: 0.7827 (mm-30) REVERT: A 136 ASN cc_start: 0.7406 (m-40) cc_final: 0.6589 (p0) REVERT: A 327 ARG cc_start: 0.6667 (mpp80) cc_final: 0.6052 (mpp80) REVERT: A 502 LYS cc_start: 0.7072 (mmtp) cc_final: 0.5577 (mmtp) REVERT: B 542 ARG cc_start: 0.8456 (mmm160) cc_final: 0.8101 (mtm110) REVERT: B 632 ASP cc_start: 0.8634 (t70) cc_final: 0.8236 (t0) REVERT: B 636 SER cc_start: 0.9178 (t) cc_final: 0.8859 (p) REVERT: H 39 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7455 (tp40) REVERT: L 17 GLN cc_start: 0.7249 (mt0) cc_final: 0.6860 (mt0) REVERT: L 27 ASP cc_start: 0.8190 (t0) cc_final: 0.7772 (m-30) REVERT: L 42 LYS cc_start: 0.8222 (mppt) cc_final: 0.7670 (mptt) REVERT: L 67 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8688 (m) REVERT: L 94 ARG cc_start: 0.6661 (mmt180) cc_final: 0.4151 (mtp180) REVERT: I 80 ASN cc_start: 0.7299 (t0) cc_final: 0.6901 (p0) REVERT: I 161 MET cc_start: 0.8730 (tpp) cc_final: 0.8372 (tpp) REVERT: I 268 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7716 (mt-10) REVERT: I 308 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8330 (mmt90) REVERT: I 318 TYR cc_start: 0.8898 (m-80) cc_final: 0.8637 (m-80) REVERT: I 371 VAL cc_start: 0.8629 (t) cc_final: 0.8376 (m) REVERT: I 502 LYS cc_start: 0.7098 (mmtp) cc_final: 0.5020 (tttp) REVERT: J 632 ASP cc_start: 0.8607 (t70) cc_final: 0.8152 (t0) REVERT: M 17 GLN cc_start: 0.7439 (mt0) cc_final: 0.7202 (mt0) REVERT: M 27 ASP cc_start: 0.8107 (t0) cc_final: 0.7728 (m-30) REVERT: M 94 ARG cc_start: 0.6339 (mmt180) cc_final: 0.3837 (mtp180) REVERT: S 49 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8008 (mm-30) REVERT: S 136 ASN cc_start: 0.7579 (m-40) cc_final: 0.6405 (p0) REVERT: S 161 MET cc_start: 0.8797 (tpp) cc_final: 0.8434 (tpp) REVERT: S 207 LYS cc_start: 0.7763 (pttt) cc_final: 0.7152 (mmtm) REVERT: S 502 LYS cc_start: 0.6858 (mmtp) cc_final: 0.5643 (mmtp) REVERT: T 632 ASP cc_start: 0.8497 (t70) cc_final: 0.8259 (t0) REVERT: U 39 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7697 (tp40) REVERT: U 105 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7863 (mm-40) REVERT: V 27 ASP cc_start: 0.8225 (t0) cc_final: 0.7851 (m-30) REVERT: V 94 ARG cc_start: 0.6467 (mmt180) cc_final: 0.4841 (mmt180) outliers start: 42 outliers final: 22 residues processed: 298 average time/residue: 0.1484 time to fit residues: 67.0987 Evaluate side-chains 288 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 262 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 67 ASN Chi-restraints excluded: chain I residue 308 ARG Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 607 ASN Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain U residue 39 GLN Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 65 optimal weight: 4.9990 chunk 3 optimal weight: 0.0980 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN L 38 GLN I 67 ASN I 103 GLN I 246 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.092176 restraints weight = 26093.261| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.20 r_work: 0.2853 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20097 Z= 0.211 Angle : 0.642 9.708 27426 Z= 0.322 Chirality : 0.047 0.288 3279 Planarity : 0.004 0.044 3339 Dihedral : 5.033 33.263 2524 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.34 % Favored : 95.40 % Rotamer: Outliers : 2.30 % Allowed : 11.00 % Favored : 86.71 % 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: 1.68 (0.27), residues: 396 sheet: 0.20 (0.20), residues: 681 loop : -0.40 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG U 71 TYR 0.020 0.002 TYR M 49 PHE 0.018 0.002 PHE H 29 TRP 0.012 0.001 TRP I 112 HIS 0.005 0.001 HIS I 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (19974) covalent geometry : angle 0.60915 / 0.31 (27093) SS BOND : bond 0.00418 / 0.26 ( 36) SS BOND : angle 1.64559 / 1.13 ( 72) hydrogen bonds : bond 0.04992 / 3.38 ( 735) hydrogen bonds : angle 4.87406 / 3.42 ( 1944) link_ALPHA1-3 : bond 0.00521 / 0.26 ( 3) link_ALPHA1-3 : angle 1.31066 / 0.79 ( 9) link_BETA1-4 : bond 0.00408 / 0.24 ( 18) link_BETA1-4 : angle 1.70792 / 1.20 ( 54) link_NAG-ASN : bond 0.00401 / 0.23 ( 66) link_NAG-ASN : angle 2.09513 / 1.48 ( 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 322 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8685 (mt-10) cc_final: 0.7834 (mm-30) REVERT: A 80 ASN cc_start: 0.6143 (p0) cc_final: 0.5935 (m-40) REVERT: A 103 GLN cc_start: 0.8322 (tt0) cc_final: 0.7939 (tt0) REVERT: A 136 ASN cc_start: 0.7376 (m-40) cc_final: 0.6531 (p0) REVERT: A 327 ARG cc_start: 0.6653 (mpp80) cc_final: 0.6283 (mpp80) REVERT: A 502 LYS cc_start: 0.7214 (mmtp) cc_final: 0.5608 (mmtp) REVERT: B 542 ARG cc_start: 0.8511 (mmm160) cc_final: 0.8092 (mtm110) REVERT: B 632 ASP cc_start: 0.8761 (t70) cc_final: 0.8320 (t0) REVERT: H 39 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7372 (tp40) REVERT: L 17 GLN cc_start: 0.7223 (mt0) cc_final: 0.6845 (mt0) REVERT: L 27 ASP cc_start: 0.8183 (t0) cc_final: 0.7739 (m-30) REVERT: L 42 LYS cc_start: 0.8262 (mppt) cc_final: 0.7880 (mptt) REVERT: L 67 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8725 (m) REVERT: L 94 ARG cc_start: 0.6672 (mmt180) cc_final: 0.3989 (mtp180) REVERT: I 117 LYS cc_start: 0.8259 (tttt) cc_final: 0.8009 (tptt) REVERT: I 136 ASN cc_start: 0.7036 (m-40) cc_final: 0.6107 (p0) REVERT: I 161 MET cc_start: 0.8851 (tpp) cc_final: 0.8440 (tpp) REVERT: I 268 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7749 (mt-10) REVERT: I 308 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8285 (mmt90) REVERT: I 318 TYR cc_start: 0.8917 (m-80) cc_final: 0.8672 (m-80) REVERT: I 327 ARG cc_start: 0.6684 (mtm180) cc_final: 0.6341 (mtm180) REVERT: I 371 VAL cc_start: 0.8649 (t) cc_final: 0.8421 (m) REVERT: I 502 LYS cc_start: 0.7226 (mmtp) cc_final: 0.4938 (tttm) REVERT: J 616 ASN cc_start: 0.8566 (t0) cc_final: 0.7799 (p0) REVERT: J 632 ASP cc_start: 0.8738 (t70) cc_final: 0.8259 (t0) REVERT: K 39 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7258 (tp40) REVERT: M 17 GLN cc_start: 0.7522 (mt0) cc_final: 0.7257 (mt0) REVERT: M 27 ASP cc_start: 0.8094 (t0) cc_final: 0.7699 (m-30) REVERT: M 94 ARG cc_start: 0.6439 (mmt180) cc_final: 0.3776 (mtp180) REVERT: S 49 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8001 (mm-30) REVERT: S 136 ASN cc_start: 0.7629 (m-40) cc_final: 0.6384 (p0) REVERT: S 161 MET cc_start: 0.8897 (tpp) cc_final: 0.8458 (tpp) REVERT: S 207 LYS cc_start: 0.7797 (pttt) cc_final: 0.7119 (mmtm) REVERT: S 308 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8417 (mtt90) REVERT: S 502 LYS cc_start: 0.7023 (mmtp) cc_final: 0.5768 (mmtp) REVERT: T 632 ASP cc_start: 0.8581 (t70) cc_final: 0.8301 (t0) REVERT: U 39 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7589 (tp40) REVERT: V 27 ASP cc_start: 0.8230 (t0) cc_final: 0.7801 (m-30) REVERT: V 94 ARG cc_start: 0.6529 (mmt180) cc_final: 0.4013 (mtp180) outliers start: 47 outliers final: 30 residues processed: 292 average time/residue: 0.1670 time to fit residues: 72.7998 Evaluate side-chains 306 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 308 ARG Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain S residue 35 TRP Chi-restraints excluded: chain S residue 308 ARG Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 39 GLN Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 188 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 125 optimal weight: 0.0040 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN I 103 GLN I 246 GLN ** S 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN T 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.125182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.099136 restraints weight = 25482.340| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.11 r_work: 0.2871 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20097 Z= 0.108 Angle : 0.556 9.501 27426 Z= 0.280 Chirality : 0.044 0.259 3279 Planarity : 0.004 0.042 3339 Dihedral : 4.738 32.474 2524 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.99 % Favored : 95.88 % Rotamer: Outliers : 1.56 % Allowed : 11.83 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2304 helix: 2.24 (0.28), residues: 378 sheet: 0.34 (0.20), residues: 681 loop : -0.35 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 83 TYR 0.019 0.001 TYR A 173 PHE 0.013 0.001 PHE S 53 TRP 0.015 0.001 TRP I 112 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (19974) covalent geometry : angle 0.52633 / 0.27 (27093) SS BOND : bond 0.00286 / 0.17 ( 36) SS BOND : angle 1.09998 / 0.78 ( 72) hydrogen bonds : bond 0.04012 / 2.70 ( 735) hydrogen bonds : angle 4.73530 / 3.30 ( 1944) link_ALPHA1-3 : bond 0.00454 / 0.23 ( 3) link_ALPHA1-3 : angle 1.41503 / 0.85 ( 9) link_BETA1-4 : bond 0.00441 / 0.25 ( 18) link_BETA1-4 : angle 1.42066 / 1.00 ( 54) link_NAG-ASN : bond 0.00306 / 0.17 ( 66) link_NAG-ASN : angle 1.97134 / 1.39 ( 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 311 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7831 (mm-30) REVERT: A 80 ASN cc_start: 0.6250 (p0) cc_final: 0.6036 (m-40) REVERT: A 136 ASN cc_start: 0.7268 (m-40) cc_final: 0.6556 (p0) REVERT: A 327 ARG cc_start: 0.6632 (mpp80) cc_final: 0.6015 (mpp80) REVERT: A 502 LYS cc_start: 0.7086 (mmtp) cc_final: 0.5477 (mmtp) REVERT: B 542 ARG cc_start: 0.8456 (mmm160) cc_final: 0.8107 (mtm110) REVERT: B 632 ASP cc_start: 0.8699 (t70) cc_final: 0.8295 (t0) REVERT: H 39 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7260 (tp40) REVERT: L 17 GLN cc_start: 0.7316 (mt0) cc_final: 0.6891 (mt0) REVERT: L 27 ASP cc_start: 0.8229 (t0) cc_final: 0.7724 (m-30) REVERT: L 42 LYS cc_start: 0.8262 (mppt) cc_final: 0.7865 (mptt) REVERT: L 67 SER cc_start: 0.9057 (p) cc_final: 0.8719 (m) REVERT: L 94 ARG cc_start: 0.6555 (mmt180) cc_final: 0.3995 (mtp180) REVERT: I 80 ASN cc_start: 0.7316 (t0) cc_final: 0.6842 (p0) REVERT: I 136 ASN cc_start: 0.7058 (m-40) cc_final: 0.6154 (p0) REVERT: I 161 MET cc_start: 0.8711 (tpp) cc_final: 0.8337 (tpp) REVERT: I 268 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7714 (mt-10) REVERT: I 308 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8474 (mmt90) REVERT: I 318 TYR cc_start: 0.8919 (m-80) cc_final: 0.8678 (m-80) REVERT: I 327 ARG cc_start: 0.6703 (mtm180) cc_final: 0.6383 (mtm180) REVERT: I 371 VAL cc_start: 0.8657 (t) cc_final: 0.8433 (m) REVERT: I 502 LYS cc_start: 0.7133 (mmtp) cc_final: 0.5019 (tttp) REVERT: J 616 ASN cc_start: 0.8465 (t0) cc_final: 0.7775 (p0) REVERT: J 632 ASP cc_start: 0.8575 (t70) cc_final: 0.8216 (t0) REVERT: K 39 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7047 (tp40) REVERT: M 17 GLN cc_start: 0.7533 (mt0) cc_final: 0.7313 (mt0) REVERT: M 27 ASP cc_start: 0.8081 (t0) cc_final: 0.7803 (m-30) REVERT: M 94 ARG cc_start: 0.6278 (mmt180) cc_final: 0.3758 (mtp180) REVERT: S 49 GLU cc_start: 0.8654 (mt-10) cc_final: 0.7972 (mm-30) REVERT: S 136 ASN cc_start: 0.7540 (m-40) cc_final: 0.6353 (p0) REVERT: S 161 MET cc_start: 0.8808 (tpp) cc_final: 0.8409 (tpp) REVERT: S 207 LYS cc_start: 0.7674 (pttt) cc_final: 0.7076 (mmtm) REVERT: S 502 LYS cc_start: 0.6906 (mmtp) cc_final: 0.5600 (mmtp) REVERT: T 632 ASP cc_start: 0.8540 (t70) cc_final: 0.8261 (t0) REVERT: U 39 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7558 (tp40) REVERT: U 105 GLN cc_start: 0.7961 (mm110) cc_final: 0.7759 (mm-40) REVERT: V 27 ASP cc_start: 0.8203 (t0) cc_final: 0.7843 (m-30) REVERT: V 94 ARG cc_start: 0.6488 (mmt180) cc_final: 0.4808 (mmt180) outliers start: 32 outliers final: 21 residues processed: 293 average time/residue: 0.1666 time to fit residues: 72.7880 Evaluate side-chains 295 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 270 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 308 ARG Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 607 ASN Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain U residue 39 GLN Chi-restraints excluded: chain U residue 70 SER Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 159 optimal weight: 0.0000 chunk 174 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 203 optimal weight: 0.0770 chunk 163 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 overall best weight: 0.8544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 607 ASN L 38 GLN I 103 GLN ** S 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN T 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.095054 restraints weight = 25841.374| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.19 r_work: 0.2861 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20097 Z= 0.112 Angle : 0.546 9.345 27426 Z= 0.275 Chirality : 0.044 0.259 3279 Planarity : 0.004 0.045 3339 Dihedral : 4.647 32.595 2524 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.04 % Favored : 95.83 % Rotamer: Outliers : 1.86 % Allowed : 11.39 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 2304 helix: 2.33 (0.27), residues: 378 sheet: 0.42 (0.20), residues: 681 loop : -0.34 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 444 TYR 0.012 0.001 TYR M 49 PHE 0.013 0.001 PHE S 53 TRP 0.015 0.001 TRP I 112 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (19974) covalent geometry : angle 0.51701 / 0.27 (27093) SS BOND : bond 0.00295 / 0.18 ( 36) SS BOND : angle 1.05093 / 0.73 ( 72) hydrogen bonds : bond 0.03981 / 2.68 ( 735) hydrogen bonds : angle 4.66818 / 3.26 ( 1944) link_ALPHA1-3 : bond 0.00469 / 0.23 ( 3) link_ALPHA1-3 : angle 1.38395 / 0.84 ( 9) link_BETA1-4 : bond 0.00415 / 0.24 ( 18) link_BETA1-4 : angle 1.43576 / 1.01 ( 54) link_NAG-ASN : bond 0.00298 / 0.16 ( 66) link_NAG-ASN : angle 1.91811 / 1.36 ( 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 307 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8703 (mt-10) cc_final: 0.7840 (mm-30) REVERT: A 136 ASN cc_start: 0.7375 (m-40) cc_final: 0.6540 (p0) REVERT: A 327 ARG cc_start: 0.6586 (mpp80) cc_final: 0.5934 (mpp80) REVERT: A 434 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.9108 (ttp) REVERT: A 502 LYS cc_start: 0.7090 (mmtp) cc_final: 0.5434 (mmtp) REVERT: B 542 ARG cc_start: 0.8511 (mmm160) cc_final: 0.8086 (mtm110) REVERT: B 632 ASP cc_start: 0.8751 (t70) cc_final: 0.8353 (t0) REVERT: H 39 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7228 (tp40) REVERT: L 27 ASP cc_start: 0.8211 (t0) cc_final: 0.7694 (m-30) REVERT: L 42 LYS cc_start: 0.8244 (mppt) cc_final: 0.7836 (mptt) REVERT: L 67 SER cc_start: 0.9065 (p) cc_final: 0.8688 (m) REVERT: L 94 ARG cc_start: 0.6544 (mmt180) cc_final: 0.3927 (mtp180) REVERT: I 80 ASN cc_start: 0.7329 (t0) cc_final: 0.6839 (p0) REVERT: I 136 ASN cc_start: 0.6997 (m-40) cc_final: 0.6064 (p0) REVERT: I 161 MET cc_start: 0.8733 (tpp) cc_final: 0.8339 (tpp) REVERT: I 268 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7734 (mt-10) REVERT: I 308 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8521 (mmt90) REVERT: I 318 TYR cc_start: 0.8934 (m-80) cc_final: 0.8686 (m-80) REVERT: I 327 ARG cc_start: 0.6684 (mtm180) cc_final: 0.6331 (mtm180) REVERT: I 371 VAL cc_start: 0.8598 (t) cc_final: 0.8389 (m) REVERT: I 502 LYS cc_start: 0.7167 (mmtp) cc_final: 0.4975 (tttp) REVERT: J 616 ASN cc_start: 0.8506 (t0) cc_final: 0.7750 (p0) REVERT: J 632 ASP cc_start: 0.8708 (t70) cc_final: 0.8260 (t0) REVERT: K 39 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7004 (tp40) REVERT: M 17 GLN cc_start: 0.7566 (mt0) cc_final: 0.7316 (mt0) REVERT: M 27 ASP cc_start: 0.8117 (t0) cc_final: 0.7827 (m-30) REVERT: M 94 ARG cc_start: 0.6224 (mmt180) cc_final: 0.3599 (mtp180) REVERT: S 49 GLU cc_start: 0.8714 (mt-10) cc_final: 0.7972 (mm-30) REVERT: S 136 ASN cc_start: 0.7527 (m-40) cc_final: 0.6280 (p0) REVERT: S 161 MET cc_start: 0.8828 (tpp) cc_final: 0.8408 (tpp) REVERT: S 207 LYS cc_start: 0.7659 (pttt) cc_final: 0.7018 (mmtm) REVERT: S 213 ILE cc_start: 0.8741 (tt) cc_final: 0.8370 (mm) REVERT: S 502 LYS cc_start: 0.6943 (mmtp) cc_final: 0.5247 (mmtp) REVERT: T 632 ASP cc_start: 0.8622 (t70) cc_final: 0.8318 (t0) REVERT: U 39 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7433 (tp40) REVERT: U 105 GLN cc_start: 0.7943 (mm110) cc_final: 0.7711 (mm-40) REVERT: V 27 ASP cc_start: 0.8180 (t0) cc_final: 0.7806 (m-30) REVERT: V 94 ARG cc_start: 0.6438 (mmt180) cc_final: 0.3978 (mtp180) outliers start: 38 outliers final: 26 residues processed: 288 average time/residue: 0.1588 time to fit residues: 68.2669 Evaluate side-chains 299 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 308 ARG Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain S residue 35 TRP Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain U residue 39 GLN Chi-restraints excluded: chain U residue 70 SER Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 226 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 607 ASN L 38 GLN I 103 GLN I 246 GLN ** S 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.094743 restraints weight = 26194.877| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.21 r_work: 0.2853 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20097 Z= 0.122 Angle : 0.550 9.277 27426 Z= 0.276 Chirality : 0.044 0.260 3279 Planarity : 0.004 0.045 3339 Dihedral : 4.620 32.449 2524 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.30 % Favored : 95.57 % Rotamer: Outliers : 1.66 % Allowed : 11.58 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2304 helix: 2.33 (0.27), residues: 378 sheet: 0.44 (0.20), residues: 681 loop : -0.33 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 503 TYR 0.017 0.001 TYR S 173 PHE 0.013 0.001 PHE S 53 TRP 0.014 0.001 TRP I 112 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (19974) covalent geometry : angle 0.52127 / 0.27 (27093) SS BOND : bond 0.00316 / 0.19 ( 36) SS BOND : angle 1.06298 / 0.74 ( 72) hydrogen bonds : bond 0.04036 / 2.72 ( 735) hydrogen bonds : angle 4.65033 / 3.25 ( 1944) link_ALPHA1-3 : bond 0.00467 / 0.23 ( 3) link_ALPHA1-3 : angle 1.37561 / 0.83 ( 9) link_BETA1-4 : bond 0.00407 / 0.23 ( 18) link_BETA1-4 : angle 1.44739 / 1.02 ( 54) link_NAG-ASN : bond 0.00295 / 0.16 ( 66) link_NAG-ASN : angle 1.89532 / 1.34 ( 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 303 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 269 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8672 (mt-10) cc_final: 0.7831 (mm-30) REVERT: A 136 ASN cc_start: 0.7382 (m-40) cc_final: 0.6571 (p0) REVERT: A 161 MET cc_start: 0.8769 (tpp) cc_final: 0.8524 (tpp) REVERT: A 327 ARG cc_start: 0.6603 (mpp80) cc_final: 0.5963 (mpp80) REVERT: A 502 LYS cc_start: 0.7106 (mmtp) cc_final: 0.5435 (mmtp) REVERT: B 542 ARG cc_start: 0.8491 (mmm160) cc_final: 0.8096 (mtm110) REVERT: B 632 ASP cc_start: 0.8719 (t70) cc_final: 0.8324 (t0) REVERT: L 27 ASP cc_start: 0.8180 (t0) cc_final: 0.7645 (m-30) REVERT: L 42 LYS cc_start: 0.8238 (mppt) cc_final: 0.7831 (mptt) REVERT: L 67 SER cc_start: 0.9064 (p) cc_final: 0.8691 (m) REVERT: L 94 ARG cc_start: 0.6560 (mmt180) cc_final: 0.3960 (mtp180) REVERT: I 80 ASN cc_start: 0.7245 (t0) cc_final: 0.6797 (p0) REVERT: I 136 ASN cc_start: 0.7014 (m-40) cc_final: 0.6108 (p0) REVERT: I 161 MET cc_start: 0.8739 (tpp) cc_final: 0.8338 (tpp) REVERT: I 268 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7711 (mt-10) REVERT: I 308 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8522 (mmt90) REVERT: I 318 TYR cc_start: 0.8923 (m-80) cc_final: 0.8678 (m-80) REVERT: I 327 ARG cc_start: 0.6663 (mtm180) cc_final: 0.6318 (mtm180) REVERT: I 371 VAL cc_start: 0.8609 (t) cc_final: 0.8401 (m) REVERT: I 502 LYS cc_start: 0.7190 (mmtp) cc_final: 0.4987 (tttp) REVERT: J 616 ASN cc_start: 0.8487 (t0) cc_final: 0.7746 (p0) REVERT: J 632 ASP cc_start: 0.8667 (t70) cc_final: 0.8224 (t0) REVERT: K 39 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7042 (tp40) REVERT: M 17 GLN cc_start: 0.7476 (mt0) cc_final: 0.7212 (mt0) REVERT: M 27 ASP cc_start: 0.8110 (t0) cc_final: 0.7833 (m-30) REVERT: M 94 ARG cc_start: 0.6262 (mmt180) cc_final: 0.3627 (mtp180) REVERT: S 49 GLU cc_start: 0.8705 (mt-10) cc_final: 0.7962 (mm-30) REVERT: S 136 ASN cc_start: 0.7539 (m-40) cc_final: 0.6317 (p0) REVERT: S 161 MET cc_start: 0.8820 (tpp) cc_final: 0.8399 (tpp) REVERT: S 207 LYS cc_start: 0.7625 (pttt) cc_final: 0.7085 (mmtm) REVERT: S 213 ILE cc_start: 0.8750 (tt) cc_final: 0.8381 (mm) REVERT: S 502 LYS cc_start: 0.6951 (mmtp) cc_final: 0.5678 (mmtp) REVERT: T 632 ASP cc_start: 0.8590 (t70) cc_final: 0.8289 (t0) REVERT: U 39 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7439 (tp40) REVERT: U 105 GLN cc_start: 0.7891 (mm110) cc_final: 0.7674 (mm-40) REVERT: V 27 ASP cc_start: 0.8182 (t0) cc_final: 0.7788 (m-30) REVERT: V 94 ARG cc_start: 0.6453 (mmt180) cc_final: 0.4020 (mtp180) outliers start: 34 outliers final: 23 residues processed: 285 average time/residue: 0.1625 time to fit residues: 68.7025 Evaluate side-chains 291 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 265 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 308 ARG Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 607 ASN Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain U residue 39 GLN Chi-restraints excluded: chain U residue 70 SER Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 102 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: 7.9990 chunk 16 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 206 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 191 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN I 103 GLN I 246 GLN ** S 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.124230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.098247 restraints weight = 25711.046| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.10 r_work: 0.2879 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.284 20097 Z= 0.214 Angle : 0.772 59.184 27426 Z= 0.453 Chirality : 0.045 0.261 3279 Planarity : 0.005 0.172 3339 Dihedral : 4.658 32.496 2524 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.49 % Rotamer: Outliers : 1.52 % Allowed : 11.97 % Favored : 86.51 % Cbeta Deviations : 0.09 % 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: 0.48 (0.18), residues: 2304 helix: 2.32 (0.27), residues: 378 sheet: 0.44 (0.20), residues: 681 loop : -0.34 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 444 TYR 0.014 0.001 TYR M 49 PHE 0.013 0.001 PHE S 53 TRP 0.013 0.001 TRP I 112 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (19974) covalent geometry : angle 0.75469 / 0.45 (27093) SS BOND : bond 0.00329 / 0.20 ( 36) SS BOND : angle 1.06435 / 0.74 ( 72) hydrogen bonds : bond 0.04101 / 2.77 ( 735) hydrogen bonds : angle 4.65163 / 3.25 ( 1944) link_ALPHA1-3 : bond 0.00459 / 0.23 ( 3) link_ALPHA1-3 : angle 1.36343 / 0.82 ( 9) link_BETA1-4 : bond 0.00418 / 0.24 ( 18) link_BETA1-4 : angle 1.45802 / 1.03 ( 54) link_NAG-ASN : bond 0.00302 / 0.16 ( 66) link_NAG-ASN : angle 1.89026 / 1.34 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5096.96 seconds wall clock time: 88 minutes 1.20 seconds (5281.20 seconds total)