Starting phenix.real_space_refine on Fri Aug 7 08:31:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yhq_72970/08_2026/9yhq_72970.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yhq_72970/08_2026/9yhq_72970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yhq_72970/08_2026/9yhq_72970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yhq_72970/08_2026/9yhq_72970.map" model { file = "/net/cci-nas-00/data/ceres_data/9yhq_72970/08_2026/9yhq_72970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yhq_72970/08_2026/9yhq_72970.cif" } resolution = 3.0 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= 0.013 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 120 5.16 5 C 12504 2.51 5 N 3354 2.21 5 O 3999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s 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: 19977 Number of models: 1 Model: "" Number of chains: 33 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: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1019 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "J" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1019 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "K" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "L" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "M" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1019 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "N" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 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 Chain: "K" 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: "L" 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: "N" 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 Time building chain proxies: 4.64, per 1000 atoms: 0.23 Number of scatterers: 19977 At special positions: 0 Unit cell: (169.32, 175.13, 136.12, 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 120 16.00 O 3999 8.00 N 3354 7.00 C 12504 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 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 K 201 " - " ASN K 26 " " NAG L 201 " - " ASN L 26 " " NAG N 201 " - " ASN N 26 " " 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: 1.81 Conformation dependent library (CDL) restraints added in 738.8 milliseconds 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4398 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 42 sheets defined 19.3% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 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 removed outlier: 3.512A pdb=" N ILE A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) 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 536 through 542 removed outlier: 4.005A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) 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: 3.633A 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: 3.598A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.666A 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: 4.155A 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: 3.620A 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: 3.596A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.671A 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: 4.167A 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: 3.615A 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: 3.595A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.681A 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: 4.153A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 100C removed outlier: 3.611A pdb=" N ARG H 100B" --> pdb=" O GLU H 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 100C removed outlier: 3.624A pdb=" N ARG J 100B" --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE J 100C" --> pdb=" O ASN J 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 100C removed outlier: 3.631A pdb=" N ARG M 100B" --> pdb=" O GLU M 99 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE M 100C" --> pdb=" O ASN M 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.576A pdb=" N THR A 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 4.637A 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: 3.594A pdb=" N THR B 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 4.661A 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: 3.582A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 4.636A 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: 3.917A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.416A 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 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 259 through 261 removed outlier: 6.435A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 12.278A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.039A 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: 11.178A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.278A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.780A 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: 6.981A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.861A 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: 3.919A 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 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 259 through 261 removed outlier: 6.434A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.348A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.030A pdb=" N ILE F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.259A pdb=" N LEU F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 10.865A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.187A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.039A 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: 11.187A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.865A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.259A pdb=" N LEU F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 12.030A pdb=" N ILE F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.348A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.791A 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: 6.982A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.860A 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: 3.906A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.429A 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 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 259 through 261 removed outlier: 6.437A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 12.025A pdb=" N ILE G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 12.272A pdb=" N LEU G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.153A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.153A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.272A pdb=" N LEU G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 12.025A pdb=" N ILE G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.767A 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: 6.972A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 5.854A 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 10 through 11 removed outlier: 6.218A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE H 33 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER H 52 " --> pdb=" O PHE H 33 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP H 35 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.218A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG H 96 " --> pdb=" O MET H 100J" (cutoff:3.500A) removed outlier: 6.481A pdb=" N MET H 100J" --> pdb=" O ARG H 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.218A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE J 33 " --> pdb=" O SER J 52 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER J 52 " --> pdb=" O PHE J 33 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP J 35 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU J 50 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.218A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ARG J 96 " --> pdb=" O MET J 100J" (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET J 100J" --> pdb=" O ARG J 96 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.327A pdb=" N GLU K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU K 33 " --> pdb=" O HIS K 49 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N HIS K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 20 through 23 removed outlier: 3.576A pdb=" N ASP K 70 " --> pdb=" O ALA K 67 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.332A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 20 through 23 removed outlier: 3.580A pdb=" N ASP L 70 " --> pdb=" O ALA L 67 " (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 10 through 11 removed outlier: 6.217A pdb=" N GLY M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE M 33 " --> pdb=" O SER M 52 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER M 52 " --> pdb=" O PHE M 33 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP M 35 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU M 50 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.217A pdb=" N GLY M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ARG M 96 " --> pdb=" O MET M 100J" (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET M 100J" --> pdb=" O ARG M 96 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.319A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE N 85 " --> pdb=" O GLN N 38 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU N 33 " --> pdb=" O HIS N 49 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N HIS N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 20 through 23 removed outlier: 3.555A pdb=" N ASP N 70 " --> pdb=" O ALA N 67 " (cutoff:3.500A) 685 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 2.32 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: 6254 1.34 - 1.46: 4459 1.46 - 1.58: 9525 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 20394 Sorted by residual: bond pdb=" C1 MAN S 6 " pdb=" O5 MAN S 6 " 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 W 6 " pdb=" O5 MAN W 6 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C1 MAN O 6 " pdb=" O5 MAN O 6 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C1 MAN O 5 " pdb=" O5 MAN O 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 MAN W 5 " pdb=" O5 MAN W 5 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.40e+00 ... (remaining 20389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 26818 1.77 - 3.55: 759 3.55 - 5.32: 99 5.32 - 7.10: 17 7.10 - 8.87: 6 Bond angle restraints: 27699 Sorted by residual: angle pdb=" C1 BMA U 3 " pdb=" O5 BMA U 3 " pdb=" C5 BMA U 3 " ideal model delta sigma weight residual 118.82 109.95 8.87 3.00e+00 1.11e-01 8.75e+00 angle pdb=" C1 BMA Q 3 " pdb=" O5 BMA Q 3 " pdb=" C5 BMA Q 3 " ideal model delta sigma weight residual 118.82 109.97 8.85 3.00e+00 1.11e-01 8.70e+00 angle pdb=" C1 BMA D 3 " pdb=" O5 BMA D 3 " pdb=" C5 BMA D 3 " ideal model delta sigma weight residual 118.82 110.00 8.82 3.00e+00 1.11e-01 8.65e+00 angle pdb=" C1 BMA W 3 " pdb=" O5 BMA W 3 " pdb=" C5 BMA W 3 " ideal model delta sigma weight residual 118.82 110.04 8.78 3.00e+00 1.11e-01 8.57e+00 angle pdb=" C1 BMA O 3 " pdb=" O5 BMA O 3 " pdb=" C5 BMA O 3 " ideal model delta sigma weight residual 118.82 110.08 8.74 3.00e+00 1.11e-01 8.49e+00 ... (remaining 27694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.73: 12840 24.73 - 49.47: 385 49.47 - 74.20: 47 74.20 - 98.93: 30 98.93 - 123.67: 81 Dihedral angle restraints: 13383 sinusoidal: 6558 harmonic: 6825 Sorted by residual: 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 66.04 -123.67 1 3.00e+01 1.11e-03 1.66e+01 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 65.99 -123.62 1 3.00e+01 1.11e-03 1.66e+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 65.98 -123.61 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 13380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.018: 3339 1.018 - 2.036: 0 2.036 - 3.055: 0 3.055 - 4.073: 0 4.073 - 5.091: 15 Chirality restraints: 3354 Sorted by residual: 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 2.56 -5.09 2.00e-01 2.50e+01 6.48e+02 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 2.56 -5.09 2.00e-01 2.50e+01 6.48e+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 2.56 -5.09 2.00e-01 2.50e+01 6.47e+02 ... (remaining 3351 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO H 14 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS M 13 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO M 14 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO M 14 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO M 14 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 13 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO J 14 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO J 14 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO J 14 " 0.023 5.00e-02 4.00e+02 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 11013 3.01 - 3.48: 18069 3.48 - 3.95: 31832 3.95 - 4.43: 36510 4.43 - 4.90: 60674 Nonbonded interactions: 158098 Sorted by model distance: nonbonded pdb=" O5 NAG D 1 " pdb=" O6 NAG D 1 " model vdw 2.535 2.432 nonbonded pdb=" O5 NAG Q 1 " pdb=" O6 NAG Q 1 " model vdw 2.537 2.432 nonbonded pdb=" O5 NAG U 1 " pdb=" O6 NAG U 1 " model vdw 2.544 2.432 nonbonded pdb=" O ASN F 156 " pdb=" OD1 ASN F 156 " model vdw 2.560 3.040 nonbonded pdb=" O ASN G 156 " pdb=" OD1 ASN G 156 " model vdw 2.563 3.040 ... (remaining 158093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain '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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.990 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: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.005 0.039 20529 Z= 0.224 Angle : 0.688 8.875 28062 Z= 0.310 Chirality : 0.339 5.091 3354 Planarity : 0.003 0.041 3399 Dihedral : 15.944 123.665 8859 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.95 % Allowed : 4.90 % Favored : 94.14 % 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: -0.56 (0.17), residues: 2313 helix: 1.23 (0.27), residues: 408 sheet: -0.07 (0.19), residues: 684 loop : -1.10 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 298 TYR 0.007 0.001 TYR H 91 PHE 0.014 0.001 PHE F 53 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS N 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (20394) covalent geometry : angle 0.66158 / 0.30 (27699) SS BOND : bond 0.00202 / 0.13 ( 42) SS BOND : angle 0.74836 / 0.52 ( 84) hydrogen bonds : bond 0.10122 / 6.58 ( 658) hydrogen bonds : angle 5.86593 / 4.20 ( 1836) link_ALPHA1-2 : bond 0.00485 / 0.24 ( 3) link_ALPHA1-2 : angle 0.37854 / 0.18 ( 9) link_ALPHA1-3 : bond 0.00187 / 0.11 ( 9) link_ALPHA1-3 : angle 0.68656 / 0.38 ( 27) link_ALPHA1-6 : bond 0.00107 / 0.06 ( 6) link_ALPHA1-6 : angle 0.41959 / 0.26 ( 18) link_BETA1-4 : bond 0.01112 / 0.59 ( 18) link_BETA1-4 : angle 1.99146 / 1.27 ( 54) link_NAG-ASN : bond 0.00430 / 0.30 ( 57) link_NAG-ASN : angle 2.25712 / 1.47 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 365 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 635 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.7080 (mt) REVERT: C 638 TYR cc_start: 0.7439 (m-10) cc_final: 0.7228 (m-10) REVERT: E 46 LYS cc_start: 0.7658 (ttpp) cc_final: 0.7425 (mptt) REVERT: E 51 THR cc_start: 0.8422 (p) cc_final: 0.8200 (p) REVERT: E 153 GLU cc_start: 0.7490 (mp0) cc_final: 0.7034 (tt0) REVERT: E 211 GLU cc_start: 0.7839 (tt0) cc_final: 0.7577 (tt0) REVERT: E 278 THR cc_start: 0.8367 (m) cc_final: 0.7832 (p) REVERT: E 490 LYS cc_start: 0.8397 (ttpt) cc_final: 0.7937 (ttpp) REVERT: F 46 LYS cc_start: 0.7681 (ttpp) cc_final: 0.7434 (mptt) REVERT: F 51 THR cc_start: 0.8443 (p) cc_final: 0.8239 (p) REVERT: F 153 GLU cc_start: 0.7420 (mp0) cc_final: 0.7066 (tt0) REVERT: F 211 GLU cc_start: 0.7842 (tt0) cc_final: 0.7553 (tt0) REVERT: F 490 LYS cc_start: 0.8396 (ttpt) cc_final: 0.7802 (ttpp) REVERT: G 51 THR cc_start: 0.8304 (p) cc_final: 0.8097 (p) REVERT: G 114 GLN cc_start: 0.7698 (mt0) cc_final: 0.7445 (mt0) REVERT: G 178 ARG cc_start: 0.7795 (ttt180) cc_final: 0.7208 (tpt170) REVERT: G 211 GLU cc_start: 0.7882 (tt0) cc_final: 0.7562 (tt0) REVERT: G 278 THR cc_start: 0.8324 (m) cc_final: 0.7745 (p) REVERT: G 490 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7739 (ttpp) REVERT: H 2 VAL cc_start: 0.6546 (OUTLIER) cc_final: 0.6282 (p) REVERT: N 4 MET cc_start: 0.6779 (mmp) cc_final: 0.6562 (mmm) outliers start: 20 outliers final: 6 residues processed: 378 average time/residue: 0.5322 time to fit residues: 231.6949 Evaluate side-chains 252 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 244 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain M residue 93 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS A 651 ASN B 618 ASN B 651 ASN C 618 ASN C 651 ASN E 80 ASN E 99 ASN E 105 HIS E 348 GLN E 356 ASN F 80 ASN F 105 HIS F 348 GLN F 356 ASN G 80 ASN G 105 HIS G 348 GLN G 356 ASN H 6 GLN J 5 GLN J 6 GLN K 42 GLN K 49 HIS L 17 GLN L 42 GLN M 6 GLN N 37 GLN N 42 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.168819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121000 restraints weight = 25900.178| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.80 r_work: 0.3287 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 20529 Z= 0.114 Angle : 0.619 11.195 28062 Z= 0.286 Chirality : 0.047 0.325 3354 Planarity : 0.004 0.060 3399 Dihedral : 9.296 76.433 4450 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.05 % Allowed : 10.90 % Favored : 86.05 % 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: -0.42 (0.17), residues: 2313 helix: 1.31 (0.27), residues: 408 sheet: 0.04 (0.20), residues: 684 loop : -1.01 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 96 TYR 0.009 0.001 TYR M 59 PHE 0.023 0.001 PHE F 53 TRP 0.007 0.001 TRP N 94 HIS 0.004 0.001 HIS L 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (20394) covalent geometry : angle 0.56034 / 0.27 (27699) SS BOND : bond 0.00411 / 0.26 ( 42) SS BOND : angle 0.81894 / 0.49 ( 84) hydrogen bonds : bond 0.03666 / 2.40 ( 658) hydrogen bonds : angle 5.11986 / 3.62 ( 1836) link_ALPHA1-2 : bond 0.00514 / 0.26 ( 3) link_ALPHA1-2 : angle 1.54676 / 0.86 ( 9) link_ALPHA1-3 : bond 0.01396 / 0.87 ( 9) link_ALPHA1-3 : angle 2.74068 / 1.93 ( 27) link_ALPHA1-6 : bond 0.00416 / 0.23 ( 6) link_ALPHA1-6 : angle 2.08943 / 1.16 ( 18) link_BETA1-4 : bond 0.00684 / 0.38 ( 18) link_BETA1-4 : angle 3.76652 / 2.96 ( 54) link_NAG-ASN : bond 0.00481 / 0.33 ( 57) link_NAG-ASN : angle 2.34002 / 1.55 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 257 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 657 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6356 (mp0) REVERT: B 542 ARG cc_start: 0.8408 (mtp180) cc_final: 0.8036 (mmm-85) REVERT: B 659 ASP cc_start: 0.7605 (t0) cc_final: 0.7404 (t0) REVERT: E 46 LYS cc_start: 0.7789 (ttpp) cc_final: 0.7428 (mptt) REVERT: E 153 GLU cc_start: 0.7905 (mp0) cc_final: 0.7185 (tt0) REVERT: E 178 ARG cc_start: 0.8328 (ttt180) cc_final: 0.7613 (tmt170) REVERT: E 278 THR cc_start: 0.8217 (m) cc_final: 0.7695 (p) REVERT: E 490 LYS cc_start: 0.8372 (ttpt) cc_final: 0.7960 (ttpp) REVERT: F 46 LYS cc_start: 0.7822 (ttpp) cc_final: 0.7440 (mptt) REVERT: F 153 GLU cc_start: 0.7847 (mp0) cc_final: 0.7217 (tt0) REVERT: F 490 LYS cc_start: 0.8383 (ttpt) cc_final: 0.7736 (ttpp) REVERT: G 114 GLN cc_start: 0.7807 (mt0) cc_final: 0.7598 (mt0) REVERT: G 153 GLU cc_start: 0.7707 (mp0) cc_final: 0.7058 (tt0) REVERT: G 178 ARG cc_start: 0.8198 (ttt180) cc_final: 0.7380 (tpt170) REVERT: G 211 GLU cc_start: 0.8041 (tt0) cc_final: 0.7823 (tt0) REVERT: G 278 THR cc_start: 0.8194 (m) cc_final: 0.7657 (p) REVERT: G 490 LYS cc_start: 0.8251 (ttpt) cc_final: 0.7794 (ttpp) REVERT: H 96 ARG cc_start: 0.8050 (ptm-80) cc_final: 0.7780 (ptm-80) REVERT: H 98 ASP cc_start: 0.7565 (t0) cc_final: 0.7315 (t0) REVERT: H 99 GLU cc_start: 0.8084 (pm20) cc_final: 0.7418 (pm20) REVERT: N 4 MET cc_start: 0.7175 (mmp) cc_final: 0.6483 (mmm) outliers start: 64 outliers final: 19 residues processed: 296 average time/residue: 0.5169 time to fit residues: 175.7695 Evaluate side-chains 255 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 352 HIS Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 15 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 20 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 66 HIS E 80 ASN E 352 HIS E 356 ASN F 66 HIS F 216 HIS F 356 ASN G 66 HIS G 356 ASN H 5 GLN M 5 GLN M 81 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.164282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116820 restraints weight = 25864.695| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.73 r_work: 0.3226 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20529 Z= 0.155 Angle : 0.620 11.266 28062 Z= 0.296 Chirality : 0.047 0.336 3354 Planarity : 0.004 0.043 3399 Dihedral : 8.602 73.526 4442 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.10 % Allowed : 11.24 % Favored : 84.67 % 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 (0.17), residues: 2313 helix: 1.18 (0.27), residues: 411 sheet: 0.04 (0.20), residues: 672 loop : -1.06 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 542 TYR 0.011 0.001 TYR J 59 PHE 0.015 0.002 PHE H 78 TRP 0.009 0.001 TRP F 338 HIS 0.004 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (20394) covalent geometry : angle 0.57066 / 0.29 (27699) SS BOND : bond 0.00210 / 0.13 ( 42) SS BOND : angle 0.93936 / 0.57 ( 84) hydrogen bonds : bond 0.03940 / 2.58 ( 658) hydrogen bonds : angle 5.04108 / 3.57 ( 1836) link_ALPHA1-2 : bond 0.00780 / 0.39 ( 3) link_ALPHA1-2 : angle 1.11811 / 0.63 ( 9) link_ALPHA1-3 : bond 0.00974 / 0.61 ( 9) link_ALPHA1-3 : angle 1.74519 / 1.17 ( 27) link_ALPHA1-6 : bond 0.00411 / 0.23 ( 6) link_ALPHA1-6 : angle 2.24120 / 1.14 ( 18) link_BETA1-4 : bond 0.00451 / 0.27 ( 18) link_BETA1-4 : angle 1.95511 / 1.41 ( 54) link_NAG-ASN : bond 0.00465 / 0.34 ( 57) link_NAG-ASN : angle 2.74243 / 1.81 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 242 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 657 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: C 535 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7794 (mpp) REVERT: E 46 LYS cc_start: 0.7830 (ttpp) cc_final: 0.7440 (mptt) REVERT: E 102 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: E 153 GLU cc_start: 0.7948 (mp0) cc_final: 0.7221 (tt0) REVERT: E 178 ARG cc_start: 0.8372 (ttt180) cc_final: 0.7580 (tpt170) REVERT: E 278 THR cc_start: 0.8222 (m) cc_final: 0.7722 (p) REVERT: E 356 ASN cc_start: 0.6523 (t0) cc_final: 0.6122 (p0) REVERT: E 490 LYS cc_start: 0.8390 (ttpt) cc_final: 0.7913 (ttpp) REVERT: F 46 LYS cc_start: 0.7842 (ttpp) cc_final: 0.7453 (mptt) REVERT: F 102 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: F 153 GLU cc_start: 0.7893 (mp0) cc_final: 0.7239 (tt0) REVERT: F 178 ARG cc_start: 0.8398 (ttt180) cc_final: 0.7508 (tpt90) REVERT: F 356 ASN cc_start: 0.6415 (t0) cc_final: 0.6185 (p0) REVERT: F 358 ILE cc_start: 0.8250 (mp) cc_final: 0.7983 (OUTLIER) REVERT: F 490 LYS cc_start: 0.8402 (ttpt) cc_final: 0.7837 (ttpp) REVERT: G 114 GLN cc_start: 0.7833 (mt0) cc_final: 0.7630 (mt0) REVERT: G 153 GLU cc_start: 0.7810 (mp0) cc_final: 0.7150 (tt0) REVERT: G 178 ARG cc_start: 0.8365 (ttt180) cc_final: 0.7564 (tpt170) REVERT: G 278 THR cc_start: 0.8224 (m) cc_final: 0.7676 (p) REVERT: G 490 LYS cc_start: 0.8306 (ttpt) cc_final: 0.7851 (ttpp) REVERT: H 96 ARG cc_start: 0.8230 (ptm-80) cc_final: 0.7897 (ptm-80) REVERT: K 30 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.6444 (mtmm) REVERT: K 45 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7582 (ttp80) REVERT: L 45 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7243 (ttp80) REVERT: M 99 GLU cc_start: 0.8083 (pm20) cc_final: 0.7665 (pm20) outliers start: 86 outliers final: 30 residues processed: 290 average time/residue: 0.5513 time to fit residues: 183.6743 Evaluate side-chains 266 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 0.0040 chunk 170 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 223 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 80 ASN E 352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.161716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114000 restraints weight = 25759.857| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.72 r_work: 0.3192 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20529 Z= 0.188 Angle : 0.648 11.120 28062 Z= 0.311 Chirality : 0.048 0.344 3354 Planarity : 0.004 0.042 3399 Dihedral : 8.024 71.124 4441 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.62 % Allowed : 11.95 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.17), residues: 2313 helix: 0.81 (0.26), residues: 429 sheet: -0.07 (0.20), residues: 684 loop : -1.05 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 542 TYR 0.012 0.001 TYR G 217 PHE 0.015 0.002 PHE M 78 TRP 0.011 0.001 TRP G 427 HIS 0.004 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (20394) covalent geometry : angle 0.59946 / 0.30 (27699) SS BOND : bond 0.00253 / 0.16 ( 42) SS BOND : angle 0.90426 / 0.57 ( 84) hydrogen bonds : bond 0.04161 / 2.71 ( 658) hydrogen bonds : angle 5.07572 / 3.60 ( 1836) link_ALPHA1-2 : bond 0.00719 / 0.36 ( 3) link_ALPHA1-2 : angle 1.18857 / 0.66 ( 9) link_ALPHA1-3 : bond 0.00956 / 0.60 ( 9) link_ALPHA1-3 : angle 2.08020 / 1.34 ( 27) link_ALPHA1-6 : bond 0.00401 / 0.23 ( 6) link_ALPHA1-6 : angle 2.33147 / 1.17 ( 18) link_BETA1-4 : bond 0.00336 / 0.21 ( 18) link_BETA1-4 : angle 2.11718 / 1.51 ( 54) link_NAG-ASN : bond 0.00489 / 0.36 ( 57) link_NAG-ASN : angle 2.74941 / 1.81 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 229 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 657 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: B 655 LYS cc_start: 0.7883 (ttpp) cc_final: 0.7657 (ttpp) REVERT: E 46 LYS cc_start: 0.7842 (ttpp) cc_final: 0.7441 (mptt) REVERT: E 97 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8265 (mtmp) REVERT: E 102 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: E 153 GLU cc_start: 0.8025 (mp0) cc_final: 0.7228 (tt0) REVERT: E 178 ARG cc_start: 0.8440 (ttt180) cc_final: 0.7621 (tpt170) REVERT: E 278 THR cc_start: 0.8275 (m) cc_final: 0.7786 (p) REVERT: E 356 ASN cc_start: 0.6649 (t0) cc_final: 0.6311 (p0) REVERT: E 490 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7909 (ttpp) REVERT: F 46 LYS cc_start: 0.7821 (ttpp) cc_final: 0.7422 (mptt) REVERT: F 153 GLU cc_start: 0.8018 (mp0) cc_final: 0.7279 (tt0) REVERT: F 178 ARG cc_start: 0.8500 (ttt180) cc_final: 0.7726 (tmt170) REVERT: F 358 ILE cc_start: 0.8283 (mp) cc_final: 0.8019 (OUTLIER) REVERT: F 490 LYS cc_start: 0.8352 (ttpt) cc_final: 0.7795 (ttpp) REVERT: G 46 LYS cc_start: 0.7988 (mptt) cc_final: 0.7717 (mttp) REVERT: G 153 GLU cc_start: 0.7914 (mp0) cc_final: 0.7153 (tt0) REVERT: G 178 ARG cc_start: 0.8458 (ttt180) cc_final: 0.7602 (tmt170) REVERT: G 231 LYS cc_start: 0.8227 (mmtp) cc_final: 0.8019 (mtpp) REVERT: G 278 THR cc_start: 0.8220 (m) cc_final: 0.7668 (p) REVERT: G 490 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7794 (ttpp) REVERT: H 58 ASN cc_start: 0.7532 (t0) cc_final: 0.6904 (t0) REVERT: H 77 GLN cc_start: 0.6963 (tt0) cc_final: 0.6746 (tt0) REVERT: H 96 ARG cc_start: 0.8344 (ptm-80) cc_final: 0.7858 (ptm-80) REVERT: J 98 ASP cc_start: 0.7721 (t0) cc_final: 0.7485 (t0) REVERT: K 30 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.6552 (mtmm) REVERT: K 45 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7518 (ttp80) REVERT: M 99 GLU cc_start: 0.8083 (pm20) cc_final: 0.7584 (pm20) outliers start: 97 outliers final: 34 residues processed: 289 average time/residue: 0.5654 time to fit residues: 186.8866 Evaluate side-chains 254 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 112 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 352 HIS E 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.162957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115051 restraints weight = 25686.524| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.74 r_work: 0.3203 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20529 Z= 0.149 Angle : 0.606 11.562 28062 Z= 0.293 Chirality : 0.047 0.336 3354 Planarity : 0.004 0.041 3399 Dihedral : 7.570 69.415 4441 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.71 % Allowed : 13.76 % Favored : 82.52 % 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: -0.55 (0.17), residues: 2313 helix: 0.88 (0.26), residues: 429 sheet: -0.03 (0.20), residues: 684 loop : -1.00 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 542 TYR 0.009 0.001 TYR G 217 PHE 0.013 0.001 PHE M 78 TRP 0.009 0.001 TRP G 427 HIS 0.004 0.001 HIS L 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (20394) covalent geometry : angle 0.55929 / 0.28 (27699) SS BOND : bond 0.00208 / 0.13 ( 42) SS BOND : angle 0.81644 / 0.54 ( 84) hydrogen bonds : bond 0.03859 / 2.51 ( 658) hydrogen bonds : angle 4.94445 / 3.51 ( 1836) link_ALPHA1-2 : bond 0.00785 / 0.39 ( 3) link_ALPHA1-2 : angle 1.18724 / 0.67 ( 9) link_ALPHA1-3 : bond 0.00991 / 0.61 ( 9) link_ALPHA1-3 : angle 1.88227 / 1.24 ( 27) link_ALPHA1-6 : bond 0.00463 / 0.26 ( 6) link_ALPHA1-6 : angle 2.32395 / 1.16 ( 18) link_BETA1-4 : bond 0.00369 / 0.23 ( 18) link_BETA1-4 : angle 1.88199 / 1.30 ( 54) link_NAG-ASN : bond 0.00465 / 0.35 ( 57) link_NAG-ASN : angle 2.62308 / 1.72 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 230 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 634 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7211 (tt0) REVERT: A 657 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: B 535 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7265 (mpt) REVERT: E 46 LYS cc_start: 0.7785 (ttpp) cc_final: 0.7404 (mptt) REVERT: E 69 TRP cc_start: 0.7231 (OUTLIER) cc_final: 0.6589 (p90) REVERT: E 102 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: E 153 GLU cc_start: 0.8071 (mp0) cc_final: 0.7191 (tt0) REVERT: E 178 ARG cc_start: 0.8466 (ttt180) cc_final: 0.7644 (tpt170) REVERT: E 278 THR cc_start: 0.8253 (m) cc_final: 0.7758 (p) REVERT: E 356 ASN cc_start: 0.6656 (t0) cc_final: 0.6347 (p0) REVERT: E 490 LYS cc_start: 0.8329 (ttpt) cc_final: 0.7847 (ttpp) REVERT: F 46 LYS cc_start: 0.7804 (ttpp) cc_final: 0.7421 (mptt) REVERT: F 153 GLU cc_start: 0.8034 (mp0) cc_final: 0.7273 (tt0) REVERT: F 178 ARG cc_start: 0.8567 (ttt180) cc_final: 0.7762 (tmt170) REVERT: F 490 LYS cc_start: 0.8360 (ttpt) cc_final: 0.7711 (ttpp) REVERT: G 98 ASN cc_start: 0.8314 (t0) cc_final: 0.8026 (t0) REVERT: G 153 GLU cc_start: 0.7950 (mp0) cc_final: 0.7143 (tt0) REVERT: G 178 ARG cc_start: 0.8474 (ttt180) cc_final: 0.7601 (tmt170) REVERT: G 231 LYS cc_start: 0.8256 (mmtp) cc_final: 0.8024 (mtpp) REVERT: G 278 THR cc_start: 0.8210 (m) cc_final: 0.7670 (p) REVERT: G 490 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7805 (ttpp) REVERT: H 58 ASN cc_start: 0.7571 (t0) cc_final: 0.6945 (t0) REVERT: H 96 ARG cc_start: 0.8338 (ptm-80) cc_final: 0.7868 (ptm-80) REVERT: J 98 ASP cc_start: 0.7685 (t0) cc_final: 0.7451 (t0) REVERT: K 30 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7517 (mppt) REVERT: K 45 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7502 (ttp80) REVERT: M 96 ARG cc_start: 0.8330 (ptm-80) cc_final: 0.8028 (ptm-80) REVERT: M 98 ASP cc_start: 0.7613 (t0) cc_final: 0.7311 (t0) outliers start: 78 outliers final: 34 residues processed: 279 average time/residue: 0.4742 time to fit residues: 151.6475 Evaluate side-chains 263 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 106 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 203 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 352 HIS F 98 ASN J 77 GLN J 81 HIS L 37 GLN M 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.164259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117429 restraints weight = 25627.940| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.63 r_work: 0.3237 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20529 Z= 0.112 Angle : 0.563 11.517 28062 Z= 0.272 Chirality : 0.045 0.332 3354 Planarity : 0.004 0.066 3399 Dihedral : 7.124 66.724 4441 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.14 % Allowed : 15.10 % Favored : 81.76 % 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: -0.37 (0.17), residues: 2313 helix: 1.35 (0.27), residues: 408 sheet: 0.05 (0.20), residues: 690 loop : -0.97 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 542 TYR 0.007 0.001 TYR E 173 PHE 0.012 0.001 PHE J 78 TRP 0.008 0.001 TRP G 112 HIS 0.004 0.001 HIS L 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (20394) covalent geometry : angle 0.51867 / 0.26 (27699) SS BOND : bond 0.00217 / 0.12 ( 42) SS BOND : angle 0.67214 / 0.46 ( 84) hydrogen bonds : bond 0.03520 / 2.31 ( 658) hydrogen bonds : angle 4.79262 / 3.40 ( 1836) link_ALPHA1-2 : bond 0.00719 / 0.36 ( 3) link_ALPHA1-2 : angle 1.25157 / 0.70 ( 9) link_ALPHA1-3 : bond 0.00977 / 0.60 ( 9) link_ALPHA1-3 : angle 1.91112 / 1.27 ( 27) link_ALPHA1-6 : bond 0.00559 / 0.32 ( 6) link_ALPHA1-6 : angle 2.27239 / 1.13 ( 18) link_BETA1-4 : bond 0.00357 / 0.22 ( 18) link_BETA1-4 : angle 1.68522 / 1.14 ( 54) link_NAG-ASN : bond 0.00451 / 0.34 ( 57) link_NAG-ASN : angle 2.47899 / 1.62 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 229 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8408 (mtmt) REVERT: B 617 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7734 (ttm-80) REVERT: C 626 MET cc_start: 0.8002 (ttt) cc_final: 0.7543 (ttm) REVERT: E 46 LYS cc_start: 0.7809 (ttpp) cc_final: 0.7465 (mptt) REVERT: E 69 TRP cc_start: 0.7251 (OUTLIER) cc_final: 0.6622 (p90) REVERT: E 98 ASN cc_start: 0.8334 (t0) cc_final: 0.8041 (t0) REVERT: E 153 GLU cc_start: 0.8047 (mp0) cc_final: 0.7171 (tt0) REVERT: E 178 ARG cc_start: 0.8460 (ttt180) cc_final: 0.7668 (tpt170) REVERT: E 211 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: E 278 THR cc_start: 0.8261 (m) cc_final: 0.7757 (p) REVERT: E 356 ASN cc_start: 0.6667 (t0) cc_final: 0.6354 (p0) REVERT: E 490 LYS cc_start: 0.8397 (ttpt) cc_final: 0.7924 (ttpp) REVERT: F 46 LYS cc_start: 0.7835 (ttpp) cc_final: 0.7482 (mptt) REVERT: F 153 GLU cc_start: 0.8028 (mp0) cc_final: 0.7311 (tt0) REVERT: F 178 ARG cc_start: 0.8554 (ttt180) cc_final: 0.7764 (tmt170) REVERT: F 490 LYS cc_start: 0.8378 (ttpt) cc_final: 0.7757 (ttpp) REVERT: G 46 LYS cc_start: 0.7990 (mptt) cc_final: 0.7564 (mttp) REVERT: G 47 ASP cc_start: 0.8482 (p0) cc_final: 0.8230 (m-30) REVERT: G 98 ASN cc_start: 0.8264 (t0) cc_final: 0.7919 (t0) REVERT: G 153 GLU cc_start: 0.7925 (mp0) cc_final: 0.7148 (tt0) REVERT: G 178 ARG cc_start: 0.8459 (ttt180) cc_final: 0.7603 (tmt170) REVERT: G 231 LYS cc_start: 0.8290 (mmtp) cc_final: 0.8049 (mtpp) REVERT: G 278 THR cc_start: 0.8210 (m) cc_final: 0.7666 (p) REVERT: G 490 LYS cc_start: 0.8321 (ttpt) cc_final: 0.7881 (ttpp) REVERT: H 58 ASN cc_start: 0.7544 (t0) cc_final: 0.6907 (t0) REVERT: H 77 GLN cc_start: 0.6866 (tt0) cc_final: 0.6477 (tt0) REVERT: H 96 ARG cc_start: 0.8251 (ptm-80) cc_final: 0.7790 (ptm-80) REVERT: J 77 GLN cc_start: 0.6652 (tt0) cc_final: 0.6174 (tm-30) REVERT: J 99 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7941 (pm20) REVERT: K 45 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7511 (ttp80) REVERT: M 96 ARG cc_start: 0.8326 (ptm-80) cc_final: 0.7999 (ptm-80) REVERT: M 98 ASP cc_start: 0.7555 (t0) cc_final: 0.7288 (t0) outliers start: 66 outliers final: 29 residues processed: 270 average time/residue: 0.5749 time to fit residues: 177.0274 Evaluate side-chains 250 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 19 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 chunk 60 optimal weight: 0.3980 chunk 186 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 352 HIS F 440 GLN G 216 HIS G 352 HIS G 440 GLN L 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113216 restraints weight = 25644.993| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.59 r_work: 0.3189 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20529 Z= 0.188 Angle : 0.635 11.264 28062 Z= 0.306 Chirality : 0.048 0.348 3354 Planarity : 0.004 0.058 3399 Dihedral : 7.278 66.979 4441 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.29 % Allowed : 15.71 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2313 helix: 0.84 (0.26), residues: 429 sheet: 0.01 (0.20), residues: 690 loop : -1.00 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 542 TYR 0.011 0.001 TYR G 217 PHE 0.015 0.002 PHE J 78 TRP 0.014 0.001 TRP G 427 HIS 0.005 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (20394) covalent geometry : angle 0.59173 / 0.30 (27699) SS BOND : bond 0.00225 / 0.14 ( 42) SS BOND : angle 1.05401 / 0.73 ( 84) hydrogen bonds : bond 0.04100 / 2.68 ( 658) hydrogen bonds : angle 4.98671 / 3.53 ( 1836) link_ALPHA1-2 : bond 0.00788 / 0.40 ( 3) link_ALPHA1-2 : angle 1.19497 / 0.66 ( 9) link_ALPHA1-3 : bond 0.00994 / 0.62 ( 9) link_ALPHA1-3 : angle 1.88552 / 1.23 ( 27) link_ALPHA1-6 : bond 0.00467 / 0.26 ( 6) link_ALPHA1-6 : angle 2.41592 / 1.20 ( 18) link_BETA1-4 : bond 0.00356 / 0.22 ( 18) link_BETA1-4 : angle 1.78771 / 1.15 ( 54) link_NAG-ASN : bond 0.00453 / 0.34 ( 57) link_NAG-ASN : angle 2.59280 / 1.70 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 220 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 657 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6283 (mp0) REVERT: B 535 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7278 (mpt) REVERT: B 617 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7715 (ttm-80) REVERT: E 46 LYS cc_start: 0.7913 (ttpp) cc_final: 0.7523 (mptt) REVERT: E 69 TRP cc_start: 0.7306 (OUTLIER) cc_final: 0.6618 (p90) REVERT: E 102 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: E 153 GLU cc_start: 0.8078 (mp0) cc_final: 0.7250 (tt0) REVERT: E 178 ARG cc_start: 0.8541 (ttt180) cc_final: 0.7774 (tpt170) REVERT: E 211 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: E 278 THR cc_start: 0.8318 (m) cc_final: 0.7810 (p) REVERT: E 356 ASN cc_start: 0.6681 (t0) cc_final: 0.6442 (p0) REVERT: E 490 LYS cc_start: 0.8445 (ttpt) cc_final: 0.7974 (ttpp) REVERT: F 46 LYS cc_start: 0.7906 (ttpp) cc_final: 0.7529 (mptt) REVERT: F 153 GLU cc_start: 0.8065 (mp0) cc_final: 0.7367 (tt0) REVERT: F 178 ARG cc_start: 0.8641 (ttt180) cc_final: 0.7830 (tmt170) REVERT: F 440 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8566 (tp-100) REVERT: F 490 LYS cc_start: 0.8476 (ttpt) cc_final: 0.7886 (ttpp) REVERT: G 46 LYS cc_start: 0.8014 (mptt) cc_final: 0.7719 (mttp) REVERT: G 98 ASN cc_start: 0.8407 (t0) cc_final: 0.8132 (t0) REVERT: G 153 GLU cc_start: 0.7945 (mp0) cc_final: 0.7186 (tt0) REVERT: G 178 ARG cc_start: 0.8541 (ttt180) cc_final: 0.7700 (tmt170) REVERT: G 231 LYS cc_start: 0.8342 (mmtp) cc_final: 0.8113 (mtpp) REVERT: G 490 LYS cc_start: 0.8393 (ttpt) cc_final: 0.7945 (ttpp) REVERT: H 58 ASN cc_start: 0.7668 (t0) cc_final: 0.7064 (t0) REVERT: H 99 GLU cc_start: 0.7888 (pm20) cc_final: 0.7283 (pm20) REVERT: J 77 GLN cc_start: 0.6764 (tt0) cc_final: 0.6325 (tm-30) REVERT: K 45 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7500 (ttp80) REVERT: L 45 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7213 (ttp80) REVERT: M 96 ARG cc_start: 0.8461 (ptm-80) cc_final: 0.8257 (ptm-80) REVERT: M 98 ASP cc_start: 0.7531 (t0) cc_final: 0.7276 (t0) outliers start: 69 outliers final: 33 residues processed: 263 average time/residue: 0.5690 time to fit residues: 171.6063 Evaluate side-chains 254 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 440 GLN Chi-restraints excluded: chain F residue 449 ILE Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 71 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 618 ASN E 352 HIS H 77 GLN M 39 GLN N 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.157568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110662 restraints weight = 25761.803| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.61 r_work: 0.3158 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 20529 Z= 0.257 Angle : 0.709 11.116 28062 Z= 0.343 Chirality : 0.050 0.364 3354 Planarity : 0.005 0.050 3399 Dihedral : 7.693 68.482 4441 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.24 % Allowed : 15.57 % Favored : 81.19 % 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: -0.74 (0.17), residues: 2313 helix: 0.55 (0.25), residues: 426 sheet: -0.02 (0.20), residues: 690 loop : -1.15 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 542 TYR 0.015 0.002 TYR G 217 PHE 0.016 0.002 PHE E 159 TRP 0.018 0.002 TRP G 427 HIS 0.004 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.26 (20394) covalent geometry : angle 0.66516 / 0.33 (27699) SS BOND : bond 0.00297 / 0.18 ( 42) SS BOND : angle 1.34131 / 0.95 ( 84) hydrogen bonds : bond 0.04584 / 2.98 ( 658) hydrogen bonds : angle 5.16248 / 3.66 ( 1836) link_ALPHA1-2 : bond 0.00816 / 0.41 ( 3) link_ALPHA1-2 : angle 1.06097 / 0.59 ( 9) link_ALPHA1-3 : bond 0.00995 / 0.62 ( 9) link_ALPHA1-3 : angle 1.82388 / 1.17 ( 27) link_ALPHA1-6 : bond 0.00508 / 0.27 ( 6) link_ALPHA1-6 : angle 2.49360 / 1.25 ( 18) link_BETA1-4 : bond 0.00365 / 0.23 ( 18) link_BETA1-4 : angle 1.88868 / 1.16 ( 54) link_NAG-ASN : bond 0.00515 / 0.37 ( 57) link_NAG-ASN : angle 2.73779 / 1.79 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 226 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 657 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6198 (mp0) REVERT: B 534 SER cc_start: 0.8367 (m) cc_final: 0.8147 (m) REVERT: B 535 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7282 (mpt) REVERT: E 46 LYS cc_start: 0.7906 (ttpp) cc_final: 0.7529 (mptt) REVERT: E 69 TRP cc_start: 0.7246 (OUTLIER) cc_final: 0.6512 (p90) REVERT: E 153 GLU cc_start: 0.8083 (mp0) cc_final: 0.7235 (tt0) REVERT: E 178 ARG cc_start: 0.8569 (ttt180) cc_final: 0.7757 (tpt170) REVERT: E 211 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: E 490 LYS cc_start: 0.8406 (ttpt) cc_final: 0.7861 (ttpp) REVERT: F 46 LYS cc_start: 0.7871 (ttpp) cc_final: 0.7486 (mptt) REVERT: F 153 GLU cc_start: 0.8111 (mp0) cc_final: 0.7323 (tt0) REVERT: F 178 ARG cc_start: 0.8651 (ttt180) cc_final: 0.7822 (tmt170) REVERT: F 490 LYS cc_start: 0.8422 (ttpt) cc_final: 0.7871 (ttpp) REVERT: G 46 LYS cc_start: 0.8007 (mptt) cc_final: 0.7706 (mttp) REVERT: G 153 GLU cc_start: 0.7998 (mp0) cc_final: 0.7192 (tt0) REVERT: G 178 ARG cc_start: 0.8555 (ttt180) cc_final: 0.7689 (tmt170) REVERT: G 231 LYS cc_start: 0.8361 (mmtp) cc_final: 0.8157 (mtpp) REVERT: G 490 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7899 (ttpp) REVERT: H 58 ASN cc_start: 0.7761 (t0) cc_final: 0.7204 (t0) REVERT: H 77 GLN cc_start: 0.6789 (tt0) cc_final: 0.6358 (tt0) REVERT: H 96 ARG cc_start: 0.8564 (ptm-80) cc_final: 0.8167 (ptm-80) REVERT: H 99 GLU cc_start: 0.7849 (pm20) cc_final: 0.7261 (pm20) REVERT: J 77 GLN cc_start: 0.6866 (tt0) cc_final: 0.6430 (tt0) REVERT: K 30 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7712 (mppt) REVERT: K 45 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7497 (ttp80) REVERT: L 45 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7208 (ttp80) REVERT: M 98 ASP cc_start: 0.7572 (t0) cc_final: 0.7288 (t0) REVERT: N 30 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7879 (mttp) outliers start: 68 outliers final: 37 residues processed: 264 average time/residue: 0.5794 time to fit residues: 174.6156 Evaluate side-chains 261 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 449 ILE Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 179 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 130 optimal weight: 0.0170 chunk 92 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 overall best weight: 1.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.160335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113799 restraints weight = 25443.475| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.60 r_work: 0.3186 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20529 Z= 0.145 Angle : 0.612 11.280 28062 Z= 0.297 Chirality : 0.046 0.345 3354 Planarity : 0.004 0.049 3399 Dihedral : 7.309 66.162 4441 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.29 % Allowed : 17.33 % Favored : 80.38 % 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: -0.56 (0.17), residues: 2313 helix: 1.01 (0.27), residues: 408 sheet: 0.08 (0.20), residues: 684 loop : -1.12 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 500 TYR 0.009 0.001 TYR G 217 PHE 0.018 0.001 PHE L 71 TRP 0.010 0.001 TRP G 112 HIS 0.003 0.001 HIS L 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (20394) covalent geometry : angle 0.56868 / 0.29 (27699) SS BOND : bond 0.00208 / 0.13 ( 42) SS BOND : angle 1.08123 / 0.76 ( 84) hydrogen bonds : bond 0.03862 / 2.53 ( 658) hydrogen bonds : angle 4.92303 / 3.49 ( 1836) link_ALPHA1-2 : bond 0.00759 / 0.38 ( 3) link_ALPHA1-2 : angle 1.16705 / 0.66 ( 9) link_ALPHA1-3 : bond 0.00926 / 0.57 ( 9) link_ALPHA1-3 : angle 1.79548 / 1.20 ( 27) link_ALPHA1-6 : bond 0.00550 / 0.31 ( 6) link_ALPHA1-6 : angle 2.36553 / 1.18 ( 18) link_BETA1-4 : bond 0.00366 / 0.22 ( 18) link_BETA1-4 : angle 1.66462 / 1.02 ( 54) link_NAG-ASN : bond 0.00462 / 0.35 ( 57) link_NAG-ASN : angle 2.54365 / 1.67 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8554 (mtmt) REVERT: A 657 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6305 (mp0) REVERT: B 535 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7333 (mpt) REVERT: B 659 ASP cc_start: 0.7570 (t0) cc_final: 0.7355 (t70) REVERT: E 46 LYS cc_start: 0.7944 (ttpp) cc_final: 0.7612 (mptt) REVERT: E 69 TRP cc_start: 0.7359 (OUTLIER) cc_final: 0.6743 (p90) REVERT: E 153 GLU cc_start: 0.8080 (mp0) cc_final: 0.7258 (tt0) REVERT: E 178 ARG cc_start: 0.8599 (ttt180) cc_final: 0.7836 (tpt170) REVERT: E 490 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8004 (ttpp) REVERT: F 46 LYS cc_start: 0.7926 (ttpp) cc_final: 0.7570 (mptt) REVERT: F 153 GLU cc_start: 0.8099 (mp0) cc_final: 0.7356 (tt0) REVERT: F 178 ARG cc_start: 0.8688 (ttt180) cc_final: 0.7897 (tmt170) REVERT: F 358 ILE cc_start: 0.8404 (mp) cc_final: 0.8153 (mt) REVERT: F 490 LYS cc_start: 0.8460 (ttpt) cc_final: 0.7899 (ttpp) REVERT: G 46 LYS cc_start: 0.8044 (mptt) cc_final: 0.7767 (mttp) REVERT: G 98 ASN cc_start: 0.8433 (t0) cc_final: 0.8159 (t0) REVERT: G 153 GLU cc_start: 0.7960 (mp0) cc_final: 0.7204 (tt0) REVERT: G 178 ARG cc_start: 0.8562 (ttt180) cc_final: 0.7736 (tmt170) REVERT: G 231 LYS cc_start: 0.8386 (mmtp) cc_final: 0.8172 (mtpp) REVERT: G 490 LYS cc_start: 0.8403 (ttpt) cc_final: 0.7953 (ttpp) REVERT: H 58 ASN cc_start: 0.7704 (t0) cc_final: 0.7154 (t0) REVERT: H 77 GLN cc_start: 0.6828 (tt0) cc_final: 0.6469 (tt0) REVERT: H 99 GLU cc_start: 0.7822 (pm20) cc_final: 0.7268 (pm20) REVERT: J 77 GLN cc_start: 0.6872 (tt0) cc_final: 0.6480 (tt0) REVERT: K 30 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.6708 (mtmm) REVERT: M 58 ASN cc_start: 0.7511 (t0) cc_final: 0.6894 (t0) REVERT: M 77 GLN cc_start: 0.6813 (tt0) cc_final: 0.6570 (tm-30) REVERT: M 98 ASP cc_start: 0.7551 (t0) cc_final: 0.7290 (t0) outliers start: 48 outliers final: 29 residues processed: 250 average time/residue: 0.5638 time to fit residues: 160.9778 Evaluate side-chains 247 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 179 optimal weight: 0.0040 chunk 52 optimal weight: 0.6980 chunk 195 optimal weight: 0.1980 chunk 184 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 59 optimal weight: 0.0970 chunk 2 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 208 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 352 HIS E 356 ASN G 352 HIS J 81 HIS N 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118914 restraints weight = 25836.508| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.66 r_work: 0.3257 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20529 Z= 0.097 Angle : 0.559 11.280 28062 Z= 0.270 Chirality : 0.044 0.331 3354 Planarity : 0.004 0.049 3399 Dihedral : 6.654 62.150 4441 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.29 % Allowed : 18.43 % Favored : 80.29 % 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: -0.35 (0.18), residues: 2313 helix: 1.30 (0.27), residues: 408 sheet: 0.05 (0.20), residues: 705 loop : -0.92 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 542 TYR 0.008 0.001 TYR E 173 PHE 0.014 0.001 PHE L 71 TRP 0.011 0.001 TRP H 103 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (20394) covalent geometry : angle 0.51878 / 0.26 (27699) SS BOND : bond 0.00179 / 0.11 ( 42) SS BOND : angle 0.98128 / 0.69 ( 84) hydrogen bonds : bond 0.03232 / 2.14 ( 658) hydrogen bonds : angle 4.62001 / 3.29 ( 1836) link_ALPHA1-2 : bond 0.00723 / 0.36 ( 3) link_ALPHA1-2 : angle 1.25243 / 0.71 ( 9) link_ALPHA1-3 : bond 0.00896 / 0.55 ( 9) link_ALPHA1-3 : angle 1.77646 / 1.21 ( 27) link_ALPHA1-6 : bond 0.00686 / 0.39 ( 6) link_ALPHA1-6 : angle 2.28273 / 1.13 ( 18) link_BETA1-4 : bond 0.00402 / 0.24 ( 18) link_BETA1-4 : angle 1.47244 / 0.92 ( 54) link_NAG-ASN : bond 0.00463 / 0.35 ( 57) link_NAG-ASN : angle 2.32846 / 1.53 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8492 (mtmt) REVERT: B 542 ARG cc_start: 0.8218 (mtp180) cc_final: 0.7925 (mmm-85) REVERT: E 46 LYS cc_start: 0.7847 (ttpp) cc_final: 0.7533 (mptt) REVERT: E 69 TRP cc_start: 0.7262 (OUTLIER) cc_final: 0.6841 (p90) REVERT: E 98 ASN cc_start: 0.8172 (t0) cc_final: 0.7864 (t0) REVERT: E 100 MET cc_start: 0.8613 (mtp) cc_final: 0.8372 (mtp) REVERT: E 153 GLU cc_start: 0.8031 (mp0) cc_final: 0.7143 (tt0) REVERT: E 178 ARG cc_start: 0.8532 (ttt180) cc_final: 0.7705 (tpt170) REVERT: E 211 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: E 356 ASN cc_start: 0.6594 (t0) cc_final: 0.6173 (p0) REVERT: E 490 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8004 (ttpp) REVERT: F 46 LYS cc_start: 0.7801 (ttpp) cc_final: 0.7462 (mptt) REVERT: F 153 GLU cc_start: 0.8029 (mp0) cc_final: 0.7244 (tt0) REVERT: F 178 ARG cc_start: 0.8633 (ttt180) cc_final: 0.7789 (tmt170) REVERT: F 490 LYS cc_start: 0.8386 (ttpt) cc_final: 0.7772 (ttpp) REVERT: G 46 LYS cc_start: 0.7992 (mptt) cc_final: 0.7638 (mttp) REVERT: G 98 ASN cc_start: 0.8162 (t0) cc_final: 0.7804 (t0) REVERT: G 153 GLU cc_start: 0.7908 (mp0) cc_final: 0.7114 (tt0) REVERT: G 178 ARG cc_start: 0.8497 (ttt180) cc_final: 0.7609 (tmt170) REVERT: G 231 LYS cc_start: 0.8381 (mmtp) cc_final: 0.8144 (mtpp) REVERT: G 490 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7880 (ttpp) REVERT: H 58 ASN cc_start: 0.7509 (t0) cc_final: 0.6939 (t0) REVERT: H 77 GLN cc_start: 0.6822 (tt0) cc_final: 0.6467 (tm-30) REVERT: H 96 ARG cc_start: 0.8178 (ptm-80) cc_final: 0.7842 (ptm-80) REVERT: H 99 GLU cc_start: 0.7786 (pm20) cc_final: 0.7225 (pm20) REVERT: J 77 GLN cc_start: 0.6870 (tt0) cc_final: 0.6566 (tt0) REVERT: J 99 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7986 (pm20) REVERT: J 100 ASN cc_start: 0.8672 (m-40) cc_final: 0.8399 (m-40) REVERT: J 100 MET cc_start: 0.8185 (mpp) cc_final: 0.7811 (mpp) REVERT: K 4 MET cc_start: 0.7300 (mmt) cc_final: 0.6616 (ttm) REVERT: K 30 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.6631 (mtmm) REVERT: M 100 ASN cc_start: 0.8606 (m-40) cc_final: 0.8300 (m-40) REVERT: N 30 LYS cc_start: 0.7868 (mtmt) cc_final: 0.7655 (mttp) outliers start: 27 outliers final: 16 residues processed: 252 average time/residue: 0.5301 time to fit residues: 152.8096 Evaluate side-chains 234 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 119 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 0.0970 chunk 166 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 618 ASN E 352 HIS G 352 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.164832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117705 restraints weight = 25986.493| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.66 r_work: 0.3242 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20529 Z= 0.111 Angle : 0.572 11.097 28062 Z= 0.275 Chirality : 0.045 0.332 3354 Planarity : 0.004 0.047 3399 Dihedral : 6.567 61.106 4441 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.00 % Allowed : 18.95 % Favored : 80.05 % 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: -0.34 (0.18), residues: 2313 helix: 1.27 (0.27), residues: 411 sheet: 0.03 (0.20), residues: 699 loop : -0.89 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 500 TYR 0.007 0.001 TYR G 217 PHE 0.015 0.001 PHE J 78 TRP 0.008 0.001 TRP F 112 HIS 0.003 0.001 HIS L 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (20394) covalent geometry : angle 0.53200 / 0.27 (27699) SS BOND : bond 0.00187 / 0.12 ( 42) SS BOND : angle 0.96353 / 0.69 ( 84) hydrogen bonds : bond 0.03345 / 2.20 ( 658) hydrogen bonds : angle 4.58625 / 3.26 ( 1836) link_ALPHA1-2 : bond 0.00707 / 0.35 ( 3) link_ALPHA1-2 : angle 1.27778 / 0.72 ( 9) link_ALPHA1-3 : bond 0.00885 / 0.55 ( 9) link_ALPHA1-3 : angle 1.78293 / 1.21 ( 27) link_ALPHA1-6 : bond 0.00682 / 0.39 ( 6) link_ALPHA1-6 : angle 2.32598 / 1.15 ( 18) link_BETA1-4 : bond 0.00415 / 0.25 ( 18) link_BETA1-4 : angle 1.49868 / 0.93 ( 54) link_NAG-ASN : bond 0.00434 / 0.33 ( 57) link_NAG-ASN : angle 2.33657 / 1.53 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7914.31 seconds wall clock time: 135 minutes 24.79 seconds (8124.79 seconds total)