Starting phenix.real_space_refine on Sat Sep 12 16:48:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xrt_22295/09_2026/6xrt_22295.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xrt_22295/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xrt_22295/09_2026/6xrt_22295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xrt_22295/09_2026/6xrt_22295.map" model { file = "/net/cci-nas-00/data/ceres_data/6xrt_22295/09_2026/6xrt_22295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xrt_22295/09_2026/6xrt_22295.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xrt_22295/09_2026/6xrt_22295.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xrt_22295/09_2026/6xrt_22295.cif" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 3.85, per 1000 atoms: 0.23 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: 1.45 Conformation dependent library (CDL) restraints added in 648.0 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: 0.73 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: 3.85 Time building geometry restraints manager: 1.83 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 - 17.99: 8452 17.99 - 35.97: 779 35.97 - 53.96: 149 53.96 - 71.94: 31 71.94 - 89.93: 17 Dihedral angle restraints: 9428 sinusoidal: 3831 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 9425 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 17.690 Find NCS groups from input model: 0.490 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 : 14.176 89.925 5694 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/Z covalent geometry : bond 0.00581 / 0.31 (16965) covalent geometry : angle 0.95322 / 0.50 (23029) SS BOND : bond 0.00309 / 0.20 ( 38) SS BOND : angle 1.83375 / 1.20 ( 76) hydrogen bonds : bond 0.29959 / 19.96 ( 401) hydrogen bonds : angle 10.93324 / 7.45 ( 1563) link_ALPHA1-2 : bond 0.01152 / 0.61 ( 1) link_ALPHA1-2 : angle 2.08606 / 1.10 ( 3) link_ALPHA1-3 : bond 0.00718 / 0.37 ( 8) link_ALPHA1-3 : angle 3.64869 / 2.76 ( 24) link_ALPHA1-6 : bond 0.00460 / 0.22 ( 7) link_ALPHA1-6 : angle 1.53660 / 1.00 ( 21) link_BETA1-4 : bond 0.00627 / 0.36 ( 26) link_BETA1-4 : angle 2.42798 / 1.59 ( 78) link_NAG-ASN : bond 0.00720 / 0.47 ( 58) link_NAG-ASN : angle 3.47842 / 2.25 ( 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 : 0.647 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: 0.7535 (p0) REVERT: G 482 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7440 (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: 0.8592 (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: 0.8325 (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: 0.1451 time to fit residues: 56.1297 Evaluate side-chains 135 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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... G 66 HIS ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 HIS G 425 ASN G 478 ASN B 590 GLN ** 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 = 0.3101 r_free = 0.3101 target = 0.036575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.030649 restraints weight = 152755.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.031469 restraints weight = 87663.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.032044 restraints weight = 60841.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.032444 restraints weight = 47102.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.032731 restraints weight = 39244.734| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 17103 Z= 0.322 Angle : 1.006 15.070 23405 Z= 0.482 Chirality : 0.053 0.355 2881 Planarity : 0.007 0.079 2802 Dihedral : 6.057 55.345 2079 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.81 % Allowed : 10.54 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % 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: -2.19 (0.18), residues: 1902 helix: -1.66 (0.25), residues: 331 sheet: -0.82 (0.25), residues: 452 loop : -1.68 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 100 TYR 0.025 0.003 TYR B 586 PHE 0.023 0.003 PHE F 383 TRP 0.036 0.003 TRP G 45 HIS 0.009 0.002 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.32 (16965) covalent geometry : angle 0.95386 / 0.47 (23029) SS BOND : bond 0.00633 / 0.36 ( 38) SS BOND : angle 1.88475 / 1.36 ( 76) hydrogen bonds : bond 0.05089 / 3.42 ( 401) hydrogen bonds : angle 5.75563 / 3.90 ( 1563) link_ALPHA1-2 : bond 0.00701 / 0.37 ( 1) link_ALPHA1-2 : angle 2.50071 / 1.35 ( 3) link_ALPHA1-3 : bond 0.00570 / 0.29 ( 8) link_ALPHA1-3 : angle 3.44791 / 2.39 ( 24) link_ALPHA1-6 : bond 0.00420 / 0.20 ( 7) link_ALPHA1-6 : angle 2.18114 / 1.52 ( 21) link_BETA1-4 : bond 0.00603 / 0.29 ( 26) link_BETA1-4 : angle 2.13116 / 1.42 ( 78) link_NAG-ASN : bond 0.00750 / 0.46 ( 58) link_NAG-ASN : angle 3.14086 / 2.11 ( 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: 31 poor density : 113 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 51 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8808 (t) REVERT: G 162 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.8496 (p) REVERT: B 542 ARG cc_start: 0.9201 (mtm180) cc_final: 0.8963 (ttp-110) REVERT: B 601 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8737 (tttp) REVERT: E 46 LYS cc_start: 0.9360 (mtpp) cc_final: 0.9025 (mmmm) REVERT: E 95 MET cc_start: 0.7851 (mmm) cc_final: 0.7482 (ttm) REVERT: E 338 TRP cc_start: 0.9253 (t-100) cc_final: 0.9021 (t-100) REVERT: E 426 MET cc_start: 0.6104 (tpp) cc_final: 0.5519 (tpp) REVERT: F 150 MET cc_start: 0.8669 (mmm) cc_final: 0.8311 (tpp) REVERT: F 271 MET cc_start: 0.8662 (mtp) cc_final: 0.8392 (mmt) REVERT: C 584 GLU cc_start: 0.9122 (tp30) cc_final: 0.8844 (tp30) REVERT: C 588 ARG cc_start: 0.7514 (mmt180) cc_final: 0.6649 (mtt180) REVERT: C 659 ASP cc_start: 0.9402 (m-30) cc_final: 0.9032 (p0) REVERT: H 5 ARG cc_start: 0.8692 (mmm160) cc_final: 0.8359 (mmm-85) REVERT: H 18 LEU cc_start: 0.9308 (tt) cc_final: 0.8718 (mp) REVERT: H 97 GLU cc_start: 0.8373 (tp30) cc_final: 0.7539 (tp30) REVERT: H 100 ASP cc_start: 0.9275 (t0) cc_final: 0.9050 (p0) REVERT: L 103 ARG cc_start: 0.8848 (tpp-160) cc_final: 0.8498 (tpp80) outliers start: 31 outliers final: 13 residues processed: 139 average time/residue: 0.1367 time to fit residues: 28.6727 Evaluate side-chains 108 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 162 THR 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: 1.9990 chunk 38 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 172 optimal weight: 0.0670 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN E 374 HIS F 114 GLN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.037720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.031614 restraints weight = 146928.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.032466 restraints weight = 85056.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.033094 restraints weight = 58808.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.033487 restraints weight = 45488.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.033786 restraints weight = 38131.831| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17103 Z= 0.117 Angle : 0.705 13.353 23405 Z= 0.327 Chirality : 0.047 0.339 2881 Planarity : 0.004 0.039 2802 Dihedral : 4.973 51.608 2072 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.46 % Allowed : 12.46 % Favored : 86.08 % 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: -1.85 (0.19), residues: 1902 helix: -1.08 (0.27), residues: 344 sheet: -0.67 (0.25), residues: 442 loop : -1.52 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 100 TYR 0.019 0.001 TYR B 643 PHE 0.026 0.001 PHE H 99 TRP 0.026 0.001 TRP F 96 HIS 0.003 0.001 HIS L 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (16965) covalent geometry : angle 0.65426 / 0.32 (23029) SS BOND : bond 0.00207 / 0.13 ( 38) SS BOND : angle 1.29282 / 0.77 ( 76) hydrogen bonds : bond 0.04257 / 2.90 ( 401) hydrogen bonds : angle 4.98848 / 3.37 ( 1563) link_ALPHA1-2 : bond 0.01059 / 0.56 ( 1) link_ALPHA1-2 : angle 1.91868 / 1.01 ( 3) link_ALPHA1-3 : bond 0.00582 / 0.30 ( 8) link_ALPHA1-3 : angle 3.02068 / 2.28 ( 24) link_ALPHA1-6 : bond 0.00366 / 0.19 ( 7) link_ALPHA1-6 : angle 1.43441 / 0.97 ( 21) link_BETA1-4 : bond 0.00416 / 0.26 ( 26) link_BETA1-4 : angle 1.60355 / 1.06 ( 78) link_NAG-ASN : bond 0.00394 / 0.28 ( 58) link_NAG-ASN : angle 2.59442 / 1.73 ( 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 134 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.9240 (mtm180) cc_final: 0.8811 (ttp-110) REVERT: B 601 LYS cc_start: 0.9066 (mmmt) cc_final: 0.8624 (tttm) REVERT: B 648 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8333 (pm20) REVERT: E 46 LYS cc_start: 0.9281 (mtpp) cc_final: 0.8965 (mmmm) REVERT: E 338 TRP cc_start: 0.9232 (t-100) cc_final: 0.9027 (t-100) REVERT: F 104 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8853 (tmm) REVERT: F 150 MET cc_start: 0.8701 (mmm) cc_final: 0.8333 (tpp) REVERT: F 271 MET cc_start: 0.8640 (mtp) cc_final: 0.8406 (mmt) REVERT: C 584 GLU cc_start: 0.9131 (tp30) cc_final: 0.8810 (tp30) REVERT: C 588 ARG cc_start: 0.7556 (mmt180) cc_final: 0.7062 (mmt180) REVERT: C 589 ASP cc_start: 0.9065 (p0) cc_final: 0.8695 (p0) REVERT: C 659 ASP cc_start: 0.9415 (m-30) cc_final: 0.9035 (p0) REVERT: H 5 ARG cc_start: 0.8734 (mmm160) cc_final: 0.8340 (mmm-85) REVERT: H 97 GLU cc_start: 0.8401 (tp30) cc_final: 0.8056 (tp30) REVERT: H 100 ASP cc_start: 0.9231 (t0) cc_final: 0.8999 (p0) REVERT: L 103 ARG cc_start: 0.8917 (tpp-160) cc_final: 0.8509 (mmm160) outliers start: 25 outliers final: 13 residues processed: 126 average time/residue: 0.1392 time to fit residues: 27.0264 Evaluate side-chains 111 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 648 GLU Chi-restraints excluded: chain E residue 128 THR 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 F residue 433 CYS Chi-restraints excluded: chain C residue 604 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 80 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN ** G 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 GLN E 478 ASN 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 = 0.3048 r_free = 0.3048 target = 0.035459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.028908 restraints weight = 148409.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.029805 restraints weight = 83595.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.030432 restraints weight = 57632.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.030875 restraints weight = 44276.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.031141 restraints weight = 36569.381| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.6033 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= 0.290 Angle : 0.873 13.696 23405 Z= 0.413 Chirality : 0.049 0.317 2881 Planarity : 0.005 0.045 2802 Dihedral : 5.449 41.465 2071 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.56 % Allowed : 15.08 % Favored : 82.35 % 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: -1.95 (0.19), residues: 1902 helix: -0.70 (0.29), residues: 335 sheet: -0.90 (0.25), residues: 443 loop : -1.68 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 100 TYR 0.017 0.002 TYR L 91 PHE 0.021 0.002 PHE F 353 TRP 0.031 0.003 TRP B 571 HIS 0.007 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.29 (16965) covalent geometry : angle 0.82236 / 0.40 (23029) SS BOND : bond 0.00396 / 0.26 ( 38) SS BOND : angle 1.69917 / 1.15 ( 76) hydrogen bonds : bond 0.04548 / 3.13 ( 401) hydrogen bonds : angle 5.12409 / 3.48 ( 1563) link_ALPHA1-2 : bond 0.00995 / 0.52 ( 1) link_ALPHA1-2 : angle 2.18310 / 1.15 ( 3) link_ALPHA1-3 : bond 0.00615 / 0.33 ( 8) link_ALPHA1-3 : angle 2.92841 / 2.05 ( 24) link_ALPHA1-6 : bond 0.00305 / 0.16 ( 7) link_ALPHA1-6 : angle 1.80005 / 1.32 ( 21) link_BETA1-4 : bond 0.00479 / 0.28 ( 26) link_BETA1-4 : angle 1.96009 / 1.30 ( 78) link_NAG-ASN : bond 0.00600 / 0.38 ( 58) link_NAG-ASN : angle 2.89353 / 2.00 ( 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 116 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 72 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 51 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8884 (t) REVERT: B 584 GLU cc_start: 0.9479 (tm-30) cc_final: 0.9232 (tm-30) REVERT: E 161 MET cc_start: 0.8782 (tpp) cc_final: 0.8548 (tpp) REVERT: F 150 MET cc_start: 0.8880 (mmm) cc_final: 0.8664 (tpp) REVERT: F 271 MET cc_start: 0.8833 (mtp) cc_final: 0.8602 (mmt) REVERT: F 426 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8021 (tmm) REVERT: F 430 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8924 (mm) REVERT: C 584 GLU cc_start: 0.9349 (tp30) cc_final: 0.8903 (tm-30) REVERT: C 589 ASP cc_start: 0.9372 (p0) cc_final: 0.8993 (p0) REVERT: H 5 ARG cc_start: 0.8767 (mmm160) cc_final: 0.8461 (mmm-85) REVERT: H 100 ASP cc_start: 0.9350 (t0) cc_final: 0.9134 (p0) REVERT: L 100 ARG cc_start: 0.8002 (mmp80) cc_final: 0.7598 (mmp80) REVERT: L 103 ARG cc_start: 0.9122 (tpp-160) cc_final: 0.8602 (tpp80) outliers start: 44 outliers final: 21 residues processed: 111 average time/residue: 0.1412 time to fit residues: 24.3750 Evaluate side-chains 92 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 432 GLN 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 128 THR 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 261 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 131 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 172 optimal weight: 0.0040 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.035937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.029331 restraints weight = 148701.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.030215 restraints weight = 85660.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.030826 restraints weight = 59687.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.031228 restraints weight = 46581.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.031542 restraints weight = 39306.338| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.6398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17103 Z= 0.199 Angle : 0.717 13.767 23405 Z= 0.338 Chirality : 0.046 0.325 2881 Planarity : 0.004 0.041 2802 Dihedral : 5.184 41.174 2071 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.98 % Allowed : 16.83 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.19), residues: 1902 helix: -0.42 (0.29), residues: 347 sheet: -0.86 (0.25), residues: 454 loop : -1.57 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 100 TYR 0.018 0.002 TYR F 435 PHE 0.015 0.001 PHE L 49 TRP 0.017 0.002 TRP E 69 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (16965) covalent geometry : angle 0.66958 / 0.33 (23029) SS BOND : bond 0.00511 / 0.29 ( 38) SS BOND : angle 1.19738 / 0.82 ( 76) hydrogen bonds : bond 0.03818 / 2.63 ( 401) hydrogen bonds : angle 4.71174 / 3.19 ( 1563) link_ALPHA1-2 : bond 0.00887 / 0.47 ( 1) link_ALPHA1-2 : angle 2.05614 / 1.08 ( 3) link_ALPHA1-3 : bond 0.00521 / 0.29 ( 8) link_ALPHA1-3 : angle 2.88291 / 2.08 ( 24) link_ALPHA1-6 : bond 0.00317 / 0.17 ( 7) link_ALPHA1-6 : angle 1.61542 / 1.15 ( 21) link_BETA1-4 : bond 0.00297 / 0.18 ( 26) link_BETA1-4 : angle 1.65122 / 1.10 ( 78) link_NAG-ASN : bond 0.00350 / 0.24 ( 58) link_NAG-ASN : angle 2.53487 / 1.73 ( 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 112 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 78 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 125 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9199 (mp) REVERT: G 434 MET cc_start: 0.9035 (mtp) cc_final: 0.8739 (mtm) REVERT: E 161 MET cc_start: 0.8726 (tpp) cc_final: 0.8508 (tpp) REVERT: E 426 MET cc_start: 0.6642 (tpp) cc_final: 0.6407 (tpp) REVERT: F 430 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8971 (mm) REVERT: F 434 MET cc_start: 0.8531 (tpp) cc_final: 0.8293 (mmm) REVERT: F 475 MET cc_start: 0.8450 (ppp) cc_final: 0.8213 (ptt) REVERT: C 584 GLU cc_start: 0.9378 (tp30) cc_final: 0.8963 (tm-30) REVERT: C 589 ASP cc_start: 0.9418 (p0) cc_final: 0.9195 (p0) REVERT: A 574 LYS cc_start: 0.9519 (mmmt) cc_final: 0.9228 (mmmt) REVERT: H 100 ASP cc_start: 0.9326 (t0) cc_final: 0.9086 (p0) REVERT: L 60 ASP cc_start: 0.8798 (t0) cc_final: 0.8478 (p0) REVERT: L 100 ARG cc_start: 0.7981 (mmp80) cc_final: 0.7744 (mmp80) REVERT: L 103 ARG cc_start: 0.9214 (tpp-160) cc_final: 0.8834 (tpp80) outliers start: 34 outliers final: 18 residues processed: 108 average time/residue: 0.1424 time to fit residues: 23.6538 Evaluate side-chains 88 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain G residue 125 LEU 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 128 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 245 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 F residue 433 CYS Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain H residue 24 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: 1.9990 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 67 ASN G 114 GLN ** 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 = 0.3095 r_free = 0.3095 target = 0.036588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.030033 restraints weight = 144309.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.030918 restraints weight = 83260.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.031563 restraints weight = 57626.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.032000 restraints weight = 44672.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.032306 restraints weight = 37254.482| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17103 Z= 0.120 Angle : 0.677 13.476 23405 Z= 0.315 Chirality : 0.046 0.318 2881 Planarity : 0.003 0.038 2802 Dihedral : 4.857 35.698 2071 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.75 % Allowed : 17.24 % Favored : 81.01 % 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: -1.49 (0.19), residues: 1902 helix: -0.18 (0.29), residues: 351 sheet: -0.43 (0.26), residues: 431 loop : -1.52 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 542 TYR 0.014 0.001 TYR E 486 PHE 0.016 0.001 PHE L 49 TRP 0.011 0.001 TRP E 45 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (16965) covalent geometry : angle 0.63233 / 0.31 (23029) SS BOND : bond 0.00278 / 0.20 ( 38) SS BOND : angle 1.21534 / 0.84 ( 76) hydrogen bonds : bond 0.03435 / 2.33 ( 401) hydrogen bonds : angle 4.36185 / 2.94 ( 1563) link_ALPHA1-2 : bond 0.01004 / 0.53 ( 1) link_ALPHA1-2 : angle 2.07408 / 1.09 ( 3) link_ALPHA1-3 : bond 0.00521 / 0.29 ( 8) link_ALPHA1-3 : angle 2.82640 / 2.10 ( 24) link_ALPHA1-6 : bond 0.00394 / 0.21 ( 7) link_ALPHA1-6 : angle 1.45064 / 0.98 ( 21) link_BETA1-4 : bond 0.00360 / 0.23 ( 26) link_BETA1-4 : angle 1.62476 / 1.08 ( 78) link_NAG-ASN : bond 0.00340 / 0.24 ( 58) link_NAG-ASN : angle 2.33059 / 1.59 ( 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 108 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: G 104 MET cc_start: 0.9054 (ptm) cc_final: 0.8492 (tmm) REVERT: G 434 MET cc_start: 0.9065 (mtp) cc_final: 0.8787 (mtm) REVERT: B 530 MET cc_start: 0.8534 (mpp) cc_final: 0.8185 (mpp) REVERT: B 535 MET cc_start: 0.9434 (mpp) cc_final: 0.8919 (mpp) REVERT: F 104 MET cc_start: 0.9272 (tmm) cc_final: 0.8990 (tmm) REVERT: F 430 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8958 (mm) REVERT: C 584 GLU cc_start: 0.9360 (tp30) cc_final: 0.8951 (tm-30) REVERT: C 589 ASP cc_start: 0.9396 (p0) cc_final: 0.9172 (p0) REVERT: A 574 LYS cc_start: 0.9540 (mmmt) cc_final: 0.9213 (mmmt) REVERT: L 60 ASP cc_start: 0.8839 (t0) cc_final: 0.8511 (p0) REVERT: L 103 ARG cc_start: 0.9215 (tpp-160) cc_final: 0.8694 (mmm160) outliers start: 30 outliers final: 18 residues processed: 106 average time/residue: 0.1301 time to fit residues: 21.7149 Evaluate side-chains 87 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain G residue 125 LEU 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 208 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 433 CYS 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 47 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 37 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 169 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 108 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3092 r_free = 0.3092 target = 0.036291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.030270 restraints weight = 147599.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.031106 restraints weight = 85932.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.031683 restraints weight = 59521.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.032088 restraints weight = 46446.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.032388 restraints weight = 38387.508| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.6708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17103 Z= 0.113 Angle : 0.655 13.288 23405 Z= 0.303 Chirality : 0.045 0.314 2881 Planarity : 0.003 0.038 2802 Dihedral : 4.678 31.755 2071 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.63 % Allowed : 17.71 % Favored : 80.66 % 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: -1.34 (0.20), residues: 1902 helix: -0.03 (0.30), residues: 351 sheet: -0.36 (0.26), residues: 429 loop : -1.42 (0.19), residues: 1122 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 0.015 0.001 PHE L 49 TRP 0.019 0.001 TRP E 69 HIS 0.004 0.001 HIS L 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (16965) covalent geometry : angle 0.61139 / 0.29 (23029) SS BOND : bond 0.00189 / 0.12 ( 38) SS BOND : angle 0.99710 / 0.66 ( 76) hydrogen bonds : bond 0.03248 / 2.21 ( 401) hydrogen bonds : angle 4.19729 / 2.83 ( 1563) link_ALPHA1-2 : bond 0.00948 / 0.50 ( 1) link_ALPHA1-2 : angle 2.01349 / 1.06 ( 3) link_ALPHA1-3 : bond 0.00509 / 0.27 ( 8) link_ALPHA1-3 : angle 2.81855 / 2.10 ( 24) link_ALPHA1-6 : bond 0.00408 / 0.21 ( 7) link_ALPHA1-6 : angle 1.42922 / 0.95 ( 21) link_BETA1-4 : bond 0.00375 / 0.22 ( 26) link_BETA1-4 : angle 1.62647 / 1.08 ( 78) link_NAG-ASN : bond 0.00316 / 0.23 ( 58) link_NAG-ASN : angle 2.26946 / 1.55 ( 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 103 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.9007 (ptm) cc_final: 0.8513 (tmm) REVERT: G 125 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9145 (mp) REVERT: G 434 MET cc_start: 0.9034 (mtp) cc_final: 0.8795 (mtm) REVERT: B 530 MET cc_start: 0.8526 (mpp) cc_final: 0.8176 (mpp) REVERT: B 535 MET cc_start: 0.9396 (mpp) cc_final: 0.8871 (mpp) REVERT: F 430 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8986 (mm) REVERT: C 584 GLU cc_start: 0.9258 (tp30) cc_final: 0.8938 (tm-30) REVERT: C 589 ASP cc_start: 0.9342 (p0) cc_final: 0.9067 (p0) REVERT: C 654 GLU cc_start: 0.9125 (tp30) cc_final: 0.8813 (tp30) REVERT: A 574 LYS cc_start: 0.9561 (mmmt) cc_final: 0.9215 (mmmt) REVERT: L 60 ASP cc_start: 0.8762 (t0) cc_final: 0.8382 (p0) REVERT: L 103 ARG cc_start: 0.9134 (tpp-160) cc_final: 0.8654 (mmm160) outliers start: 28 outliers final: 21 residues processed: 100 average time/residue: 0.1244 time to fit residues: 19.9875 Evaluate side-chains 95 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain G residue 125 LEU 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 416 LEU Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 433 CYS 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 11 VAL Chi-restraints excluded: chain L residue 21 ILE 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: 8.9990 chunk 116 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 315 GLN ** L 66 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 = 0.2985 r_free = 0.2985 target = 0.034133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.028250 restraints weight = 148110.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.029065 restraints weight = 83651.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.029621 restraints weight = 57417.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.030025 restraints weight = 44355.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.030314 restraints weight = 36620.528| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.7613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17103 Z= 0.301 Angle : 0.833 13.766 23405 Z= 0.394 Chirality : 0.048 0.319 2881 Planarity : 0.005 0.059 2802 Dihedral : 5.404 30.733 2071 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.15 % Allowed : 17.82 % Favored : 80.02 % 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: -1.66 (0.19), residues: 1902 helix: -0.19 (0.29), residues: 341 sheet: -0.80 (0.24), residues: 473 loop : -1.56 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 94 TYR 0.017 0.002 TYR L 91 PHE 0.020 0.002 PHE F 382 TRP 0.025 0.003 TRP E 69 HIS 0.006 0.002 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.30 (16965) covalent geometry : angle 0.78701 / 0.38 (23029) SS BOND : bond 0.00363 / 0.25 ( 38) SS BOND : angle 1.44266 / 0.94 ( 76) hydrogen bonds : bond 0.03972 / 2.70 ( 401) hydrogen bonds : angle 4.77862 / 3.23 ( 1563) link_ALPHA1-2 : bond 0.00775 / 0.41 ( 1) link_ALPHA1-2 : angle 2.10184 / 1.10 ( 3) link_ALPHA1-3 : bond 0.00559 / 0.30 ( 8) link_ALPHA1-3 : angle 2.88653 / 1.98 ( 24) link_ALPHA1-6 : bond 0.00322 / 0.17 ( 7) link_ALPHA1-6 : angle 1.78905 / 1.33 ( 21) link_BETA1-4 : bond 0.00362 / 0.22 ( 26) link_BETA1-4 : angle 1.89146 / 1.27 ( 78) link_NAG-ASN : bond 0.00583 / 0.38 ( 58) link_NAG-ASN : angle 2.70458 / 1.85 ( 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 97 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 60 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: G 104 MET cc_start: 0.9039 (ptm) cc_final: 0.8502 (tmm) REVERT: G 434 MET cc_start: 0.9109 (mtp) cc_final: 0.8833 (mtm) REVERT: B 530 MET cc_start: 0.8615 (mpp) cc_final: 0.8321 (mpp) REVERT: B 535 MET cc_start: 0.9408 (mpp) cc_final: 0.8871 (mpp) REVERT: F 100 MET cc_start: 0.9202 (mmm) cc_final: 0.8982 (mmp) REVERT: F 104 MET cc_start: 0.9119 (tmm) cc_final: 0.8854 (tmm) REVERT: F 430 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9058 (mm) REVERT: C 584 GLU cc_start: 0.9297 (tp30) cc_final: 0.8950 (tm-30) REVERT: C 589 ASP cc_start: 0.9438 (p0) cc_final: 0.9044 (p0) REVERT: C 654 GLU cc_start: 0.9274 (tp30) cc_final: 0.9009 (tp30) REVERT: A 574 LYS cc_start: 0.9575 (mmmt) cc_final: 0.9226 (mmmt) REVERT: A 626 MET cc_start: 0.9219 (ppp) cc_final: 0.8857 (ppp) outliers start: 37 outliers final: 26 residues processed: 94 average time/residue: 0.1222 time to fit residues: 18.5463 Evaluate side-chains 87 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain G residue 161 MET 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 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 433 CYS 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 H residue 24 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 114 GLN L 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.035521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.029569 restraints weight = 142073.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.030449 restraints weight = 78733.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.031062 restraints weight = 52668.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.031460 restraints weight = 40153.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.031773 restraints weight = 33075.332| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.7573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17103 Z= 0.118 Angle : 0.684 13.536 23405 Z= 0.318 Chirality : 0.046 0.319 2881 Planarity : 0.003 0.038 2802 Dihedral : 4.925 29.760 2071 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.51 % Allowed : 18.29 % Favored : 80.20 % 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: -1.29 (0.20), residues: 1902 helix: 0.11 (0.30), residues: 345 sheet: -0.38 (0.26), residues: 437 loop : -1.40 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 100 TYR 0.013 0.001 TYR E 486 PHE 0.012 0.001 PHE L 49 TRP 0.038 0.002 TRP E 69 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (16965) covalent geometry : angle 0.64057 / 0.31 (23029) SS BOND : bond 0.00241 / 0.15 ( 38) SS BOND : angle 1.13083 / 0.77 ( 76) hydrogen bonds : bond 0.03278 / 2.23 ( 401) hydrogen bonds : angle 4.28954 / 2.90 ( 1563) link_ALPHA1-2 : bond 0.00887 / 0.47 ( 1) link_ALPHA1-2 : angle 2.04444 / 1.07 ( 3) link_ALPHA1-3 : bond 0.00523 / 0.29 ( 8) link_ALPHA1-3 : angle 2.78241 / 2.04 ( 24) link_ALPHA1-6 : bond 0.00415 / 0.22 ( 7) link_ALPHA1-6 : angle 1.44814 / 0.99 ( 21) link_BETA1-4 : bond 0.00347 / 0.21 ( 26) link_BETA1-4 : angle 1.66855 / 1.12 ( 78) link_NAG-ASN : bond 0.00341 / 0.24 ( 58) link_NAG-ASN : angle 2.31985 / 1.59 ( 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 98 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.8975 (ptm) cc_final: 0.8478 (tmm) REVERT: G 434 MET cc_start: 0.9100 (mtp) cc_final: 0.8840 (mtm) REVERT: B 530 MET cc_start: 0.8632 (mpp) cc_final: 0.8340 (mpp) REVERT: B 535 MET cc_start: 0.9390 (mpp) cc_final: 0.8836 (mpp) REVERT: E 95 MET cc_start: 0.9254 (ppp) cc_final: 0.8945 (ppp) REVERT: F 104 MET cc_start: 0.9170 (tmm) cc_final: 0.8913 (tmm) REVERT: C 584 GLU cc_start: 0.9262 (tp30) cc_final: 0.9005 (tm-30) REVERT: C 589 ASP cc_start: 0.9389 (p0) cc_final: 0.9106 (p0) REVERT: C 626 MET cc_start: 0.7638 (mmm) cc_final: 0.7437 (tpt) REVERT: C 654 GLU cc_start: 0.9208 (tp30) cc_final: 0.8826 (tp30) REVERT: A 530 MET cc_start: 0.7064 (pmm) cc_final: 0.6780 (pmm) REVERT: A 574 LYS cc_start: 0.9597 (mmmt) cc_final: 0.9208 (mmmt) REVERT: L 103 ARG cc_start: 0.9224 (tpp-160) cc_final: 0.8731 (mmm160) outliers start: 26 outliers final: 20 residues processed: 95 average time/residue: 0.1302 time to fit residues: 19.4736 Evaluate side-chains 89 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 106 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.034964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.028881 restraints weight = 154106.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.029743 restraints weight = 86578.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.030344 restraints weight = 58901.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.030784 restraints weight = 45018.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.031026 restraints weight = 36951.510| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.7911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 17103 Z= 0.236 Angle : 0.753 13.637 23405 Z= 0.353 Chirality : 0.046 0.316 2881 Planarity : 0.004 0.046 2802 Dihedral : 5.112 29.241 2071 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.46 % Allowed : 18.40 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.19), residues: 1902 helix: -0.07 (0.30), residues: 347 sheet: -0.70 (0.25), residues: 478 loop : -1.38 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 100 TYR 0.012 0.001 TYR F 484 PHE 0.015 0.002 PHE L 49 TRP 0.030 0.002 TRP E 69 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.24 (16965) covalent geometry : angle 0.70807 / 0.34 (23029) SS BOND : bond 0.00305 / 0.21 ( 38) SS BOND : angle 1.30248 / 0.86 ( 76) hydrogen bonds : bond 0.03542 / 2.42 ( 401) hydrogen bonds : angle 4.48111 / 3.03 ( 1563) link_ALPHA1-2 : bond 0.00790 / 0.42 ( 1) link_ALPHA1-2 : angle 2.10478 / 1.10 ( 3) link_ALPHA1-3 : bond 0.00604 / 0.32 ( 8) link_ALPHA1-3 : angle 2.78529 / 1.97 ( 24) link_ALPHA1-6 : bond 0.00293 / 0.17 ( 7) link_ALPHA1-6 : angle 1.63624 / 1.18 ( 21) link_BETA1-4 : bond 0.00291 / 0.17 ( 26) link_BETA1-4 : angle 1.76626 / 1.19 ( 78) link_NAG-ASN : bond 0.00442 / 0.29 ( 58) link_NAG-ASN : angle 2.50532 / 1.72 ( 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 92 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.9006 (ptm) cc_final: 0.8555 (tmm) REVERT: G 434 MET cc_start: 0.9108 (mtp) cc_final: 0.8834 (mtm) REVERT: B 530 MET cc_start: 0.8682 (mpp) cc_final: 0.8402 (mpp) REVERT: B 535 MET cc_start: 0.9377 (mpp) cc_final: 0.8822 (mpp) REVERT: E 95 MET cc_start: 0.9348 (ppp) cc_final: 0.9037 (ppp) REVERT: C 584 GLU cc_start: 0.9241 (tp30) cc_final: 0.8967 (tm-30) REVERT: C 589 ASP cc_start: 0.9426 (p0) cc_final: 0.9154 (p0) REVERT: C 654 GLU cc_start: 0.9292 (tp30) cc_final: 0.8959 (tp30) REVERT: A 530 MET cc_start: 0.7116 (pmm) cc_final: 0.6793 (pmm) REVERT: A 574 LYS cc_start: 0.9602 (mmmt) cc_final: 0.9231 (mmmt) outliers start: 25 outliers final: 21 residues processed: 89 average time/residue: 0.1240 time to fit residues: 17.9002 Evaluate side-chains 86 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 46 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 182 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.035405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.029486 restraints weight = 139702.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.030337 restraints weight = 77955.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.030869 restraints weight = 52947.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.031301 restraints weight = 41124.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.031597 restraints weight = 33626.786| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.7951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17103 Z= 0.139 Angle : 0.693 13.588 23405 Z= 0.322 Chirality : 0.046 0.315 2881 Planarity : 0.004 0.039 2802 Dihedral : 4.920 28.906 2071 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.22 % Allowed : 18.58 % Favored : 80.20 % 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: -1.31 (0.20), residues: 1902 helix: 0.19 (0.30), residues: 340 sheet: -0.56 (0.25), residues: 480 loop : -1.37 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 100 TYR 0.012 0.001 TYR E 486 PHE 0.013 0.001 PHE L 49 TRP 0.031 0.002 TRP E 69 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (16965) covalent geometry : angle 0.64968 / 0.31 (23029) SS BOND : bond 0.00237 / 0.15 ( 38) SS BOND : angle 1.14862 / 0.76 ( 76) hydrogen bonds : bond 0.03221 / 2.18 ( 401) hydrogen bonds : angle 4.26582 / 2.88 ( 1563) link_ALPHA1-2 : bond 0.00853 / 0.45 ( 1) link_ALPHA1-2 : angle 2.02912 / 1.06 ( 3) link_ALPHA1-3 : bond 0.00503 / 0.27 ( 8) link_ALPHA1-3 : angle 2.74551 / 1.99 ( 24) link_ALPHA1-6 : bond 0.00370 / 0.20 ( 7) link_ALPHA1-6 : angle 1.47000 / 1.01 ( 21) link_BETA1-4 : bond 0.00322 / 0.19 ( 26) link_BETA1-4 : angle 1.69793 / 1.14 ( 78) link_NAG-ASN : bond 0.00326 / 0.23 ( 58) link_NAG-ASN : angle 2.34270 / 1.60 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2197.29 seconds wall clock time: 39 minutes 30.71 seconds (2370.71 seconds total)