Starting phenix.real_space_refine on Thu Mar 5 05:55:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x9s_22109/03_2026/6x9s_22109.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x9s_22109/03_2026/6x9s_22109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x9s_22109/03_2026/6x9s_22109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x9s_22109/03_2026/6x9s_22109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x9s_22109/03_2026/6x9s_22109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x9s_22109/03_2026/6x9s_22109.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19590 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "J" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "M" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "T" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "U" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "V" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "T" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.42, per 1000 atoms: 0.23 Number of scatterers: 19590 At special positions: 0 Unit cell: (122.57, 127.72, 150.38, 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=2.14 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=2.11 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.06 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.14 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=2.11 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 119 " - pdb=" SG CYS S 205 " distance=2.06 Simple disulfide: pdb=" SG CYS S 126 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS S 131 " - pdb=" SG CYS S 157 " distance=2.02 Simple disulfide: pdb=" SG CYS S 218 " - pdb=" SG CYS S 247 " distance=2.03 Simple disulfide: pdb=" SG CYS S 228 " - pdb=" SG CYS S 239 " distance=2.14 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=2.11 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: 1.77 Conformation dependent library (CDL) restraints added in 866.8 milliseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 45 sheets defined 21.4% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.195A 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: 4.015A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.172A 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: 3.763A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.437A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.542A 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 removed outlier: 3.602A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) 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: 4.195A 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: 4.015A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.172A 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: 3.763A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 removed outlier: 4.438A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.542A 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 removed outlier: 3.602A pdb=" N GLN J 658 " --> pdb=" O GLU J 654 " (cutoff:3.500A) 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: 4.195A 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: 4.015A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.171A 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: 3.764A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 523 through 528 removed outlier: 4.437A pdb=" N GLY T 527 " --> pdb=" O GLY T 524 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 removed outlier: 3.542A 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 removed outlier: 3.603A pdb=" N GLN T 658 " --> pdb=" O GLU T 654 " (cutoff:3.500A) 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: 3.776A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.540A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.657A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.179A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 271 through 274 removed outlier: 12.179A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.555A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=11, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.031A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=13, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.644A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.644A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=16, first strand: chain 'I' and resid 494 through 498 Processing sheet with id=17, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.776A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=19, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=20, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=21, first strand: chain 'I' and resid 201 through 203 removed outlier: 6.540A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'I' and resid 259 through 261 removed outlier: 3.657A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.871A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.179A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'I' and resid 271 through 274 removed outlier: 12.179A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 11.871A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.555A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'K' and resid 3 through 8 Processing sheet with id=26, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.032A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=28, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.643A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.643A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=31, first strand: chain 'S' and resid 494 through 498 Processing sheet with id=32, first strand: chain 'S' and resid 45 through 47 removed outlier: 3.776A pdb=" N ILE S 225 " --> pdb=" O VAL S 245 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL S 242 " --> pdb=" O LEU S 86 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'S' and resid 75 through 76 Processing sheet with id=34, first strand: chain 'S' and resid 91 through 94 Processing sheet with id=35, first strand: chain 'S' and resid 169 through 177 Processing sheet with id=36, first strand: chain 'S' and resid 201 through 203 removed outlier: 6.540A pdb=" N THR S 202 " --> pdb=" O TYR S 435 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'S' and resid 259 through 261 removed outlier: 3.658A pdb=" N GLY S 451 " --> pdb=" O LEU S 260 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLY S 441 " --> pdb=" O ASN S 300 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN S 300 " --> pdb=" O GLY S 441 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY S 451 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR S 290 " --> pdb=" O GLY S 451 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N ILE S 453 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N PHE S 288 " --> pdb=" O ILE S 453 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR S 455 " --> pdb=" O VAL S 286 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N VAL S 286 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP S 457 " --> pdb=" O ILE S 284 " (cutoff:3.500A) removed outlier: 12.178A pdb=" N ILE S 284 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE S 382 " --> pdb=" O LYS S 421 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'S' and resid 271 through 274 removed outlier: 12.178A pdb=" N ILE S 284 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP S 457 " --> pdb=" O ILE S 284 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N VAL S 286 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR S 455 " --> pdb=" O VAL S 286 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N PHE S 288 " --> pdb=" O ILE S 453 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N ILE S 453 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR S 290 " --> pdb=" O GLY S 451 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY S 451 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN S 300 " --> pdb=" O GLY S 441 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLY S 441 " --> pdb=" O ASN S 300 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'S' and resid 304 through 312 removed outlier: 6.555A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'U' and resid 3 through 8 Processing sheet with id=41, first strand: chain 'U' and resid 11 through 12 removed outlier: 6.031A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'U' and resid 11 through 12 Processing sheet with id=43, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.644A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP V 35 " --> pdb=" O MET V 47 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.644A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'V' and resid 19 through 24 789 hydrogen bonds defined for protein. 2025 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3525 1.31 - 1.44: 5410 1.44 - 1.57: 10801 1.57 - 1.69: 64 1.69 - 1.82: 174 Bond restraints: 19974 Sorted by residual: bond pdb=" C1 NAG B 703 " pdb=" O5 NAG B 703 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG T 703 " pdb=" O5 NAG T 703 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG J 703 " pdb=" O5 NAG J 703 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.88e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 23225 2.34 - 4.67: 3343 4.67 - 7.01: 456 7.01 - 9.35: 57 9.35 - 11.68: 12 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N PRO M 7 " pdb=" CA PRO M 7 " pdb=" C PRO M 7 " ideal model delta sigma weight residual 110.70 122.38 -11.68 1.22e+00 6.72e-01 9.17e+01 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 122.38 -11.68 1.22e+00 6.72e-01 9.16e+01 angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 122.38 -11.68 1.22e+00 6.72e-01 9.16e+01 angle pdb=" C GLU S 492 " pdb=" N PRO S 493 " pdb=" CA PRO S 493 " ideal model delta sigma weight residual 119.56 127.33 -7.77 1.01e+00 9.80e-01 5.92e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 127.30 -7.74 1.01e+00 9.80e-01 5.87e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 12609 21.89 - 43.79: 276 43.79 - 65.68: 108 65.68 - 87.57: 33 87.57 - 109.46: 12 Dihedral angle restraints: 13038 sinusoidal: 6291 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 93.00 163.30 -70.30 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS S 228 " pdb=" SG CYS S 228 " pdb=" SG CYS S 239 " pdb=" CB CYS S 239 " ideal model delta sinusoidal sigma weight residual 93.00 163.30 -70.30 1 1.00e+01 1.00e-02 6.36e+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 93.00 163.27 -70.27 1 1.00e+01 1.00e-02 6.36e+01 ... (remaining 13035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2249 0.093 - 0.185: 796 0.185 - 0.278: 204 0.278 - 0.370: 27 0.370 - 0.463: 3 Chirality restraints: 3279 Sorted by residual: 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 1.52e+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 1.52e+02 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.50e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.057 2.00e-02 2.50e+03 4.71e-02 2.77e+01 pdb=" C7 NAG B 702 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.076 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " 0.057 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" C7 NAG T 702 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " -0.076 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " -0.057 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" C7 NAG J 702 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " -0.042 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.012 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 6654 2.84 - 3.36: 16547 3.36 - 3.87: 32269 3.87 - 4.39: 37908 4.39 - 4.90: 63051 Nonbonded interactions: 156429 Sorted by model distance: nonbonded pdb=" N ASN I 355 " pdb=" OD1 ASN I 355 " model vdw 2.329 3.120 nonbonded pdb=" N ASN A 355 " pdb=" OD1 ASN A 355 " model vdw 2.329 3.120 nonbonded pdb=" N ASN S 355 " pdb=" OD1 ASN S 355 " model vdw 2.330 3.120 nonbonded pdb=" N LEU K 100A" pdb=" N GLN K 100B" model vdw 2.331 2.560 nonbonded pdb=" N LEU H 100A" pdb=" N GLN H 100B" model vdw 2.332 2.560 ... (remaining 156424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.050 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 0.145 20097 Z= 1.285 Angle : 1.723 11.683 27426 Z= 1.112 Chirality : 0.099 0.463 3279 Planarity : 0.009 0.061 3339 Dihedral : 11.649 109.464 8598 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.65 % Favored : 96.09 % 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: 0.54 (0.17), residues: 2304 helix: -0.30 (0.25), residues: 387 sheet: 0.81 (0.20), residues: 666 loop : 0.48 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 53 TYR 0.054 0.008 TYR L 36 PHE 0.036 0.006 PHE I 383 TRP 0.065 0.011 TRP S 479 HIS 0.006 0.002 HIS H 82A Details of bonding type rmsd covalent geometry : bond 0.02479 (19974) covalent geometry : angle 1.69511 (27093) SS BOND : bond 0.04003 ( 36) SS BOND : angle 2.75150 ( 72) hydrogen bonds : bond 0.16341 ( 744) hydrogen bonds : angle 7.00542 ( 2025) link_ALPHA1-3 : bond 0.03405 ( 3) link_ALPHA1-3 : angle 2.80175 ( 9) link_BETA1-4 : bond 0.02706 ( 18) link_BETA1-4 : angle 3.80411 ( 54) link_NAG-ASN : bond 0.03269 ( 66) link_NAG-ASN : angle 3.29133 ( 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 453 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 444 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7835 (mtp) cc_final: 0.7634 (mtp) REVERT: H 82 MET cc_start: 0.8617 (mtt) cc_final: 0.8401 (mtt) REVERT: L 94 ARG cc_start: 0.5628 (mmt180) cc_final: 0.4648 (mtm-85) REVERT: I 277 ILE cc_start: 0.8783 (tp) cc_final: 0.8521 (tp) REVERT: M 94 ARG cc_start: 0.5849 (mmt180) cc_final: 0.4832 (mtm-85) REVERT: V 94 ARG cc_start: 0.5814 (mmt180) cc_final: 0.4800 (mtm-85) outliers start: 9 outliers final: 4 residues processed: 447 average time/residue: 0.1658 time to fit residues: 106.5711 Evaluate side-chains 265 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 261 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain T residue 618 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 HIS I 103 GLN I 246 GLN I 302 ASN ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN M 39 HIS ** S 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 114 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.142029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109573 restraints weight = 24871.817| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.43 r_work: 0.2964 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20097 Z= 0.159 Angle : 0.706 8.136 27426 Z= 0.360 Chirality : 0.047 0.214 3279 Planarity : 0.004 0.041 3339 Dihedral : 7.992 66.177 4343 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.26 % Favored : 96.48 % Rotamer: Outliers : 1.76 % Allowed : 4.79 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.17), residues: 2304 helix: 1.22 (0.27), residues: 402 sheet: 0.47 (0.19), residues: 675 loop : 0.17 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 444 TYR 0.013 0.001 TYR M 96 PHE 0.020 0.002 PHE S 383 TRP 0.017 0.001 TRP S 479 HIS 0.006 0.001 HIS U 82A Details of bonding type rmsd covalent geometry : bond 0.00348 (19974) covalent geometry : angle 0.66283 (27093) SS BOND : bond 0.00365 ( 36) SS BOND : angle 0.89541 ( 72) hydrogen bonds : bond 0.05261 ( 744) hydrogen bonds : angle 5.57972 ( 2025) link_ALPHA1-3 : bond 0.00663 ( 3) link_ALPHA1-3 : angle 2.30609 ( 9) link_BETA1-4 : bond 0.00541 ( 18) link_BETA1-4 : angle 2.12178 ( 54) link_NAG-ASN : bond 0.00312 ( 66) link_NAG-ASN : angle 2.65951 ( 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 347 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 311 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: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.7952 (mt0) cc_final: 0.7481 (tt0) REVERT: A 232 LYS cc_start: 0.8259 (mttt) cc_final: 0.7894 (ptpt) REVERT: H 23 ARG cc_start: 0.8387 (tpt170) cc_final: 0.8184 (ttm-80) REVERT: H 75 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8274 (mttp) REVERT: L 54 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.7950 (mtp-110) REVERT: L 94 ARG cc_start: 0.5885 (mmt180) cc_final: 0.3700 (mtm-85) REVERT: I 375 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.9014 (p) REVERT: I 434 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.9054 (ttp) REVERT: K 46 GLU cc_start: 0.8831 (tt0) cc_final: 0.8628 (tt0) REVERT: M 54 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8228 (mtp-110) REVERT: M 85 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8097 (t0) REVERT: M 94 ARG cc_start: 0.5805 (mmt180) cc_final: 0.3573 (mtm-85) REVERT: S 107 ASP cc_start: 0.8718 (m-30) cc_final: 0.8499 (m-30) REVERT: S 434 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.9105 (ttp) REVERT: U 18 LEU cc_start: 0.8361 (tp) cc_final: 0.8077 (tp) REVERT: V 54 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8184 (mtp-110) REVERT: V 94 ARG cc_start: 0.6170 (mmt180) cc_final: 0.3869 (mtm-85) outliers start: 36 outliers final: 24 residues processed: 332 average time/residue: 0.1589 time to fit residues: 77.3706 Evaluate side-chains 265 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 186 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 374 HIS ** H 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS ** K 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 374 HIS S 377 ASN V 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.135766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.101761 restraints weight = 25014.254| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.63 r_work: 0.2823 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20097 Z= 0.229 Angle : 0.685 8.405 27426 Z= 0.347 Chirality : 0.047 0.230 3279 Planarity : 0.004 0.053 3339 Dihedral : 7.076 59.817 4341 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.86 % Favored : 95.88 % Rotamer: Outliers : 2.49 % Allowed : 6.65 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2304 helix: 1.19 (0.27), residues: 399 sheet: 0.40 (0.20), residues: 642 loop : -0.04 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 71 TYR 0.016 0.002 TYR V 49 PHE 0.021 0.002 PHE I 383 TRP 0.012 0.002 TRP H 103 HIS 0.005 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00547 (19974) covalent geometry : angle 0.64851 (27093) SS BOND : bond 0.00424 ( 36) SS BOND : angle 1.04740 ( 72) hydrogen bonds : bond 0.05537 ( 744) hydrogen bonds : angle 5.19789 ( 2025) link_ALPHA1-3 : bond 0.00980 ( 3) link_ALPHA1-3 : angle 1.05593 ( 9) link_BETA1-4 : bond 0.00540 ( 18) link_BETA1-4 : angle 1.64071 ( 54) link_NAG-ASN : bond 0.00336 ( 66) link_NAG-ASN : angle 2.51916 ( 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 302 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 251 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8033 (mt0) cc_final: 0.7610 (tt0) REVERT: A 136 ASN cc_start: 0.7781 (m-40) cc_final: 0.7538 (m-40) REVERT: A 232 LYS cc_start: 0.8374 (mttt) cc_final: 0.7998 (ptpt) REVERT: B 634 GLU cc_start: 0.8355 (tt0) cc_final: 0.8056 (tt0) REVERT: H 23 ARG cc_start: 0.8445 (tpt170) cc_final: 0.8235 (ttm-80) REVERT: L 49 TYR cc_start: 0.9338 (p90) cc_final: 0.8856 (p90) REVERT: L 54 ARG cc_start: 0.8644 (mtm-85) cc_final: 0.8043 (mtp-110) REVERT: L 94 ARG cc_start: 0.6185 (mmt180) cc_final: 0.3632 (mtm-85) REVERT: J 636 SER cc_start: 0.9047 (t) cc_final: 0.8793 (p) REVERT: K 46 GLU cc_start: 0.8947 (tt0) cc_final: 0.8732 (tt0) REVERT: M 54 ARG cc_start: 0.8698 (mtm-85) cc_final: 0.8302 (mtp-110) REVERT: M 94 ARG cc_start: 0.6085 (mmt180) cc_final: 0.3558 (mtm-85) REVERT: S 434 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.9242 (ttp) REVERT: U 30 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.8995 (m) REVERT: V 54 ARG cc_start: 0.8644 (mtm-85) cc_final: 0.8231 (mtp-110) REVERT: V 86 TYR cc_start: 0.8397 (m-80) cc_final: 0.8162 (m-10) REVERT: V 94 ARG cc_start: 0.6238 (mmt180) cc_final: 0.3767 (mtm-85) outliers start: 51 outliers final: 40 residues processed: 283 average time/residue: 0.1558 time to fit residues: 65.0103 Evaluate side-chains 275 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 599 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 68 THR 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 85 ASP Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 159 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.098289 restraints weight = 24942.731| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.61 r_work: 0.2787 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20097 Z= 0.222 Angle : 0.662 8.184 27426 Z= 0.334 Chirality : 0.047 0.230 3279 Planarity : 0.005 0.057 3339 Dihedral : 6.205 49.923 4335 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.60 % Favored : 95.27 % Rotamer: Outliers : 2.64 % Allowed : 7.28 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2304 helix: 1.37 (0.27), residues: 381 sheet: 0.29 (0.20), residues: 669 loop : -0.31 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 444 TYR 0.018 0.002 TYR V 49 PHE 0.019 0.002 PHE S 383 TRP 0.011 0.002 TRP A 479 HIS 0.005 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00536 (19974) covalent geometry : angle 0.62885 (27093) SS BOND : bond 0.00426 ( 36) SS BOND : angle 0.95331 ( 72) hydrogen bonds : bond 0.05311 ( 744) hydrogen bonds : angle 5.03383 ( 2025) link_ALPHA1-3 : bond 0.00864 ( 3) link_ALPHA1-3 : angle 0.91518 ( 9) link_BETA1-4 : bond 0.00518 ( 18) link_BETA1-4 : angle 1.54375 ( 54) link_NAG-ASN : bond 0.00313 ( 66) link_NAG-ASN : angle 2.36492 ( 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 308 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 254 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8049 (mt0) cc_final: 0.7700 (tt0) REVERT: A 213 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8223 (mm) REVERT: B 636 SER cc_start: 0.9047 (t) cc_final: 0.8780 (p) REVERT: H 82 MET cc_start: 0.8921 (mtt) cc_final: 0.8698 (mtm) REVERT: L 17 GLN cc_start: 0.6817 (mt0) cc_final: 0.6584 (tp40) REVERT: L 49 TYR cc_start: 0.9383 (p90) cc_final: 0.8927 (p90) REVERT: L 94 ARG cc_start: 0.6216 (mmt180) cc_final: 0.3662 (mtm-85) REVERT: I 232 LYS cc_start: 0.8252 (mttp) cc_final: 0.8050 (ptpp) REVERT: M 53 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8826 (mm-40) REVERT: M 54 ARG cc_start: 0.8693 (mtm-85) cc_final: 0.8316 (mtp-110) REVERT: M 85 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8049 (t0) REVERT: M 94 ARG cc_start: 0.6198 (mmt180) cc_final: 0.3523 (mtm-85) REVERT: S 434 MET cc_start: 0.9444 (OUTLIER) cc_final: 0.9226 (ttp) REVERT: U 30 SER cc_start: 0.9235 (OUTLIER) cc_final: 0.9010 (m) REVERT: V 54 ARG cc_start: 0.8584 (mtm-85) cc_final: 0.8171 (mtp-110) REVERT: V 94 ARG cc_start: 0.6412 (mmt180) cc_final: 0.3752 (mtm-85) outliers start: 54 outliers final: 38 residues processed: 291 average time/residue: 0.1663 time to fit residues: 70.7952 Evaluate side-chains 284 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 102 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: 6.9990 chunk 184 optimal weight: 7.9990 chunk 180 optimal weight: 0.2980 chunk 228 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN I 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.095430 restraints weight = 24976.504| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.66 r_work: 0.2873 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 20097 Z= 0.240 Angle : 0.678 8.992 27426 Z= 0.338 Chirality : 0.047 0.296 3279 Planarity : 0.005 0.058 3339 Dihedral : 5.946 45.897 4335 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 3.18 % Allowed : 7.28 % Favored : 89.54 % 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: -0.02 (0.17), residues: 2304 helix: 1.27 (0.27), residues: 384 sheet: 0.18 (0.20), residues: 648 loop : -0.47 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 444 TYR 0.018 0.002 TYR V 49 PHE 0.019 0.002 PHE I 383 TRP 0.012 0.002 TRP I 427 HIS 0.005 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00584 (19974) covalent geometry : angle 0.64254 (27093) SS BOND : bond 0.00443 ( 36) SS BOND : angle 1.01078 ( 72) hydrogen bonds : bond 0.05434 ( 744) hydrogen bonds : angle 4.98292 ( 2025) link_ALPHA1-3 : bond 0.00975 ( 3) link_ALPHA1-3 : angle 0.95788 ( 9) link_BETA1-4 : bond 0.00449 ( 18) link_BETA1-4 : angle 1.49221 ( 54) link_NAG-ASN : bond 0.00361 ( 66) link_NAG-ASN : angle 2.47694 ( 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 306 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 241 time to evaluate : 0.842 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 114 GLN cc_start: 0.8005 (mt0) cc_final: 0.7673 (tt0) REVERT: A 151 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7915 (ttm170) REVERT: A 355 ASN cc_start: 0.7356 (p0) cc_final: 0.6935 (t0) REVERT: B 636 SER cc_start: 0.9053 (t) cc_final: 0.8831 (p) REVERT: L 49 TYR cc_start: 0.9358 (p90) cc_final: 0.8903 (p90) REVERT: L 94 ARG cc_start: 0.6158 (mmt180) cc_final: 0.3659 (mtm-85) REVERT: I 232 LYS cc_start: 0.8265 (mttp) cc_final: 0.7924 (ptpt) REVERT: I 381 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7972 (tp30) REVERT: K 82 LEU cc_start: 0.7775 (mt) cc_final: 0.7482 (mt) REVERT: M 42 LYS cc_start: 0.8508 (mmmm) cc_final: 0.7458 (mtmm) REVERT: M 53 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8772 (mm-40) REVERT: M 54 ARG cc_start: 0.8670 (mtm-85) cc_final: 0.8297 (mtp-110) REVERT: M 94 ARG cc_start: 0.6118 (mmt180) cc_final: 0.3439 (mtm-85) REVERT: S 434 MET cc_start: 0.9452 (OUTLIER) cc_final: 0.9227 (ttp) REVERT: U 30 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8972 (m) REVERT: V 42 LYS cc_start: 0.8647 (mmmm) cc_final: 0.8396 (mmmm) REVERT: V 47 MET cc_start: 0.9083 (mmm) cc_final: 0.8699 (mmm) REVERT: V 54 ARG cc_start: 0.8560 (mtm-85) cc_final: 0.8146 (mtp-110) REVERT: V 94 ARG cc_start: 0.6320 (mmt180) cc_final: 0.3774 (mtm-85) outliers start: 65 outliers final: 49 residues processed: 285 average time/residue: 0.1620 time to fit residues: 67.5274 Evaluate side-chains 287 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 455 THR Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 534 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 85 ASP 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: 3.9990 chunk 178 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.105579 restraints weight = 24505.711| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.42 r_work: 0.2921 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20097 Z= 0.109 Angle : 0.560 10.305 27426 Z= 0.280 Chirality : 0.043 0.226 3279 Planarity : 0.004 0.057 3339 Dihedral : 5.307 41.098 4335 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.69 % Favored : 96.18 % Rotamer: Outliers : 1.42 % Allowed : 9.63 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2304 helix: 2.13 (0.28), residues: 363 sheet: 0.20 (0.19), residues: 699 loop : -0.39 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 444 TYR 0.015 0.001 TYR V 49 PHE 0.014 0.001 PHE I 383 TRP 0.010 0.001 TRP A 479 HIS 0.004 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00238 (19974) covalent geometry : angle 0.52799 (27093) SS BOND : bond 0.00256 ( 36) SS BOND : angle 0.58944 ( 72) hydrogen bonds : bond 0.04105 ( 744) hydrogen bonds : angle 4.72534 ( 2025) link_ALPHA1-3 : bond 0.00898 ( 3) link_ALPHA1-3 : angle 1.06423 ( 9) link_BETA1-4 : bond 0.00402 ( 18) link_BETA1-4 : angle 1.41831 ( 54) link_NAG-ASN : bond 0.00197 ( 66) link_NAG-ASN : angle 2.13782 ( 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 300 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 271 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8169 (mttm) REVERT: A 114 GLN cc_start: 0.7850 (mt0) cc_final: 0.7649 (tt0) REVERT: A 213 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8212 (mm) REVERT: L 49 TYR cc_start: 0.9265 (p90) cc_final: 0.8818 (p90) REVERT: L 94 ARG cc_start: 0.5851 (mmt180) cc_final: 0.3532 (mtm-85) REVERT: I 114 GLN cc_start: 0.7928 (mt0) cc_final: 0.7454 (tt0) REVERT: I 213 ILE cc_start: 0.8230 (tt) cc_final: 0.7955 (mm) REVERT: K 46 GLU cc_start: 0.8923 (tt0) cc_final: 0.8688 (tt0) REVERT: M 42 LYS cc_start: 0.8484 (mmmm) cc_final: 0.7310 (mtmm) REVERT: M 53 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8773 (mm-40) REVERT: M 54 ARG cc_start: 0.8624 (mtm-85) cc_final: 0.7984 (mtp-110) REVERT: M 85 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7977 (t0) REVERT: M 94 ARG cc_start: 0.5929 (mmt180) cc_final: 0.3470 (mtm-85) REVERT: U 30 SER cc_start: 0.9128 (OUTLIER) cc_final: 0.8904 (m) REVERT: U 43 LYS cc_start: 0.7567 (mppt) cc_final: 0.7183 (mmmm) REVERT: U 100 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9129 (mp) REVERT: V 42 LYS cc_start: 0.8582 (mmmm) cc_final: 0.8353 (mmmm) REVERT: V 47 MET cc_start: 0.9050 (mmm) cc_final: 0.8695 (mmm) REVERT: V 54 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.7898 (mtp-110) REVERT: V 85 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8240 (t0) REVERT: V 94 ARG cc_start: 0.6196 (mmt180) cc_final: 0.3777 (mtm-85) outliers start: 29 outliers final: 14 residues processed: 293 average time/residue: 0.1758 time to fit residues: 74.1185 Evaluate side-chains 258 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 85 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 65 optimal weight: 0.0370 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 20 optimal weight: 0.0870 chunk 225 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.100632 restraints weight = 25113.588| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.61 r_work: 0.2828 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20097 Z= 0.118 Angle : 0.564 9.457 27426 Z= 0.281 Chirality : 0.044 0.317 3279 Planarity : 0.004 0.058 3339 Dihedral : 5.124 36.580 4335 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 1.76 % Allowed : 9.53 % Favored : 88.71 % 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: 0.31 (0.18), residues: 2304 helix: 2.01 (0.27), residues: 381 sheet: 0.21 (0.19), residues: 732 loop : -0.34 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 178 TYR 0.016 0.001 TYR V 49 PHE 0.014 0.001 PHE S 383 TRP 0.009 0.001 TRP A 479 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00269 (19974) covalent geometry : angle 0.52760 (27093) SS BOND : bond 0.00336 ( 36) SS BOND : angle 0.70726 ( 72) hydrogen bonds : bond 0.04121 ( 744) hydrogen bonds : angle 4.63038 ( 2025) link_ALPHA1-3 : bond 0.00926 ( 3) link_ALPHA1-3 : angle 1.15731 ( 9) link_BETA1-4 : bond 0.00418 ( 18) link_BETA1-4 : angle 1.36000 ( 54) link_NAG-ASN : bond 0.00210 ( 66) link_NAG-ASN : angle 2.26932 ( 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 294 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8122 (mttm) REVERT: A 151 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7561 (ttm170) REVERT: A 213 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8259 (mm) REVERT: B 635 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8355 (tt) REVERT: H 100 TYR cc_start: 0.9008 (p90) cc_final: 0.8592 (p90) REVERT: L 49 TYR cc_start: 0.9249 (p90) cc_final: 0.8764 (p90) REVERT: L 94 ARG cc_start: 0.5652 (mmt180) cc_final: 0.3599 (mtm-85) REVERT: I 114 GLN cc_start: 0.7893 (mt0) cc_final: 0.7475 (tt0) REVERT: I 381 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7817 (tp30) REVERT: I 434 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.9036 (ttp) REVERT: K 46 GLU cc_start: 0.8834 (tt0) cc_final: 0.8593 (tt0) REVERT: M 42 LYS cc_start: 0.8412 (mmmm) cc_final: 0.7326 (mtmm) REVERT: M 53 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8766 (mm-40) REVERT: M 54 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8057 (mtp-110) REVERT: M 94 ARG cc_start: 0.5666 (mmt180) cc_final: 0.3543 (mtm-85) REVERT: S 161 MET cc_start: 0.9146 (tpt) cc_final: 0.8808 (tpt) REVERT: U 30 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8878 (m) REVERT: U 43 LYS cc_start: 0.7496 (mppt) cc_final: 0.7109 (mmmm) REVERT: U 100 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9155 (mp) REVERT: V 47 MET cc_start: 0.8989 (mmm) cc_final: 0.8626 (mmm) REVERT: V 54 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.7951 (mtp-110) REVERT: V 85 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8283 (t0) REVERT: V 94 ARG cc_start: 0.5932 (mmt180) cc_final: 0.3783 (mtm-85) outliers start: 36 outliers final: 21 residues processed: 285 average time/residue: 0.1679 time to fit residues: 69.6262 Evaluate side-chains 273 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 599 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 85 ASP 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: 4.9990 chunk 173 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.098420 restraints weight = 25133.381| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.72 r_work: 0.2809 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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 0.035 20097 Z= 0.147 Angle : 0.579 8.076 27426 Z= 0.290 Chirality : 0.044 0.240 3279 Planarity : 0.004 0.057 3339 Dihedral : 5.103 33.801 4335 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 2.20 % Allowed : 9.29 % Favored : 88.51 % 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: 0.32 (0.18), residues: 2304 helix: 1.99 (0.27), residues: 381 sheet: 0.27 (0.19), residues: 714 loop : -0.35 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 444 TYR 0.015 0.001 TYR V 49 PHE 0.015 0.002 PHE I 383 TRP 0.009 0.001 TRP A 479 HIS 0.004 0.001 HIS H 82A Details of bonding type rmsd covalent geometry : bond 0.00348 (19974) covalent geometry : angle 0.54639 (27093) SS BOND : bond 0.00302 ( 36) SS BOND : angle 0.79999 ( 72) hydrogen bonds : bond 0.04423 ( 744) hydrogen bonds : angle 4.65036 ( 2025) link_ALPHA1-3 : bond 0.00837 ( 3) link_ALPHA1-3 : angle 1.25182 ( 9) link_BETA1-4 : bond 0.00397 ( 18) link_BETA1-4 : angle 1.36591 ( 54) link_NAG-ASN : bond 0.00223 ( 66) link_NAG-ASN : angle 2.19686 ( 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 297 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8190 (mttm) REVERT: A 213 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8248 (mm) REVERT: B 635 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8339 (tt) REVERT: L 17 GLN cc_start: 0.6757 (mt0) cc_final: 0.6549 (tp-100) REVERT: L 49 TYR cc_start: 0.9307 (p90) cc_final: 0.8801 (p90) REVERT: L 94 ARG cc_start: 0.6153 (mmt180) cc_final: 0.3719 (mtm-85) REVERT: I 381 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7946 (tp30) REVERT: I 434 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.9163 (ttp) REVERT: K 46 GLU cc_start: 0.8972 (tt0) cc_final: 0.8745 (tt0) REVERT: K 82 LEU cc_start: 0.7979 (mt) cc_final: 0.7733 (mt) REVERT: M 42 LYS cc_start: 0.8455 (mmmm) cc_final: 0.7445 (mtmm) REVERT: M 53 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8804 (mm-40) REVERT: M 54 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8071 (mtp-110) REVERT: M 94 ARG cc_start: 0.5994 (mmt180) cc_final: 0.3340 (mtm-85) REVERT: S 161 MET cc_start: 0.9269 (tpt) cc_final: 0.8959 (tpt) REVERT: T 626 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8603 (mtp) REVERT: U 30 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8907 (m) REVERT: U 43 LYS cc_start: 0.7564 (mppt) cc_final: 0.7095 (mmmm) REVERT: U 100 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9155 (mp) REVERT: V 54 ARG cc_start: 0.8517 (mtm-85) cc_final: 0.7943 (mtp-110) REVERT: V 85 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8258 (t0) REVERT: V 86 TYR cc_start: 0.8356 (m-80) cc_final: 0.8050 (m-10) REVERT: V 94 ARG cc_start: 0.6402 (mmt180) cc_final: 0.3714 (mtm-85) outliers start: 45 outliers final: 34 residues processed: 282 average time/residue: 0.1695 time to fit residues: 69.6725 Evaluate side-chains 283 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 599 SER Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 27 ASP Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 85 ASP 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: 3.9990 chunk 32 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.129613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.094687 restraints weight = 25072.037| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.71 r_work: 0.2771 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20097 Z= 0.258 Angle : 0.688 14.226 27426 Z= 0.342 Chirality : 0.048 0.390 3279 Planarity : 0.005 0.056 3339 Dihedral : 5.606 38.261 4335 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 2.44 % Allowed : 9.24 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2304 helix: 1.24 (0.27), residues: 399 sheet: 0.06 (0.19), residues: 684 loop : -0.44 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 444 TYR 0.015 0.002 TYR V 49 PHE 0.018 0.002 PHE S 383 TRP 0.012 0.002 TRP T 631 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00631 (19974) covalent geometry : angle 0.64788 (27093) SS BOND : bond 0.00473 ( 36) SS BOND : angle 1.11701 ( 72) hydrogen bonds : bond 0.05488 ( 744) hydrogen bonds : angle 4.88690 ( 2025) link_ALPHA1-3 : bond 0.00771 ( 3) link_ALPHA1-3 : angle 1.46504 ( 9) link_BETA1-4 : bond 0.00389 ( 18) link_BETA1-4 : angle 1.45650 ( 54) link_NAG-ASN : bond 0.00354 ( 66) link_NAG-ASN : angle 2.63896 ( 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 285 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 235 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8673 (mmtt) cc_final: 0.8287 (mttm) REVERT: A 213 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8392 (mm) REVERT: L 49 TYR cc_start: 0.9425 (p90) cc_final: 0.8937 (p90) REVERT: L 94 ARG cc_start: 0.6499 (mmt180) cc_final: 0.3895 (mtm-85) REVERT: I 434 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.9170 (ttp) REVERT: M 42 LYS cc_start: 0.8457 (mmmm) cc_final: 0.7353 (mtmm) REVERT: M 53 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8856 (mm-40) REVERT: M 54 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8073 (mtp-110) REVERT: M 94 ARG cc_start: 0.6287 (mmt180) cc_final: 0.3566 (mtm-85) REVERT: S 161 MET cc_start: 0.9267 (tpt) cc_final: 0.8927 (tpt) REVERT: U 30 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8915 (m) REVERT: U 34 MET cc_start: 0.9132 (mtm) cc_final: 0.8878 (mtp) REVERT: U 43 LYS cc_start: 0.7572 (mppt) cc_final: 0.7083 (mmmm) REVERT: U 82 LEU cc_start: 0.8272 (mt) cc_final: 0.7979 (mt) REVERT: U 100 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9152 (mp) REVERT: V 54 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.8187 (mtp-110) REVERT: V 85 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8311 (t0) REVERT: V 86 TYR cc_start: 0.8495 (m-80) cc_final: 0.8220 (m-10) REVERT: V 94 ARG cc_start: 0.6444 (mmt180) cc_final: 0.3830 (mtm-85) outliers start: 50 outliers final: 39 residues processed: 269 average time/residue: 0.1735 time to fit residues: 67.4595 Evaluate side-chains 275 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 27 ASP Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 226 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 208 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.099886 restraints weight = 25207.328| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.69 r_work: 0.2958 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20097 Z= 0.114 Angle : 0.573 10.519 27426 Z= 0.286 Chirality : 0.043 0.318 3279 Planarity : 0.004 0.056 3339 Dihedral : 5.167 34.782 4335 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.88 % Rotamer: Outliers : 1.66 % Allowed : 10.31 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 2304 helix: 1.96 (0.27), residues: 381 sheet: 0.30 (0.19), residues: 681 loop : -0.46 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 444 TYR 0.016 0.001 TYR V 49 PHE 0.013 0.001 PHE I 383 TRP 0.009 0.001 TRP I 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00252 (19974) covalent geometry : angle 0.53782 (27093) SS BOND : bond 0.00283 ( 36) SS BOND : angle 0.62560 ( 72) hydrogen bonds : bond 0.04151 ( 744) hydrogen bonds : angle 4.67946 ( 2025) link_ALPHA1-3 : bond 0.00702 ( 3) link_ALPHA1-3 : angle 1.35461 ( 9) link_BETA1-4 : bond 0.00352 ( 18) link_BETA1-4 : angle 1.41976 ( 54) link_NAG-ASN : bond 0.00210 ( 66) link_NAG-ASN : angle 2.26880 ( 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 297 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8156 (mttm) REVERT: A 213 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8223 (mm) REVERT: A 271 MET cc_start: 0.8759 (mmt) cc_final: 0.8514 (mmm) REVERT: H 100 TYR cc_start: 0.8975 (p90) cc_final: 0.8501 (p90) REVERT: L 17 GLN cc_start: 0.7374 (mp10) cc_final: 0.7105 (pm20) REVERT: L 49 TYR cc_start: 0.9251 (p90) cc_final: 0.8691 (p90) REVERT: L 94 ARG cc_start: 0.5750 (mmt180) cc_final: 0.3780 (mtm-85) REVERT: I 114 GLN cc_start: 0.7848 (mt0) cc_final: 0.7437 (tt0) REVERT: K 46 GLU cc_start: 0.8854 (tt0) cc_final: 0.8634 (tt0) REVERT: M 42 LYS cc_start: 0.8448 (mmmm) cc_final: 0.7388 (mtmm) REVERT: M 53 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8837 (mm-40) REVERT: M 54 ARG cc_start: 0.8642 (mtm-85) cc_final: 0.8061 (mtp-110) REVERT: M 94 ARG cc_start: 0.5654 (mmt180) cc_final: 0.3529 (mtm-85) REVERT: S 95 MET cc_start: 0.9226 (ptm) cc_final: 0.9014 (ttp) REVERT: S 161 MET cc_start: 0.9096 (tpt) cc_final: 0.8751 (tpt) REVERT: T 626 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8344 (mtp) REVERT: U 30 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8819 (m) REVERT: U 34 MET cc_start: 0.8838 (mtm) cc_final: 0.8584 (mtp) REVERT: U 43 LYS cc_start: 0.7537 (mppt) cc_final: 0.7105 (mmmm) REVERT: U 82 LEU cc_start: 0.8242 (mt) cc_final: 0.7992 (mt) REVERT: V 47 MET cc_start: 0.8991 (mmm) cc_final: 0.8642 (mmm) REVERT: V 54 ARG cc_start: 0.8480 (mtm-85) cc_final: 0.7962 (mtp-110) REVERT: V 85 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8232 (t0) REVERT: V 86 TYR cc_start: 0.8330 (m-80) cc_final: 0.8056 (m-10) REVERT: V 94 ARG cc_start: 0.5977 (mmt180) cc_final: 0.3804 (mtm-85) outliers start: 34 outliers final: 27 residues processed: 284 average time/residue: 0.1622 time to fit residues: 67.0280 Evaluate side-chains 285 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 254 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 485 LYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 626 MET Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 27 ASP Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 27 optimal weight: 0.0470 chunk 223 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 175 optimal weight: 0.0000 chunk 191 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.135790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.101137 restraints weight = 25134.727| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.74 r_work: 0.2869 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20097 Z= 0.100 Angle : 0.538 8.786 27426 Z= 0.269 Chirality : 0.043 0.250 3279 Planarity : 0.004 0.056 3339 Dihedral : 4.782 32.613 4335 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 1.52 % Allowed : 10.85 % Favored : 87.63 % 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: 1.95 (0.27), residues: 399 sheet: 0.63 (0.19), residues: 753 loop : -0.53 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 444 TYR 0.016 0.001 TYR V 49 PHE 0.013 0.001 PHE S 383 TRP 0.010 0.001 TRP K 36 HIS 0.002 0.000 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00221 (19974) covalent geometry : angle 0.50761 (27093) SS BOND : bond 0.00197 ( 36) SS BOND : angle 0.57093 ( 72) hydrogen bonds : bond 0.03733 ( 744) hydrogen bonds : angle 4.51346 ( 2025) link_ALPHA1-3 : bond 0.00708 ( 3) link_ALPHA1-3 : angle 1.35284 ( 9) link_BETA1-4 : bond 0.00384 ( 18) link_BETA1-4 : angle 1.37113 ( 54) link_NAG-ASN : bond 0.00199 ( 66) link_NAG-ASN : angle 2.02529 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4924.14 seconds wall clock time: 85 minutes 10.30 seconds (5110.30 seconds total)