Starting phenix.real_space_refine on Sun Sep 13 21:19:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v4n_21042/09_2026/6v4n_21042_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v4n_21042/09_2026/6v4n_21042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v4n_21042/09_2026/6v4n_21042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v4n_21042/09_2026/6v4n_21042.map" model { file = "/net/cci-nas-00/data/ceres_data/6v4n_21042/09_2026/6v4n_21042_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v4n_21042/09_2026/6v4n_21042_neut.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 164 5.16 5 C 16130 2.51 5 N 4318 2.21 5 O 5250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25866 Number of models: 1 Model: "" Number of chains: 40 Chain: "I" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 371} Chain: "M" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3028 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 371} Chain: "N" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 371} Chain: "W" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3028 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 371} Chain: "A" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 203} Chain breaks: 1 Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 203} Chain breaks: 1 Chain: "D" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 203} Chain breaks: 1 Chain: "H" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 203} Chain breaks: 1 Chain: "B" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1648 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "E" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1648 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "G" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1648 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "L" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1648 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' CA': 1, 'BMA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' CA': 1, 'BMA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "M" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "N" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "W" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 6.81, per 1000 atoms: 0.26 Number of scatterers: 25866 At special positions: 0 Unit cell: (163.9, 163.9, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 164 16.00 O 5250 8.00 N 4318 7.00 C 16130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS I 87 " - pdb=" SG CYS I 420 " distance=1.88 Simple disulfide: pdb=" SG CYS I 122 " - pdb=" SG CYS I 127 " distance=2.03 Simple disulfide: pdb=" SG CYS I 182 " - pdb=" SG CYS I 229 " distance=2.03 Simple disulfide: pdb=" SG CYS I 231 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 277 " - pdb=" SG CYS I 291 " distance=2.03 Simple disulfide: pdb=" SG CYS I 279 " - pdb=" SG CYS I 289 " distance=2.03 Simple disulfide: pdb=" SG CYS I 318 " - pdb=" SG CYS I 337 " distance=2.03 Simple disulfide: pdb=" SG CYS I 424 " - pdb=" SG CYS I 447 " distance=2.03 Simple disulfide: pdb=" SG CYS M 87 " - pdb=" SG CYS M 420 " distance=2.03 Simple disulfide: pdb=" SG CYS M 122 " - pdb=" SG CYS M 127 " distance=2.03 Simple disulfide: pdb=" SG CYS M 182 " - pdb=" SG CYS M 229 " distance=2.03 Simple disulfide: pdb=" SG CYS M 231 " - pdb=" SG CYS M 236 " distance=2.03 Simple disulfide: pdb=" SG CYS M 277 " - pdb=" SG CYS M 291 " distance=2.03 Simple disulfide: pdb=" SG CYS M 279 " - pdb=" SG CYS M 289 " distance=2.03 Simple disulfide: pdb=" SG CYS M 318 " - pdb=" SG CYS M 337 " distance=2.03 Simple disulfide: pdb=" SG CYS M 424 " - pdb=" SG CYS M 447 " distance=2.03 Simple disulfide: pdb=" SG CYS N 87 " - pdb=" SG CYS N 420 " distance=2.04 Simple disulfide: pdb=" SG CYS N 122 " - pdb=" SG CYS N 127 " distance=2.03 Simple disulfide: pdb=" SG CYS N 182 " - pdb=" SG CYS N 229 " distance=2.03 Simple disulfide: pdb=" SG CYS N 231 " - pdb=" SG CYS N 236 " distance=2.03 Simple disulfide: pdb=" SG CYS N 277 " - pdb=" SG CYS N 291 " distance=2.03 Simple disulfide: pdb=" SG CYS N 279 " - pdb=" SG CYS N 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 318 " - pdb=" SG CYS N 337 " distance=2.03 Simple disulfide: pdb=" SG CYS N 424 " - pdb=" SG CYS N 447 " distance=2.03 Simple disulfide: pdb=" SG CYS W 87 " - pdb=" SG CYS W 420 " distance=2.04 Simple disulfide: pdb=" SG CYS W 122 " - pdb=" SG CYS W 127 " distance=2.03 Simple disulfide: pdb=" SG CYS W 182 " - pdb=" SG CYS W 229 " distance=2.03 Simple disulfide: pdb=" SG CYS W 231 " - pdb=" SG CYS W 236 " distance=2.03 Simple disulfide: pdb=" SG CYS W 277 " - pdb=" SG CYS W 291 " distance=2.03 Simple disulfide: pdb=" SG CYS W 279 " - pdb=" SG CYS W 289 " distance=2.03 Simple disulfide: pdb=" SG CYS W 318 " - pdb=" SG CYS W 337 " distance=2.03 Simple disulfide: pdb=" SG CYS W 424 " - pdb=" SG CYS W 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA M 508 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA N 508 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG F 1 " - " ASN I 144 " " NAG J 1 " - " ASN I 463 " " NAG K 1 " - " ASN I 284 " " NAG O 1 " - " ASN M 144 " " NAG P 1 " - " ASN M 463 " " NAG Q 1 " - " ASN M 284 " " NAG R 1 " - " ASN N 144 " " NAG S 1 " - " ASN N 463 " " NAG T 1 " - " ASN N 284 " " NAG U 1 " - " ASN W 144 " " NAG V 1 " - " ASN W 463 " " NAG X 1 " - " ASN W 284 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.0 seconds 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5988 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 76 sheets defined 3.6% alpha, 46.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'I' and resid 99 through 104 removed outlier: 3.595A pdb=" N GLY I 104 " --> pdb=" O HIS I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 147 removed outlier: 4.704A pdb=" N ARG I 147 " --> pdb=" O ASN I 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'N' and resid 99 through 103 Processing helix chain 'W' and resid 99 through 103 Processing helix chain 'W' and resid 143 through 147 removed outlier: 4.707A pdb=" N ARG W 147 " --> pdb=" O ASN W 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 187 through 189 No H-bonds generated for 'chain 'D' and resid 187 through 189' Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 182 through 189 removed outlier: 4.206A pdb=" N HIS B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 182 through 189 removed outlier: 4.205A pdb=" N HIS E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 182 through 189 removed outlier: 4.206A pdb=" N HIS G 189 " --> pdb=" O ASP G 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 182 through 189 removed outlier: 4.205A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 92 through 98 removed outlier: 5.438A pdb=" N LYS I 94 " --> pdb=" O CYS I 447 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N CYS I 447 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU I 96 " --> pdb=" O ILE I 445 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER I 440 " --> pdb=" O HIS I 431 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 113 through 122 removed outlier: 4.840A pdb=" N LEU I 113 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA I 136 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE I 115 " --> pdb=" O HIS I 134 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N HIS I 134 " --> pdb=" O ILE I 115 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU I 117 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU I 132 " --> pdb=" O GLU I 117 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU I 156 " --> pdb=" O HIS I 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 178 through 183 removed outlier: 3.710A pdb=" N SER I 178 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU I 202 " --> pdb=" O THR I 213 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR I 213 " --> pdb=" O LEU I 202 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE I 204 " --> pdb=" O THR I 211 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA I 209 " --> pdb=" O TYR I 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AA5, first strand: chain 'I' and resid 222 through 224 removed outlier: 3.975A pdb=" N ASP I 242 " --> pdb=" O GLU I 250 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU I 250 " --> pdb=" O ASP I 242 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS I 263 " --> pdb=" O LYS I 255 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG I 257 " --> pdb=" O ILE I 261 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE I 261 " --> pdb=" O ARG I 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 268 through 269 removed outlier: 6.512A pdb=" N THR I 268 " --> pdb=" O ILE I 314 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N LEU I 316 " --> pdb=" O THR I 268 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG I 292 " --> pdb=" O GLU I 276 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU I 276 " --> pdb=" O ARG I 292 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 352 through 356 removed outlier: 7.931A pdb=" N MET I 375 " --> pdb=" O VAL I 401 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL I 401 " --> pdb=" O MET I 375 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET I 377 " --> pdb=" O VAL I 399 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL I 399 " --> pdb=" O MET I 377 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU I 379 " --> pdb=" O SER I 397 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 92 through 98 removed outlier: 5.416A pdb=" N LYS M 94 " --> pdb=" O CYS M 447 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS M 447 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU M 96 " --> pdb=" O ILE M 445 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER M 440 " --> pdb=" O HIS M 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 113 through 122 removed outlier: 4.852A pdb=" N LEU M 113 " --> pdb=" O ALA M 136 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA M 136 " --> pdb=" O LEU M 113 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ILE M 115 " --> pdb=" O HIS M 134 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS M 134 " --> pdb=" O ILE M 115 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLU M 117 " --> pdb=" O LEU M 132 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU M 132 " --> pdb=" O GLU M 117 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU M 156 " --> pdb=" O HIS M 173 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 178 through 183 removed outlier: 3.706A pdb=" N SER M 178 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU M 202 " --> pdb=" O THR M 213 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR M 213 " --> pdb=" O LEU M 202 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE M 204 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA M 209 " --> pdb=" O TYR M 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 222 through 224 removed outlier: 3.544A pdb=" N ASN M 230 " --> pdb=" O TYR M 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 222 through 224 removed outlier: 3.970A pdb=" N ASP M 242 " --> pdb=" O GLU M 250 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU M 250 " --> pdb=" O ASP M 242 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS M 263 " --> pdb=" O LYS M 255 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG M 257 " --> pdb=" O ILE M 261 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE M 261 " --> pdb=" O ARG M 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 268 through 269 removed outlier: 6.509A pdb=" N THR M 268 " --> pdb=" O ILE M 314 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N LEU M 316 " --> pdb=" O THR M 268 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG M 292 " --> pdb=" O GLU M 276 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU M 276 " --> pdb=" O ARG M 292 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 352 through 356 removed outlier: 7.926A pdb=" N MET M 375 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL M 401 " --> pdb=" O MET M 375 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET M 377 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL M 399 " --> pdb=" O MET M 377 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU M 379 " --> pdb=" O SER M 397 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 92 through 98 removed outlier: 5.472A pdb=" N LYS N 94 " --> pdb=" O CYS N 447 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N CYS N 447 " --> pdb=" O LYS N 94 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU N 96 " --> pdb=" O ILE N 445 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER N 440 " --> pdb=" O HIS N 431 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 113 through 122 removed outlier: 4.864A pdb=" N LEU N 113 " --> pdb=" O ALA N 136 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ALA N 136 " --> pdb=" O LEU N 113 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE N 115 " --> pdb=" O HIS N 134 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N HIS N 134 " --> pdb=" O ILE N 115 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLU N 117 " --> pdb=" O LEU N 132 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU N 132 " --> pdb=" O GLU N 117 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU N 156 " --> pdb=" O HIS N 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 178 through 183 removed outlier: 3.705A pdb=" N SER N 178 " --> pdb=" O VAL N 193 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU N 202 " --> pdb=" O THR N 213 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR N 213 " --> pdb=" O LEU N 202 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE N 204 " --> pdb=" O THR N 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA N 209 " --> pdb=" O TYR N 206 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 222 through 224 removed outlier: 3.546A pdb=" N ASN N 230 " --> pdb=" O TYR N 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 222 through 224 removed outlier: 3.980A pdb=" N ASP N 242 " --> pdb=" O GLU N 250 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU N 250 " --> pdb=" O ASP N 242 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS N 263 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG N 257 " --> pdb=" O ILE N 261 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE N 261 " --> pdb=" O ARG N 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 268 through 269 removed outlier: 6.497A pdb=" N THR N 268 " --> pdb=" O ILE N 314 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N LEU N 316 " --> pdb=" O THR N 268 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG N 292 " --> pdb=" O GLU N 276 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU N 276 " --> pdb=" O ARG N 292 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 352 through 356 removed outlier: 7.929A pdb=" N MET N 375 " --> pdb=" O VAL N 401 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL N 401 " --> pdb=" O MET N 375 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N MET N 377 " --> pdb=" O VAL N 399 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL N 399 " --> pdb=" O MET N 377 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU N 379 " --> pdb=" O SER N 397 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 92 through 98 removed outlier: 5.431A pdb=" N LYS W 94 " --> pdb=" O CYS W 447 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS W 447 " --> pdb=" O LYS W 94 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU W 96 " --> pdb=" O ILE W 445 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER W 440 " --> pdb=" O HIS W 431 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 113 through 122 removed outlier: 4.849A pdb=" N LEU W 113 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA W 136 " --> pdb=" O LEU W 113 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE W 115 " --> pdb=" O HIS W 134 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N HIS W 134 " --> pdb=" O ILE W 115 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLU W 117 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU W 132 " --> pdb=" O GLU W 117 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU W 156 " --> pdb=" O HIS W 173 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 178 through 183 removed outlier: 3.736A pdb=" N SER W 178 " --> pdb=" O VAL W 193 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU W 202 " --> pdb=" O THR W 213 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR W 213 " --> pdb=" O LEU W 202 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE W 204 " --> pdb=" O THR W 211 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA W 209 " --> pdb=" O TYR W 206 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 222 through 224 Processing sheet with id=AC8, first strand: chain 'W' and resid 222 through 224 removed outlier: 3.963A pdb=" N ASP W 242 " --> pdb=" O GLU W 250 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU W 250 " --> pdb=" O ASP W 242 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS W 263 " --> pdb=" O LYS W 255 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG W 257 " --> pdb=" O ILE W 261 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE W 261 " --> pdb=" O ARG W 257 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 268 through 269 removed outlier: 6.513A pdb=" N THR W 268 " --> pdb=" O ILE W 314 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N LEU W 316 " --> pdb=" O THR W 268 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG W 292 " --> pdb=" O GLU W 276 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU W 276 " --> pdb=" O ARG W 292 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 352 through 356 removed outlier: 7.937A pdb=" N MET W 375 " --> pdb=" O VAL W 401 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL W 401 " --> pdb=" O MET W 375 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N MET W 377 " --> pdb=" O VAL W 399 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL W 399 " --> pdb=" O MET W 377 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU W 379 " --> pdb=" O SER W 397 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.947A pdb=" N TYR A 33 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP A 34 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR A 50 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.903A pdb=" N VAL A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP A 96 " --> pdb=" O MET A 100I" (cutoff:3.500A) removed outlier: 5.385A pdb=" N MET A 100I" --> pdb=" O ASP A 96 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 120 through 124 removed outlier: 4.883A pdb=" N ALA A 137 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 184 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY A 139 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL A 182 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU A 141 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER A 180 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 178 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 181 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 120 through 124 removed outlier: 4.883A pdb=" N ALA A 137 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 184 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY A 139 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL A 182 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU A 141 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER A 180 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 178 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 151 through 154 Processing sheet with id=AD8, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.948A pdb=" N TYR C 33 " --> pdb=" O GLY C 95 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR C 50 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.903A pdb=" N VAL C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP C 96 " --> pdb=" O MET C 100I" (cutoff:3.500A) removed outlier: 5.385A pdb=" N MET C 100I" --> pdb=" O ASP C 96 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.883A pdb=" N ALA C 137 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 184 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 181 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.883A pdb=" N ALA C 137 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 184 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AE5, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.947A pdb=" N TYR D 33 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.903A pdb=" N VAL D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP D 96 " --> pdb=" O MET D 100I" (cutoff:3.500A) removed outlier: 5.384A pdb=" N MET D 100I" --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 120 through 124 removed outlier: 4.882A pdb=" N ALA D 137 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL D 184 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU D 178 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 181 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 120 through 124 removed outlier: 4.882A pdb=" N ALA D 137 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL D 184 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU D 178 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.947A pdb=" N TYR H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.905A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP H 96 " --> pdb=" O MET H 100I" (cutoff:3.500A) removed outlier: 5.385A pdb=" N MET H 100I" --> pdb=" O ASP H 96 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 120 through 124 removed outlier: 4.882A pdb=" N ALA H 137 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL H 184 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY H 139 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL H 182 " --> pdb=" O GLY H 139 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU H 141 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER H 180 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS H 143 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU H 178 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL H 181 " --> pdb=" O HIS H 164 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 120 through 124 removed outlier: 4.882A pdb=" N ALA H 137 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL H 184 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY H 139 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL H 182 " --> pdb=" O GLY H 139 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU H 141 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER H 180 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS H 143 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU H 178 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 151 through 154 Processing sheet with id=AF8, first strand: chain 'B' and resid 4 through 7 removed outlier: 12.098A pdb=" N CYS B 23 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 11.080A pdb=" N THR B 74 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N ALA B 25 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 11.843A pdb=" N THR B 72 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 11.444A pdb=" N GLN B 27 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP B 70 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AG1, first strand: chain 'B' and resid 53 through 54 removed outlier: 5.603A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 115 through 116 removed outlier: 5.856A pdb=" N LEU B 135 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER B 177 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN B 137 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 175 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 130 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 115 through 116 removed outlier: 5.856A pdb=" N LEU B 135 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER B 177 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN B 137 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 175 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 178 " --> pdb=" O GLN B 160 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 153 through 155 removed outlier: 3.511A pdb=" N VAL B 150 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP B 148 " --> pdb=" O GLN B 155 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 4 through 7 removed outlier: 12.098A pdb=" N CYS E 23 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 11.081A pdb=" N THR E 74 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N ALA E 25 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N THR E 72 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 11.445A pdb=" N GLN E 27 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP E 70 " --> pdb=" O GLN E 27 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 12 through 13 Processing sheet with id=AG7, first strand: chain 'E' and resid 53 through 54 removed outlier: 5.602A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 115 through 116 removed outlier: 5.857A pdb=" N LEU E 135 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER E 177 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN E 137 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU E 175 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 130 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 115 through 116 removed outlier: 5.857A pdb=" N LEU E 135 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER E 177 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN E 137 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU E 175 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR E 178 " --> pdb=" O GLN E 160 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 153 through 155 removed outlier: 3.510A pdb=" N VAL E 150 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 4 through 7 removed outlier: 12.097A pdb=" N CYS G 23 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 11.081A pdb=" N THR G 74 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N ALA G 25 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N THR G 72 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 11.444A pdb=" N GLN G 27 " --> pdb=" O ASP G 70 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP G 70 " --> pdb=" O GLN G 27 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AH4, first strand: chain 'G' and resid 53 through 54 removed outlier: 5.603A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE G 48 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 115 through 116 removed outlier: 5.857A pdb=" N LEU G 135 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER G 177 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN G 137 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU G 175 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA G 130 " --> pdb=" O LEU G 181 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 115 through 116 removed outlier: 5.857A pdb=" N LEU G 135 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER G 177 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN G 137 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU G 175 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR G 178 " --> pdb=" O GLN G 160 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 153 through 155 removed outlier: 3.511A pdb=" N VAL G 150 " --> pdb=" O ALA G 153 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TRP G 148 " --> pdb=" O GLN G 155 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 4 through 7 removed outlier: 12.098A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 11.082A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.923A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.445A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AI1, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.602A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 115 through 116 removed outlier: 5.856A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA L 130 " --> pdb=" O LEU L 181 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 115 through 116 removed outlier: 5.856A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR L 178 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 153 through 155 removed outlier: 3.511A pdb=" N VAL L 150 " --> pdb=" O ALA L 153 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2079 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: 6.21 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8176 1.34 - 1.47: 6959 1.47 - 1.60: 10916 1.60 - 1.72: 5 1.72 - 1.85: 228 Bond restraints: 26284 Sorted by residual: bond pdb=" C1 NAG R 1 " pdb=" C2 NAG R 1 " ideal model delta sigma weight residual 1.532 1.641 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C1 NAG J 1 " pdb=" C2 NAG J 1 " ideal model delta sigma weight residual 1.532 1.638 -0.106 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C1 NAG K 1 " pdb=" C2 NAG K 1 " ideal model delta sigma weight residual 1.532 1.629 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C ASN N 144 " pdb=" N GLY N 145 " ideal model delta sigma weight residual 1.331 1.398 -0.068 1.46e-02 4.69e+03 2.16e+01 bond pdb=" N ASN N 144 " pdb=" CA ASN N 144 " ideal model delta sigma weight residual 1.457 1.412 0.046 1.29e-02 6.01e+03 1.25e+01 ... (remaining 26279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 34310 1.85 - 3.71: 1193 3.71 - 5.56: 120 5.56 - 7.42: 28 7.42 - 9.27: 11 Bond angle restraints: 35662 Sorted by residual: angle pdb=" CA TYR N 143 " pdb=" C TYR N 143 " pdb=" N ASN N 144 " ideal model delta sigma weight residual 117.48 111.23 6.25 1.41e+00 5.03e-01 1.96e+01 angle pdb=" C ASN N 144 " pdb=" N GLY N 145 " pdb=" CA GLY N 145 " ideal model delta sigma weight residual 121.41 129.77 -8.36 1.96e+00 2.60e-01 1.82e+01 angle pdb=" O TYR N 143 " pdb=" C TYR N 143 " pdb=" N ASN N 144 " ideal model delta sigma weight residual 122.23 127.50 -5.27 1.30e+00 5.92e-01 1.64e+01 angle pdb=" N ASP C 100A" pdb=" CA ASP C 100A" pdb=" C ASP C 100A" ideal model delta sigma weight residual 110.80 119.38 -8.58 2.13e+00 2.20e-01 1.62e+01 angle pdb=" N ASP D 100A" pdb=" CA ASP D 100A" pdb=" C ASP D 100A" ideal model delta sigma weight residual 110.80 119.37 -8.57 2.13e+00 2.20e-01 1.62e+01 ... (remaining 35657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.12: 15036 22.12 - 44.23: 900 44.23 - 66.35: 151 66.35 - 88.47: 61 88.47 - 110.59: 32 Dihedral angle restraints: 16180 sinusoidal: 6774 harmonic: 9406 Sorted by residual: dihedral pdb=" CA THR H 191 " pdb=" C THR H 191 " pdb=" N GLN H 192 " pdb=" CA GLN H 192 " ideal model delta harmonic sigma weight residual -180.00 -136.82 -43.18 0 5.00e+00 4.00e-02 7.46e+01 dihedral pdb=" CA THR A 191 " pdb=" C THR A 191 " pdb=" N GLN A 192 " pdb=" CA GLN A 192 " ideal model delta harmonic sigma weight residual -180.00 -136.85 -43.15 0 5.00e+00 4.00e-02 7.45e+01 dihedral pdb=" CA THR D 191 " pdb=" C THR D 191 " pdb=" N GLN D 192 " pdb=" CA GLN D 192 " ideal model delta harmonic sigma weight residual 180.00 -136.85 -43.15 0 5.00e+00 4.00e-02 7.45e+01 ... (remaining 16177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 4009 0.336 - 0.672: 4 0.672 - 1.008: 0 1.008 - 1.344: 2 1.344 - 1.680: 3 Chirality restraints: 4018 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.76e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-02 2.50e+03 2.84e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.33e+02 ... (remaining 4015 not shown) Planarity restraints: 4524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.333 2.00e-02 2.50e+03 2.82e-01 9.97e+02 pdb=" C7 NAG J 1 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.493 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " -0.212 2.00e-02 2.50e+03 1.81e-01 4.07e+02 pdb=" C7 NAG K 1 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.035 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " 0.296 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.090 2.00e-02 2.50e+03 7.43e-02 6.89e+01 pdb=" C7 NAG K 2 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.068 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.118 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.015 2.00e-02 2.50e+03 ... (remaining 4521 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 297 2.57 - 3.15: 20986 3.15 - 3.74: 37661 3.74 - 4.32: 60018 4.32 - 4.90: 98598 Nonbonded interactions: 217560 Sorted by model distance: nonbonded pdb=" O HOH W 606 " pdb=" O HOH W 630 " model vdw 1.991 3.040 nonbonded pdb=" O HOH M 606 " pdb=" O HOH M 638 " model vdw 1.991 3.040 nonbonded pdb=" O HOH I 608 " pdb=" O HOH I 629 " model vdw 1.991 3.040 nonbonded pdb=" O HOH N 607 " pdb=" O HOH N 636 " model vdw 1.991 3.040 nonbonded pdb=" NH1 ARG W 116 " pdb=" OE2 GLU W 117 " model vdw 2.108 3.120 ... (remaining 217555 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' selection = chain 'C' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } ncs_group { reference = (chain 'I' and resid 77 through 466) selection = (chain 'M' and resid 77 through 466) selection = (chain 'N' and resid 77 through 466) selection = (chain 'W' and resid 77 through 466) } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.05 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.040 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.350 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.010 0.256 26364 Z= 0.430 Angle : 1.048 44.224 35854 Z= 0.478 Chirality : 0.074 1.680 4018 Planarity : 0.007 0.282 4512 Dihedral : 16.017 110.586 10048 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.42 % Favored : 93.55 % Rotamer: Outliers : 1.03 % Allowed : 1.71 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.13), residues: 3254 helix: -3.78 (0.49), residues: 64 sheet: -1.35 (0.13), residues: 1316 loop : -2.69 (0.11), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 154 TYR 0.025 0.002 TYR H 33 PHE 0.017 0.002 PHE H 91 TRP 0.015 0.002 TRP W 177 HIS 0.006 0.001 HIS M 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00949 / 0.39 (26284) covalent geometry : angle 0.79098 / 0.41 (35662) SS BOND : bond 0.02266 / 1.51 ( 48) SS BOND : angle 4.12469 / 2.82 ( 96) hydrogen bonds : bond 0.19692 / 13.37 ( 748) hydrogen bonds : angle 8.47058 / 5.83 ( 2079) link_BETA1-4 : bond 0.07079 / 5.13 ( 20) link_BETA1-4 : angle 7.18214 / 4.56 ( 60) link_NAG-ASN : bond 0.14600 / 8.03 ( 12) link_NAG-ASN : angle 18.51675 / 12.93 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 331 time to evaluate : 1.030 Fit side-chains REVERT: W 194 ASP cc_start: 0.7386 (p0) cc_final: 0.6900 (p0) REVERT: A 6 GLU cc_start: 0.8797 (mp0) cc_final: 0.8560 (mp0) REVERT: A 27 ASP cc_start: 0.8486 (t0) cc_final: 0.8270 (t70) REVERT: A 96 ASP cc_start: 0.8162 (t0) cc_final: 0.7856 (t0) REVERT: A 180 SER cc_start: 0.6716 (OUTLIER) cc_final: 0.6436 (p) REVERT: C 6 GLU cc_start: 0.8837 (mp0) cc_final: 0.8616 (mp0) REVERT: C 27 ASP cc_start: 0.8590 (t0) cc_final: 0.8335 (t70) REVERT: C 96 ASP cc_start: 0.8107 (t0) cc_final: 0.7745 (t0) REVERT: D 6 GLU cc_start: 0.8852 (mp0) cc_final: 0.8606 (mp0) REVERT: D 27 ASP cc_start: 0.8474 (t0) cc_final: 0.8259 (t70) REVERT: D 96 ASP cc_start: 0.8148 (t0) cc_final: 0.7841 (t0) REVERT: H 6 GLU cc_start: 0.8750 (mp0) cc_final: 0.8513 (mp0) REVERT: H 96 ASP cc_start: 0.8144 (t0) cc_final: 0.7823 (t0) outliers start: 29 outliers final: 9 residues processed: 355 average time/residue: 0.7902 time to fit residues: 318.4403 Evaluate side-chains 254 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.0050 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 100EGLN D 60 ASN H 100EGLN B 100 GLN B 155 GLN E 100 GLN E 155 GLN G 100 GLN G 155 GLN L 100 GLN L 155 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.150105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.085090 restraints weight = 29347.062| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.85 r_work: 0.2831 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26364 Z= 0.132 Angle : 0.679 8.101 35854 Z= 0.349 Chirality : 0.047 0.158 4018 Planarity : 0.005 0.071 4512 Dihedral : 10.471 70.320 4225 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.36 % Allowed : 8.89 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.98 (0.13), residues: 3254 helix: -3.54 (0.44), residues: 64 sheet: -0.66 (0.14), residues: 1358 loop : -1.78 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 150 TYR 0.014 0.001 TYR B 186 PHE 0.010 0.002 PHE L 209 TRP 0.012 0.001 TRP N 456 HIS 0.007 0.001 HIS M 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (26284) covalent geometry : angle 0.66125 / 0.34 (35662) SS BOND : bond 0.00530 / 0.35 ( 48) SS BOND : angle 1.61032 / 1.04 ( 96) hydrogen bonds : bond 0.04060 / 2.72 ( 748) hydrogen bonds : angle 6.15894 / 4.21 ( 2079) link_BETA1-4 : bond 0.00493 / 0.29 ( 20) link_BETA1-4 : angle 2.07379 / 1.45 ( 60) link_NAG-ASN : bond 0.00577 / 0.33 ( 12) link_NAG-ASN : angle 3.36801 / 2.17 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 79 ARG cc_start: 0.8417 (mtp180) cc_final: 0.8175 (ttp80) REVERT: I 392 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7477 (mp0) REVERT: M 250 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8529 (tt0) REVERT: N 125 LYS cc_start: 0.8094 (pmtt) cc_final: 0.7850 (tttt) REVERT: N 369 MET cc_start: 0.8704 (mmm) cc_final: 0.8466 (mmm) REVERT: N 392 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7403 (mp0) REVERT: W 194 ASP cc_start: 0.8594 (p0) cc_final: 0.8244 (p0) REVERT: A 3 GLN cc_start: 0.8312 (tm-30) cc_final: 0.8021 (mt0) REVERT: A 6 GLU cc_start: 0.8675 (mp0) cc_final: 0.8469 (mp0) REVERT: A 13 ARG cc_start: 0.7746 (mmm-85) cc_final: 0.7418 (mmm-85) REVERT: A 52 TYR cc_start: 0.9294 (OUTLIER) cc_final: 0.8996 (m-80) REVERT: A 96 ASP cc_start: 0.8690 (t0) cc_final: 0.8478 (t0) REVERT: C 13 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7443 (mmm-85) REVERT: C 27 ASP cc_start: 0.8787 (t0) cc_final: 0.8574 (t70) REVERT: C 52 TYR cc_start: 0.9289 (OUTLIER) cc_final: 0.8990 (m-80) REVERT: C 96 ASP cc_start: 0.8712 (t0) cc_final: 0.8459 (t0) REVERT: D 3 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8041 (mt0) REVERT: D 6 GLU cc_start: 0.8734 (mp0) cc_final: 0.8499 (mp0) REVERT: D 13 ARG cc_start: 0.7709 (mmm-85) cc_final: 0.7385 (mmm-85) REVERT: D 52 TYR cc_start: 0.9318 (OUTLIER) cc_final: 0.9013 (m-80) REVERT: D 96 ASP cc_start: 0.8755 (t0) cc_final: 0.8498 (t0) REVERT: D 148 GLU cc_start: 0.8089 (mt-10) cc_final: 0.6901 (pp20) REVERT: H 3 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7979 (mt0) REVERT: H 13 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7474 (mmm-85) REVERT: H 52 TYR cc_start: 0.9285 (OUTLIER) cc_final: 0.8987 (m-80) REVERT: H 96 ASP cc_start: 0.8693 (t0) cc_final: 0.8470 (t0) REVERT: E 3 GLN cc_start: 0.8215 (mm110) cc_final: 0.7927 (mm110) REVERT: G 3 GLN cc_start: 0.8273 (mm110) cc_final: 0.8072 (mp-120) REVERT: G 79 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7638 (mm-40) REVERT: L 3 GLN cc_start: 0.8383 (mm110) cc_final: 0.8097 (mp-120) REVERT: L 79 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7592 (mt0) outliers start: 38 outliers final: 16 residues processed: 283 average time/residue: 0.7162 time to fit residues: 232.5022 Evaluate side-chains 250 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 142 optimal weight: 0.5980 chunk 153 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 303 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 169 ASN M 169 ASN N 169 ASN W 169 ASN A 35 ASN A 60 ASN C 35 ASN C 100EGLN D 35 ASN H 35 ASN H 100EGLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.146359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.079852 restraints weight = 29245.553| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.88 r_work: 0.2741 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 26364 Z= 0.195 Angle : 0.674 8.180 35854 Z= 0.347 Chirality : 0.048 0.154 4018 Planarity : 0.005 0.055 4512 Dihedral : 7.787 59.393 4222 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.39 % Allowed : 11.67 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.14), residues: 3254 helix: -3.17 (0.47), residues: 64 sheet: -0.31 (0.14), residues: 1410 loop : -1.44 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG W 102 TYR 0.021 0.002 TYR I 383 PHE 0.012 0.002 PHE D 91 TRP 0.016 0.002 TRP N 456 HIS 0.007 0.001 HIS W 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (26284) covalent geometry : angle 0.65867 / 0.34 (35662) SS BOND : bond 0.00256 / 0.16 ( 48) SS BOND : angle 1.58893 / 1.10 ( 96) hydrogen bonds : bond 0.04120 / 2.71 ( 748) hydrogen bonds : angle 5.84225 / 4.00 ( 2079) link_BETA1-4 : bond 0.00442 / 0.26 ( 20) link_BETA1-4 : angle 2.29998 / 1.64 ( 60) link_NAG-ASN : bond 0.00501 / 0.28 ( 12) link_NAG-ASN : angle 2.68804 / 1.66 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 392 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7500 (mp0) REVERT: M 125 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8135 (mptp) REVERT: M 135 TYR cc_start: 0.9570 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: M 250 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8594 (tt0) REVERT: N 229 CYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8246 (p) REVERT: N 334 THR cc_start: 0.9218 (p) cc_final: 0.8975 (p) REVERT: N 392 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7479 (mp0) REVERT: N 414 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8654 (mt-10) REVERT: W 194 ASP cc_start: 0.8705 (p0) cc_final: 0.8350 (p0) REVERT: A 3 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8029 (mt0) REVERT: A 13 ARG cc_start: 0.7789 (mmm-85) cc_final: 0.7437 (mmm-85) REVERT: A 72 ASP cc_start: 0.8056 (t0) cc_final: 0.7675 (t0) REVERT: A 96 ASP cc_start: 0.8686 (t0) cc_final: 0.8403 (t0) REVERT: C 6 GLU cc_start: 0.8803 (mp0) cc_final: 0.8489 (mp0) REVERT: C 13 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7557 (mmm160) REVERT: C 72 ASP cc_start: 0.8076 (t0) cc_final: 0.7675 (OUTLIER) REVERT: C 96 ASP cc_start: 0.8703 (t0) cc_final: 0.8446 (t0) REVERT: D 3 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8008 (mt0) REVERT: D 13 ARG cc_start: 0.7740 (mmm-85) cc_final: 0.7513 (mmm160) REVERT: D 72 ASP cc_start: 0.8061 (t0) cc_final: 0.7667 (OUTLIER) REVERT: D 96 ASP cc_start: 0.8698 (t0) cc_final: 0.8437 (t0) REVERT: H 3 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7995 (mt0) REVERT: H 6 GLU cc_start: 0.8806 (mp0) cc_final: 0.8525 (mp0) REVERT: H 13 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7568 (mmm160) REVERT: H 72 ASP cc_start: 0.8107 (t0) cc_final: 0.7737 (t0) REVERT: H 96 ASP cc_start: 0.8688 (t0) cc_final: 0.8392 (t0) REVERT: B 79 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7556 (mm110) REVERT: E 3 GLN cc_start: 0.8297 (mm110) cc_final: 0.8031 (mm110) REVERT: E 79 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7567 (mm110) REVERT: G 3 GLN cc_start: 0.8323 (mm110) cc_final: 0.8038 (mp-120) REVERT: G 79 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7571 (mm110) REVERT: L 3 GLN cc_start: 0.8282 (mm110) cc_final: 0.7985 (mp-120) REVERT: L 79 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7582 (mm110) outliers start: 39 outliers final: 20 residues processed: 280 average time/residue: 0.7434 time to fit residues: 238.0683 Evaluate side-chains 258 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 414 GLU Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 168 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 225 optimal weight: 4.9990 chunk 196 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 225 GLN B 6 GLN E 6 GLN G 6 GLN L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.147862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.080506 restraints weight = 28986.401| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.90 r_work: 0.2759 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26364 Z= 0.150 Angle : 0.615 8.228 35854 Z= 0.318 Chirality : 0.046 0.145 4018 Planarity : 0.005 0.052 4512 Dihedral : 6.834 59.508 4222 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.64 % Allowed : 12.85 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % 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: -1.15 (0.14), residues: 3254 helix: -2.80 (0.49), residues: 64 sheet: -0.06 (0.14), residues: 1394 loop : -1.27 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 24 TYR 0.016 0.002 TYR I 383 PHE 0.011 0.001 PHE I 130 TRP 0.014 0.001 TRP N 456 HIS 0.007 0.001 HIS M 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (26284) covalent geometry : angle 0.60471 / 0.32 (35662) SS BOND : bond 0.00247 / 0.16 ( 48) SS BOND : angle 1.36927 / 0.93 ( 96) hydrogen bonds : bond 0.03555 / 2.32 ( 748) hydrogen bonds : angle 5.50978 / 3.77 ( 2079) link_BETA1-4 : bond 0.00427 / 0.26 ( 20) link_BETA1-4 : angle 1.83680 / 1.31 ( 60) link_NAG-ASN : bond 0.00357 / 0.18 ( 12) link_NAG-ASN : angle 2.06761 / 1.24 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 245 time to evaluate : 1.030 Fit side-chains REVERT: I 392 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7473 (mp0) REVERT: M 125 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8090 (mptp) REVERT: M 135 TYR cc_start: 0.9578 (OUTLIER) cc_final: 0.7403 (m-80) REVERT: N 125 LYS cc_start: 0.8124 (pmtt) cc_final: 0.7867 (tttt) REVERT: N 334 THR cc_start: 0.9220 (p) cc_final: 0.8986 (p) REVERT: N 392 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7328 (mp0) REVERT: N 414 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8647 (mt-10) REVERT: W 194 ASP cc_start: 0.8784 (p0) cc_final: 0.8471 (p0) REVERT: A 3 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7951 (mt0) REVERT: A 72 ASP cc_start: 0.8025 (t0) cc_final: 0.7681 (t0) REVERT: A 96 ASP cc_start: 0.8707 (t0) cc_final: 0.8457 (t0) REVERT: C 6 GLU cc_start: 0.8759 (mp0) cc_final: 0.8511 (mp0) REVERT: C 96 ASP cc_start: 0.8683 (t0) cc_final: 0.8449 (t0) REVERT: D 3 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7917 (mt0) REVERT: D 96 ASP cc_start: 0.8723 (t0) cc_final: 0.8453 (t0) REVERT: H 3 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7912 (mt0) REVERT: H 72 ASP cc_start: 0.8130 (t0) cc_final: 0.7754 (t0) REVERT: H 96 ASP cc_start: 0.8718 (t0) cc_final: 0.8439 (t0) REVERT: B 3 GLN cc_start: 0.8289 (mm110) cc_final: 0.7827 (mp-120) REVERT: B 4 MET cc_start: 0.9222 (mmp) cc_final: 0.8998 (mmp) REVERT: B 79 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7466 (mm110) REVERT: E 3 GLN cc_start: 0.8347 (mm110) cc_final: 0.8055 (mm110) REVERT: E 79 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7512 (mm110) REVERT: G 3 GLN cc_start: 0.8340 (mm110) cc_final: 0.7939 (mp-120) REVERT: G 4 MET cc_start: 0.9197 (mmp) cc_final: 0.8975 (mmp) REVERT: G 79 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7495 (mm110) REVERT: L 3 GLN cc_start: 0.8271 (mm110) cc_final: 0.7853 (mp-120) REVERT: L 4 MET cc_start: 0.9195 (mmp) cc_final: 0.8949 (mmp) REVERT: L 79 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7507 (mm110) outliers start: 46 outliers final: 20 residues processed: 285 average time/residue: 0.7240 time to fit residues: 237.3916 Evaluate side-chains 251 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 414 GLU Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 165 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 247 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 314 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN C 76 ASN D 76 ASN H 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.148638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.081493 restraints weight = 29106.422| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.93 r_work: 0.2779 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26364 Z= 0.122 Angle : 0.572 8.051 35854 Z= 0.297 Chirality : 0.044 0.151 4018 Planarity : 0.005 0.050 4512 Dihedral : 6.511 59.815 4218 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.21 % Allowed : 13.85 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.14), residues: 3254 helix: -2.17 (0.59), residues: 64 sheet: 0.16 (0.14), residues: 1382 loop : -1.16 (0.13), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 13 TYR 0.013 0.001 TYR I 383 PHE 0.010 0.001 PHE I 119 TRP 0.014 0.001 TRP N 456 HIS 0.007 0.001 HIS N 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (26284) covalent geometry : angle 0.56201 / 0.29 (35662) SS BOND : bond 0.00224 / 0.14 ( 48) SS BOND : angle 1.36954 / 0.93 ( 96) hydrogen bonds : bond 0.03266 / 2.13 ( 748) hydrogen bonds : angle 5.25103 / 3.58 ( 2079) link_BETA1-4 : bond 0.00424 / 0.27 ( 20) link_BETA1-4 : angle 1.56633 / 1.11 ( 60) link_NAG-ASN : bond 0.00274 / 0.15 ( 12) link_NAG-ASN : angle 1.84487 / 1.09 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.907 Fit side-chains REVERT: I 135 TYR cc_start: 0.9577 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: I 392 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7382 (mp0) REVERT: M 125 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8027 (mptp) REVERT: M 135 TYR cc_start: 0.9581 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: N 87 CYS cc_start: 0.5116 (OUTLIER) cc_final: 0.4914 (m) REVERT: N 125 LYS cc_start: 0.8072 (pmtt) cc_final: 0.7855 (tttt) REVERT: N 135 TYR cc_start: 0.9584 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: N 334 THR cc_start: 0.9240 (p) cc_final: 0.9013 (p) REVERT: N 338 GLU cc_start: 0.8322 (pm20) cc_final: 0.7969 (pm20) REVERT: N 392 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7322 (mp0) REVERT: N 414 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8662 (mt-10) REVERT: W 135 TYR cc_start: 0.9577 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: W 194 ASP cc_start: 0.8775 (p0) cc_final: 0.8435 (p0) REVERT: A 3 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7899 (mt0) REVERT: A 72 ASP cc_start: 0.8083 (t0) cc_final: 0.7734 (t0) REVERT: A 96 ASP cc_start: 0.8709 (t0) cc_final: 0.8491 (t0) REVERT: A 105 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8785 (mttm) REVERT: C 72 ASP cc_start: 0.8071 (t0) cc_final: 0.7710 (OUTLIER) REVERT: C 96 ASP cc_start: 0.8693 (t0) cc_final: 0.8473 (t0) REVERT: D 3 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7871 (mt0) REVERT: D 72 ASP cc_start: 0.8076 (t0) cc_final: 0.7709 (OUTLIER) REVERT: D 96 ASP cc_start: 0.8722 (t0) cc_final: 0.8503 (t0) REVERT: H 3 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7852 (mt0) REVERT: H 13 ARG cc_start: 0.7842 (mmm160) cc_final: 0.7593 (mmm160) REVERT: H 72 ASP cc_start: 0.8124 (t0) cc_final: 0.7737 (t0) REVERT: H 96 ASP cc_start: 0.8709 (t0) cc_final: 0.8487 (t0) REVERT: B 3 GLN cc_start: 0.8266 (mm110) cc_final: 0.7781 (mp-120) REVERT: B 4 MET cc_start: 0.9196 (mmp) cc_final: 0.8872 (mmp) REVERT: E 3 GLN cc_start: 0.8321 (mm110) cc_final: 0.8027 (mm110) REVERT: G 3 GLN cc_start: 0.8329 (mm110) cc_final: 0.7938 (mp-120) REVERT: G 4 MET cc_start: 0.9181 (mmp) cc_final: 0.8915 (mmp) REVERT: L 3 GLN cc_start: 0.8279 (mm110) cc_final: 0.7843 (mp-120) REVERT: L 4 MET cc_start: 0.9184 (mmp) cc_final: 0.8976 (mmp) outliers start: 34 outliers final: 16 residues processed: 254 average time/residue: 0.7146 time to fit residues: 207.8162 Evaluate side-chains 238 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 414 GLU Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 52 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 55 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 87 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 66.8201 > 50:) chunk 53 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 168 optimal weight: 10.0000 chunk 232 optimal weight: 40.0000 chunk 289 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 225 GLN W 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.146096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.078462 restraints weight = 29039.005| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.87 r_work: 0.2725 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 26364 Z= 0.244 Angle : 0.673 8.035 35854 Z= 0.348 Chirality : 0.048 0.147 4018 Planarity : 0.005 0.053 4512 Dihedral : 6.790 59.047 4218 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.57 % Allowed : 14.20 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3254 helix: -2.17 (0.59), residues: 64 sheet: 0.23 (0.14), residues: 1400 loop : -1.13 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 13 TYR 0.025 0.002 TYR I 383 PHE 0.012 0.002 PHE N 130 TRP 0.014 0.002 TRP N 456 HIS 0.008 0.001 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 (26284) covalent geometry : angle 0.65842 / 0.34 (35662) SS BOND : bond 0.00381 / 0.25 ( 48) SS BOND : angle 1.80416 / 1.24 ( 96) hydrogen bonds : bond 0.03930 / 2.56 ( 748) hydrogen bonds : angle 5.51796 / 3.77 ( 2079) link_BETA1-4 : bond 0.00401 / 0.24 ( 20) link_BETA1-4 : angle 2.11328 / 1.52 ( 60) link_NAG-ASN : bond 0.00727 / 0.42 ( 12) link_NAG-ASN : angle 2.21760 / 1.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 1.020 Fit side-chains REVERT: I 392 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7524 (mp0) REVERT: M 125 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8133 (mptp) REVERT: N 334 THR cc_start: 0.9247 (p) cc_final: 0.9026 (p) REVERT: N 392 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7474 (mp0) REVERT: W 194 ASP cc_start: 0.8909 (p0) cc_final: 0.8642 (p0) REVERT: A 3 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7930 (mt0) REVERT: A 72 ASP cc_start: 0.8145 (t0) cc_final: 0.7739 (t0) REVERT: A 96 ASP cc_start: 0.8705 (t0) cc_final: 0.8458 (t0) REVERT: A 105 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8791 (mttm) REVERT: C 72 ASP cc_start: 0.8172 (t0) cc_final: 0.7799 (OUTLIER) REVERT: C 96 ASP cc_start: 0.8694 (t0) cc_final: 0.8476 (t0) REVERT: D 3 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7900 (mt0) REVERT: D 72 ASP cc_start: 0.8161 (t0) cc_final: 0.7773 (OUTLIER) REVERT: D 96 ASP cc_start: 0.8729 (t0) cc_final: 0.8515 (t0) REVERT: H 3 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7893 (mt0) REVERT: H 69 MET cc_start: 0.9378 (mtt) cc_final: 0.9143 (mtt) REVERT: H 72 ASP cc_start: 0.8195 (t0) cc_final: 0.7775 (t0) REVERT: H 96 ASP cc_start: 0.8708 (t0) cc_final: 0.8450 (t0) REVERT: B 3 GLN cc_start: 0.8301 (mm110) cc_final: 0.7836 (mp-120) REVERT: B 4 MET cc_start: 0.9228 (mmp) cc_final: 0.8974 (mmp) REVERT: E 3 GLN cc_start: 0.8317 (mm110) cc_final: 0.8042 (mm110) REVERT: G 3 GLN cc_start: 0.8372 (mm110) cc_final: 0.7999 (mm110) REVERT: G 4 MET cc_start: 0.9196 (mmp) cc_final: 0.8992 (mmp) REVERT: L 3 GLN cc_start: 0.8316 (mm110) cc_final: 0.7900 (mp-120) outliers start: 44 outliers final: 29 residues processed: 279 average time/residue: 0.6839 time to fit residues: 220.3358 Evaluate side-chains 257 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 31 optimal weight: 5.9990 chunk 267 optimal weight: 0.8980 chunk 250 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 283 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 90 optimal weight: 0.4980 chunk 132 optimal weight: 3.9990 chunk 316 optimal weight: 30.0000 chunk 198 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 171 GLN H 171 GLN E 79 GLN G 79 GLN L 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.146774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.079132 restraints weight = 29089.195| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.90 r_work: 0.2738 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26364 Z= 0.190 Angle : 0.626 8.491 35854 Z= 0.325 Chirality : 0.046 0.138 4018 Planarity : 0.005 0.050 4512 Dihedral : 6.623 58.937 4218 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.57 % Allowed : 14.60 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3254 helix: -2.05 (0.61), residues: 64 sheet: 0.29 (0.14), residues: 1388 loop : -1.07 (0.13), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 13 TYR 0.020 0.002 TYR I 383 PHE 0.012 0.002 PHE I 119 TRP 0.014 0.002 TRP N 456 HIS 0.007 0.001 HIS M 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (26284) covalent geometry : angle 0.61542 / 0.32 (35662) SS BOND : bond 0.00309 / 0.20 ( 48) SS BOND : angle 1.48059 / 1.03 ( 96) hydrogen bonds : bond 0.03635 / 2.37 ( 748) hydrogen bonds : angle 5.38206 / 3.68 ( 2079) link_BETA1-4 : bond 0.00407 / 0.25 ( 20) link_BETA1-4 : angle 1.79243 / 1.28 ( 60) link_NAG-ASN : bond 0.00503 / 0.28 ( 12) link_NAG-ASN : angle 2.03633 / 1.20 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: I 229 CYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8486 (p) REVERT: I 392 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7520 (mp0) REVERT: M 125 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8173 (mppt) REVERT: M 229 CYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8244 (p) REVERT: N 125 LYS cc_start: 0.8116 (pmtt) cc_final: 0.7877 (tttt) REVERT: N 229 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8265 (p) REVERT: N 334 THR cc_start: 0.9256 (p) cc_final: 0.9038 (p) REVERT: N 392 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7483 (mp0) REVERT: W 194 ASP cc_start: 0.8938 (p0) cc_final: 0.8670 (p0) REVERT: A 3 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7918 (mt0) REVERT: A 69 MET cc_start: 0.9429 (mtt) cc_final: 0.9217 (mtt) REVERT: A 72 ASP cc_start: 0.8144 (t0) cc_final: 0.7733 (t0) REVERT: A 96 ASP cc_start: 0.8716 (t0) cc_final: 0.8483 (t0) REVERT: A 105 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8774 (mttm) REVERT: C 69 MET cc_start: 0.9427 (mtt) cc_final: 0.9208 (mtt) REVERT: C 72 ASP cc_start: 0.8134 (t0) cc_final: 0.7765 (OUTLIER) REVERT: C 96 ASP cc_start: 0.8697 (t0) cc_final: 0.8478 (t0) REVERT: D 3 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7893 (mt0) REVERT: D 69 MET cc_start: 0.9413 (mtt) cc_final: 0.9213 (mtt) REVERT: D 72 ASP cc_start: 0.8144 (t0) cc_final: 0.7759 (t0) REVERT: D 96 ASP cc_start: 0.8729 (t0) cc_final: 0.8514 (t0) REVERT: H 3 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7885 (mt0) REVERT: H 69 MET cc_start: 0.9334 (mtt) cc_final: 0.9107 (mtt) REVERT: H 72 ASP cc_start: 0.8196 (t0) cc_final: 0.7781 (t0) REVERT: H 96 ASP cc_start: 0.8712 (t0) cc_final: 0.8493 (t0) REVERT: B 3 GLN cc_start: 0.8310 (mm110) cc_final: 0.7823 (mp-120) REVERT: B 4 MET cc_start: 0.9217 (mmp) cc_final: 0.9016 (mmp) REVERT: E 3 GLN cc_start: 0.8310 (mm110) cc_final: 0.8034 (mm110) REVERT: G 3 GLN cc_start: 0.8386 (mm110) cc_final: 0.8112 (mm110) REVERT: L 3 GLN cc_start: 0.8283 (mm110) cc_final: 0.7833 (mp-120) REVERT: L 4 MET cc_start: 0.9174 (mmp) cc_final: 0.8868 (mmp) outliers start: 44 outliers final: 27 residues processed: 264 average time/residue: 0.6797 time to fit residues: 207.3927 Evaluate side-chains 252 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 317 optimal weight: 5.9990 chunk 258 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 232 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN B 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.148200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.080920 restraints weight = 29001.307| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.91 r_work: 0.2764 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26364 Z= 0.125 Angle : 0.566 8.448 35854 Z= 0.294 Chirality : 0.044 0.135 4018 Planarity : 0.004 0.049 4512 Dihedral : 6.297 59.033 4218 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.53 % Allowed : 14.85 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3254 helix: -1.96 (0.62), residues: 64 sheet: 0.44 (0.14), residues: 1372 loop : -0.99 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 13 TYR 0.013 0.001 TYR I 383 PHE 0.010 0.001 PHE N 119 TRP 0.014 0.001 TRP N 456 HIS 0.007 0.001 HIS W 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (26284) covalent geometry : angle 0.55757 / 0.29 (35662) SS BOND : bond 0.00239 / 0.16 ( 48) SS BOND : angle 1.17446 / 0.81 ( 96) hydrogen bonds : bond 0.03225 / 2.11 ( 748) hydrogen bonds : angle 5.13520 / 3.51 ( 2079) link_BETA1-4 : bond 0.00431 / 0.27 ( 20) link_BETA1-4 : angle 1.50213 / 1.06 ( 60) link_NAG-ASN : bond 0.00265 / 0.14 ( 12) link_NAG-ASN : angle 1.79282 / 1.08 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 392 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7364 (mp0) REVERT: M 125 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8113 (mppt) REVERT: M 135 TYR cc_start: 0.9588 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: N 334 THR cc_start: 0.9251 (p) cc_final: 0.9035 (p) REVERT: N 392 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7333 (mp0) REVERT: N 414 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8722 (mt-10) REVERT: W 194 ASP cc_start: 0.8875 (p0) cc_final: 0.8597 (p0) REVERT: W 400 MET cc_start: 0.9378 (mtm) cc_final: 0.9171 (mtm) REVERT: A 3 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7905 (mt0) REVERT: A 52 TYR cc_start: 0.9432 (OUTLIER) cc_final: 0.8978 (t80) REVERT: A 72 ASP cc_start: 0.8172 (t0) cc_final: 0.7780 (t0) REVERT: A 96 ASP cc_start: 0.8737 (t0) cc_final: 0.8524 (t0) REVERT: A 105 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8776 (mttm) REVERT: C 72 ASP cc_start: 0.8103 (t0) cc_final: 0.7733 (t0) REVERT: C 96 ASP cc_start: 0.8723 (t0) cc_final: 0.8513 (t0) REVERT: D 3 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7876 (mt0) REVERT: D 69 MET cc_start: 0.9415 (mtt) cc_final: 0.9215 (mtt) REVERT: D 72 ASP cc_start: 0.8085 (t0) cc_final: 0.7715 (t0) REVERT: D 96 ASP cc_start: 0.8739 (t0) cc_final: 0.8518 (t0) REVERT: H 3 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7865 (mt0) REVERT: H 13 ARG cc_start: 0.7955 (mmm160) cc_final: 0.7646 (mmm160) REVERT: H 69 MET cc_start: 0.9369 (mtt) cc_final: 0.9154 (mtt) REVERT: H 72 ASP cc_start: 0.8158 (t0) cc_final: 0.7756 (t0) REVERT: H 96 ASP cc_start: 0.8721 (t0) cc_final: 0.8506 (t0) REVERT: B 3 GLN cc_start: 0.8317 (mm110) cc_final: 0.7794 (mp-120) REVERT: B 4 MET cc_start: 0.9194 (mmp) cc_final: 0.8852 (mmp) REVERT: B 27 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8097 (pt0) REVERT: E 3 GLN cc_start: 0.8324 (mm110) cc_final: 0.8077 (mm110) REVERT: G 3 GLN cc_start: 0.8366 (mm110) cc_final: 0.7962 (mm110) REVERT: G 4 MET cc_start: 0.9147 (mmp) cc_final: 0.8912 (mmp) REVERT: L 3 GLN cc_start: 0.8260 (mm110) cc_final: 0.7772 (mp-120) REVERT: L 4 MET cc_start: 0.9112 (mmp) cc_final: 0.8760 (mmp) outliers start: 43 outliers final: 27 residues processed: 251 average time/residue: 0.7404 time to fit residues: 213.5067 Evaluate side-chains 241 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 414 GLU Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 353 VAL Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain B residue 27 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 32 optimal weight: 2.9990 chunk 304 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 258 optimal weight: 9.9990 chunk 195 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 211 optimal weight: 30.0000 chunk 267 optimal weight: 10.0000 chunk 168 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.146517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.078831 restraints weight = 29126.053| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.90 r_work: 0.2728 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 26364 Z= 0.206 Angle : 0.633 7.940 35854 Z= 0.328 Chirality : 0.046 0.140 4018 Planarity : 0.005 0.052 4512 Dihedral : 6.489 58.670 4218 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.57 % Allowed : 15.13 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3254 helix: -1.95 (0.61), residues: 64 sheet: 0.37 (0.14), residues: 1412 loop : -0.96 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG W 260 TYR 0.023 0.002 TYR I 383 PHE 0.012 0.002 PHE N 119 TRP 0.013 0.002 TRP N 456 HIS 0.007 0.001 HIS W 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (26284) covalent geometry : angle 0.62216 / 0.33 (35662) SS BOND : bond 0.00367 / 0.24 ( 48) SS BOND : angle 1.51975 / 1.08 ( 96) hydrogen bonds : bond 0.03709 / 2.42 ( 748) hydrogen bonds : angle 5.35497 / 3.66 ( 2079) link_BETA1-4 : bond 0.00418 / 0.26 ( 20) link_BETA1-4 : angle 1.87716 / 1.34 ( 60) link_NAG-ASN : bond 0.00610 / 0.35 ( 12) link_NAG-ASN : angle 2.04849 / 1.20 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 392 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7504 (mp0) REVERT: M 125 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8167 (mppt) REVERT: M 229 CYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8247 (p) REVERT: N 334 THR cc_start: 0.9260 (p) cc_final: 0.9050 (p) REVERT: N 392 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7372 (mp0) REVERT: W 194 ASP cc_start: 0.9006 (p0) cc_final: 0.8747 (p0) REVERT: A 3 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7918 (mt0) REVERT: A 72 ASP cc_start: 0.8211 (t0) cc_final: 0.7788 (t0) REVERT: A 96 ASP cc_start: 0.8721 (t0) cc_final: 0.8492 (t0) REVERT: A 105 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8771 (mttm) REVERT: C 72 ASP cc_start: 0.8153 (t0) cc_final: 0.7790 (t0) REVERT: C 96 ASP cc_start: 0.8704 (t0) cc_final: 0.8487 (t0) REVERT: D 3 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7901 (mt0) REVERT: D 69 MET cc_start: 0.9378 (mtt) cc_final: 0.9168 (mtt) REVERT: D 72 ASP cc_start: 0.8166 (t0) cc_final: 0.7788 (t0) REVERT: D 96 ASP cc_start: 0.8728 (t0) cc_final: 0.8515 (t0) REVERT: H 3 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7885 (mt0) REVERT: H 13 ARG cc_start: 0.7982 (mmm160) cc_final: 0.7572 (mmm-85) REVERT: H 69 MET cc_start: 0.9336 (mtt) cc_final: 0.9111 (mtt) REVERT: H 72 ASP cc_start: 0.8187 (t0) cc_final: 0.7764 (t0) REVERT: H 96 ASP cc_start: 0.8715 (t0) cc_final: 0.8501 (t0) REVERT: B 3 GLN cc_start: 0.8324 (mm110) cc_final: 0.7863 (mm110) REVERT: B 4 MET cc_start: 0.9228 (mmp) cc_final: 0.9013 (mmp) REVERT: B 27 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: E 3 GLN cc_start: 0.8309 (mm110) cc_final: 0.8067 (mm110) REVERT: G 3 GLN cc_start: 0.8304 (mm110) cc_final: 0.8025 (mm110) REVERT: L 3 GLN cc_start: 0.8281 (mm110) cc_final: 0.7811 (mm110) REVERT: L 4 MET cc_start: 0.9177 (mmp) cc_final: 0.8856 (mmp) outliers start: 44 outliers final: 34 residues processed: 266 average time/residue: 0.6885 time to fit residues: 211.7985 Evaluate side-chains 260 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 353 VAL Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain B residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 180 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 315 optimal weight: 50.0000 chunk 276 optimal weight: 30.0000 chunk 291 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.147703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.080338 restraints weight = 28919.289| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.90 r_work: 0.2754 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26364 Z= 0.137 Angle : 0.579 7.982 35854 Z= 0.301 Chirality : 0.044 0.137 4018 Planarity : 0.004 0.063 4512 Dihedral : 6.290 58.884 4218 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.46 % Allowed : 15.27 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3254 helix: -1.89 (0.61), residues: 64 sheet: 0.41 (0.14), residues: 1400 loop : -0.92 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG W 260 TYR 0.015 0.001 TYR I 383 PHE 0.011 0.001 PHE N 119 TRP 0.013 0.001 TRP N 456 HIS 0.007 0.001 HIS M 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (26284) covalent geometry : angle 0.57002 / 0.30 (35662) SS BOND : bond 0.00303 / 0.19 ( 48) SS BOND : angle 1.31536 / 0.91 ( 96) hydrogen bonds : bond 0.03342 / 2.18 ( 748) hydrogen bonds : angle 5.17397 / 3.53 ( 2079) link_BETA1-4 : bond 0.00421 / 0.26 ( 20) link_BETA1-4 : angle 1.57521 / 1.12 ( 60) link_NAG-ASN : bond 0.00326 / 0.18 ( 12) link_NAG-ASN : angle 1.85884 / 1.11 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 392 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7371 (mp0) REVERT: M 87 CYS cc_start: 0.5100 (OUTLIER) cc_final: 0.4856 (m) REVERT: M 125 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8167 (mppt) REVERT: M 135 TYR cc_start: 0.9590 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: N 334 THR cc_start: 0.9250 (p) cc_final: 0.9039 (p) REVERT: N 392 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7317 (mp0) REVERT: W 194 ASP cc_start: 0.8919 (p0) cc_final: 0.8657 (p0) REVERT: W 400 MET cc_start: 0.9384 (mtm) cc_final: 0.9147 (mtm) REVERT: A 3 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7905 (mt0) REVERT: A 72 ASP cc_start: 0.8194 (t0) cc_final: 0.7801 (t0) REVERT: A 96 ASP cc_start: 0.8723 (t0) cc_final: 0.8504 (t0) REVERT: A 105 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8771 (mttm) REVERT: C 72 ASP cc_start: 0.8104 (t0) cc_final: 0.7728 (t0) REVERT: C 96 ASP cc_start: 0.8703 (t0) cc_final: 0.8478 (t0) REVERT: D 3 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7878 (mt0) REVERT: D 72 ASP cc_start: 0.8095 (t0) cc_final: 0.7731 (t0) REVERT: D 96 ASP cc_start: 0.8735 (t0) cc_final: 0.8522 (t0) REVERT: H 3 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7866 (mt0) REVERT: H 13 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7561 (mmm-85) REVERT: H 69 MET cc_start: 0.9363 (mtt) cc_final: 0.9148 (mtt) REVERT: H 72 ASP cc_start: 0.8167 (t0) cc_final: 0.7758 (t0) REVERT: H 96 ASP cc_start: 0.8717 (t0) cc_final: 0.8491 (t0) REVERT: B 3 GLN cc_start: 0.8330 (mm110) cc_final: 0.7882 (mm110) REVERT: B 4 MET cc_start: 0.9201 (mmp) cc_final: 0.8998 (mmp) REVERT: B 27 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8105 (pt0) REVERT: G 3 GLN cc_start: 0.8290 (mm110) cc_final: 0.8019 (mm110) REVERT: L 3 GLN cc_start: 0.8279 (mm110) cc_final: 0.7813 (mm110) REVERT: L 4 MET cc_start: 0.9143 (mmp) cc_final: 0.8839 (mmp) outliers start: 41 outliers final: 33 residues processed: 257 average time/residue: 0.7001 time to fit residues: 206.8686 Evaluate side-chains 254 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 353 VAL Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain B residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 274 optimal weight: 20.0000 chunk 321 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 310 optimal weight: 0.9990 chunk 197 optimal weight: 9.9990 chunk 269 optimal weight: 2.9990 chunk 292 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 320 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.147309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.079812 restraints weight = 28812.383| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.91 r_work: 0.2745 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26364 Z= 0.158 Angle : 0.595 7.799 35854 Z= 0.308 Chirality : 0.045 0.138 4018 Planarity : 0.005 0.059 4512 Dihedral : 6.284 58.664 4218 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.46 % Allowed : 15.42 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3254 helix: -1.84 (0.60), residues: 64 sheet: 0.45 (0.14), residues: 1396 loop : -0.91 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 260 TYR 0.019 0.002 TYR I 383 PHE 0.011 0.001 PHE W 119 TRP 0.013 0.001 TRP N 456 HIS 0.007 0.001 HIS W 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (26284) covalent geometry : angle 0.58413 / 0.31 (35662) SS BOND : bond 0.00338 / 0.21 ( 48) SS BOND : angle 1.45441 / 1.00 ( 96) hydrogen bonds : bond 0.03465 / 2.26 ( 748) hydrogen bonds : angle 5.20941 / 3.56 ( 2079) link_BETA1-4 : bond 0.00423 / 0.26 ( 20) link_BETA1-4 : angle 1.69281 / 1.20 ( 60) link_NAG-ASN : bond 0.00437 / 0.25 ( 12) link_NAG-ASN : angle 1.90838 / 1.13 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12081.53 seconds wall clock time: 205 minutes 58.78 seconds (12358.78 seconds total)