Starting phenix.real_space_refine on Fri Aug 7 08:35:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yho_72969/08_2026/9yho_72969.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yho_72969/08_2026/9yho_72969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yho_72969/08_2026/9yho_72969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yho_72969/08_2026/9yho_72969.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yho_72969/08_2026/9yho_72969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yho_72969/08_2026/9yho_72969.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 117 5.16 5 C 12537 2.51 5 N 3300 2.21 5 O 4008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19962 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 970 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "B" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 970 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 970 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "E" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3395 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3395 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3395 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1048 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "J" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1048 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "K" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 845 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "L" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 845 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "M" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1048 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "N" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 845 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "D" 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: "I" 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "P" 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: "Q" 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: "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: "S" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "T" 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: "U" 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: "V" 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: "W" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" 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: "F" 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: "G" 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 Time building chain proxies: 4.62, per 1000 atoms: 0.23 Number of scatterers: 19962 At special positions: 0 Unit cell: (163.904, 160.576, 133.12, 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 117 16.00 O 4008 8.00 N 3300 7.00 C 12537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS E 501 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 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 ALPHA1-2 " MAN O 5 " - " MAN O 6 " " MAN S 5 " - " MAN S 6 " " MAN W 5 " - " MAN W 6 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA O 3 " - " MAN O 8 " " MAN O 4 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 8 " " MAN S 4 " - " MAN S 5 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 8 " " MAN W 4 " - " MAN W 5 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 7 " " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 7 " " BMA W 3 " - " MAN W 4 " " MAN W 4 " - " MAN W 7 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG B 701 " - " ASN B 611 " " NAG C 701 " - " ASN C 611 " " NAG D 1 " - " ASN E 262 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 156 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 230 " " NAG E 607 " - " ASN E 234 " " NAG E 608 " - " ASN E 241 " " NAG E 609 " - " ASN E 276 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 344 " " NAG E 612 " - " ASN E 392 " " NAG E 613 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 160 " " NAG F 605 " - " ASN F 197 " " NAG F 606 " - " ASN F 230 " " NAG F 607 " - " ASN F 234 " " NAG F 608 " - " ASN F 241 " " NAG F 609 " - " ASN F 276 " " NAG F 610 " - " ASN F 301 " " NAG F 611 " - " ASN F 344 " " NAG F 612 " - " ASN F 392 " " NAG F 613 " - " ASN F 448 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 160 " " NAG G 605 " - " ASN G 197 " " NAG G 606 " - " ASN G 230 " " NAG G 607 " - " ASN G 234 " " NAG G 608 " - " ASN G 241 " " NAG G 609 " - " ASN G 276 " " NAG G 610 " - " ASN G 301 " " NAG G 611 " - " ASN G 344 " " NAG G 612 " - " ASN G 392 " " NAG G 613 " - " ASN G 448 " " NAG I 1 " - " ASN E 295 " " NAG O 1 " - " ASN E 332 " " NAG P 1 " - " ASN E 386 " " NAG Q 1 " - " ASN F 262 " " NAG R 1 " - " ASN F 295 " " NAG S 1 " - " ASN F 332 " " NAG T 1 " - " ASN F 386 " " NAG U 1 " - " ASN G 262 " " NAG V 1 " - " ASN G 295 " " NAG W 1 " - " ASN G 332 " " NAG X 1 " - " ASN G 386 " Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 745.2 milliseconds 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4410 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 42 sheets defined 20.9% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 573 through 596 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 653 through 663 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 573 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 649 Processing helix chain 'B' and resid 653 through 663 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 649 Processing helix chain 'C' and resid 653 through 663 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.687A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.545A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 474 through 483 removed outlier: 4.193A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.686A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 353 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.544A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 474 through 483 removed outlier: 4.193A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 117 Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.687A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.544A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 474 through 483 removed outlier: 4.193A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.792A pdb=" N GLN H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.052A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 100D Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.792A pdb=" N GLN J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 removed outlier: 4.051A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 100D Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.948A pdb=" N VAL K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.948A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.792A pdb=" N GLN M 64 " --> pdb=" O PRO M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 83 through 87 removed outlier: 4.052A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 100D Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.948A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.600A pdb=" N THR A 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL E 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.609A pdb=" N THR B 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL F 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 603 through 609 removed outlier: 3.609A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.848A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.680A pdb=" N PHE E 53 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS E 218 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AA7, first strand: chain 'E' and resid 169 through 174 Processing sheet with id=AA8, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.438A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 12.207A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.210A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.207A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 301 through 308 removed outlier: 6.716A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.848A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.681A pdb=" N PHE F 53 " --> pdb=" O CYS F 218 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS F 218 " --> pdb=" O PHE F 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 91 through 93 Processing sheet with id=AB6, first strand: chain 'F' and resid 169 through 174 Processing sheet with id=AB7, first strand: chain 'F' and resid 260 through 261 removed outlier: 6.437A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N ILE F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.207A pdb=" N LEU F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.210A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.207A pdb=" N LEU F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N ILE F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 301 through 308 removed outlier: 6.716A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.848A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.681A pdb=" N PHE G 53 " --> pdb=" O CYS G 218 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS G 218 " --> pdb=" O PHE G 53 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 91 through 93 Processing sheet with id=AC5, first strand: chain 'G' and resid 169 through 174 Processing sheet with id=AC6, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.438A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N ILE G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 12.207A pdb=" N LEU G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.210A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.207A pdb=" N LEU G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N ILE G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 301 through 308 removed outlier: 6.716A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.864A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP H 35 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR H 52 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU H 33 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.865A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR J 50 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP J 35 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR J 52 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU J 33 " --> pdb=" O TYR J 52 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.513A pdb=" N THR K 5 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG K 24 " --> pdb=" O THR K 5 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.838A pdb=" N GLU K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU K 46 " --> pdb=" O LEU K 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.838A pdb=" N GLU K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.513A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.838A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.838A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.865A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR M 50 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TRP M 35 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR M 52 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU M 33 " --> pdb=" O TYR M 52 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.513A pdb=" N THR N 5 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG N 24 " --> pdb=" O THR N 5 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.838A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU N 46 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.838A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 1926 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: 4.10 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6196 1.34 - 1.46: 4381 1.46 - 1.58: 9655 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 20382 Sorted by residual: bond pdb=" C1 MAN S 8 " pdb=" O5 MAN S 8 " ideal model delta sigma weight residual 1.399 1.432 -0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C1 MAN W 8 " pdb=" O5 MAN W 8 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" C1 MAN W 7 " pdb=" O5 MAN W 7 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" C1 MAN S 7 " pdb=" O5 MAN S 7 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 MAN O 8 " pdb=" O5 MAN O 8 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 20377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 26876 1.79 - 3.59: 708 3.59 - 5.38: 78 5.38 - 7.17: 16 7.17 - 8.96: 9 Bond angle restraints: 27687 Sorted by residual: angle pdb=" C1 BMA Q 3 " pdb=" O5 BMA Q 3 " pdb=" C5 BMA Q 3 " ideal model delta sigma weight residual 118.82 109.86 8.96 3.00e+00 1.11e-01 8.93e+00 angle pdb=" C1 BMA D 3 " pdb=" O5 BMA D 3 " pdb=" C5 BMA D 3 " ideal model delta sigma weight residual 118.82 109.92 8.90 3.00e+00 1.11e-01 8.81e+00 angle pdb=" C1 BMA U 3 " pdb=" O5 BMA U 3 " pdb=" C5 BMA U 3 " ideal model delta sigma weight residual 118.82 109.93 8.89 3.00e+00 1.11e-01 8.78e+00 angle pdb=" C1 BMA O 3 " pdb=" O5 BMA O 3 " pdb=" C5 BMA O 3 " ideal model delta sigma weight residual 118.82 110.59 8.23 3.00e+00 1.11e-01 7.53e+00 angle pdb=" C1 BMA S 3 " pdb=" O5 BMA S 3 " pdb=" C5 BMA S 3 " ideal model delta sigma weight residual 118.82 110.59 8.23 3.00e+00 1.11e-01 7.52e+00 ... (remaining 27682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.61: 12852 24.61 - 49.22: 315 49.22 - 73.83: 36 73.83 - 98.44: 30 98.44 - 123.06: 81 Dihedral angle restraints: 13314 sinusoidal: 6444 harmonic: 6870 Sorted by residual: dihedral pdb=" O2 MAN W 8 " pdb=" C2 MAN W 8 " pdb=" C3 MAN W 8 " pdb=" O3 MAN W 8 " ideal model delta sinusoidal sigma weight residual -57.63 65.43 -123.06 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" O2 MAN S 8 " pdb=" C2 MAN S 8 " pdb=" C3 MAN S 8 " pdb=" O3 MAN S 8 " ideal model delta sinusoidal sigma weight residual -57.63 65.42 -123.05 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" O2 MAN O 8 " pdb=" C2 MAN O 8 " pdb=" C3 MAN O 8 " pdb=" O3 MAN O 8 " ideal model delta sinusoidal sigma weight residual -57.63 65.38 -123.01 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 13311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.016: 3333 1.016 - 2.033: 0 2.033 - 3.049: 0 3.049 - 4.066: 0 4.066 - 5.082: 15 Chirality restraints: 3348 Sorted by residual: chirality pdb=" C4 NAG F 604 " pdb=" C3 NAG F 604 " pdb=" C5 NAG F 604 " pdb=" O4 NAG F 604 " both_signs ideal model delta sigma weight residual False -2.53 2.55 -5.08 2.00e-01 2.50e+01 6.46e+02 chirality pdb=" C4 NAG G 604 " pdb=" C3 NAG G 604 " pdb=" C5 NAG G 604 " pdb=" O4 NAG G 604 " both_signs ideal model delta sigma weight residual False -2.53 2.55 -5.08 2.00e-01 2.50e+01 6.45e+02 chirality pdb=" C4 NAG E 604 " pdb=" C3 NAG E 604 " pdb=" C5 NAG E 604 " pdb=" O4 NAG E 604 " both_signs ideal model delta sigma weight residual False -2.53 2.55 -5.08 2.00e-01 2.50e+01 6.45e+02 ... (remaining 3345 not shown) Planarity restraints: 3444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU N 11 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO N 12 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO N 12 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO N 12 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 11 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO L 12 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO L 12 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 12 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 11 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO K 12 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO K 12 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO K 12 " -0.017 5.00e-02 4.00e+02 ... (remaining 3441 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 11948 3.03 - 3.50: 18250 3.50 - 3.96: 31032 3.96 - 4.43: 36056 4.43 - 4.90: 58659 Nonbonded interactions: 155945 Sorted by model distance: nonbonded pdb=" O ASN F 156 " pdb=" OD1 ASN F 156 " model vdw 2.562 3.040 nonbonded pdb=" O ASN G 156 " pdb=" OD1 ASN G 156 " model vdw 2.563 3.040 nonbonded pdb=" O ASN E 156 " pdb=" OD1 ASN E 156 " model vdw 2.563 3.040 nonbonded pdb=" OD1 ASN G 156 " pdb=" O5 NAG G 603 " model vdw 2.574 3.040 nonbonded pdb=" OD1 ASN E 156 " pdb=" O5 NAG E 603 " model vdw 2.574 3.040 ... (remaining 155940 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'W' } 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: 3.380 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: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 19.450 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.004 0.041 20514 Z= 0.218 Angle : 0.662 8.964 28041 Z= 0.292 Chirality : 0.338 5.082 3348 Planarity : 0.003 0.030 3390 Dihedral : 15.300 123.056 8778 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.57 % Allowed : 5.44 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.18), residues: 2325 helix: 1.36 (0.28), residues: 414 sheet: 0.49 (0.20), residues: 699 loop : -1.18 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 350 TYR 0.015 0.001 TYR J 50 PHE 0.008 0.001 PHE H 78 TRP 0.006 0.001 TRP G 338 HIS 0.002 0.001 HIS M 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 (20382) covalent geometry : angle 0.64315 / 0.29 (27687) SS BOND : bond 0.00239 / 0.14 ( 42) SS BOND : angle 0.66754 / 0.47 ( 84) hydrogen bonds : bond 0.12969 / 8.37 ( 678) hydrogen bonds : angle 6.01049 / 4.14 ( 1926) link_ALPHA1-2 : bond 0.00175 / 0.09 ( 3) link_ALPHA1-2 : angle 0.65521 / 0.36 ( 9) link_ALPHA1-3 : bond 0.00410 / 0.25 ( 9) link_ALPHA1-3 : angle 0.87026 / 0.51 ( 27) link_ALPHA1-6 : bond 0.00238 / 0.13 ( 6) link_ALPHA1-6 : angle 1.40162 / 0.87 ( 18) link_BETA1-4 : bond 0.01292 / 0.69 ( 18) link_BETA1-4 : angle 2.24264 / 1.45 ( 54) link_NAG-ASN : bond 0.00346 / 0.25 ( 54) link_NAG-ASN : angle 1.72703 / 1.14 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 429 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 612 SER cc_start: 0.8138 (t) cc_final: 0.7868 (m) REVERT: E 106 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7090 (mt-10) REVERT: E 189 LYS cc_start: 0.7297 (mmtm) cc_final: 0.6506 (mttp) REVERT: E 213 ILE cc_start: 0.8852 (mm) cc_final: 0.8517 (tt) REVERT: F 106 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6993 (mt-10) REVERT: F 189 LYS cc_start: 0.7301 (mmtm) cc_final: 0.6586 (mttp) REVERT: F 428 GLN cc_start: 0.8801 (mp10) cc_final: 0.8483 (mt0) REVERT: F 467 THR cc_start: 0.8700 (m) cc_final: 0.8329 (m) REVERT: G 106 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7104 (mt-10) REVERT: G 189 LYS cc_start: 0.7506 (mmtm) cc_final: 0.6791 (mttp) REVERT: G 290 THR cc_start: 0.8748 (t) cc_final: 0.8541 (p) REVERT: G 467 THR cc_start: 0.8891 (m) cc_final: 0.8608 (m) REVERT: H 20 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7195 (tt) REVERT: H 63 LEU cc_start: 0.6684 (tp) cc_final: 0.6445 (tt) REVERT: H 87 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7870 (t) REVERT: J 20 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6405 (tt) REVERT: L 45 GLN cc_start: 0.7841 (pm20) cc_final: 0.7352 (pt0) REVERT: M 20 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.5712 (tt) outliers start: 12 outliers final: 5 residues processed: 438 average time/residue: 0.1555 time to fit residues: 104.1884 Evaluate side-chains 285 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 276 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.0870 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN B 590 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN E 80 ASN E 103 GLN E 105 HIS E 130 GLN E 428 GLN E 440 GLN F 80 ASN F 103 GLN F 105 HIS F 130 GLN F 356 ASN F 440 GLN G 80 ASN G 103 GLN G 105 HIS G 130 GLN G 356 ASN G 440 GLN H 58 HIS H 76 ASN J 58 HIS M 58 HIS M 95 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113917 restraints weight = 29086.948| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.40 r_work: 0.3278 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20514 Z= 0.113 Angle : 0.681 21.466 28041 Z= 0.302 Chirality : 0.047 0.324 3348 Planarity : 0.004 0.062 3390 Dihedral : 9.459 73.438 4413 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.44 % Allowed : 9.12 % Favored : 88.44 % 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: -0.27 (0.17), residues: 2325 helix: 1.51 (0.28), residues: 414 sheet: 0.53 (0.20), residues: 666 loop : -1.22 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 178 TYR 0.018 0.001 TYR J 50 PHE 0.017 0.001 PHE F 53 TRP 0.011 0.001 TRP M 103 HIS 0.002 0.000 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (20382) covalent geometry : angle 0.59615 / 0.28 (27687) SS BOND : bond 0.00292 / 0.20 ( 42) SS BOND : angle 1.18081 / 0.77 ( 84) hydrogen bonds : bond 0.03510 / 2.28 ( 678) hydrogen bonds : angle 4.85485 / 3.38 ( 1926) link_ALPHA1-2 : bond 0.00098 / 0.05 ( 3) link_ALPHA1-2 : angle 1.62550 / 0.92 ( 9) link_ALPHA1-3 : bond 0.01365 / 0.86 ( 9) link_ALPHA1-3 : angle 2.68554 / 1.81 ( 27) link_ALPHA1-6 : bond 0.00461 / 0.24 ( 6) link_ALPHA1-6 : angle 1.95107 / 1.24 ( 18) link_BETA1-4 : bond 0.00901 / 0.50 ( 18) link_BETA1-4 : angle 6.17508 / 4.12 ( 54) link_NAG-ASN : bond 0.00454 / 0.32 ( 54) link_NAG-ASN : angle 2.09149 / 1.49 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 302 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 612 SER cc_start: 0.8164 (t) cc_final: 0.7839 (m) REVERT: A 635 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.6771 (pt) REVERT: B 655 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7819 (ttmt) REVERT: E 106 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7267 (mt-10) REVERT: E 125 LEU cc_start: 0.8592 (tp) cc_final: 0.8059 (tp) REVERT: E 189 LYS cc_start: 0.7328 (mmtm) cc_final: 0.6457 (mttp) REVERT: E 213 ILE cc_start: 0.8773 (mm) cc_final: 0.8491 (mt) REVERT: E 349 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7975 (mp) REVERT: F 106 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7112 (mt-10) REVERT: F 189 LYS cc_start: 0.7311 (mmtm) cc_final: 0.6514 (mttp) REVERT: F 213 ILE cc_start: 0.8639 (tt) cc_final: 0.8361 (pt) REVERT: F 428 GLN cc_start: 0.8783 (mp10) cc_final: 0.8523 (mt0) REVERT: G 106 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7337 (mt-10) REVERT: G 189 LYS cc_start: 0.7433 (mmtm) cc_final: 0.6650 (mttp) REVERT: G 207 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7476 (mmpt) REVERT: G 290 THR cc_start: 0.8876 (t) cc_final: 0.8592 (p) REVERT: G 370 GLU cc_start: 0.8380 (mp0) cc_final: 0.8137 (mp0) REVERT: H 33 LEU cc_start: 0.8767 (mp) cc_final: 0.8542 (mp) REVERT: H 63 LEU cc_start: 0.6498 (tp) cc_final: 0.6259 (tt) REVERT: H 76 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.6741 (t0) REVERT: L 27 GLN cc_start: 0.7125 (tt0) cc_final: 0.6609 (tm-30) REVERT: L 45 GLN cc_start: 0.7763 (pm20) cc_final: 0.7248 (pt0) REVERT: N 27 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7512 (tm-30) outliers start: 51 outliers final: 21 residues processed: 333 average time/residue: 0.1378 time to fit residues: 72.8190 Evaluate side-chains 296 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 271 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 108 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 10 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 191 optimal weight: 0.0980 chunk 102 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 222 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 216 HIS F 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108398 restraints weight = 28996.842| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.17 r_work: 0.3207 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20514 Z= 0.142 Angle : 0.618 11.061 28041 Z= 0.291 Chirality : 0.047 0.289 3348 Planarity : 0.004 0.045 3390 Dihedral : 8.177 66.027 4406 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.63 % Allowed : 9.93 % Favored : 87.44 % 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: -0.33 (0.18), residues: 2325 helix: 1.37 (0.28), residues: 417 sheet: 0.34 (0.20), residues: 708 loop : -1.16 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 500 TYR 0.017 0.001 TYR H 50 PHE 0.016 0.002 PHE F 53 TRP 0.011 0.001 TRP A 631 HIS 0.003 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (20382) covalent geometry : angle 0.57161 / 0.28 (27687) SS BOND : bond 0.00236 / 0.15 ( 42) SS BOND : angle 1.11350 / 0.66 ( 84) hydrogen bonds : bond 0.03679 / 2.41 ( 678) hydrogen bonds : angle 4.75741 / 3.30 ( 1926) link_ALPHA1-2 : bond 0.00255 / 0.13 ( 3) link_ALPHA1-2 : angle 1.45528 / 0.83 ( 9) link_ALPHA1-3 : bond 0.01263 / 0.77 ( 9) link_ALPHA1-3 : angle 2.04896 / 1.25 ( 27) link_ALPHA1-6 : bond 0.00272 / 0.15 ( 6) link_ALPHA1-6 : angle 1.96027 / 1.14 ( 18) link_BETA1-4 : bond 0.00413 / 0.26 ( 18) link_BETA1-4 : angle 2.99649 / 2.36 ( 54) link_NAG-ASN : bond 0.00491 / 0.36 ( 54) link_NAG-ASN : angle 2.32510 / 1.67 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 289 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 612 SER cc_start: 0.8318 (t) cc_final: 0.7961 (m) REVERT: A 635 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.6783 (pt) REVERT: B 617 ARG cc_start: 0.8392 (mtp-110) cc_final: 0.8181 (mtp-110) REVERT: B 655 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7891 (ttmt) REVERT: E 51 THR cc_start: 0.8595 (p) cc_final: 0.8349 (p) REVERT: E 106 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7243 (mt-10) REVERT: E 189 LYS cc_start: 0.7268 (mmtm) cc_final: 0.6383 (mttp) REVERT: E 213 ILE cc_start: 0.8750 (mm) cc_final: 0.8442 (mt) REVERT: F 106 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7124 (mt-10) REVERT: F 189 LYS cc_start: 0.7337 (mmtm) cc_final: 0.6530 (mttp) REVERT: F 213 ILE cc_start: 0.8571 (tt) cc_final: 0.8358 (pt) REVERT: F 428 GLN cc_start: 0.8845 (mp10) cc_final: 0.8587 (mt0) REVERT: G 56 SER cc_start: 0.8044 (t) cc_final: 0.7776 (m) REVERT: G 106 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7351 (mt-10) REVERT: G 189 LYS cc_start: 0.7428 (mmtm) cc_final: 0.6564 (mttp) REVERT: G 207 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7410 (mmpt) REVERT: G 424 ILE cc_start: 0.9077 (mm) cc_final: 0.8859 (mm) REVERT: H 33 LEU cc_start: 0.8901 (mp) cc_final: 0.8656 (mp) REVERT: H 64 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: H 76 ASN cc_start: 0.6974 (t0) cc_final: 0.6745 (t0) REVERT: L 27 GLN cc_start: 0.7110 (tt0) cc_final: 0.6555 (tm-30) REVERT: L 45 GLN cc_start: 0.7796 (pm20) cc_final: 0.7308 (pt0) REVERT: M 56 THR cc_start: 0.8409 (m) cc_final: 0.8052 (p) REVERT: M 76 ASN cc_start: 0.6532 (t0) cc_final: 0.6085 (t0) REVERT: N 4 MET cc_start: 0.7336 (ptp) cc_final: 0.7097 (ptp) REVERT: N 27 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7507 (tm-30) outliers start: 55 outliers final: 40 residues processed: 312 average time/residue: 0.1425 time to fit residues: 69.1020 Evaluate side-chains 310 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 233 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 214 optimal weight: 0.1980 chunk 205 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.140264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101847 restraints weight = 29480.913| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.42 r_work: 0.3100 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20514 Z= 0.244 Angle : 0.715 12.056 28041 Z= 0.341 Chirality : 0.049 0.309 3348 Planarity : 0.004 0.041 3390 Dihedral : 7.868 57.760 4406 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.76 % Favored : 94.15 % Rotamer: Outliers : 3.49 % Allowed : 10.65 % Favored : 85.86 % 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: -0.68 (0.17), residues: 2325 helix: 0.91 (0.27), residues: 417 sheet: 0.06 (0.20), residues: 726 loop : -1.30 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 500 TYR 0.021 0.002 TYR H 50 PHE 0.017 0.002 PHE E 317 TRP 0.011 0.001 TRP M 47 HIS 0.006 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.24 (20382) covalent geometry : angle 0.66998 / 0.33 (27687) SS BOND : bond 0.00388 / 0.20 ( 42) SS BOND : angle 1.17746 / 0.71 ( 84) hydrogen bonds : bond 0.04411 / 2.93 ( 678) hydrogen bonds : angle 4.97151 / 3.43 ( 1926) link_ALPHA1-2 : bond 0.00128 / 0.06 ( 3) link_ALPHA1-2 : angle 1.56326 / 0.86 ( 9) link_ALPHA1-3 : bond 0.01121 / 0.69 ( 9) link_ALPHA1-3 : angle 2.27222 / 1.42 ( 27) link_ALPHA1-6 : bond 0.00346 / 0.19 ( 6) link_ALPHA1-6 : angle 2.04857 / 1.19 ( 18) link_BETA1-4 : bond 0.00484 / 0.30 ( 18) link_BETA1-4 : angle 2.07085 / 1.42 ( 54) link_NAG-ASN : bond 0.00586 / 0.39 ( 54) link_NAG-ASN : angle 2.85395 / 2.09 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 273 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7303 (pt) REVERT: B 655 LYS cc_start: 0.8288 (ttmm) cc_final: 0.8046 (ttmt) REVERT: E 51 THR cc_start: 0.8867 (p) cc_final: 0.8627 (p) REVERT: E 106 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7319 (mt-10) REVERT: E 189 LYS cc_start: 0.7437 (mmtm) cc_final: 0.6531 (mttp) REVERT: E 296 CYS cc_start: 0.7793 (m) cc_final: 0.7489 (m) REVERT: F 106 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7287 (mt-10) REVERT: F 189 LYS cc_start: 0.7413 (mmtm) cc_final: 0.6525 (mtmm) REVERT: F 213 ILE cc_start: 0.8755 (tt) cc_final: 0.8442 (pt) REVERT: F 264 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7788 (p) REVERT: F 428 GLN cc_start: 0.8884 (mp10) cc_final: 0.8645 (mt0) REVERT: G 56 SER cc_start: 0.8420 (t) cc_final: 0.8145 (m) REVERT: G 106 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7445 (mt-10) REVERT: G 189 LYS cc_start: 0.7426 (mmtm) cc_final: 0.6545 (mttp) REVERT: H 76 ASN cc_start: 0.7219 (t0) cc_final: 0.6898 (t0) REVERT: H 86 ASP cc_start: 0.6965 (t70) cc_final: 0.6706 (t70) REVERT: K 27 GLN cc_start: 0.6910 (tt0) cc_final: 0.6412 (tm-30) REVERT: K 45 GLN cc_start: 0.8246 (pm20) cc_final: 0.7759 (pm20) REVERT: K 61 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7481 (mtp180) REVERT: L 27 GLN cc_start: 0.7265 (tt0) cc_final: 0.6636 (tm-30) REVERT: M 110 THR cc_start: 0.7461 (m) cc_final: 0.7142 (p) REVERT: N 27 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7628 (tm-30) outliers start: 73 outliers final: 53 residues processed: 314 average time/residue: 0.1415 time to fit residues: 70.0583 Evaluate side-chains 308 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 253 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 144 optimal weight: 0.8980 chunk 226 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 196 optimal weight: 8.9990 chunk 197 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN C 616 ASN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN G 428 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.103932 restraints weight = 28630.091| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.32 r_work: 0.3162 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20514 Z= 0.114 Angle : 0.605 11.687 28041 Z= 0.286 Chirality : 0.046 0.316 3348 Planarity : 0.003 0.039 3390 Dihedral : 6.986 56.326 4405 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 2.63 % Allowed : 12.66 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.18), residues: 2325 helix: 1.23 (0.28), residues: 414 sheet: 0.21 (0.20), residues: 711 loop : -1.24 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 81 TYR 0.015 0.001 TYR H 50 PHE 0.014 0.001 PHE F 53 TRP 0.009 0.001 TRP M 47 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (20382) covalent geometry : angle 0.55708 / 0.28 (27687) SS BOND : bond 0.00165 / 0.10 ( 42) SS BOND : angle 0.94280 / 0.57 ( 84) hydrogen bonds : bond 0.03483 / 2.30 ( 678) hydrogen bonds : angle 4.65317 / 3.23 ( 1926) link_ALPHA1-2 : bond 0.00384 / 0.19 ( 3) link_ALPHA1-2 : angle 1.66881 / 0.90 ( 9) link_ALPHA1-3 : bond 0.01026 / 0.64 ( 9) link_ALPHA1-3 : angle 2.03386 / 1.28 ( 27) link_ALPHA1-6 : bond 0.00512 / 0.29 ( 6) link_ALPHA1-6 : angle 2.01016 / 1.15 ( 18) link_BETA1-4 : bond 0.00430 / 0.27 ( 18) link_BETA1-4 : angle 1.82348 / 1.35 ( 54) link_NAG-ASN : bond 0.00592 / 0.40 ( 54) link_NAG-ASN : angle 2.72057 / 1.96 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 270 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7225 (pt) REVERT: B 655 LYS cc_start: 0.8255 (ttmm) cc_final: 0.8019 (ttmt) REVERT: C 660 LEU cc_start: 0.8554 (tt) cc_final: 0.7819 (mt) REVERT: E 106 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7322 (mt-10) REVERT: E 189 LYS cc_start: 0.7440 (mmtm) cc_final: 0.6550 (mttp) REVERT: E 296 CYS cc_start: 0.7646 (m) cc_final: 0.7328 (m) REVERT: F 106 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7224 (mt-10) REVERT: F 189 LYS cc_start: 0.7397 (mmtm) cc_final: 0.6578 (mttp) REVERT: F 213 ILE cc_start: 0.8727 (tt) cc_final: 0.8494 (pt) REVERT: F 428 GLN cc_start: 0.8877 (mp10) cc_final: 0.8619 (mt0) REVERT: G 56 SER cc_start: 0.8264 (t) cc_final: 0.8043 (m) REVERT: G 106 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7424 (mt-10) REVERT: G 189 LYS cc_start: 0.7432 (mmtm) cc_final: 0.6562 (mttp) REVERT: G 207 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7400 (mmpt) REVERT: H 76 ASN cc_start: 0.7169 (t0) cc_final: 0.6912 (t0) REVERT: K 27 GLN cc_start: 0.6784 (tt0) cc_final: 0.6156 (tm-30) REVERT: K 45 GLN cc_start: 0.8191 (pm20) cc_final: 0.7679 (pm20) REVERT: L 27 GLN cc_start: 0.7145 (tt0) cc_final: 0.6509 (tm-30) REVERT: L 45 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.6971 (pt0) REVERT: M 110 THR cc_start: 0.7466 (m) cc_final: 0.7257 (p) REVERT: N 27 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7518 (tm-30) REVERT: N 28 LYS cc_start: 0.8867 (mmtp) cc_final: 0.8647 (mmtp) outliers start: 55 outliers final: 34 residues processed: 301 average time/residue: 0.1289 time to fit residues: 60.8690 Evaluate side-chains 295 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 258 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 500 ARG Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 20 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN G 67 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.138796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101710 restraints weight = 28767.957| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.32 r_work: 0.3132 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20514 Z= 0.167 Angle : 0.635 11.590 28041 Z= 0.301 Chirality : 0.046 0.303 3348 Planarity : 0.003 0.037 3390 Dihedral : 6.829 54.856 4405 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 3.39 % Allowed : 12.51 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.18), residues: 2325 helix: 1.06 (0.27), residues: 417 sheet: 0.13 (0.20), residues: 714 loop : -1.31 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 617 TYR 0.017 0.001 TYR H 50 PHE 0.015 0.001 PHE F 53 TRP 0.009 0.001 TRP M 47 HIS 0.005 0.001 HIS K 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (20382) covalent geometry : angle 0.58770 / 0.29 (27687) SS BOND : bond 0.00210 / 0.14 ( 42) SS BOND : angle 1.04013 / 0.60 ( 84) hydrogen bonds : bond 0.03713 / 2.46 ( 678) hydrogen bonds : angle 4.67793 / 3.24 ( 1926) link_ALPHA1-2 : bond 0.00294 / 0.15 ( 3) link_ALPHA1-2 : angle 1.46633 / 0.80 ( 9) link_ALPHA1-3 : bond 0.01025 / 0.64 ( 9) link_ALPHA1-3 : angle 2.06830 / 1.29 ( 27) link_ALPHA1-6 : bond 0.00410 / 0.24 ( 6) link_ALPHA1-6 : angle 2.04150 / 1.14 ( 18) link_BETA1-4 : bond 0.00411 / 0.26 ( 18) link_BETA1-4 : angle 1.80131 / 1.27 ( 54) link_NAG-ASN : bond 0.00516 / 0.35 ( 54) link_NAG-ASN : angle 2.79469 / 2.03 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 258 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7303 (pt) REVERT: B 655 LYS cc_start: 0.8312 (ttmm) cc_final: 0.8056 (ttmt) REVERT: C 624 ASP cc_start: 0.8322 (m-30) cc_final: 0.7882 (m-30) REVERT: E 51 THR cc_start: 0.8845 (p) cc_final: 0.8583 (p) REVERT: E 106 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7336 (mt-10) REVERT: E 189 LYS cc_start: 0.7439 (mmtm) cc_final: 0.6531 (mttp) REVERT: E 296 CYS cc_start: 0.7710 (m) cc_final: 0.7412 (m) REVERT: F 106 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7270 (mt-10) REVERT: F 189 LYS cc_start: 0.7411 (mmtm) cc_final: 0.6585 (mttp) REVERT: F 213 ILE cc_start: 0.8764 (tt) cc_final: 0.8505 (pt) REVERT: F 428 GLN cc_start: 0.8876 (mp10) cc_final: 0.8616 (mt0) REVERT: F 475 MET cc_start: 0.7345 (mmt) cc_final: 0.7050 (mmt) REVERT: G 56 SER cc_start: 0.8292 (t) cc_final: 0.8086 (m) REVERT: G 106 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7427 (mt-10) REVERT: G 189 LYS cc_start: 0.7431 (mmtm) cc_final: 0.6566 (mttp) REVERT: G 370 GLU cc_start: 0.8424 (mp0) cc_final: 0.8203 (mp0) REVERT: H 55 GLU cc_start: 0.8238 (mp0) cc_final: 0.7986 (mp0) REVERT: H 76 ASN cc_start: 0.7180 (t0) cc_final: 0.6894 (t0) REVERT: J 64 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6494 (tm-30) REVERT: K 27 GLN cc_start: 0.6773 (tt0) cc_final: 0.6146 (tm-30) REVERT: K 45 GLN cc_start: 0.8208 (pm20) cc_final: 0.7689 (pm20) REVERT: L 27 GLN cc_start: 0.7132 (tt0) cc_final: 0.6519 (tm-30) REVERT: L 45 GLN cc_start: 0.7670 (pm20) cc_final: 0.7041 (pt0) REVERT: M 110 THR cc_start: 0.7503 (m) cc_final: 0.7171 (p) REVERT: N 27 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7588 (tm-30) REVERT: N 28 LYS cc_start: 0.8881 (mmtp) cc_final: 0.8658 (mmtp) outliers start: 71 outliers final: 49 residues processed: 304 average time/residue: 0.1426 time to fit residues: 68.2068 Evaluate side-chains 304 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 253 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 500 ARG Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 207 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 151 optimal weight: 0.6980 chunk 165 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN G 428 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN N 45 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101132 restraints weight = 28673.360| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.10 r_work: 0.3099 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20514 Z= 0.223 Angle : 0.695 11.378 28041 Z= 0.330 Chirality : 0.048 0.310 3348 Planarity : 0.004 0.037 3390 Dihedral : 6.904 54.070 4404 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.76 % Favored : 94.19 % Rotamer: Outliers : 3.68 % Allowed : 12.27 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 2325 helix: 0.84 (0.27), residues: 417 sheet: 0.15 (0.20), residues: 684 loop : -1.50 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 350 TYR 0.018 0.002 TYR H 50 PHE 0.015 0.002 PHE F 53 TRP 0.011 0.001 TRP M 47 HIS 0.006 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (20382) covalent geometry : angle 0.64910 / 0.32 (27687) SS BOND : bond 0.00251 / 0.16 ( 42) SS BOND : angle 1.14859 / 0.68 ( 84) hydrogen bonds : bond 0.04282 / 2.84 ( 678) hydrogen bonds : angle 4.87454 / 3.36 ( 1926) link_ALPHA1-2 : bond 0.00320 / 0.16 ( 3) link_ALPHA1-2 : angle 1.96025 / 0.97 ( 9) link_ALPHA1-3 : bond 0.01106 / 0.69 ( 9) link_ALPHA1-3 : angle 2.10350 / 1.30 ( 27) link_ALPHA1-6 : bond 0.00485 / 0.27 ( 6) link_ALPHA1-6 : angle 2.10966 / 1.19 ( 18) link_BETA1-4 : bond 0.00431 / 0.27 ( 18) link_BETA1-4 : angle 1.82715 / 1.20 ( 54) link_NAG-ASN : bond 0.00526 / 0.36 ( 54) link_NAG-ASN : angle 2.87940 / 2.07 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 267 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 ARG cc_start: 0.8810 (mmm-85) cc_final: 0.8589 (mtm-85) REVERT: B 656 ASN cc_start: 0.8337 (m-40) cc_final: 0.8017 (m-40) REVERT: C 638 TYR cc_start: 0.8109 (m-80) cc_final: 0.7797 (m-10) REVERT: E 51 THR cc_start: 0.9011 (p) cc_final: 0.8765 (p) REVERT: E 106 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7347 (mt-10) REVERT: E 189 LYS cc_start: 0.7471 (mmtm) cc_final: 0.6585 (mttp) REVERT: E 246 GLN cc_start: 0.7268 (pt0) cc_final: 0.6391 (tp-100) REVERT: F 56 SER cc_start: 0.8324 (t) cc_final: 0.8067 (m) REVERT: F 106 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7372 (mt-10) REVERT: F 189 LYS cc_start: 0.7459 (mmtm) cc_final: 0.6633 (mttp) REVERT: F 213 ILE cc_start: 0.8817 (tt) cc_final: 0.8448 (pt) REVERT: F 428 GLN cc_start: 0.8883 (mp10) cc_final: 0.8656 (mt0) REVERT: F 475 MET cc_start: 0.7209 (mmt) cc_final: 0.6841 (mmt) REVERT: G 56 SER cc_start: 0.8434 (t) cc_final: 0.8164 (m) REVERT: G 106 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7426 (mt-10) REVERT: G 189 LYS cc_start: 0.7381 (mmtm) cc_final: 0.6547 (mttp) REVERT: G 370 GLU cc_start: 0.8453 (mp0) cc_final: 0.8214 (mp0) REVERT: G 475 MET cc_start: 0.7122 (mmt) cc_final: 0.6884 (mmm) REVERT: H 64 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6429 (tm-30) REVERT: J 64 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6514 (tm-30) REVERT: K 27 GLN cc_start: 0.6868 (tt0) cc_final: 0.6203 (tm-30) REVERT: K 45 GLN cc_start: 0.8247 (pm20) cc_final: 0.7261 (pt0) REVERT: K 62 PHE cc_start: 0.7985 (m-80) cc_final: 0.7414 (m-80) REVERT: L 27 GLN cc_start: 0.7268 (tt0) cc_final: 0.6591 (tm-30) REVERT: M 20 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7104 (tt) REVERT: M 67 VAL cc_start: 0.6145 (p) cc_final: 0.5929 (p) REVERT: M 110 THR cc_start: 0.7917 (m) cc_final: 0.7630 (p) REVERT: N 27 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7484 (tm-30) REVERT: N 28 LYS cc_start: 0.8899 (mmtp) cc_final: 0.8659 (mmtp) outliers start: 77 outliers final: 56 residues processed: 312 average time/residue: 0.1289 time to fit residues: 63.4157 Evaluate side-chains 308 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 249 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 500 ARG Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 92 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 194 optimal weight: 2.9990 chunk 125 optimal weight: 0.0980 chunk 174 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN K 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103076 restraints weight = 29244.021| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.41 r_work: 0.3118 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20514 Z= 0.134 Angle : 0.623 11.627 28041 Z= 0.295 Chirality : 0.046 0.306 3348 Planarity : 0.003 0.036 3390 Dihedral : 6.571 53.396 4402 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.18 % Rotamer: Outliers : 2.91 % Allowed : 13.61 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2325 helix: 1.12 (0.28), residues: 414 sheet: 0.04 (0.20), residues: 720 loop : -1.36 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 542 TYR 0.014 0.001 TYR H 50 PHE 0.014 0.001 PHE F 53 TRP 0.010 0.001 TRP E 112 HIS 0.005 0.001 HIS N 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (20382) covalent geometry : angle 0.57654 / 0.29 (27687) SS BOND : bond 0.00237 / 0.13 ( 42) SS BOND : angle 1.02721 / 0.61 ( 84) hydrogen bonds : bond 0.03603 / 2.38 ( 678) hydrogen bonds : angle 4.66373 / 3.23 ( 1926) link_ALPHA1-2 : bond 0.00378 / 0.19 ( 3) link_ALPHA1-2 : angle 1.73160 / 0.91 ( 9) link_ALPHA1-3 : bond 0.00996 / 0.62 ( 9) link_ALPHA1-3 : angle 1.95502 / 1.23 ( 27) link_ALPHA1-6 : bond 0.00479 / 0.27 ( 6) link_ALPHA1-6 : angle 2.00119 / 1.12 ( 18) link_BETA1-4 : bond 0.00432 / 0.27 ( 18) link_BETA1-4 : angle 1.54326 / 1.02 ( 54) link_NAG-ASN : bond 0.00516 / 0.36 ( 54) link_NAG-ASN : angle 2.79948 / 2.01 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 257 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 ARG cc_start: 0.8814 (mmm-85) cc_final: 0.8589 (mtm-85) REVERT: B 656 ASN cc_start: 0.8322 (m-40) cc_final: 0.8016 (m-40) REVERT: C 542 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8226 (mtm-85) REVERT: C 638 TYR cc_start: 0.8090 (m-80) cc_final: 0.7816 (m-10) REVERT: C 660 LEU cc_start: 0.8579 (tt) cc_final: 0.7885 (mt) REVERT: E 51 THR cc_start: 0.8938 (p) cc_final: 0.8675 (p) REVERT: E 106 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7318 (mt-10) REVERT: E 189 LYS cc_start: 0.7452 (mmtm) cc_final: 0.6551 (mttp) REVERT: E 246 GLN cc_start: 0.7426 (pt0) cc_final: 0.6542 (tp-100) REVERT: F 106 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7266 (mt-10) REVERT: F 189 LYS cc_start: 0.7430 (mmtm) cc_final: 0.6607 (mttp) REVERT: F 213 ILE cc_start: 0.8810 (tt) cc_final: 0.8450 (pt) REVERT: F 428 GLN cc_start: 0.8879 (mp10) cc_final: 0.8644 (mt0) REVERT: F 475 MET cc_start: 0.7184 (mmt) cc_final: 0.6817 (mmt) REVERT: G 51 THR cc_start: 0.8883 (p) cc_final: 0.8623 (p) REVERT: G 56 SER cc_start: 0.8294 (t) cc_final: 0.8057 (m) REVERT: G 106 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7421 (mt-10) REVERT: G 189 LYS cc_start: 0.7377 (mmtm) cc_final: 0.6527 (mttp) REVERT: G 370 GLU cc_start: 0.8451 (mp0) cc_final: 0.8189 (mp0) REVERT: H 76 ASN cc_start: 0.6937 (OUTLIER) cc_final: 0.6635 (t0) REVERT: J 64 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6409 (tm-30) REVERT: K 27 GLN cc_start: 0.6796 (tt0) cc_final: 0.6138 (tm-30) REVERT: K 45 GLN cc_start: 0.8204 (pm20) cc_final: 0.7259 (pt0) REVERT: K 62 PHE cc_start: 0.7920 (m-80) cc_final: 0.7377 (m-80) REVERT: L 27 GLN cc_start: 0.7195 (tt0) cc_final: 0.6517 (tm-30) REVERT: L 45 GLN cc_start: 0.7994 (pm20) cc_final: 0.7208 (pt0) REVERT: M 20 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7029 (tt) REVERT: M 67 VAL cc_start: 0.6042 (p) cc_final: 0.5796 (p) REVERT: M 110 THR cc_start: 0.7833 (m) cc_final: 0.7580 (p) REVERT: N 27 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7415 (tm-30) REVERT: N 28 LYS cc_start: 0.8903 (mmtp) cc_final: 0.8662 (mmtp) REVERT: N 45 GLN cc_start: 0.8072 (pm20) cc_final: 0.7071 (pt0) outliers start: 61 outliers final: 51 residues processed: 294 average time/residue: 0.1279 time to fit residues: 58.9825 Evaluate side-chains 303 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 249 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 500 ARG Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 92 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 196 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102958 restraints weight = 29129.962| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.38 r_work: 0.3117 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20514 Z= 0.147 Angle : 0.626 11.594 28041 Z= 0.296 Chirality : 0.046 0.306 3348 Planarity : 0.003 0.034 3390 Dihedral : 6.501 53.586 4402 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.96 % Allowed : 13.47 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2325 helix: 1.07 (0.28), residues: 417 sheet: 0.04 (0.20), residues: 717 loop : -1.34 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 617 TYR 0.015 0.001 TYR H 50 PHE 0.015 0.001 PHE F 53 TRP 0.010 0.001 TRP M 47 HIS 0.005 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (20382) covalent geometry : angle 0.58140 / 0.29 (27687) SS BOND : bond 0.00203 / 0.13 ( 42) SS BOND : angle 1.00747 / 0.60 ( 84) hydrogen bonds : bond 0.03613 / 2.39 ( 678) hydrogen bonds : angle 4.62678 / 3.20 ( 1926) link_ALPHA1-2 : bond 0.00339 / 0.17 ( 3) link_ALPHA1-2 : angle 1.54945 / 0.83 ( 9) link_ALPHA1-3 : bond 0.00979 / 0.61 ( 9) link_ALPHA1-3 : angle 1.90545 / 1.20 ( 27) link_ALPHA1-6 : bond 0.00452 / 0.26 ( 6) link_ALPHA1-6 : angle 2.01211 / 1.12 ( 18) link_BETA1-4 : bond 0.00441 / 0.27 ( 18) link_BETA1-4 : angle 1.54936 / 1.02 ( 54) link_NAG-ASN : bond 0.00493 / 0.35 ( 54) link_NAG-ASN : angle 2.75285 / 1.98 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 252 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 ARG cc_start: 0.8827 (mmm-85) cc_final: 0.8596 (mtm-85) REVERT: A 635 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7590 (mt) REVERT: B 656 ASN cc_start: 0.8333 (m-40) cc_final: 0.8042 (m-40) REVERT: C 542 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.8237 (mtm-85) REVERT: C 638 TYR cc_start: 0.8115 (m-80) cc_final: 0.7851 (m-10) REVERT: C 660 LEU cc_start: 0.8583 (tt) cc_final: 0.7894 (mt) REVERT: E 51 THR cc_start: 0.8931 (p) cc_final: 0.8674 (p) REVERT: E 106 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7306 (mt-10) REVERT: E 189 LYS cc_start: 0.7456 (mmtm) cc_final: 0.6558 (mttp) REVERT: E 246 GLN cc_start: 0.7424 (pt0) cc_final: 0.6552 (tp-100) REVERT: F 106 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7263 (mt-10) REVERT: F 189 LYS cc_start: 0.7427 (mmtm) cc_final: 0.6598 (mttp) REVERT: F 213 ILE cc_start: 0.8804 (tt) cc_final: 0.8460 (pt) REVERT: F 290 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8519 (p) REVERT: F 428 GLN cc_start: 0.8870 (mp10) cc_final: 0.8640 (mt0) REVERT: F 475 MET cc_start: 0.7199 (mmt) cc_final: 0.6845 (mmt) REVERT: G 51 THR cc_start: 0.8908 (p) cc_final: 0.8653 (p) REVERT: G 56 SER cc_start: 0.8286 (t) cc_final: 0.8052 (m) REVERT: G 106 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7419 (mt-10) REVERT: G 189 LYS cc_start: 0.7360 (mmtm) cc_final: 0.6520 (mttp) REVERT: G 370 GLU cc_start: 0.8477 (mp0) cc_final: 0.8203 (mp0) REVERT: J 64 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6417 (tm-30) REVERT: K 27 GLN cc_start: 0.6833 (tt0) cc_final: 0.6152 (tm-30) REVERT: K 45 GLN cc_start: 0.8208 (pm20) cc_final: 0.7292 (pt0) REVERT: L 27 GLN cc_start: 0.7234 (tt0) cc_final: 0.6553 (tm-30) REVERT: L 45 GLN cc_start: 0.7970 (pm20) cc_final: 0.7145 (pt0) REVERT: M 67 VAL cc_start: 0.6109 (p) cc_final: 0.5869 (p) REVERT: M 110 THR cc_start: 0.7795 (m) cc_final: 0.7550 (p) REVERT: N 27 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7419 (tm-30) REVERT: N 28 LYS cc_start: 0.8909 (mmtp) cc_final: 0.8661 (mmtp) REVERT: N 45 GLN cc_start: 0.8110 (pm20) cc_final: 0.7065 (pt0) REVERT: N 91 THR cc_start: 0.8705 (p) cc_final: 0.8450 (p) outliers start: 62 outliers final: 53 residues processed: 290 average time/residue: 0.1304 time to fit residues: 59.1167 Evaluate side-chains 306 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 250 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 500 ARG Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 616 ASN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102013 restraints weight = 28604.683| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.11 r_work: 0.3110 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20514 Z= 0.200 Angle : 0.663 11.521 28041 Z= 0.316 Chirality : 0.047 0.311 3348 Planarity : 0.004 0.034 3390 Dihedral : 6.613 53.663 4402 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.96 % Allowed : 13.66 % Favored : 83.38 % 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: -0.79 (0.17), residues: 2325 helix: 0.91 (0.27), residues: 420 sheet: -0.01 (0.20), residues: 717 loop : -1.39 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 617 TYR 0.016 0.001 TYR H 50 PHE 0.016 0.002 PHE F 53 TRP 0.011 0.001 TRP M 47 HIS 0.006 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (20382) covalent geometry : angle 0.61911 / 0.31 (27687) SS BOND : bond 0.00241 / 0.15 ( 42) SS BOND : angle 1.08439 / 0.66 ( 84) hydrogen bonds : bond 0.03898 / 2.58 ( 678) hydrogen bonds : angle 4.68302 / 3.23 ( 1926) link_ALPHA1-2 : bond 0.00294 / 0.15 ( 3) link_ALPHA1-2 : angle 1.58751 / 0.85 ( 9) link_ALPHA1-3 : bond 0.01021 / 0.64 ( 9) link_ALPHA1-3 : angle 1.92310 / 1.20 ( 27) link_ALPHA1-6 : bond 0.00414 / 0.23 ( 6) link_ALPHA1-6 : angle 2.05267 / 1.14 ( 18) link_BETA1-4 : bond 0.00434 / 0.27 ( 18) link_BETA1-4 : angle 1.66887 / 1.07 ( 54) link_NAG-ASN : bond 0.00496 / 0.34 ( 54) link_NAG-ASN : angle 2.80219 / 2.01 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 255 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 635 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7667 (mt) REVERT: B 656 ASN cc_start: 0.8387 (m-40) cc_final: 0.8104 (m-40) REVERT: C 638 TYR cc_start: 0.8140 (m-80) cc_final: 0.7875 (m-10) REVERT: C 660 LEU cc_start: 0.8609 (tt) cc_final: 0.7914 (mt) REVERT: E 51 THR cc_start: 0.8984 (p) cc_final: 0.8736 (p) REVERT: E 106 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7353 (mt-10) REVERT: E 189 LYS cc_start: 0.7447 (mmtm) cc_final: 0.6573 (mttp) REVERT: E 246 GLN cc_start: 0.7405 (pt0) cc_final: 0.6624 (tp-100) REVERT: F 106 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7316 (mt-10) REVERT: F 189 LYS cc_start: 0.7449 (mmtm) cc_final: 0.6625 (mttp) REVERT: F 213 ILE cc_start: 0.8831 (tt) cc_final: 0.8457 (pt) REVERT: F 290 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8564 (p) REVERT: F 428 GLN cc_start: 0.8865 (mp10) cc_final: 0.8647 (mt0) REVERT: F 475 MET cc_start: 0.7209 (mmt) cc_final: 0.6866 (mmt) REVERT: G 51 THR cc_start: 0.8997 (p) cc_final: 0.8744 (p) REVERT: G 56 SER cc_start: 0.8348 (t) cc_final: 0.8124 (m) REVERT: G 106 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7422 (mt-10) REVERT: G 189 LYS cc_start: 0.7349 (mmtm) cc_final: 0.6521 (mttp) REVERT: G 246 GLN cc_start: 0.7266 (pt0) cc_final: 0.6437 (tp-100) REVERT: G 370 GLU cc_start: 0.8471 (mp0) cc_final: 0.8200 (mp0) REVERT: H 64 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6447 (tm-30) REVERT: H 76 ASN cc_start: 0.7045 (OUTLIER) cc_final: 0.6674 (t0) REVERT: J 64 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6383 (tm-30) REVERT: K 27 GLN cc_start: 0.6930 (tt0) cc_final: 0.6389 (tm-30) REVERT: K 45 GLN cc_start: 0.8250 (pm20) cc_final: 0.7355 (pt0) REVERT: L 27 GLN cc_start: 0.7344 (tt0) cc_final: 0.6599 (tm-30) REVERT: L 45 GLN cc_start: 0.8050 (pm20) cc_final: 0.7274 (pt0) REVERT: M 67 VAL cc_start: 0.6185 (p) cc_final: 0.5966 (p) REVERT: M 86 ASP cc_start: 0.6768 (t70) cc_final: 0.6545 (t70) REVERT: M 110 THR cc_start: 0.7898 (m) cc_final: 0.7626 (p) REVERT: N 27 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7461 (tm-30) REVERT: N 28 LYS cc_start: 0.8917 (mmtp) cc_final: 0.8665 (mmtp) REVERT: N 45 GLN cc_start: 0.8130 (pm20) cc_final: 0.7086 (pt0) REVERT: N 91 THR cc_start: 0.8749 (p) cc_final: 0.8497 (p) outliers start: 62 outliers final: 52 residues processed: 291 average time/residue: 0.1371 time to fit residues: 62.9592 Evaluate side-chains 307 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 250 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 500 ARG Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 207 LYS Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 6 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 121 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.138386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101742 restraints weight = 29156.207| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.34 r_work: 0.3124 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20514 Z= 0.125 Angle : 0.621 11.621 28041 Z= 0.295 Chirality : 0.046 0.306 3348 Planarity : 0.004 0.070 3390 Dihedral : 6.456 53.414 4402 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.72 % Allowed : 13.99 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2325 helix: 1.10 (0.27), residues: 417 sheet: 0.02 (0.20), residues: 717 loop : -1.31 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 542 TYR 0.015 0.001 TYR H 50 PHE 0.016 0.001 PHE H 78 TRP 0.011 0.001 TRP A 614 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (20382) covalent geometry : angle 0.57709 / 0.29 (27687) SS BOND : bond 0.00180 / 0.11 ( 42) SS BOND : angle 0.98339 / 0.59 ( 84) hydrogen bonds : bond 0.03494 / 2.31 ( 678) hydrogen bonds : angle 4.59220 / 3.17 ( 1926) link_ALPHA1-2 : bond 0.00336 / 0.17 ( 3) link_ALPHA1-2 : angle 1.61106 / 0.86 ( 9) link_ALPHA1-3 : bond 0.00935 / 0.58 ( 9) link_ALPHA1-3 : angle 1.83863 / 1.18 ( 27) link_ALPHA1-6 : bond 0.00514 / 0.29 ( 6) link_ALPHA1-6 : angle 1.94500 / 1.09 ( 18) link_BETA1-4 : bond 0.00460 / 0.28 ( 18) link_BETA1-4 : angle 1.50007 / 0.98 ( 54) link_NAG-ASN : bond 0.00496 / 0.35 ( 54) link_NAG-ASN : angle 2.72659 / 1.95 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4284.55 seconds wall clock time: 74 minutes 30.51 seconds (4470.51 seconds total)