Starting phenix.real_space_refine on Wed Mar 4 23:00:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xrt_22295/03_2026/6xrt_22295.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xrt_22295/03_2026/6xrt_22295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xrt_22295/03_2026/6xrt_22295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xrt_22295/03_2026/6xrt_22295.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xrt_22295/03_2026/6xrt_22295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xrt_22295/03_2026/6xrt_22295.map" } resolution = 3.9 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= 0.014 sd= 0.071 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 115 5.16 5 C 10380 2.51 5 N 2761 2.21 5 O 3391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16647 Number of models: 1 Model: "" Number of chains: 32 Chain: "G" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "B" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "E" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "F" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3500 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "C" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1005 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "A" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 2 Chain: "H" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1038 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 795 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" 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: "M" 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: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" 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: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.71, per 1000 atoms: 0.22 Number of scatterers: 16647 At special positions: 0 Unit cell: (127.33, 132.68, 163.71, 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 115 16.00 O 3391 8.00 N 2761 7.00 C 10380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 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=2.04 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=2.04 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 G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " 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 E 501 " - pdb=" SG CYS C 605 " 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=2.04 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=2.04 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 F 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 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 V 4 " - " MAN V 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 6 " " MAN J 4 " - " MAN J 5 " " BMA N 3 " - " MAN N 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 6 " - " MAN V 7 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 6 " " MAN V 6 " - " MAN V 8 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " 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 T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG D 1 " - " ASN G 88 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 608 " - " ASN E 197 " " NAG E 609 " - " ASN E 234 " " NAG E 615 " - " ASN E 276 " " NAG E 616 " - " ASN E 295 " " NAG E 617 " - " ASN E 301 " " NAG E 618 " - " ASN E 332 " " NAG E 619 " - " ASN E 339 " " NAG E 620 " - " ASN E 355 " " NAG E 621 " - " ASN E 363 " " NAG E 622 " - " ASN E 386 " " NAG E 623 " - " ASN E 392 " " NAG E 624 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 616 " - " ASN F 197 " " NAG F 617 " - " ASN F 234 " " NAG F 625 " - " ASN F 301 " " NAG F 626 " - " ASN F 332 " " NAG F 627 " - " ASN F 339 " " NAG F 628 " - " ASN F 355 " " NAG F 629 " - " ASN F 363 " " NAG F 630 " - " ASN F 386 " " NAG F 631 " - " ASN F 392 " " NAG G 603 " - " ASN G 133 " " NAG G 624 " - " ASN G 276 " " NAG G 627 " - " ASN G 301 " " NAG G 628 " - " ASN G 332 " " NAG G 629 " - " ASN G 339 " " NAG G 630 " - " ASN G 355 " " NAG G 631 " - " ASN G 363 " " NAG G 634 " - " ASN G 392 " " NAG I 1 " - " ASN G 156 " " NAG J 1 " - " ASN G 160 " " NAG K 1 " - " ASN G 197 " " NAG M 1 " - " ASN G 234 " " NAG N 1 " - " ASN G 262 " " NAG O 1 " - " ASN G 295 " " NAG P 1 " - " ASN G 386 " " NAG Q 1 " - " ASN G 448 " " NAG R 1 " - " ASN E 156 " " NAG S 1 " - " ASN E 160 " " NAG T 1 " - " ASN E 262 " " NAG U 1 " - " ASN F 156 " " NAG V 1 " - " ASN F 160 " " NAG W 1 " - " ASN F 262 " " NAG X 1 " - " ASN F 276 " " NAG Y 1 " - " ASN F 295 " " NAG Z 1 " - " ASN F 448 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 482.5 milliseconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3620 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 44 sheets defined 20.1% alpha, 57.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'G' and resid 99 through 117 removed outlier: 4.497A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.504A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL G 127 " --> pdb=" O PRO G 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 127' Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.548A pdb=" N VAL G 345 " --> pdb=" O THR G 341 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG G 350 " --> pdb=" O VAL G 346 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.737A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 479 removed outlier: 4.015A pdb=" N ASP G 477 " --> pdb=" O ASP G 474 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN G 478 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP G 479 " --> pdb=" O ARG G 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 474 through 479' Processing helix chain 'B' and resid 532 through 535 removed outlier: 3.886A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.932A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 removed outlier: 3.875A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 4.269A pdb=" N SER B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 633 removed outlier: 3.540A pdb=" N ASP B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 628 through 633' Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 645 through 659 removed outlier: 3.974A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.538A pdb=" N ASP E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 344 Processing helix chain 'E' and resid 345 through 351 removed outlier: 3.618A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 460 through 464 removed outlier: 3.936A pdb=" N SER E 463 " --> pdb=" O SER E 460 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR E 464 " --> pdb=" O THR E 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 460 through 464' Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.903A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 484 No H-bonds generated for 'chain 'E' and resid 482 through 484' Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.096A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 335 through 348 removed outlier: 4.233A pdb=" N GLU F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR F 341 " --> pdb=" O THR F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 351 No H-bonds generated for 'chain 'F' and resid 349 through 351' Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.818A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 381 removed outlier: 4.008A pdb=" N GLY F 380 " --> pdb=" O ASN F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 392 removed outlier: 3.640A pdb=" N PHE F 391 " --> pdb=" O SER F 388 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN F 392 " --> pdb=" O GLY F 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 388 through 392' Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 569 through 587 removed outlier: 3.812A pdb=" N ILE C 573 " --> pdb=" O THR C 569 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 595 Processing helix chain 'C' and resid 631 through 635 Processing helix chain 'C' and resid 638 through 661 removed outlier: 4.346A pdb=" N ILE C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR C 643 " --> pdb=" O THR C 639 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.927A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 595 removed outlier: 3.621A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.136A pdb=" N SER A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 633 removed outlier: 3.537A pdb=" N TRP A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 637 removed outlier: 5.902A pdb=" N ASN A 637 " --> pdb=" O GLU A 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 637' Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.828A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 655 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 660 " --> pdb=" O ASN A 656 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 removed outlier: 4.055A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.826A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.664A pdb=" N ALA G 224 " --> pdb=" O VAL G 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.567A pdb=" N GLN G 170 " --> pdb=" O MET G 161 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET G 161 " --> pdb=" O GLN G 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 259 through 261 removed outlier: 4.170A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 9.580A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.973A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.617A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.615A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.617A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.973A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.580A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG G 469 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 304 through 308 Processing sheet with id=AA8, first strand: chain 'G' and resid 423 through 424 removed outlier: 3.543A pdb=" N ILE G 424 " --> pdb=" O MET G 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 494 through 495 removed outlier: 3.635A pdb=" N CYS C 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.639A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 226 " --> pdb=" O LYS E 487 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL E 245 " --> pdb=" O ILE E 225 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 53 through 55 removed outlier: 4.175A pdb=" N PHE E 53 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS E 218 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.819A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 169 through 177 removed outlier: 4.102A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 202 through 203 removed outlier: 7.245A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.630A pdb=" N MET E 271 " --> pdb=" O GLN E 287 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN E 287 " --> pdb=" O MET E 271 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.641A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 259 through 261 removed outlier: 5.610A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.641A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.656A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 416 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS E 331 " --> pdb=" O LEU E 416 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.641A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 468 through 470 removed outlier: 5.610A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.641A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN E 287 " --> pdb=" O MET E 271 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET E 271 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.630A pdb=" N MET E 271 " --> pdb=" O GLN E 287 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN E 287 " --> pdb=" O MET E 271 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS E 331 " --> pdb=" O LEU E 416 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 416 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 315 through 322 removed outlier: 6.736A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.641A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.656A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 416 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS E 331 " --> pdb=" O LEU E 416 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 468 through 470 removed outlier: 5.610A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.641A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS E 331 " --> pdb=" O LEU E 416 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 416 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 359 through 361 removed outlier: 4.179A pdb=" N ILE E 359 " --> pdb=" O TRP E 395 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 35 through 40 removed outlier: 3.597A pdb=" N THR F 37 " --> pdb=" O ALA F 497 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA F 497 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.659A pdb=" N LYS F 487 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 226 " --> pdb=" O LYS F 487 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 91 through 93 removed outlier: 3.610A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY F 237 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 169 through 177 removed outlier: 3.522A pdb=" N SER F 158 " --> pdb=" O GLN F 130 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS F 189 " --> pdb=" O CYS F 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 202 through 203 removed outlier: 7.607A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.668A pdb=" N VAL F 286 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.170A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 10.997A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.372A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 10.997A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.170A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 286 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN F 301 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 374 through 375 removed outlier: 3.520A pdb=" N CYS F 331 " --> pdb=" O LEU F 416 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 286 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.170A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 10.997A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.372A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 10.997A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.170A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 286 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE F 359 " --> pdb=" O TRP F 395 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 374 through 375 removed outlier: 3.520A pdb=" N CYS F 331 " --> pdb=" O LEU F 416 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.658A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE F 359 " --> pdb=" O TRP F 395 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 322 through 323 removed outlier: 4.295A pdb=" N ASN F 301 " --> pdb=" O ILE F 323 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS F 331 " --> pdb=" O LEU F 416 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 393 through 395 removed outlier: 3.887A pdb=" N ILE F 359 " --> pdb=" O TRP F 395 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN F 301 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 393 through 395 removed outlier: 3.887A pdb=" N ILE F 359 " --> pdb=" O TRP F 395 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS F 331 " --> pdb=" O LEU F 416 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 306 through 308 Processing sheet with id=AE3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.677A pdb=" N VAL H 12 " --> pdb=" O ILE H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'H' and resid 18 through 23 removed outlier: 3.551A pdb=" N LEU H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 46 through 51 removed outlier: 6.986A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HIS H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 7.048A pdb=" N TRP H 35A" --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 46 through 51 removed outlier: 6.986A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HIS H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 7.048A pdb=" N TRP H 35A" --> pdb=" O HIS H 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.626A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS L 23 " --> pdb=" O ALA L 71 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 44 through 46 574 hydrogen bonds defined for protein. 1563 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: 2.75 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2722 1.32 - 1.45: 4966 1.45 - 1.58: 9125 1.58 - 1.71: 1 1.71 - 1.84: 151 Bond restraints: 16965 Sorted by residual: bond pdb=" N VAL C 608 " pdb=" CA VAL C 608 " ideal model delta sigma weight residual 1.454 1.490 -0.036 7.70e-03 1.69e+04 2.17e+01 bond pdb=" OH TYS H 100D" pdb=" S TYS H 100D" ideal model delta sigma weight residual 1.679 1.595 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C3 BMA I 3 " pdb=" O3 BMA I 3 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C3 BMA J 3 " pdb=" O3 BMA J 3 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C PRO L 44 " pdb=" O PRO L 44 " ideal model delta sigma weight residual 1.234 1.193 0.040 1.14e-02 7.69e+03 1.24e+01 ... (remaining 16960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 22221 2.42 - 4.84: 689 4.84 - 7.26: 101 7.26 - 9.68: 15 9.68 - 12.10: 3 Bond angle restraints: 23029 Sorted by residual: angle pdb=" CA PHE L 49 " pdb=" CB PHE L 49 " pdb=" CG PHE L 49 " ideal model delta sigma weight residual 113.80 121.28 -7.48 1.00e+00 1.00e+00 5.59e+01 angle pdb=" N ARG F 166 " pdb=" CA ARG F 166 " pdb=" C ARG F 166 " ideal model delta sigma weight residual 112.93 106.46 6.47 1.12e+00 7.97e-01 3.34e+01 angle pdb=" C ARG G 308 " pdb=" N ILE G 309 " pdb=" CA ILE G 309 " ideal model delta sigma weight residual 120.56 113.85 6.71 1.28e+00 6.10e-01 2.75e+01 angle pdb=" C PHE L 49 " pdb=" CA PHE L 49 " pdb=" CB PHE L 49 " ideal model delta sigma weight residual 110.42 120.66 -10.24 1.99e+00 2.53e-01 2.65e+01 angle pdb=" C LEU L 46 " pdb=" N VAL L 47 " pdb=" CA VAL L 47 " ideal model delta sigma weight residual 123.08 118.12 4.96 1.01e+00 9.80e-01 2.41e+01 ... (remaining 23024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 10632 24.09 - 48.17: 643 48.17 - 72.26: 108 72.26 - 96.34: 60 96.34 - 120.43: 37 Dihedral angle restraints: 11480 sinusoidal: 5883 harmonic: 5597 Sorted by residual: dihedral pdb=" C PHE L 49 " pdb=" N PHE L 49 " pdb=" CA PHE L 49 " pdb=" CB PHE L 49 " ideal model delta harmonic sigma weight residual -122.60 -141.47 18.87 0 2.50e+00 1.60e-01 5.70e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -147.72 61.72 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual -86.00 -25.81 -60.19 1 1.00e+01 1.00e-02 4.83e+01 ... (remaining 11477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2794 0.139 - 0.279: 57 0.279 - 0.418: 25 0.418 - 0.557: 3 0.557 - 0.697: 2 Chirality restraints: 2881 Sorted by residual: chirality pdb=" CA PHE L 49 " pdb=" N PHE L 49 " pdb=" C PHE L 49 " pdb=" CB PHE L 49 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA THR L 42 " pdb=" N THR L 42 " pdb=" C THR L 42 " pdb=" CB THR L 42 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" CA TYS H 100D" pdb=" N TYS H 100D" pdb=" C TYS H 100D" pdb=" CB TYS H 100D" both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.25e+00 ... (remaining 2878 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 624 " 0.343 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG G 624 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG G 624 " 0.070 2.00e-02 2.50e+03 pdb=" N2 NAG G 624 " -0.524 2.00e-02 2.50e+03 pdb=" O7 NAG G 624 " 0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 703 " -0.236 2.00e-02 2.50e+03 2.01e-01 5.05e+02 pdb=" C7 NAG A 703 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG A 703 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 703 " 0.331 2.00e-02 2.50e+03 pdb=" O7 NAG A 703 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 701 " 0.225 2.00e-02 2.50e+03 1.87e-01 4.38e+02 pdb=" C7 NAG A 701 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A 701 " 0.161 2.00e-02 2.50e+03 pdb=" N2 NAG A 701 " -0.307 2.00e-02 2.50e+03 pdb=" O7 NAG A 701 " -0.014 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4209 2.80 - 3.33: 14378 3.33 - 3.85: 25965 3.85 - 4.38: 28548 4.38 - 4.90: 48951 Nonbonded interactions: 122051 Sorted by model distance: nonbonded pdb=" OG1 THR G 37 " pdb=" O CYS B 604 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR E 139 " pdb=" OD1 ASP E 141 " model vdw 2.291 3.040 nonbonded pdb=" N ASP L 52 " pdb=" OD1 ASP L 52 " model vdw 2.309 3.120 nonbonded pdb=" O LEU E 369 " pdb=" OG1 THR E 373 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR F 37 " pdb=" O CYS A 604 " model vdw 2.326 3.040 ... (remaining 122046 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 520 through 702) selection = (chain 'B' and (resid 520 through 545 or resid 569 through 624 or resid 626 thro \ ugh 702)) selection = (chain 'C' and (resid 520 through 545 or resid 569 through 624 or resid 626 thro \ ugh 702)) } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = (chain 'E' and (resid 32 through 58 or resid 66 through 185 or resid 189 through \ 398 or resid 412 through 618)) selection = (chain 'F' and (resid 32 through 185 or resid 189 through 398 or resid 412 throu \ gh 628)) selection = (chain 'G' and (resid 32 through 58 or resid 66 through 398 or resid 412 through \ 634)) } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'T' selection = chain 'U' } ncs_group { reference = 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.550 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 : 0.006 0.084 17103 Z= 0.312 Angle : 1.015 16.438 23405 Z= 0.510 Chirality : 0.067 0.697 2881 Planarity : 0.009 0.297 2802 Dihedral : 17.056 120.428 7746 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.93 % Allowed : 0.93 % Favored : 98.14 % Cbeta Deviations : 0.22 % 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: -2.77 (0.17), residues: 1902 helix: -3.39 (0.20), residues: 316 sheet: -0.44 (0.28), residues: 370 loop : -1.94 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 444 TYR 0.022 0.002 TYR E 486 PHE 0.043 0.002 PHE L 49 TRP 0.039 0.002 TRP F 96 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00581 (16965) covalent geometry : angle 0.95322 (23029) SS BOND : bond 0.00309 ( 38) SS BOND : angle 1.83375 ( 76) hydrogen bonds : bond 0.29959 ( 401) hydrogen bonds : angle 10.93324 ( 1563) link_ALPHA1-2 : bond 0.01152 ( 1) link_ALPHA1-2 : angle 2.08606 ( 3) link_ALPHA1-3 : bond 0.00718 ( 8) link_ALPHA1-3 : angle 3.64869 ( 24) link_ALPHA1-6 : bond 0.00460 ( 7) link_ALPHA1-6 : angle 1.53660 ( 21) link_BETA1-4 : bond 0.00627 ( 26) link_BETA1-4 : angle 2.42798 ( 78) link_NAG-ASN : bond 0.00720 ( 58) link_NAG-ASN : angle 3.47842 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 249 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 195 ASN cc_start: 0.8016 (p0) cc_final: 0.7534 (p0) REVERT: G 482 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7441 (mp0) REVERT: B 542 ARG cc_start: 0.9048 (mtm180) cc_final: 0.8784 (mtm-85) REVERT: B 601 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8800 (tttt) REVERT: B 643 TYR cc_start: 0.8972 (m-10) cc_final: 0.8705 (m-10) REVERT: B 647 GLU cc_start: 0.8824 (pm20) cc_final: 0.8593 (pm20) REVERT: E 46 LYS cc_start: 0.9226 (mtpp) cc_final: 0.8994 (mmmm) REVERT: E 94 ASN cc_start: 0.9036 (t0) cc_final: 0.8700 (t0) REVERT: E 95 MET cc_start: 0.7751 (mmm) cc_final: 0.6934 (ttm) REVERT: E 127 VAL cc_start: 0.8166 (m) cc_final: 0.7361 (p) REVERT: E 309 ILE cc_start: 0.7940 (tt) cc_final: 0.7572 (pt) REVERT: E 338 TRP cc_start: 0.8999 (t-100) cc_final: 0.8722 (t-100) REVERT: E 477 ASP cc_start: 0.8928 (m-30) cc_final: 0.8636 (m-30) REVERT: E 484 TYR cc_start: 0.8790 (p90) cc_final: 0.8495 (p90) REVERT: F 284 ILE cc_start: 0.8644 (mm) cc_final: 0.8141 (mp) REVERT: F 381 GLU cc_start: 0.8203 (tp30) cc_final: 0.6946 (tm-30) REVERT: F 383 PHE cc_start: 0.7697 (m-80) cc_final: 0.7210 (m-80) REVERT: C 588 ARG cc_start: 0.7096 (mmt180) cc_final: 0.6024 (mtt180) REVERT: C 626 MET cc_start: 0.7771 (mmm) cc_final: 0.7074 (tpt) REVERT: C 659 ASP cc_start: 0.9430 (m-30) cc_final: 0.9080 (p0) REVERT: A 592 LEU cc_start: 0.8827 (tp) cc_final: 0.8591 (tp) REVERT: A 593 LEU cc_start: 0.9304 (tp) cc_final: 0.8958 (tp) REVERT: A 596 TRP cc_start: 0.8496 (m-10) cc_final: 0.8151 (m-90) REVERT: A 648 GLU cc_start: 0.8965 (pt0) cc_final: 0.8428 (pp20) REVERT: A 657 GLU cc_start: 0.8597 (mp0) cc_final: 0.8073 (pm20) REVERT: H 5 ARG cc_start: 0.8817 (mmm160) cc_final: 0.8380 (mmm-85) REVERT: H 18 LEU cc_start: 0.8968 (tt) cc_final: 0.8665 (mp) REVERT: H 77 GLN cc_start: 0.8550 (mt0) cc_final: 0.8326 (tp-100) REVERT: H 80 LEU cc_start: 0.8949 (tp) cc_final: 0.8100 (tp) REVERT: H 102 LEU cc_start: 0.8863 (mt) cc_final: 0.8662 (mt) REVERT: L 86 TYR cc_start: 0.8523 (m-80) cc_final: 0.8178 (m-80) REVERT: L 103 ARG cc_start: 0.8721 (tpp-160) cc_final: 0.8349 (mmm160) outliers start: 16 outliers final: 6 residues processed: 263 average time/residue: 0.1447 time to fit residues: 55.4824 Evaluate side-chains 136 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 52 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 HIS G 425 ASN G 478 ASN E 195 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS A 616 ASN A 651 ASN H 1 GLN ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.036813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.030835 restraints weight = 150337.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.031668 restraints weight = 87406.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.032230 restraints weight = 60475.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.032629 restraints weight = 47090.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.032900 restraints weight = 39395.400| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 17103 Z= 0.309 Angle : 0.963 14.253 23405 Z= 0.456 Chirality : 0.052 0.392 2881 Planarity : 0.006 0.063 2802 Dihedral : 13.068 97.890 4131 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.75 % Allowed : 10.25 % Favored : 88.00 % 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: -2.10 (0.19), residues: 1902 helix: -1.53 (0.25), residues: 331 sheet: -0.66 (0.25), residues: 462 loop : -1.69 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 588 TYR 0.023 0.003 TYR B 586 PHE 0.021 0.003 PHE F 383 TRP 0.034 0.003 TRP G 479 HIS 0.007 0.002 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00657 (16965) covalent geometry : angle 0.89976 (23029) SS BOND : bond 0.00477 ( 38) SS BOND : angle 1.89422 ( 76) hydrogen bonds : bond 0.05098 ( 401) hydrogen bonds : angle 5.74439 ( 1563) link_ALPHA1-2 : bond 0.01538 ( 1) link_ALPHA1-2 : angle 4.84681 ( 3) link_ALPHA1-3 : bond 0.00696 ( 8) link_ALPHA1-3 : angle 4.45218 ( 24) link_ALPHA1-6 : bond 0.00384 ( 7) link_ALPHA1-6 : angle 2.36955 ( 21) link_BETA1-4 : bond 0.00336 ( 26) link_BETA1-4 : angle 2.35788 ( 78) link_NAG-ASN : bond 0.00638 ( 58) link_NAG-ASN : angle 3.10591 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 51 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8793 (t) REVERT: B 542 ARG cc_start: 0.9232 (mtm180) cc_final: 0.8809 (mtm-85) REVERT: B 601 LYS cc_start: 0.9147 (mmmt) cc_final: 0.8758 (tttp) REVERT: E 46 LYS cc_start: 0.9337 (mtpp) cc_final: 0.9011 (mmmm) REVERT: E 95 MET cc_start: 0.7955 (mmm) cc_final: 0.7403 (ttm) REVERT: E 338 TRP cc_start: 0.9266 (t-100) cc_final: 0.9044 (t-100) REVERT: E 426 MET cc_start: 0.6058 (tpp) cc_final: 0.5407 (tpp) REVERT: F 52 LEU cc_start: 0.8966 (mt) cc_final: 0.8749 (mt) REVERT: F 271 MET cc_start: 0.8711 (mtp) cc_final: 0.8342 (mmt) REVERT: F 475 MET cc_start: 0.8314 (ppp) cc_final: 0.7898 (ppp) REVERT: C 584 GLU cc_start: 0.9118 (tp30) cc_final: 0.8733 (tp30) REVERT: C 588 ARG cc_start: 0.7482 (mmt180) cc_final: 0.6558 (mtt180) REVERT: C 659 ASP cc_start: 0.9412 (m-30) cc_final: 0.9039 (p0) REVERT: H 18 LEU cc_start: 0.9308 (tt) cc_final: 0.8866 (mm) REVERT: H 97 GLU cc_start: 0.8478 (tp30) cc_final: 0.7602 (tp30) REVERT: H 100 GLU cc_start: 0.8621 (tt0) cc_final: 0.7907 (tm-30) REVERT: H 100 ASP cc_start: 0.9320 (t0) cc_final: 0.9054 (p0) REVERT: L 103 ARG cc_start: 0.8837 (tpp-160) cc_final: 0.8476 (tpp80) outliers start: 30 outliers final: 14 residues processed: 140 average time/residue: 0.1395 time to fit residues: 29.6167 Evaluate side-chains 107 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 479 TRP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 160 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 172 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 HIS ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS F 114 GLN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS C 630 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.037107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.031062 restraints weight = 147246.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.031913 restraints weight = 86028.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.032486 restraints weight = 59771.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.032894 restraints weight = 46365.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.033190 restraints weight = 38860.728| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17103 Z= 0.173 Angle : 0.748 13.658 23405 Z= 0.347 Chirality : 0.048 0.372 2881 Planarity : 0.004 0.039 2802 Dihedral : 11.363 97.722 4123 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.63 % Allowed : 12.58 % Favored : 85.79 % 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: -1.81 (0.19), residues: 1902 helix: -0.80 (0.28), residues: 338 sheet: -0.72 (0.25), residues: 445 loop : -1.56 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 542 TYR 0.022 0.002 TYR B 643 PHE 0.030 0.001 PHE H 99 TRP 0.024 0.002 TRP F 96 HIS 0.004 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00372 (16965) covalent geometry : angle 0.69300 (23029) SS BOND : bond 0.01238 ( 38) SS BOND : angle 1.09692 ( 76) hydrogen bonds : bond 0.04639 ( 401) hydrogen bonds : angle 5.04397 ( 1563) link_ALPHA1-2 : bond 0.01053 ( 1) link_ALPHA1-2 : angle 3.25888 ( 3) link_ALPHA1-3 : bond 0.00906 ( 8) link_ALPHA1-3 : angle 3.68144 ( 24) link_ALPHA1-6 : bond 0.00630 ( 7) link_ALPHA1-6 : angle 1.65564 ( 21) link_BETA1-4 : bond 0.00483 ( 26) link_BETA1-4 : angle 1.82285 ( 78) link_NAG-ASN : bond 0.00387 ( 58) link_NAG-ASN : angle 2.69125 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.9308 (mtm180) cc_final: 0.8839 (mtm-85) REVERT: B 601 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8668 (tttt) REVERT: E 338 TRP cc_start: 0.9277 (t-100) cc_final: 0.9042 (t-100) REVERT: E 426 MET cc_start: 0.6338 (tpp) cc_final: 0.5898 (tpp) REVERT: F 104 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8883 (tmm) REVERT: F 271 MET cc_start: 0.8757 (mtp) cc_final: 0.8534 (mmt) REVERT: C 584 GLU cc_start: 0.9192 (tp30) cc_final: 0.8760 (tm-30) REVERT: C 589 ASP cc_start: 0.9165 (p0) cc_final: 0.8817 (p0) REVERT: C 659 ASP cc_start: 0.9452 (m-30) cc_final: 0.9054 (p0) REVERT: L 103 ARG cc_start: 0.8924 (tpp-160) cc_final: 0.8501 (mmm160) outliers start: 28 outliers final: 14 residues processed: 124 average time/residue: 0.1352 time to fit residues: 25.7760 Evaluate side-chains 102 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 104 MET Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 80 optimal weight: 6.9990 chunk 52 optimal weight: 0.0060 chunk 163 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 0.3980 chunk 143 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 overall best weight: 2.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.036417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.030405 restraints weight = 145528.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.031246 restraints weight = 84737.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.031811 restraints weight = 58837.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.032159 restraints weight = 45683.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.032480 restraints weight = 38793.653| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17103 Z= 0.163 Angle : 0.710 13.288 23405 Z= 0.327 Chirality : 0.047 0.296 2881 Planarity : 0.004 0.041 2802 Dihedral : 9.449 89.572 4123 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.05 % Favored : 93.90 % Rotamer: Outliers : 1.69 % Allowed : 14.68 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.19), residues: 1902 helix: -0.41 (0.29), residues: 339 sheet: -0.66 (0.26), residues: 431 loop : -1.52 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 100 TYR 0.013 0.001 TYR B 638 PHE 0.014 0.001 PHE L 49 TRP 0.017 0.001 TRP E 96 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00356 (16965) covalent geometry : angle 0.65827 (23029) SS BOND : bond 0.00307 ( 38) SS BOND : angle 1.22114 ( 76) hydrogen bonds : bond 0.03712 ( 401) hydrogen bonds : angle 4.65906 ( 1563) link_ALPHA1-2 : bond 0.01189 ( 1) link_ALPHA1-2 : angle 3.64962 ( 3) link_ALPHA1-3 : bond 0.01449 ( 8) link_ALPHA1-3 : angle 3.03270 ( 24) link_ALPHA1-6 : bond 0.00838 ( 7) link_ALPHA1-6 : angle 1.44088 ( 21) link_BETA1-4 : bond 0.00319 ( 26) link_BETA1-4 : angle 1.88820 ( 78) link_NAG-ASN : bond 0.00357 ( 58) link_NAG-ASN : angle 2.54947 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.9342 (mtm180) cc_final: 0.8994 (ttp-110) REVERT: E 150 MET cc_start: 0.7918 (mmm) cc_final: 0.7696 (mmm) REVERT: E 338 TRP cc_start: 0.9262 (t-100) cc_final: 0.9034 (t-100) REVERT: E 426 MET cc_start: 0.7037 (tpp) cc_final: 0.6837 (tpp) REVERT: E 475 MET cc_start: 0.8612 (ptt) cc_final: 0.8410 (ptt) REVERT: F 104 MET cc_start: 0.9116 (tmm) cc_final: 0.8805 (tmm) REVERT: F 150 MET cc_start: 0.8646 (mmm) cc_final: 0.8268 (tpp) REVERT: F 426 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7824 (ppp) REVERT: C 584 GLU cc_start: 0.9255 (tp30) cc_final: 0.8652 (tm-30) REVERT: C 588 ARG cc_start: 0.7788 (mmt180) cc_final: 0.7073 (mmt180) REVERT: C 589 ASP cc_start: 0.9258 (p0) cc_final: 0.8860 (p0) REVERT: A 574 LYS cc_start: 0.9428 (mmmt) cc_final: 0.8811 (tptm) REVERT: H 100 ASP cc_start: 0.9266 (t0) cc_final: 0.8964 (p0) REVERT: L 103 ARG cc_start: 0.8975 (tpp-160) cc_final: 0.8531 (mmm160) outliers start: 29 outliers final: 18 residues processed: 112 average time/residue: 0.1367 time to fit residues: 23.6756 Evaluate side-chains 99 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 131 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 GLN E 478 ASN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.034948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.028928 restraints weight = 152581.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.029723 restraints weight = 88266.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.030307 restraints weight = 61475.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.030666 restraints weight = 47896.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.030950 restraints weight = 40460.952| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.6676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 17103 Z= 0.288 Angle : 0.843 13.882 23405 Z= 0.399 Chirality : 0.049 0.273 2881 Planarity : 0.005 0.051 2802 Dihedral : 9.346 83.780 4123 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.91 % Allowed : 15.78 % Favored : 81.30 % 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: -1.77 (0.19), residues: 1902 helix: -0.35 (0.29), residues: 333 sheet: -0.85 (0.25), residues: 456 loop : -1.60 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 100 TYR 0.017 0.002 TYR L 91 PHE 0.021 0.002 PHE F 382 TRP 0.024 0.002 TRP E 69 HIS 0.006 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00620 (16965) covalent geometry : angle 0.79530 (23029) SS BOND : bond 0.00527 ( 38) SS BOND : angle 1.39960 ( 76) hydrogen bonds : bond 0.04301 ( 401) hydrogen bonds : angle 5.00442 ( 1563) link_ALPHA1-2 : bond 0.02025 ( 1) link_ALPHA1-2 : angle 4.02708 ( 3) link_ALPHA1-3 : bond 0.01202 ( 8) link_ALPHA1-3 : angle 2.69398 ( 24) link_ALPHA1-6 : bond 0.00515 ( 7) link_ALPHA1-6 : angle 1.71681 ( 21) link_BETA1-4 : bond 0.00378 ( 26) link_BETA1-4 : angle 1.97424 ( 78) link_NAG-ASN : bond 0.00517 ( 58) link_NAG-ASN : angle 2.76690 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 74 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 150 MET cc_start: 0.9328 (mmp) cc_final: 0.9007 (mmp) REVERT: G 161 MET cc_start: 0.8727 (mmm) cc_final: 0.8409 (mmt) REVERT: G 434 MET cc_start: 0.9084 (mtp) cc_final: 0.8833 (mtm) REVERT: B 535 MET cc_start: 0.9442 (mpp) cc_final: 0.8938 (mpp) REVERT: B 584 GLU cc_start: 0.9453 (tm-30) cc_final: 0.9178 (tm-30) REVERT: E 150 MET cc_start: 0.8206 (mmm) cc_final: 0.7908 (mmm) REVERT: E 161 MET cc_start: 0.8760 (tpp) cc_final: 0.8554 (tpp) REVERT: E 271 MET cc_start: 0.8210 (mpp) cc_final: 0.7988 (mpp) REVERT: F 114 GLN cc_start: 0.9527 (OUTLIER) cc_final: 0.9288 (tm-30) REVERT: F 430 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8931 (mm) REVERT: C 584 GLU cc_start: 0.9334 (tp30) cc_final: 0.8927 (tm-30) REVERT: C 589 ASP cc_start: 0.9382 (p0) cc_final: 0.8957 (p0) REVERT: A 530 MET cc_start: 0.7033 (pmm) cc_final: 0.6642 (pmm) REVERT: A 574 LYS cc_start: 0.9512 (mmmt) cc_final: 0.9148 (mmmt) REVERT: A 626 MET cc_start: 0.9131 (ppp) cc_final: 0.8121 (ppp) REVERT: H 100 GLU cc_start: 0.8949 (pt0) cc_final: 0.8609 (pm20) REVERT: H 100 ASP cc_start: 0.9386 (t0) cc_final: 0.9086 (p0) REVERT: L 60 ASP cc_start: 0.8826 (t0) cc_final: 0.8464 (p0) REVERT: L 103 ARG cc_start: 0.9209 (tpp-160) cc_final: 0.8849 (tpp80) outliers start: 50 outliers final: 29 residues processed: 118 average time/residue: 0.1151 time to fit residues: 21.7292 Evaluate side-chains 96 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 88 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 41 optimal weight: 0.0050 chunk 128 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 67 ASN G 98 ASN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN L 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.035533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.029480 restraints weight = 150373.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.030311 restraints weight = 87134.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.030870 restraints weight = 60785.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.031264 restraints weight = 47455.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.031569 restraints weight = 39594.114| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17103 Z= 0.161 Angle : 0.701 13.660 23405 Z= 0.327 Chirality : 0.046 0.256 2881 Planarity : 0.004 0.047 2802 Dihedral : 8.656 78.623 4123 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.98 % Allowed : 17.59 % Favored : 80.43 % 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: -1.53 (0.19), residues: 1902 helix: -0.07 (0.30), residues: 335 sheet: -0.68 (0.25), residues: 435 loop : -1.48 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 100 TYR 0.012 0.001 TYR E 486 PHE 0.018 0.001 PHE L 49 TRP 0.029 0.002 TRP E 69 HIS 0.003 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00357 (16965) covalent geometry : angle 0.65297 (23029) SS BOND : bond 0.00239 ( 38) SS BOND : angle 1.20945 ( 76) hydrogen bonds : bond 0.03593 ( 401) hydrogen bonds : angle 4.58005 ( 1563) link_ALPHA1-2 : bond 0.02216 ( 1) link_ALPHA1-2 : angle 4.38480 ( 3) link_ALPHA1-3 : bond 0.00923 ( 8) link_ALPHA1-3 : angle 2.40076 ( 24) link_ALPHA1-6 : bond 0.00642 ( 7) link_ALPHA1-6 : angle 1.53162 ( 21) link_BETA1-4 : bond 0.00332 ( 26) link_BETA1-4 : angle 1.78137 ( 78) link_NAG-ASN : bond 0.00342 ( 58) link_NAG-ASN : angle 2.47597 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.9065 (ptm) cc_final: 0.8435 (tmm) REVERT: G 434 MET cc_start: 0.9112 (mtp) cc_final: 0.8784 (mtm) REVERT: B 535 MET cc_start: 0.9446 (mpp) cc_final: 0.8886 (mpp) REVERT: E 150 MET cc_start: 0.8260 (mmm) cc_final: 0.7916 (mmm) REVERT: E 271 MET cc_start: 0.8189 (mpp) cc_final: 0.7957 (mpp) REVERT: E 426 MET cc_start: 0.6706 (tpp) cc_final: 0.6315 (tpp) REVERT: F 114 GLN cc_start: 0.9523 (OUTLIER) cc_final: 0.9316 (tm-30) REVERT: F 150 MET cc_start: 0.8618 (tpp) cc_final: 0.8224 (tpp) REVERT: F 430 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8969 (mm) REVERT: C 584 GLU cc_start: 0.9340 (tp30) cc_final: 0.8942 (tm-30) REVERT: C 589 ASP cc_start: 0.9423 (p0) cc_final: 0.9181 (p0) REVERT: A 530 MET cc_start: 0.7234 (pmm) cc_final: 0.7010 (pmm) REVERT: A 574 LYS cc_start: 0.9544 (mmmt) cc_final: 0.9234 (mmmt) REVERT: H 100 GLU cc_start: 0.9010 (pt0) cc_final: 0.8765 (pm20) REVERT: H 100 ASP cc_start: 0.9401 (t0) cc_final: 0.9078 (p0) REVERT: L 60 ASP cc_start: 0.8857 (t0) cc_final: 0.8528 (p0) REVERT: L 103 ARG cc_start: 0.9265 (tpp-160) cc_final: 0.8747 (mmm160) outliers start: 34 outliers final: 21 residues processed: 98 average time/residue: 0.1269 time to fit residues: 19.5652 Evaluate side-chains 90 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 201 CYS Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 37 optimal weight: 0.0050 chunk 19 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 overall best weight: 1.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 130 GLN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.035994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.029951 restraints weight = 150284.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.030777 restraints weight = 86838.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.031339 restraints weight = 60822.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.031737 restraints weight = 47346.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.032030 restraints weight = 39478.523| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.7009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17103 Z= 0.124 Angle : 0.668 13.407 23405 Z= 0.309 Chirality : 0.046 0.281 2881 Planarity : 0.003 0.039 2802 Dihedral : 8.040 70.336 4123 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.51 % Allowed : 18.05 % Favored : 80.43 % 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: -1.36 (0.19), residues: 1902 helix: 0.01 (0.30), residues: 346 sheet: -0.40 (0.26), residues: 426 loop : -1.43 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 585 TYR 0.015 0.001 TYR E 486 PHE 0.013 0.001 PHE L 49 TRP 0.021 0.001 TRP E 69 HIS 0.004 0.001 HIS H 34 Details of bonding type rmsd covalent geometry : bond 0.00278 (16965) covalent geometry : angle 0.62204 (23029) SS BOND : bond 0.00193 ( 38) SS BOND : angle 1.15666 ( 76) hydrogen bonds : bond 0.03247 ( 401) hydrogen bonds : angle 4.30629 ( 1563) link_ALPHA1-2 : bond 0.02440 ( 1) link_ALPHA1-2 : angle 4.42309 ( 3) link_ALPHA1-3 : bond 0.00864 ( 8) link_ALPHA1-3 : angle 2.13995 ( 24) link_ALPHA1-6 : bond 0.00685 ( 7) link_ALPHA1-6 : angle 1.45177 ( 21) link_BETA1-4 : bond 0.00402 ( 26) link_BETA1-4 : angle 1.77052 ( 78) link_NAG-ASN : bond 0.00332 ( 58) link_NAG-ASN : angle 2.37845 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.8992 (ptm) cc_final: 0.8439 (tmm) REVERT: G 161 MET cc_start: 0.8509 (mmm) cc_final: 0.8307 (mmt) REVERT: G 271 MET cc_start: 0.8363 (mmt) cc_final: 0.8090 (mmm) REVERT: G 434 MET cc_start: 0.9041 (mtp) cc_final: 0.8776 (mtm) REVERT: B 535 MET cc_start: 0.9402 (mpp) cc_final: 0.8860 (mpp) REVERT: E 150 MET cc_start: 0.8243 (mmm) cc_final: 0.7857 (mmm) REVERT: F 104 MET cc_start: 0.9230 (tmm) cc_final: 0.8964 (tmm) REVERT: F 114 GLN cc_start: 0.9441 (OUTLIER) cc_final: 0.9226 (tm-30) REVERT: F 430 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8957 (mm) REVERT: C 584 GLU cc_start: 0.9250 (tp30) cc_final: 0.8959 (tm-30) REVERT: C 589 ASP cc_start: 0.9344 (p0) cc_final: 0.9072 (p0) REVERT: C 654 GLU cc_start: 0.9177 (tp30) cc_final: 0.8763 (tp30) REVERT: A 574 LYS cc_start: 0.9595 (mmmt) cc_final: 0.9231 (mmmt) REVERT: H 100 GLU cc_start: 0.8970 (pt0) cc_final: 0.8721 (pm20) REVERT: H 100 ASP cc_start: 0.9307 (t0) cc_final: 0.9012 (p0) REVERT: L 60 ASP cc_start: 0.8773 (t0) cc_final: 0.8426 (p0) REVERT: L 103 ARG cc_start: 0.9152 (tpp-160) cc_final: 0.8690 (mmm160) outliers start: 26 outliers final: 17 residues processed: 102 average time/residue: 0.1182 time to fit residues: 19.3254 Evaluate side-chains 89 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 201 CYS Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 41 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 15 optimal weight: 0.0870 chunk 98 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.034625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.028703 restraints weight = 143748.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.029530 restraints weight = 80225.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.030121 restraints weight = 54455.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.030459 restraints weight = 41560.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.030769 restraints weight = 35024.147| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.7596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 17103 Z= 0.261 Angle : 0.773 13.742 23405 Z= 0.362 Chirality : 0.047 0.263 2881 Planarity : 0.004 0.055 2802 Dihedral : 8.247 63.847 4123 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.21 % Allowed : 18.11 % Favored : 79.67 % 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: -1.61 (0.19), residues: 1902 helix: -0.14 (0.29), residues: 349 sheet: -0.76 (0.25), residues: 458 loop : -1.54 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 100 TYR 0.015 0.002 TYR L 91 PHE 0.016 0.002 PHE F 382 TRP 0.016 0.002 TRP H 35A HIS 0.005 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00566 (16965) covalent geometry : angle 0.72419 (23029) SS BOND : bond 0.00283 ( 38) SS BOND : angle 1.39143 ( 76) hydrogen bonds : bond 0.03743 ( 401) hydrogen bonds : angle 4.63341 ( 1563) link_ALPHA1-2 : bond 0.02368 ( 1) link_ALPHA1-2 : angle 4.81438 ( 3) link_ALPHA1-3 : bond 0.00694 ( 8) link_ALPHA1-3 : angle 2.58633 ( 24) link_ALPHA1-6 : bond 0.00436 ( 7) link_ALPHA1-6 : angle 1.62994 ( 21) link_BETA1-4 : bond 0.00339 ( 26) link_BETA1-4 : angle 1.92678 ( 78) link_NAG-ASN : bond 0.00477 ( 58) link_NAG-ASN : angle 2.61386 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 65 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.9078 (ptm) cc_final: 0.8486 (tmm) REVERT: G 434 MET cc_start: 0.9108 (mtp) cc_final: 0.8822 (mtm) REVERT: B 535 MET cc_start: 0.9419 (mpp) cc_final: 0.8872 (mpp) REVERT: E 150 MET cc_start: 0.8357 (mmm) cc_final: 0.7921 (mmm) REVERT: F 114 GLN cc_start: 0.9519 (OUTLIER) cc_final: 0.9273 (tm-30) REVERT: F 430 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8909 (mm) REVERT: F 434 MET cc_start: 0.8657 (mmm) cc_final: 0.8307 (tpp) REVERT: C 584 GLU cc_start: 0.9297 (tp30) cc_final: 0.8962 (tm-30) REVERT: C 589 ASP cc_start: 0.9451 (p0) cc_final: 0.9040 (p0) REVERT: C 654 GLU cc_start: 0.9263 (tp30) cc_final: 0.8912 (tp30) REVERT: A 574 LYS cc_start: 0.9633 (mmmt) cc_final: 0.9342 (mmmt) REVERT: A 657 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: H 100 ASP cc_start: 0.9367 (t0) cc_final: 0.9120 (p0) outliers start: 38 outliers final: 25 residues processed: 99 average time/residue: 0.1107 time to fit residues: 18.1078 Evaluate side-chains 93 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 201 CYS Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 82 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.034667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.028832 restraints weight = 143617.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.029650 restraints weight = 79469.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.030236 restraints weight = 54054.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.030633 restraints weight = 41149.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.030927 restraints weight = 33968.291| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.7877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17103 Z= 0.226 Angle : 0.743 13.776 23405 Z= 0.346 Chirality : 0.046 0.273 2881 Planarity : 0.004 0.050 2802 Dihedral : 8.076 58.488 4123 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.92 % Allowed : 18.23 % Favored : 79.85 % 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: -1.54 (0.19), residues: 1902 helix: -0.00 (0.29), residues: 343 sheet: -0.69 (0.25), residues: 452 loop : -1.53 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 100 TYR 0.010 0.001 TYR F 486 PHE 0.012 0.001 PHE L 49 TRP 0.018 0.002 TRP E 69 HIS 0.004 0.001 HIS H 34 Details of bonding type rmsd covalent geometry : bond 0.00488 (16965) covalent geometry : angle 0.69542 (23029) SS BOND : bond 0.00290 ( 38) SS BOND : angle 1.38247 ( 76) hydrogen bonds : bond 0.03531 ( 401) hydrogen bonds : angle 4.53752 ( 1563) link_ALPHA1-2 : bond 0.02737 ( 1) link_ALPHA1-2 : angle 5.03474 ( 3) link_ALPHA1-3 : bond 0.00699 ( 8) link_ALPHA1-3 : angle 2.39619 ( 24) link_ALPHA1-6 : bond 0.00452 ( 7) link_ALPHA1-6 : angle 1.53960 ( 21) link_BETA1-4 : bond 0.00303 ( 26) link_BETA1-4 : angle 1.82688 ( 78) link_NAG-ASN : bond 0.00378 ( 58) link_NAG-ASN : angle 2.54891 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.9026 (ptm) cc_final: 0.8499 (tmm) REVERT: G 150 MET cc_start: 0.9132 (mmp) cc_final: 0.8924 (mmp) REVERT: G 434 MET cc_start: 0.9126 (mtp) cc_final: 0.8856 (mtm) REVERT: B 535 MET cc_start: 0.9380 (mpp) cc_final: 0.8765 (mpp) REVERT: F 104 MET cc_start: 0.9156 (tmm) cc_final: 0.8914 (tmm) REVERT: F 114 GLN cc_start: 0.9503 (OUTLIER) cc_final: 0.9277 (tm-30) REVERT: F 430 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8973 (mm) REVERT: C 530 MET cc_start: 0.8909 (mtp) cc_final: 0.8504 (mtm) REVERT: C 584 GLU cc_start: 0.9286 (tp30) cc_final: 0.8964 (tm-30) REVERT: C 589 ASP cc_start: 0.9446 (p0) cc_final: 0.9162 (p0) REVERT: C 654 GLU cc_start: 0.9269 (tp30) cc_final: 0.8909 (tp30) REVERT: A 574 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9355 (mmmt) REVERT: A 657 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8399 (mp0) REVERT: H 100 ASP cc_start: 0.9314 (t0) cc_final: 0.9100 (p0) outliers start: 33 outliers final: 25 residues processed: 97 average time/residue: 0.1142 time to fit residues: 18.1394 Evaluate side-chains 93 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 201 CYS Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 106 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 72 HIS F 302 ASN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.035307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.028310 restraints weight = 141100.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.029147 restraints weight = 85740.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.029732 restraints weight = 61572.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.030152 restraints weight = 48804.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.030442 restraints weight = 41598.041| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.8151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17103 Z= 0.214 Angle : 0.738 13.711 23405 Z= 0.344 Chirality : 0.046 0.274 2881 Planarity : 0.004 0.050 2802 Dihedral : 7.987 57.270 4123 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.81 % Allowed : 18.58 % Favored : 79.62 % 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: -1.58 (0.19), residues: 1902 helix: -0.22 (0.29), residues: 361 sheet: -0.70 (0.25), residues: 455 loop : -1.51 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 100 TYR 0.011 0.001 TYR A 638 PHE 0.011 0.001 PHE F 382 TRP 0.043 0.002 TRP E 69 HIS 0.004 0.001 HIS H 34 Details of bonding type rmsd covalent geometry : bond 0.00464 (16965) covalent geometry : angle 0.68958 (23029) SS BOND : bond 0.00291 ( 38) SS BOND : angle 1.39966 ( 76) hydrogen bonds : bond 0.03469 ( 401) hydrogen bonds : angle 4.50639 ( 1563) link_ALPHA1-2 : bond 0.02684 ( 1) link_ALPHA1-2 : angle 5.00273 ( 3) link_ALPHA1-3 : bond 0.00618 ( 8) link_ALPHA1-3 : angle 2.35180 ( 24) link_ALPHA1-6 : bond 0.00453 ( 7) link_ALPHA1-6 : angle 1.51872 ( 21) link_BETA1-4 : bond 0.00317 ( 26) link_BETA1-4 : angle 1.87212 ( 78) link_NAG-ASN : bond 0.00384 ( 58) link_NAG-ASN : angle 2.53844 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.9047 (ptm) cc_final: 0.8525 (tmm) REVERT: G 434 MET cc_start: 0.9106 (mtp) cc_final: 0.8838 (mtt) REVERT: B 535 MET cc_start: 0.9356 (mpp) cc_final: 0.8728 (mpp) REVERT: F 104 MET cc_start: 0.9157 (tmm) cc_final: 0.8908 (tmm) REVERT: F 114 GLN cc_start: 0.9474 (OUTLIER) cc_final: 0.9267 (tm-30) REVERT: C 530 MET cc_start: 0.8916 (mtp) cc_final: 0.8517 (mtm) REVERT: C 584 GLU cc_start: 0.9280 (tp30) cc_final: 0.8990 (tm-30) REVERT: C 589 ASP cc_start: 0.9448 (p0) cc_final: 0.9153 (p0) REVERT: A 657 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8459 (mp0) REVERT: H 100 ASP cc_start: 0.9266 (t0) cc_final: 0.9024 (p0) REVERT: L 52 ASP cc_start: 0.9266 (p0) cc_final: 0.8851 (m-30) outliers start: 31 outliers final: 26 residues processed: 98 average time/residue: 0.1135 time to fit residues: 18.1463 Evaluate side-chains 94 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 201 CYS Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 46 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.034754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.028918 restraints weight = 142460.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.029759 restraints weight = 79193.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.030331 restraints weight = 53606.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.030754 restraints weight = 40856.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.031036 restraints weight = 33484.444| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.8282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17103 Z= 0.186 Angle : 0.718 13.666 23405 Z= 0.334 Chirality : 0.046 0.279 2881 Planarity : 0.004 0.046 2802 Dihedral : 7.851 57.105 4123 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.57 % Allowed : 18.93 % Favored : 79.50 % 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: -1.50 (0.19), residues: 1902 helix: -0.19 (0.28), residues: 367 sheet: -0.54 (0.25), residues: 453 loop : -1.51 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 100 TYR 0.012 0.001 TYR E 486 PHE 0.012 0.001 PHE H 99 TRP 0.018 0.002 TRP E 69 HIS 0.004 0.001 HIS H 34 Details of bonding type rmsd covalent geometry : bond 0.00406 (16965) covalent geometry : angle 0.67057 (23029) SS BOND : bond 0.00262 ( 38) SS BOND : angle 1.24822 ( 76) hydrogen bonds : bond 0.03367 ( 401) hydrogen bonds : angle 4.42098 ( 1563) link_ALPHA1-2 : bond 0.02880 ( 1) link_ALPHA1-2 : angle 5.08945 ( 3) link_ALPHA1-3 : bond 0.00629 ( 8) link_ALPHA1-3 : angle 2.24408 ( 24) link_ALPHA1-6 : bond 0.00474 ( 7) link_ALPHA1-6 : angle 1.47209 ( 21) link_BETA1-4 : bond 0.00326 ( 26) link_BETA1-4 : angle 1.85082 ( 78) link_NAG-ASN : bond 0.00343 ( 58) link_NAG-ASN : angle 2.49559 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2057.09 seconds wall clock time: 37 minutes 2.13 seconds (2222.13 seconds total)