Starting phenix.real_space_refine on Wed Sep 25 04:45:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfq_34724/09_2024/8hfq_34724.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfq_34724/09_2024/8hfq_34724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfq_34724/09_2024/8hfq_34724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfq_34724/09_2024/8hfq_34724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfq_34724/09_2024/8hfq_34724.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfq_34724/09_2024/8hfq_34724.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 34029 2.51 5 N 9412 2.21 5 O 10557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 54193 Number of models: 1 Model: "" Number of chains: 76 Chain: "A" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "B" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "C" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "D" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "E" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "F" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "G" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "H" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "I" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "J" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "K" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "L" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "M" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "N" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "O" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "P" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "Q" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "R" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "S" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "T" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "U" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "V" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "W" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "X" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "Y" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "Z" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "a" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "b" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "c" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "d" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "e" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "f" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "g" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "h" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "i" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "j" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "k" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2282 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 13, 'TRANS': 275} Chain: "l" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2164 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 6, 'TRANS': 265} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 626 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "n" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1619 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.11, per 1000 atoms: 0.50 Number of scatterers: 54193 At special positions: 0 Unit cell: (171.2, 180.83, 182.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 195 16.00 O 10557 8.00 N 9412 7.00 C 34029 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=66, symmetry=0 Number of additional bonds: simple=66, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.38 Conformation dependent library (CDL) restraints added in 5.6 seconds 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12612 Finding SS restraints... Secondary structure from input PDB file: 356 helices and 3 sheets defined 81.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 20 through 47 removed outlier: 4.157A pdb=" N ASN A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ALA A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.544A pdb=" N GLN A 68 " --> pdb=" O TYR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 102 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 125 through 140 removed outlier: 4.204A pdb=" N TYR A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 172 removed outlier: 3.847A pdb=" N TYR A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 removed outlier: 4.157A pdb=" N VAL B 8 " --> pdb=" O VAL B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 33 through 47 Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 75 through 100 Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 153 through 172 removed outlier: 3.775A pdb=" N VAL B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 20 through 47 removed outlier: 4.099A pdb=" N ASN C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ALA C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 77 through 102 Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 125 through 140 removed outlier: 4.117A pdb=" N TYR C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 172 removed outlier: 3.716A pdb=" N TYR C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 removed outlier: 4.019A pdb=" N VAL D 8 " --> pdb=" O VAL D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 47 removed outlier: 4.447A pdb=" N ASN D 35 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LYS D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 75 through 100 Processing helix chain 'D' and resid 102 through 109 Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'D' and resid 123 through 143 Processing helix chain 'D' and resid 153 through 170 Processing helix chain 'E' and resid 3 through 15 Processing helix chain 'E' and resid 20 through 63 removed outlier: 4.412A pdb=" N ASN E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 69 Processing helix chain 'E' and resid 77 through 102 removed outlier: 3.511A pdb=" N LYS E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 Processing helix chain 'E' and resid 114 through 122 Processing helix chain 'E' and resid 125 through 139 removed outlier: 4.178A pdb=" N TYR E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 172 removed outlier: 3.562A pdb=" N TYR E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 16 removed outlier: 4.082A pdb=" N VAL F 8 " --> pdb=" O VAL F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 47 removed outlier: 4.455A pdb=" N ASN F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS F 36 " --> pdb=" O ALA F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 75 through 100 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 112 through 120 Processing helix chain 'F' and resid 123 through 143 Processing helix chain 'F' and resid 153 through 170 Processing helix chain 'G' and resid 3 through 15 Processing helix chain 'G' and resid 20 through 47 removed outlier: 4.353A pdb=" N ASN G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ALA G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 64 through 68 removed outlier: 3.635A pdb=" N GLN G 68 " --> pdb=" O TYR G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 102 Processing helix chain 'G' and resid 104 through 111 Processing helix chain 'G' and resid 114 through 122 Processing helix chain 'G' and resid 125 through 140 removed outlier: 4.042A pdb=" N TYR G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 172 removed outlier: 3.814A pdb=" N TYR G 163 " --> pdb=" O GLU G 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 16 removed outlier: 3.885A pdb=" N VAL H 8 " --> pdb=" O VAL H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 47 removed outlier: 4.432A pdb=" N ASN H 35 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LYS H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 75 through 100 Processing helix chain 'H' and resid 102 through 109 Processing helix chain 'H' and resid 112 through 121 Processing helix chain 'H' and resid 123 through 143 Processing helix chain 'H' and resid 153 through 170 Processing helix chain 'I' and resid 3 through 15 Processing helix chain 'I' and resid 20 through 47 removed outlier: 3.976A pdb=" N ASN I 35 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ALA I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 64 through 67 Processing helix chain 'I' and resid 77 through 102 Processing helix chain 'I' and resid 104 through 111 Processing helix chain 'I' and resid 114 through 122 Processing helix chain 'I' and resid 125 through 139 removed outlier: 4.124A pdb=" N TYR I 129 " --> pdb=" O SER I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 172 Processing helix chain 'J' and resid 3 through 15 removed outlier: 4.208A pdb=" N VAL J 8 " --> pdb=" O VAL J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 47 removed outlier: 4.432A pdb=" N ASN J 35 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYS J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 75 through 100 Processing helix chain 'J' and resid 102 through 109 Processing helix chain 'J' and resid 112 through 121 Processing helix chain 'J' and resid 123 through 143 removed outlier: 3.522A pdb=" N ASN J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 170 removed outlier: 3.558A pdb=" N VAL J 157 " --> pdb=" O CYS J 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 Processing helix chain 'K' and resid 20 through 47 removed outlier: 4.402A pdb=" N ASN K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 63 Processing helix chain 'K' and resid 64 through 69 removed outlier: 3.695A pdb=" N GLN K 68 " --> pdb=" O PRO K 64 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR K 69 " --> pdb=" O TYR K 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 64 through 69' Processing helix chain 'K' and resid 77 through 102 removed outlier: 3.518A pdb=" N LYS K 81 " --> pdb=" O ASP K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 111 Processing helix chain 'K' and resid 114 through 122 Processing helix chain 'K' and resid 125 through 140 removed outlier: 4.137A pdb=" N TYR K 129 " --> pdb=" O SER K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 172 Processing helix chain 'L' and resid 3 through 16 removed outlier: 4.331A pdb=" N VAL L 8 " --> pdb=" O VAL L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 47 removed outlier: 4.335A pdb=" N ASN L 35 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 63 through 68 removed outlier: 4.473A pdb=" N ILE L 67 " --> pdb=" O GLN L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 100 removed outlier: 4.148A pdb=" N ARG L 78 " --> pdb=" O TYR L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 109 removed outlier: 3.566A pdb=" N CYS L 109 " --> pdb=" O LEU L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 121 Processing helix chain 'L' and resid 123 through 143 Processing helix chain 'L' and resid 153 through 170 Processing helix chain 'M' and resid 3 through 15 Processing helix chain 'M' and resid 20 through 47 removed outlier: 4.331A pdb=" N ASN M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALA M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 64 through 69 removed outlier: 3.742A pdb=" N GLN M 68 " --> pdb=" O PRO M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 102 Processing helix chain 'M' and resid 104 through 111 Processing helix chain 'M' and resid 114 through 122 Processing helix chain 'M' and resid 125 through 140 removed outlier: 4.122A pdb=" N TYR M 129 " --> pdb=" O SER M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 172 removed outlier: 3.561A pdb=" N ASP M 148 " --> pdb=" O GLY M 144 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR M 163 " --> pdb=" O GLU M 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 16 removed outlier: 4.141A pdb=" N VAL N 8 " --> pdb=" O VAL N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 47 removed outlier: 4.392A pdb=" N ASN N 35 " --> pdb=" O VAL N 31 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS N 36 " --> pdb=" O ALA N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 63 Processing helix chain 'N' and resid 75 through 100 Processing helix chain 'N' and resid 102 through 109 Processing helix chain 'N' and resid 112 through 121 Processing helix chain 'N' and resid 123 through 143 Processing helix chain 'N' and resid 153 through 169 Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 20 through 47 removed outlier: 4.268A pdb=" N ASN O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA O 36 " --> pdb=" O ARG O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 63 Processing helix chain 'O' and resid 64 through 67 Processing helix chain 'O' and resid 77 through 102 Processing helix chain 'O' and resid 104 through 111 Processing helix chain 'O' and resid 114 through 122 Processing helix chain 'O' and resid 125 through 140 removed outlier: 4.147A pdb=" N TYR O 129 " --> pdb=" O SER O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 172 Processing helix chain 'P' and resid 3 through 15 removed outlier: 4.029A pdb=" N VAL P 8 " --> pdb=" O VAL P 4 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG P 15 " --> pdb=" O GLN P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 47 removed outlier: 4.352A pdb=" N ASN P 35 " --> pdb=" O VAL P 31 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LYS P 36 " --> pdb=" O ALA P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 63 Processing helix chain 'P' and resid 75 through 100 Processing helix chain 'P' and resid 102 through 109 Processing helix chain 'P' and resid 112 through 121 Processing helix chain 'P' and resid 123 through 143 Processing helix chain 'P' and resid 153 through 170 Processing helix chain 'Q' and resid 3 through 15 Processing helix chain 'Q' and resid 20 through 63 removed outlier: 4.169A pdb=" N ASN Q 35 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN Q 49 " --> pdb=" O THR Q 45 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N SER Q 50 " --> pdb=" O ASP Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 68 Processing helix chain 'Q' and resid 77 through 102 Processing helix chain 'Q' and resid 104 through 111 Processing helix chain 'Q' and resid 114 through 122 Processing helix chain 'Q' and resid 125 through 140 removed outlier: 4.102A pdb=" N TYR Q 129 " --> pdb=" O SER Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 172 removed outlier: 3.587A pdb=" N TYR Q 163 " --> pdb=" O GLU Q 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 16 removed outlier: 3.910A pdb=" N VAL R 8 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 47 removed outlier: 4.357A pdb=" N ASN R 35 " --> pdb=" O VAL R 31 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 63 Processing helix chain 'R' and resid 64 through 67 Processing helix chain 'R' and resid 75 through 100 Processing helix chain 'R' and resid 102 through 108 Processing helix chain 'R' and resid 112 through 121 Processing helix chain 'R' and resid 123 through 143 Processing helix chain 'R' and resid 153 through 170 Processing helix chain 'S' and resid 3 through 15 Processing helix chain 'S' and resid 20 through 47 removed outlier: 4.225A pdb=" N ASN S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA S 36 " --> pdb=" O ARG S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 63 Processing helix chain 'S' and resid 64 through 69 Processing helix chain 'S' and resid 77 through 102 Processing helix chain 'S' and resid 104 through 111 Processing helix chain 'S' and resid 114 through 122 Processing helix chain 'S' and resid 125 through 140 removed outlier: 4.040A pdb=" N TYR S 129 " --> pdb=" O SER S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 172 removed outlier: 3.626A pdb=" N ASP S 148 " --> pdb=" O GLY S 144 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU S 159 " --> pdb=" O ASP S 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 16 removed outlier: 4.010A pdb=" N VAL T 8 " --> pdb=" O VAL T 4 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG T 15 " --> pdb=" O GLN T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 47 removed outlier: 4.436A pdb=" N ASN T 35 " --> pdb=" O VAL T 31 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LYS T 36 " --> pdb=" O ALA T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 63 Processing helix chain 'T' and resid 75 through 100 Processing helix chain 'T' and resid 102 through 109 Processing helix chain 'T' and resid 112 through 121 Processing helix chain 'T' and resid 123 through 143 Processing helix chain 'T' and resid 153 through 170 Processing helix chain 'U' and resid 3 through 15 Processing helix chain 'U' and resid 20 through 47 removed outlier: 4.294A pdb=" N ASN U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA U 36 " --> pdb=" O ARG U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 63 Processing helix chain 'U' and resid 64 through 68 removed outlier: 3.710A pdb=" N GLN U 68 " --> pdb=" O TYR U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 102 Processing helix chain 'U' and resid 104 through 110 Processing helix chain 'U' and resid 114 through 122 Processing helix chain 'U' and resid 125 through 140 removed outlier: 4.118A pdb=" N TYR U 129 " --> pdb=" O SER U 125 " (cutoff:3.500A) Processing helix chain 'U' and resid 144 through 172 removed outlier: 3.656A pdb=" N TYR U 163 " --> pdb=" O GLU U 159 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 16 removed outlier: 4.034A pdb=" N VAL V 8 " --> pdb=" O VAL V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 20 through 33 Processing helix chain 'V' and resid 33 through 47 Processing helix chain 'V' and resid 47 through 63 Processing helix chain 'V' and resid 75 through 100 Processing helix chain 'V' and resid 102 through 109 Processing helix chain 'V' and resid 112 through 120 Processing helix chain 'V' and resid 123 through 143 Processing helix chain 'V' and resid 153 through 170 Processing helix chain 'W' and resid 3 through 15 Processing helix chain 'W' and resid 20 through 47 removed outlier: 4.233A pdb=" N ASN W 35 " --> pdb=" O LEU W 31 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA W 36 " --> pdb=" O ARG W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 63 Processing helix chain 'W' and resid 64 through 67 Processing helix chain 'W' and resid 77 through 102 Processing helix chain 'W' and resid 104 through 111 Processing helix chain 'W' and resid 114 through 122 Processing helix chain 'W' and resid 125 through 140 removed outlier: 4.205A pdb=" N TYR W 129 " --> pdb=" O SER W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 144 through 172 removed outlier: 3.624A pdb=" N GLU W 159 " --> pdb=" O ASP W 145 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR W 163 " --> pdb=" O GLU W 159 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 16 removed outlier: 3.831A pdb=" N VAL X 8 " --> pdb=" O VAL X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 47 removed outlier: 4.480A pdb=" N ASN X 35 " --> pdb=" O VAL X 31 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LYS X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 64 through 67 Processing helix chain 'X' and resid 75 through 100 Processing helix chain 'X' and resid 102 through 109 Processing helix chain 'X' and resid 112 through 121 Processing helix chain 'X' and resid 123 through 143 Processing helix chain 'X' and resid 153 through 170 Processing helix chain 'Y' and resid 3 through 15 Processing helix chain 'Y' and resid 20 through 47 removed outlier: 3.538A pdb=" N LEU Y 24 " --> pdb=" O SER Y 20 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN Y 35 " --> pdb=" O LEU Y 31 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA Y 36 " --> pdb=" O ARG Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 63 Processing helix chain 'Y' and resid 64 through 69 Processing helix chain 'Y' and resid 77 through 102 Processing helix chain 'Y' and resid 104 through 111 Processing helix chain 'Y' and resid 114 through 122 removed outlier: 3.586A pdb=" N ILE Y 118 " --> pdb=" O GLY Y 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 125 through 140 removed outlier: 4.148A pdb=" N TYR Y 129 " --> pdb=" O SER Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 144 through 171 removed outlier: 3.547A pdb=" N SER Y 162 " --> pdb=" O ASP Y 148 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR Y 163 " --> pdb=" O GLU Y 159 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 16 removed outlier: 4.157A pdb=" N VAL Z 8 " --> pdb=" O VAL Z 4 " (cutoff:3.500A) Processing helix chain 'Z' and resid 20 through 47 removed outlier: 4.377A pdb=" N ASN Z 35 " --> pdb=" O VAL Z 31 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LYS Z 36 " --> pdb=" O ALA Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 63 Processing helix chain 'Z' and resid 75 through 100 Processing helix chain 'Z' and resid 102 through 108 Processing helix chain 'Z' and resid 112 through 121 Processing helix chain 'Z' and resid 123 through 143 Processing helix chain 'Z' and resid 153 through 172 removed outlier: 3.781A pdb=" N VAL Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 15 Processing helix chain 'a' and resid 20 through 47 removed outlier: 4.233A pdb=" N ASN a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALA a 36 " --> pdb=" O ARG a 32 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 63 Processing helix chain 'a' and resid 64 through 69 removed outlier: 3.627A pdb=" N GLN a 68 " --> pdb=" O PRO a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 102 Processing helix chain 'a' and resid 104 through 111 Processing helix chain 'a' and resid 114 through 122 Processing helix chain 'a' and resid 125 through 140 removed outlier: 4.074A pdb=" N TYR a 129 " --> pdb=" O SER a 125 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 172 Processing helix chain 'b' and resid 3 through 16 removed outlier: 3.899A pdb=" N VAL b 8 " --> pdb=" O VAL b 4 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG b 15 " --> pdb=" O GLN b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 20 through 33 Processing helix chain 'b' and resid 33 through 47 Processing helix chain 'b' and resid 47 through 63 Processing helix chain 'b' and resid 64 through 67 Processing helix chain 'b' and resid 75 through 100 Processing helix chain 'b' and resid 102 through 109 Processing helix chain 'b' and resid 112 through 121 Processing helix chain 'b' and resid 123 through 143 Processing helix chain 'b' and resid 153 through 170 Processing helix chain 'c' and resid 3 through 15 Processing helix chain 'c' and resid 20 through 47 removed outlier: 4.074A pdb=" N ASN c 35 " --> pdb=" O LEU c 31 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ALA c 36 " --> pdb=" O ARG c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 47 through 63 Processing helix chain 'c' and resid 64 through 69 Processing helix chain 'c' and resid 77 through 102 Processing helix chain 'c' and resid 104 through 111 Processing helix chain 'c' and resid 114 through 122 Processing helix chain 'c' and resid 125 through 140 removed outlier: 4.196A pdb=" N TYR c 129 " --> pdb=" O SER c 125 " (cutoff:3.500A) Processing helix chain 'c' and resid 144 through 172 removed outlier: 3.707A pdb=" N TYR c 163 " --> pdb=" O GLU c 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 16 removed outlier: 3.994A pdb=" N VAL d 8 " --> pdb=" O VAL d 4 " (cutoff:3.500A) Processing helix chain 'd' and resid 20 through 47 removed outlier: 4.303A pdb=" N ASN d 35 " --> pdb=" O VAL d 31 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LYS d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 47 through 63 Processing helix chain 'd' and resid 75 through 100 Processing helix chain 'd' and resid 102 through 109 Processing helix chain 'd' and resid 112 through 121 Processing helix chain 'd' and resid 123 through 143 Processing helix chain 'd' and resid 153 through 170 Processing helix chain 'e' and resid 3 through 16 Processing helix chain 'e' and resid 20 through 47 removed outlier: 4.424A pdb=" N ASN e 35 " --> pdb=" O LEU e 31 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA e 36 " --> pdb=" O ARG e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 63 Processing helix chain 'e' and resid 64 through 69 removed outlier: 3.548A pdb=" N GLN e 68 " --> pdb=" O PRO e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 77 through 102 Processing helix chain 'e' and resid 104 through 111 Processing helix chain 'e' and resid 114 through 122 Processing helix chain 'e' and resid 125 through 140 removed outlier: 4.222A pdb=" N TYR e 129 " --> pdb=" O SER e 125 " (cutoff:3.500A) Processing helix chain 'e' and resid 144 through 172 Processing helix chain 'f' and resid 3 through 16 removed outlier: 4.085A pdb=" N VAL f 8 " --> pdb=" O VAL f 4 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 33 Processing helix chain 'f' and resid 33 through 47 Processing helix chain 'f' and resid 47 through 63 Processing helix chain 'f' and resid 64 through 67 Processing helix chain 'f' and resid 75 through 100 Processing helix chain 'f' and resid 102 through 109 Processing helix chain 'f' and resid 112 through 121 Processing helix chain 'f' and resid 123 through 143 Processing helix chain 'f' and resid 153 through 170 Processing helix chain 'g' and resid 3 through 15 Processing helix chain 'g' and resid 20 through 47 removed outlier: 4.106A pdb=" N ASN g 35 " --> pdb=" O LEU g 31 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALA g 36 " --> pdb=" O ARG g 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 63 Processing helix chain 'g' and resid 64 through 69 removed outlier: 3.593A pdb=" N GLN g 68 " --> pdb=" O PRO g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 102 Processing helix chain 'g' and resid 104 through 111 Processing helix chain 'g' and resid 114 through 122 Processing helix chain 'g' and resid 125 through 140 removed outlier: 4.202A pdb=" N TYR g 129 " --> pdb=" O SER g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 144 through 172 removed outlier: 3.526A pdb=" N GLU g 159 " --> pdb=" O ASP g 145 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR g 163 " --> pdb=" O GLU g 159 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 16 Processing helix chain 'h' and resid 20 through 33 Processing helix chain 'h' and resid 33 through 47 Processing helix chain 'h' and resid 47 through 63 Processing helix chain 'h' and resid 75 through 100 Processing helix chain 'h' and resid 102 through 109 Processing helix chain 'h' and resid 112 through 121 Processing helix chain 'h' and resid 123 through 143 Processing helix chain 'h' and resid 153 through 170 Processing helix chain 'i' and resid 3 through 16 Processing helix chain 'i' and resid 20 through 47 removed outlier: 4.288A pdb=" N ASN i 35 " --> pdb=" O LEU i 31 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA i 36 " --> pdb=" O ARG i 32 " (cutoff:3.500A) Processing helix chain 'i' and resid 47 through 63 Processing helix chain 'i' and resid 64 through 69 removed outlier: 3.630A pdb=" N GLN i 68 " --> pdb=" O PRO i 64 " (cutoff:3.500A) Processing helix chain 'i' and resid 77 through 102 Processing helix chain 'i' and resid 104 through 111 Processing helix chain 'i' and resid 114 through 122 Processing helix chain 'i' and resid 125 through 140 removed outlier: 4.184A pdb=" N TYR i 129 " --> pdb=" O SER i 125 " (cutoff:3.500A) Processing helix chain 'i' and resid 144 through 172 Processing helix chain 'j' and resid 3 through 16 removed outlier: 4.174A pdb=" N VAL j 8 " --> pdb=" O VAL j 4 " (cutoff:3.500A) Processing helix chain 'j' and resid 20 through 33 Processing helix chain 'j' and resid 33 through 47 Processing helix chain 'j' and resid 47 through 63 Processing helix chain 'j' and resid 75 through 100 Processing helix chain 'j' and resid 102 through 109 Processing helix chain 'j' and resid 112 through 121 Processing helix chain 'j' and resid 123 through 143 Processing helix chain 'j' and resid 153 through 170 removed outlier: 3.511A pdb=" N VAL j 157 " --> pdb=" O CYS j 153 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 17 Processing helix chain 'k' and resid 28 through 43 Processing helix chain 'k' and resid 50 through 54 removed outlier: 3.615A pdb=" N ARG k 54 " --> pdb=" O ASP k 51 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 64 removed outlier: 3.623A pdb=" N ASN k 64 " --> pdb=" O SER k 60 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 79 Processing helix chain 'k' and resid 79 through 87 Processing helix chain 'k' and resid 91 through 104 Processing helix chain 'k' and resid 110 through 135 removed outlier: 4.030A pdb=" N VAL k 114 " --> pdb=" O SER k 110 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE k 126 " --> pdb=" O GLU k 122 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N ASP k 127 " --> pdb=" O ASN k 123 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA k 128 " --> pdb=" O GLN k 124 " (cutoff:3.500A) Processing helix chain 'k' and resid 136 through 143 Processing helix chain 'k' and resid 160 through 171 removed outlier: 3.734A pdb=" N PHE k 164 " --> pdb=" O ARG k 160 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR k 165 " --> pdb=" O THR k 161 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE k 168 " --> pdb=" O PHE k 164 " (cutoff:3.500A) Processing helix chain 'k' and resid 189 through 195 removed outlier: 3.719A pdb=" N GLN k 195 " --> pdb=" O THR k 191 " (cutoff:3.500A) Processing helix chain 'k' and resid 229 through 233 Processing helix chain 'k' and resid 267 through 279 Processing helix chain 'l' and resid 3 through 11 removed outlier: 3.572A pdb=" N ARG l 9 " --> pdb=" O VAL l 5 " (cutoff:3.500A) Processing helix chain 'l' and resid 12 through 17 Processing helix chain 'l' and resid 28 through 43 Processing helix chain 'l' and resid 50 through 54 removed outlier: 3.547A pdb=" N GLU l 53 " --> pdb=" O MET l 50 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG l 54 " --> pdb=" O SER l 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 50 through 54' Processing helix chain 'l' and resid 55 through 64 Processing helix chain 'l' and resid 68 through 78 Processing helix chain 'l' and resid 79 through 87 Processing helix chain 'l' and resid 91 through 103 Processing helix chain 'l' and resid 110 through 135 removed outlier: 3.687A pdb=" N ILE l 114 " --> pdb=" O ASP l 110 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N TYR l 126 " --> pdb=" O HIS l 122 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N GLU l 127 " --> pdb=" O GLN l 123 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA l 128 " --> pdb=" O GLY l 124 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR l 133 " --> pdb=" O GLU l 129 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE l 134 " --> pdb=" O ILE l 130 " (cutoff:3.500A) Processing helix chain 'l' and resid 136 through 143 Processing helix chain 'l' and resid 161 through 172 removed outlier: 3.984A pdb=" N PHE l 165 " --> pdb=" O LYS l 161 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER l 166 " --> pdb=" O THR l 162 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE l 169 " --> pdb=" O PHE l 165 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN l 170 " --> pdb=" O SER l 166 " (cutoff:3.500A) Processing helix chain 'l' and resid 190 through 195 removed outlier: 3.570A pdb=" N ALA l 195 " --> pdb=" O THR l 191 " (cutoff:3.500A) Processing helix chain 'l' and resid 204 through 209 removed outlier: 3.504A pdb=" N GLU l 209 " --> pdb=" O SER l 206 " (cutoff:3.500A) Processing helix chain 'l' and resid 252 through 263 Processing helix chain 'm' and resid 15 through 18 Processing helix chain 'm' and resid 55 through 66 Processing helix chain 'm' and resid 81 through 85 removed outlier: 3.899A pdb=" N THR m 85 " --> pdb=" O LEU m 82 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 17 removed outlier: 3.558A pdb=" N VAL n 17 " --> pdb=" O ASN n 14 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 54 Processing helix chain 'n' and resid 60 through 64 Processing helix chain 'n' and resid 65 through 74 Processing helix chain 'n' and resid 78 through 88 Processing helix chain 'n' and resid 89 through 96 Processing helix chain 'n' and resid 101 through 114 Processing helix chain 'n' and resid 120 through 146 removed outlier: 3.843A pdb=" N LYS n 124 " --> pdb=" O SER n 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE n 129 " --> pdb=" O ILE n 125 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL n 130 " --> pdb=" O ALA n 126 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU n 136 " --> pdb=" O ALA n 132 " (cutoff:3.500A) Proline residue: n 137 - end of helix Processing helix chain 'n' and resid 146 through 154 Processing helix chain 'n' and resid 175 through 179 Processing helix chain 'n' and resid 183 through 194 Processing sheet with id=AA1, first strand: chain 'k' and resid 259 through 264 removed outlier: 7.100A pdb=" N LEU k 238 " --> pdb=" O PRO k 287 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG k 240 " --> pdb=" O ILE k 285 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE k 285 " --> pdb=" O ARG k 240 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU k 242 " --> pdb=" O ALA k 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'l' and resid 243 through 249 removed outlier: 6.519A pdb=" N ILE l 228 " --> pdb=" O VAL l 267 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL l 267 " --> pdb=" O ILE l 228 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'm' and resid 47 through 52 removed outlier: 7.771A pdb=" N LEU m 20 " --> pdb=" O PRO m 75 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL m 22 " --> pdb=" O ILE m 73 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE m 73 " --> pdb=" O VAL m 22 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU m 24 " --> pdb=" O VAL m 71 " (cutoff:3.500A) 4006 hydrogen bonds defined for protein. 11931 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: 21.44 Time building geometry restraints manager: 13.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 9338 1.31 - 1.43: 14377 1.43 - 1.56: 31007 1.56 - 1.69: 86 1.69 - 1.82: 300 Bond restraints: 55108 Sorted by residual: bond pdb=" C3C CYC j 201 " pdb=" C4C CYC j 201 " ideal model delta sigma weight residual 1.514 1.719 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C4C CYC B 201 " pdb=" NC CYC B 201 " ideal model delta sigma weight residual 1.377 1.211 0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" NB CYC B 201 " pdb=" C4B CYC B 201 " ideal model delta sigma weight residual 1.369 1.534 -0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" NB CYC L 201 " pdb=" C4B CYC L 201 " ideal model delta sigma weight residual 1.369 1.533 -0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" NB CYC H 201 " pdb=" C4B CYC H 201 " ideal model delta sigma weight residual 1.369 1.533 -0.164 2.00e-02 2.50e+03 6.69e+01 ... (remaining 55103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 71430 2.61 - 5.21: 2273 5.21 - 7.82: 938 7.82 - 10.43: 265 10.43 - 13.03: 53 Bond angle restraints: 74959 Sorted by residual: angle pdb=" N GLU k 183 " pdb=" CA GLU k 183 " pdb=" C GLU k 183 " ideal model delta sigma weight residual 108.67 95.64 13.03 1.55e+00 4.16e-01 7.07e+01 angle pdb=" C MET n 179 " pdb=" N PRO n 180 " pdb=" CA PRO n 180 " ideal model delta sigma weight residual 120.31 127.80 -7.49 9.80e-01 1.04e+00 5.84e+01 angle pdb=" N GLN l 160 " pdb=" CA GLN l 160 " pdb=" C GLN l 160 " ideal model delta sigma weight residual 110.50 120.48 -9.98 1.41e+00 5.03e-01 5.01e+01 angle pdb=" N TYR B 74 " pdb=" CA TYR B 74 " pdb=" CB TYR B 74 " ideal model delta sigma weight residual 110.35 118.07 -7.72 1.12e+00 7.97e-01 4.75e+01 angle pdb=" N PRO L 145 " pdb=" CD PRO L 145 " pdb=" CG PRO L 145 " ideal model delta sigma weight residual 103.20 94.01 9.19 1.50e+00 4.44e-01 3.75e+01 ... (remaining 74954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 30837 17.88 - 35.77: 2469 35.77 - 53.65: 531 53.65 - 71.54: 144 71.54 - 89.42: 69 Dihedral angle restraints: 34050 sinusoidal: 14297 harmonic: 19753 Sorted by residual: dihedral pdb=" CD ARG T 78 " pdb=" NE ARG T 78 " pdb=" CZ ARG T 78 " pdb=" NH1 ARG T 78 " ideal model delta sinusoidal sigma weight residual 0.00 -47.55 47.55 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CD ARG T 77 " pdb=" NE ARG T 77 " pdb=" CZ ARG T 77 " pdb=" NH1 ARG T 77 " ideal model delta sinusoidal sigma weight residual 0.00 -44.34 44.34 1 1.00e+01 1.00e-02 2.73e+01 dihedral pdb=" CA MET C 1 " pdb=" C MET C 1 " pdb=" N LYS C 2 " pdb=" CA LYS C 2 " ideal model delta harmonic sigma weight residual -180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 34047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 7644 0.100 - 0.201: 444 0.201 - 0.301: 55 0.301 - 0.401: 34 0.401 - 0.501: 21 Chirality restraints: 8198 Sorted by residual: chirality pdb=" CB THR B 75 " pdb=" CA THR B 75 " pdb=" OG1 THR B 75 " pdb=" CG2 THR B 75 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" C2C CYC d 202 " pdb=" C1C CYC d 202 " pdb=" C3C CYC d 202 " pdb=" CMC CYC d 202 " both_signs ideal model delta sigma weight residual False -2.52 -2.97 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" C2C CYC f 202 " pdb=" C1C CYC f 202 " pdb=" C3C CYC f 202 " pdb=" CMC CYC f 202 " both_signs ideal model delta sigma weight residual False -2.52 -2.97 0.44 2.00e-01 2.50e+01 4.88e+00 ... (remaining 8195 not shown) Planarity restraints: 9826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG T 78 " 0.805 9.50e-02 1.11e+02 3.61e-01 7.92e+01 pdb=" NE ARG T 78 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG T 78 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG T 78 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG T 78 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG T 77 " 0.775 9.50e-02 1.11e+02 3.48e-01 7.35e+01 pdb=" NE ARG T 77 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG T 77 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG T 77 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG T 77 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG U 32 " 0.544 9.50e-02 1.11e+02 2.45e-01 4.11e+01 pdb=" NE ARG U 32 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG U 32 " -0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG U 32 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG U 32 " 0.031 2.00e-02 2.50e+03 ... (remaining 9823 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 528 2.52 - 3.11: 39890 3.11 - 3.71: 96688 3.71 - 4.30: 139137 4.30 - 4.90: 224484 Nonbonded interactions: 500727 Sorted by model distance: nonbonded pdb=" OE1 GLU l 141 " pdb=" NH2 ARG l 158 " model vdw 1.919 3.120 nonbonded pdb=" NH1 ARG m 61 " pdb=" CBB CYC h 201 " model vdw 1.951 3.540 nonbonded pdb=" NE ARG l 180 " pdb=" O2D CYC Z 201 " model vdw 2.028 2.496 nonbonded pdb=" O ALA l 77 " pdb=" OH TYR l 126 " model vdw 2.030 3.040 nonbonded pdb=" OD1 ASP l 33 " pdb=" NH2 ARG l 63 " model vdw 2.057 3.120 ... (remaining 500722 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 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 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: 0.080 Extract box with map and model: 1.570 Check model and map are aligned: 0.320 Set scattering table: 0.390 Process input model: 101.790 Find NCS groups from input model: 3.200 Set up NCS constraints: 0.550 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: 0.020 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.012 0.205 55108 Z= 0.807 Angle : 1.310 13.033 74959 Z= 0.602 Chirality : 0.062 0.501 8198 Planarity : 0.010 0.361 9826 Dihedral : 14.441 89.419 21438 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.65 % Favored : 98.24 % Rotamer: Outliers : 0.45 % Allowed : 0.66 % Favored : 98.88 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.09), residues: 6771 helix: -0.33 (0.06), residues: 5087 sheet: 0.28 (0.62), residues: 48 loop : -1.15 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP U 128 HIS 0.014 0.002 HIS G 140 PHE 0.033 0.002 PHE Q 28 TYR 0.030 0.002 TYR n 103 ARG 0.038 0.001 ARG U 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1521 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1497 time to evaluate : 4.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 GLN cc_start: 0.7298 (mt0) cc_final: 0.7082 (mt0) REVERT: A 42 LYS cc_start: 0.8191 (tmtt) cc_final: 0.7837 (tmtp) REVERT: A 116 ASP cc_start: 0.7125 (m-30) cc_final: 0.6843 (m-30) REVERT: A 134 LYS cc_start: 0.8025 (mmtp) cc_final: 0.7800 (tppp) REVERT: A 139 ASN cc_start: 0.8101 (m110) cc_final: 0.7891 (m110) REVERT: B 1 MET cc_start: 0.7740 (ptp) cc_final: 0.7476 (ptp) REVERT: B 36 LYS cc_start: 0.8236 (mttm) cc_final: 0.7819 (mtpt) REVERT: C 35 ASN cc_start: 0.8352 (m-40) cc_final: 0.8094 (m110) REVERT: C 131 GLU cc_start: 0.7819 (tp30) cc_final: 0.7416 (tp30) REVERT: D 23 GLN cc_start: 0.7207 (tt0) cc_final: 0.6765 (tt0) REVERT: D 25 ASP cc_start: 0.7379 (m-30) cc_final: 0.6832 (m-30) REVERT: D 92 TYR cc_start: 0.8881 (m-80) cc_final: 0.8634 (m-80) REVERT: D 132 GLN cc_start: 0.7269 (mm-40) cc_final: 0.7049 (mm-40) REVERT: D 148 ILE cc_start: 0.7483 (tt) cc_final: 0.7242 (tt) REVERT: D 166 ARG cc_start: 0.7638 (ptm160) cc_final: 0.7212 (ptp-170) REVERT: E 17 ARG cc_start: 0.7193 (ptt90) cc_final: 0.6958 (ptm-80) REVERT: E 42 LYS cc_start: 0.7525 (tptt) cc_final: 0.7267 (tptm) REVERT: E 120 ARG cc_start: 0.7269 (ttm110) cc_final: 0.6979 (ttm-80) REVERT: E 165 ASP cc_start: 0.7539 (m-30) cc_final: 0.7103 (m-30) REVERT: G 131 GLU cc_start: 0.7804 (tp30) cc_final: 0.7514 (tp30) REVERT: G 169 ASN cc_start: 0.8426 (m-40) cc_final: 0.7888 (m-40) REVERT: H 107 ASP cc_start: 0.8025 (m-30) cc_final: 0.7713 (m-30) REVERT: H 114 ARG cc_start: 0.7585 (ttm110) cc_final: 0.6997 (ttp-170) REVERT: H 134 MET cc_start: 0.8563 (mtm) cc_final: 0.8345 (mtp) REVERT: I 11 THR cc_start: 0.8267 (m) cc_final: 0.7984 (m) REVERT: I 20 SER cc_start: 0.8319 (p) cc_final: 0.8021 (p) REVERT: I 42 LYS cc_start: 0.7428 (ttmm) cc_final: 0.7079 (ttpt) REVERT: I 47 ASN cc_start: 0.7739 (t0) cc_final: 0.7328 (t0) REVERT: I 49 GLN cc_start: 0.6981 (tp-100) cc_final: 0.6605 (pm20) REVERT: I 50 SER cc_start: 0.8375 (t) cc_final: 0.7980 (p) REVERT: I 109 GLU cc_start: 0.6377 (mm-30) cc_final: 0.6087 (mm-30) REVERT: I 143 SER cc_start: 0.6175 (p) cc_final: 0.5968 (m) REVERT: J 33 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6886 (mm-30) REVERT: J 115 GLU cc_start: 0.7723 (mp0) cc_final: 0.7406 (mp0) REVERT: K 53 ASN cc_start: 0.7214 (m-40) cc_final: 0.6847 (m110) REVERT: K 72 ASN cc_start: 0.7678 (m-40) cc_final: 0.7442 (m110) REVERT: K 117 GLU cc_start: 0.6859 (mp0) cc_final: 0.6608 (mp0) REVERT: L 3 ASP cc_start: 0.7756 (p0) cc_final: 0.7473 (p0) REVERT: M 49 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7408 (pm20) REVERT: M 134 LYS cc_start: 0.8660 (mttm) cc_final: 0.8445 (mttp) REVERT: M 159 GLU cc_start: 0.6803 (tm-30) cc_final: 0.5752 (tm-30) REVERT: N 107 ASP cc_start: 0.7492 (m-30) cc_final: 0.7192 (m-30) REVERT: O 10 SER cc_start: 0.8399 (m) cc_final: 0.8180 (m) REVERT: O 42 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7653 (ttmp) REVERT: Q 39 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7178 (tm130) REVERT: Q 47 ASN cc_start: 0.7690 (t0) cc_final: 0.7279 (t0) REVERT: Q 148 ASP cc_start: 0.6947 (m-30) cc_final: 0.6662 (m-30) REVERT: R 1 MET cc_start: 0.7382 (ptp) cc_final: 0.6787 (ptp) REVERT: R 30 THR cc_start: 0.8417 (m) cc_final: 0.8175 (m) REVERT: S 35 ASN cc_start: 0.8513 (m-40) cc_final: 0.8261 (m-40) REVERT: T 146 ASN cc_start: 0.7211 (m-40) cc_final: 0.6982 (m-40) REVERT: U 116 ASP cc_start: 0.6970 (p0) cc_final: 0.6632 (p0) REVERT: U 143 SER cc_start: 0.8132 (p) cc_final: 0.7829 (p) REVERT: V 39 ASP cc_start: 0.7808 (m-30) cc_final: 0.7452 (m-30) REVERT: V 135 LYS cc_start: 0.8378 (tttt) cc_final: 0.8093 (ttmt) REVERT: V 152 ASP cc_start: 0.6404 (t0) cc_final: 0.6131 (t0) REVERT: W 143 SER cc_start: 0.7634 (p) cc_final: 0.7417 (p) REVERT: X 25 ASP cc_start: 0.6337 (m-30) cc_final: 0.6060 (m-30) REVERT: X 101 ASP cc_start: 0.7846 (t70) cc_final: 0.7632 (t70) REVERT: X 132 GLN cc_start: 0.7824 (mm110) cc_final: 0.7608 (mm-40) REVERT: Y 1 MET cc_start: 0.6608 (mtm) cc_final: 0.6120 (mtm) REVERT: Y 11 THR cc_start: 0.7872 (m) cc_final: 0.6860 (p) REVERT: Y 15 GLN cc_start: 0.7724 (mp10) cc_final: 0.7292 (mp10) REVERT: Y 20 SER cc_start: 0.7836 (p) cc_final: 0.7612 (p) REVERT: Z 101 ASP cc_start: 0.7434 (t0) cc_final: 0.7139 (t0) REVERT: Z 132 GLN cc_start: 0.7043 (mm-40) cc_final: 0.6442 (mt0) REVERT: a 15 GLN cc_start: 0.8129 (mt0) cc_final: 0.7904 (mt0) REVERT: a 65 TYR cc_start: 0.7757 (p90) cc_final: 0.7449 (p90) REVERT: a 67 THR cc_start: 0.7145 (m) cc_final: 0.6761 (p) REVERT: a 131 GLU cc_start: 0.7588 (tp30) cc_final: 0.7264 (tp30) REVERT: a 159 GLU cc_start: 0.7104 (tt0) cc_final: 0.6903 (tt0) REVERT: b 11 GLN cc_start: 0.7587 (mt0) cc_final: 0.6791 (mt0) REVERT: b 135 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7829 (tttt) REVERT: c 49 GLN cc_start: 0.7389 (tp-100) cc_final: 0.7187 (pm20) REVERT: c 53 ASN cc_start: 0.8542 (m-40) cc_final: 0.8127 (m110) REVERT: c 68 GLN cc_start: 0.7290 (mt0) cc_final: 0.7053 (mt0) REVERT: c 162 SER cc_start: 0.7891 (m) cc_final: 0.7669 (t) REVERT: d 133 LYS cc_start: 0.8409 (mttm) cc_final: 0.8117 (mttm) REVERT: d 134 MET cc_start: 0.8743 (mtm) cc_final: 0.8466 (mtm) REVERT: d 159 GLU cc_start: 0.7821 (tt0) cc_final: 0.7469 (tt0) REVERT: e 42 LYS cc_start: 0.7432 (ttpt) cc_final: 0.7192 (tptm) REVERT: e 53 ASN cc_start: 0.7860 (m-40) cc_final: 0.7625 (m110) REVERT: e 120 ARG cc_start: 0.7483 (ttm110) cc_final: 0.7248 (ttp80) REVERT: e 123 ASP cc_start: 0.7485 (t0) cc_final: 0.7085 (t0) REVERT: e 161 ASN cc_start: 0.7285 (m-40) cc_final: 0.7049 (m-40) REVERT: f 22 SER cc_start: 0.7829 (p) cc_final: 0.7590 (p) REVERT: f 156 ILE cc_start: 0.8470 (tp) cc_final: 0.8270 (mp) REVERT: g 45 THR cc_start: 0.8095 (m) cc_final: 0.7837 (m) REVERT: h 87 GLU cc_start: 0.7355 (tt0) cc_final: 0.7117 (mt-10) REVERT: i 42 LYS cc_start: 0.7304 (tttm) cc_final: 0.6900 (tppt) REVERT: i 70 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6841 (mm110) REVERT: i 139 ASN cc_start: 0.7868 (m110) cc_final: 0.7655 (m110) REVERT: i 148 ASP cc_start: 0.8063 (m-30) cc_final: 0.7819 (m-30) REVERT: j 10 SER cc_start: 0.7601 (p) cc_final: 0.7358 (t) REVERT: j 103 SER cc_start: 0.7761 (p) cc_final: 0.7412 (p) REVERT: j 107 ASP cc_start: 0.6758 (m-30) cc_final: 0.6460 (m-30) REVERT: l 5 VAL cc_start: 0.7750 (p) cc_final: 0.7522 (p) REVERT: m 66 MET cc_start: 0.7148 (mtm) cc_final: 0.6703 (mtm) REVERT: n 55 ASN cc_start: 0.7752 (m-40) cc_final: 0.7202 (t0) REVERT: n 134 LYS cc_start: 0.7538 (mttp) cc_final: 0.7106 (mttp) REVERT: n 142 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6903 (tp30) outliers start: 24 outliers final: 3 residues processed: 1508 average time/residue: 1.5220 time to fit residues: 2830.0161 Evaluate side-chains 945 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 941 time to evaluate : 4.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain n residue 142 GLU Chi-restraints excluded: chain n residue 170 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 570 optimal weight: 0.9990 chunk 512 optimal weight: 0.3980 chunk 284 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 345 optimal weight: 0.5980 chunk 273 optimal weight: 0.6980 chunk 529 optimal weight: 0.9990 chunk 205 optimal weight: 0.7980 chunk 322 optimal weight: 2.9990 chunk 394 optimal weight: 1.9990 chunk 613 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 25 GLN A 33 GLN A 140 HIS B 72 ASN C 15 GLN D 11 GLN D 72 ASN E 39 GLN E 47 ASN E 53 ASN E 70 GLN E 78 GLN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 169 ASN J 47 ASN K 15 GLN K 47 ASN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 ASN L 68 GLN M 15 GLN M 35 ASN N 68 GLN N 132 GLN O 33 GLN O 72 ASN P 68 GLN P 132 GLN Q 35 ASN Q 139 ASN Q 140 HIS R 65 GLN S 57 GLN T 47 ASN T 72 ASN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 ASN ** U 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 35 ASN V 111 ASN V 146 ASN W 33 GLN W 47 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 GLN a 39 GLN a 53 ASN a 61 ASN a 119 ASN a 169 ASN b 72 ASN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN ** e 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN e 140 HIS g 39 GLN g 57 GLN g 61 ASN g 140 HIS h 11 GLN h 35 ASN h 63 GLN h 68 GLN h 72 ASN i 49 GLN i 140 HIS j 132 GLN k 102 HIS k 124 GLN k 270 GLN l 197 ASN m 84 HIS n 57 GLN ** n 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 75 GLN n 141 ASN n 186 HIS Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 55108 Z= 0.190 Angle : 0.673 11.529 74959 Z= 0.321 Chirality : 0.038 0.231 8198 Planarity : 0.005 0.078 9826 Dihedral : 9.990 89.704 10022 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.20 % Favored : 98.76 % Rotamer: Outliers : 2.46 % Allowed : 10.55 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.09), residues: 6771 helix: 1.03 (0.07), residues: 5154 sheet: 0.31 (0.61), residues: 48 loop : -0.55 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 128 HIS 0.007 0.002 HIS C 140 PHE 0.013 0.001 PHE b 98 TYR 0.026 0.001 TYR B 74 ARG 0.009 0.001 ARG n 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1049 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLN cc_start: 0.8073 (tp-100) cc_final: 0.7742 (tp40) REVERT: A 116 ASP cc_start: 0.7128 (m-30) cc_final: 0.6800 (m-30) REVERT: A 134 LYS cc_start: 0.7991 (mmtp) cc_final: 0.7737 (tppp) REVERT: A 159 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6924 (tt0) REVERT: B 135 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7650 (ttpt) REVERT: C 33 GLN cc_start: 0.8376 (tp-100) cc_final: 0.8143 (tp-100) REVERT: D 15 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.6000 (mtp-110) REVERT: D 23 GLN cc_start: 0.7296 (tt0) cc_final: 0.6880 (tt0) REVERT: D 141 ILE cc_start: 0.8212 (pp) cc_final: 0.7949 (mt) REVERT: D 145 PRO cc_start: 0.7305 (Cg_endo) cc_final: 0.7100 (Cg_exo) REVERT: E 1 MET cc_start: 0.6299 (ttt) cc_final: 0.5215 (ttt) REVERT: E 46 ASP cc_start: 0.7188 (p0) cc_final: 0.6980 (p0) REVERT: E 120 ARG cc_start: 0.6926 (ttm110) cc_final: 0.6700 (ttm110) REVERT: G 33 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: G 131 GLU cc_start: 0.7879 (tp30) cc_final: 0.7543 (tp30) REVERT: G 169 ASN cc_start: 0.8553 (m-40) cc_final: 0.8174 (m110) REVERT: H 11 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.6645 (mt0) REVERT: H 33 GLU cc_start: 0.7244 (mm-30) cc_final: 0.7023 (mm-30) REVERT: H 107 ASP cc_start: 0.7912 (m-30) cc_final: 0.7700 (m-30) REVERT: H 134 MET cc_start: 0.8576 (mtm) cc_final: 0.8309 (mtp) REVERT: I 42 LYS cc_start: 0.7389 (ttmm) cc_final: 0.7103 (ttpt) REVERT: I 47 ASN cc_start: 0.7619 (t0) cc_final: 0.7385 (t0) REVERT: I 49 GLN cc_start: 0.7005 (tp-100) cc_final: 0.6564 (pm20) REVERT: I 50 SER cc_start: 0.8375 (t) cc_final: 0.7997 (p) REVERT: I 143 SER cc_start: 0.6773 (p) cc_final: 0.6537 (m) REVERT: J 33 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6729 (tp30) REVERT: J 115 GLU cc_start: 0.7759 (mp0) cc_final: 0.7453 (mp0) REVERT: J 159 GLU cc_start: 0.7835 (tt0) cc_final: 0.7477 (tt0) REVERT: K 53 ASN cc_start: 0.7270 (m-40) cc_final: 0.6869 (m110) REVERT: K 110 TYR cc_start: 0.8258 (m-10) cc_final: 0.8055 (m-80) REVERT: K 117 GLU cc_start: 0.6800 (mp0) cc_final: 0.6454 (mp0) REVERT: K 137 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8008 (mtmm) REVERT: L 165 ASP cc_start: 0.7443 (m-30) cc_final: 0.7190 (m-30) REVERT: M 20 SER cc_start: 0.8479 (p) cc_final: 0.8249 (m) REVERT: M 49 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7495 (pm20) REVERT: M 134 LYS cc_start: 0.8575 (mttm) cc_final: 0.8329 (mttp) REVERT: N 107 ASP cc_start: 0.7373 (m-30) cc_final: 0.7067 (m-30) REVERT: N 115 GLU cc_start: 0.7217 (mp0) cc_final: 0.6887 (mp0) REVERT: O 159 GLU cc_start: 0.7783 (tp30) cc_final: 0.7531 (tt0) REVERT: P 107 ASP cc_start: 0.7125 (m-30) cc_final: 0.6839 (m-30) REVERT: Q 33 GLN cc_start: 0.6655 (tt0) cc_final: 0.6454 (tt0) REVERT: Q 39 GLN cc_start: 0.7645 (tm-30) cc_final: 0.7218 (tm-30) REVERT: Q 136 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8693 (mp) REVERT: Q 148 ASP cc_start: 0.7381 (m-30) cc_final: 0.7118 (m-30) REVERT: R 1 MET cc_start: 0.7420 (ptp) cc_final: 0.6792 (ptp) REVERT: R 106 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7135 (tp30) REVERT: S 35 ASN cc_start: 0.8513 (m-40) cc_final: 0.8238 (m-40) REVERT: T 15 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7519 (mtm110) REVERT: T 135 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7835 (ttpt) REVERT: U 143 SER cc_start: 0.8167 (p) cc_final: 0.7933 (p) REVERT: V 117 TYR cc_start: 0.8642 (m-10) cc_final: 0.8415 (m-10) REVERT: V 152 ASP cc_start: 0.6822 (t0) cc_final: 0.6420 (t0) REVERT: W 1 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5590 (ttt) REVERT: W 78 GLN cc_start: 0.7539 (tp40) cc_final: 0.7192 (tp40) REVERT: W 143 SER cc_start: 0.7759 (p) cc_final: 0.7554 (p) REVERT: X 25 ASP cc_start: 0.6490 (m-30) cc_final: 0.6207 (m-30) REVERT: X 33 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6693 (mm-30) REVERT: X 132 GLN cc_start: 0.7664 (mm110) cc_final: 0.7395 (mm110) REVERT: Y 1 MET cc_start: 0.6696 (mtm) cc_final: 0.6195 (mtm) REVERT: Y 11 THR cc_start: 0.8051 (m) cc_final: 0.7623 (p) REVERT: Y 68 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6947 (mt0) REVERT: Z 114 ARG cc_start: 0.7635 (tpt-90) cc_final: 0.7240 (tpp-160) REVERT: a 67 THR cc_start: 0.7511 (m) cc_final: 0.7211 (p) REVERT: b 11 GLN cc_start: 0.7637 (mt0) cc_final: 0.7390 (mt0) REVERT: b 36 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7679 (mtpt) REVERT: b 106 GLU cc_start: 0.6707 (mm-30) cc_final: 0.5939 (mm-30) REVERT: c 11 THR cc_start: 0.8302 (t) cc_final: 0.8010 (m) REVERT: c 49 GLN cc_start: 0.7430 (tp-100) cc_final: 0.7061 (pm20) REVERT: c 53 ASN cc_start: 0.8448 (m-40) cc_final: 0.8033 (m110) REVERT: c 68 GLN cc_start: 0.7280 (mt0) cc_final: 0.7022 (mt0) REVERT: c 69 THR cc_start: 0.7890 (p) cc_final: 0.7682 (t) REVERT: d 111 ASN cc_start: 0.8261 (t0) cc_final: 0.7907 (t0) REVERT: d 133 LYS cc_start: 0.8400 (mttm) cc_final: 0.8119 (mttm) REVERT: d 134 MET cc_start: 0.8800 (mtm) cc_final: 0.8461 (mtm) REVERT: d 159 GLU cc_start: 0.7785 (tt0) cc_final: 0.7454 (tt0) REVERT: e 42 LYS cc_start: 0.7647 (ttpt) cc_final: 0.7291 (tptm) REVERT: e 53 ASN cc_start: 0.7985 (m-40) cc_final: 0.7713 (m110) REVERT: e 117 GLU cc_start: 0.7061 (mp0) cc_final: 0.6259 (mp0) REVERT: e 123 ASP cc_start: 0.7546 (t0) cc_final: 0.7163 (t0) REVERT: e 161 ASN cc_start: 0.7779 (m-40) cc_final: 0.7549 (m-40) REVERT: e 162 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.8025 (p) REVERT: f 25 ASP cc_start: 0.6207 (m-30) cc_final: 0.5896 (m-30) REVERT: f 35 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7344 (m-40) REVERT: f 132 GLN cc_start: 0.6714 (mp10) cc_final: 0.6497 (mm-40) REVERT: g 47 ASN cc_start: 0.8142 (t0) cc_final: 0.7907 (t0) REVERT: g 131 GLU cc_start: 0.7029 (tp30) cc_final: 0.6668 (tp30) REVERT: h 11 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7467 (mt0) REVERT: h 79 MET cc_start: 0.8758 (tpp) cc_final: 0.8324 (tpp) REVERT: i 42 LYS cc_start: 0.7348 (tttm) cc_final: 0.7056 (tppt) REVERT: i 70 GLN cc_start: 0.7099 (mm-40) cc_final: 0.6854 (mm110) REVERT: j 62 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6977 (tt0) REVERT: j 106 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.5728 (pm20) REVERT: j 107 ASP cc_start: 0.7191 (m-30) cc_final: 0.6944 (m-30) REVERT: j 159 GLU cc_start: 0.7376 (tt0) cc_final: 0.6892 (tm-30) REVERT: l 41 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7325 (ttt-90) REVERT: m 19 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6804 (tpm170) REVERT: m 30 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6768 (mm-40) REVERT: m 35 ASP cc_start: 0.6527 (m-30) cc_final: 0.6244 (m-30) REVERT: m 66 MET cc_start: 0.7017 (mtm) cc_final: 0.6672 (mtm) REVERT: n 29 ARG cc_start: 0.7113 (ttm110) cc_final: 0.6433 (mtt90) REVERT: n 55 ASN cc_start: 0.7752 (m-40) cc_final: 0.7326 (t0) REVERT: n 73 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8473 (mttt) REVERT: n 134 LYS cc_start: 0.7457 (mttp) cc_final: 0.7011 (mttp) outliers start: 130 outliers final: 32 residues processed: 1111 average time/residue: 1.5075 time to fit residues: 2071.1048 Evaluate side-chains 975 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 926 time to evaluate : 4.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain G residue 33 GLN Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 79 MET Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain a residue 164 LEU Chi-restraints excluded: chain b residue 36 LYS Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 162 SER Chi-restraints excluded: chain f residue 35 ASN Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain h residue 11 GLN Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 62 GLU Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 8 GLN Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain n residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 341 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 510 optimal weight: 0.8980 chunk 418 optimal weight: 0.0770 chunk 169 optimal weight: 5.9990 chunk 614 optimal weight: 5.9990 chunk 664 optimal weight: 4.9990 chunk 547 optimal weight: 0.9980 chunk 609 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 493 optimal weight: 3.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS B 11 GLN C 35 ASN D 11 GLN D 47 ASN D 111 ASN E 33 GLN E 39 GLN E 47 ASN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 169 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 47 ASN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN M 39 GLN N 132 GLN P 146 ASN Q 139 ASN R 68 GLN R 132 GLN S 139 ASN ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN U 15 GLN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 ASN U 78 GLN U 140 HIS V 111 ASN V 146 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 47 ASN ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN ** Z 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 GLN a 61 ASN a 169 ASN b 72 ASN b 132 GLN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN e 72 ASN e 139 ASN g 39 GLN h 68 GLN i 39 GLN i 140 HIS j 132 GLN k 270 GLN n 74 ASN n 141 ASN n 147 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 55108 Z= 0.237 Angle : 0.651 11.760 74959 Z= 0.313 Chirality : 0.039 0.205 8198 Planarity : 0.005 0.084 9826 Dihedral : 10.382 173.556 10012 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.17 % Favored : 98.80 % Rotamer: Outliers : 2.80 % Allowed : 12.23 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.10), residues: 6771 helix: 1.55 (0.07), residues: 5158 sheet: 0.53 (0.62), residues: 48 loop : -0.32 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP i 128 HIS 0.012 0.002 HIS M 140 PHE 0.016 0.002 PHE b 98 TYR 0.025 0.002 TYR B 74 ARG 0.065 0.001 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1016 time to evaluate : 4.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7215 (m-30) cc_final: 0.6918 (m-30) REVERT: A 134 LYS cc_start: 0.8102 (mmtp) cc_final: 0.7849 (tppp) REVERT: A 159 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7220 (tt0) REVERT: B 11 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: B 87 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7271 (tt0) REVERT: B 133 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8000 (mttm) REVERT: B 135 LYS cc_start: 0.7910 (ttpp) cc_final: 0.7635 (ttpt) REVERT: C 13 ASP cc_start: 0.7771 (t0) cc_final: 0.7566 (t0) REVERT: C 50 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7945 (p) REVERT: C 131 GLU cc_start: 0.7955 (tp30) cc_final: 0.7727 (tp30) REVERT: D 15 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6149 (ttm-80) REVERT: D 23 GLN cc_start: 0.7637 (tt0) cc_final: 0.7304 (tt0) REVERT: D 148 ILE cc_start: 0.7593 (tt) cc_final: 0.7378 (tt) REVERT: E 1 MET cc_start: 0.6668 (ttt) cc_final: 0.5877 (ttt) REVERT: E 25 GLN cc_start: 0.8327 (mt0) cc_final: 0.8034 (mt0) REVERT: E 120 ARG cc_start: 0.6895 (ttm110) cc_final: 0.6634 (ttm110) REVERT: G 117 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7168 (pm20) REVERT: G 131 GLU cc_start: 0.7922 (tp30) cc_final: 0.7607 (tp30) REVERT: G 169 ASN cc_start: 0.8544 (m-40) cc_final: 0.8174 (m110) REVERT: H 11 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.6667 (mt0) REVERT: H 68 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6306 (pp30) REVERT: H 134 MET cc_start: 0.8687 (mtm) cc_final: 0.8416 (mtp) REVERT: I 42 LYS cc_start: 0.7389 (ttmm) cc_final: 0.7126 (ttpt) REVERT: I 47 ASN cc_start: 0.7681 (t0) cc_final: 0.7451 (t0) REVERT: I 49 GLN cc_start: 0.7065 (tp-100) cc_final: 0.6558 (pm20) REVERT: I 50 SER cc_start: 0.8449 (t) cc_final: 0.7984 (p) REVERT: I 143 SER cc_start: 0.7181 (p) cc_final: 0.6786 (m) REVERT: J 15 ARG cc_start: 0.7120 (mtm-85) cc_final: 0.6830 (mtm110) REVERT: J 33 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6689 (tp30) REVERT: J 115 GLU cc_start: 0.7835 (mp0) cc_final: 0.7498 (mp0) REVERT: J 150 ARG cc_start: 0.6649 (mmt90) cc_final: 0.6123 (mmt-90) REVERT: J 159 GLU cc_start: 0.7853 (tt0) cc_final: 0.7529 (tt0) REVERT: K 53 ASN cc_start: 0.7316 (m-40) cc_final: 0.6927 (m110) REVERT: K 81 LYS cc_start: 0.8431 (mttm) cc_final: 0.8128 (mttt) REVERT: K 110 TYR cc_start: 0.8486 (m-10) cc_final: 0.8126 (m-80) REVERT: K 117 GLU cc_start: 0.6948 (mp0) cc_final: 0.6628 (mp0) REVERT: K 137 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7996 (mtmm) REVERT: K 159 GLU cc_start: 0.7691 (tt0) cc_final: 0.7489 (tt0) REVERT: L 25 ASP cc_start: 0.6845 (m-30) cc_final: 0.6332 (m-30) REVERT: L 132 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.6318 (mp10) REVERT: M 49 GLN cc_start: 0.7954 (tp-100) cc_final: 0.7471 (pm20) REVERT: M 134 LYS cc_start: 0.8558 (mttm) cc_final: 0.8321 (mttp) REVERT: N 107 ASP cc_start: 0.7619 (m-30) cc_final: 0.7298 (m-30) REVERT: N 115 GLU cc_start: 0.7219 (mp0) cc_final: 0.6913 (mp0) REVERT: O 123 ASP cc_start: 0.7605 (t0) cc_final: 0.7403 (t70) REVERT: P 22 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8153 (t) REVERT: P 107 ASP cc_start: 0.7335 (m-30) cc_final: 0.7081 (m-30) REVERT: Q 148 ASP cc_start: 0.7479 (m-30) cc_final: 0.7255 (m-30) REVERT: R 1 MET cc_start: 0.7688 (ptp) cc_final: 0.6974 (ptp) REVERT: R 68 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6265 (mp-120) REVERT: R 165 ASP cc_start: 0.7568 (m-30) cc_final: 0.7257 (m-30) REVERT: S 35 ASN cc_start: 0.8613 (m-40) cc_final: 0.8358 (m-40) REVERT: S 116 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6948 (m-30) REVERT: U 77 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7553 (p0) REVERT: U 125 SER cc_start: 0.8730 (m) cc_final: 0.8423 (t) REVERT: V 117 TYR cc_start: 0.8643 (m-10) cc_final: 0.8282 (m-10) REVERT: V 152 ASP cc_start: 0.7218 (t0) cc_final: 0.6725 (t0) REVERT: W 78 GLN cc_start: 0.7825 (tp40) cc_final: 0.7551 (tp40) REVERT: W 82 ASP cc_start: 0.7697 (m-30) cc_final: 0.7397 (m-30) REVERT: X 25 ASP cc_start: 0.6582 (m-30) cc_final: 0.6318 (m-30) REVERT: X 33 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6856 (mm-30) REVERT: X 132 GLN cc_start: 0.7709 (mm110) cc_final: 0.7426 (mm-40) REVERT: Y 1 MET cc_start: 0.6819 (mtm) cc_final: 0.6368 (mtm) REVERT: Y 11 THR cc_start: 0.8065 (m) cc_final: 0.7774 (p) REVERT: Y 39 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7322 (mt0) REVERT: Y 68 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.6975 (mt0) REVERT: Y 117 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6560 (tt0) REVERT: a 65 TYR cc_start: 0.8014 (p90) cc_final: 0.7684 (p90) REVERT: a 67 THR cc_start: 0.7383 (m) cc_final: 0.7067 (p) REVERT: a 81 LYS cc_start: 0.7778 (mttp) cc_final: 0.7557 (mmtp) REVERT: a 159 GLU cc_start: 0.6863 (tt0) cc_final: 0.6551 (mt-10) REVERT: b 86 MET cc_start: 0.8291 (mmm) cc_final: 0.8044 (mmm) REVERT: b 106 GLU cc_start: 0.6597 (mm-30) cc_final: 0.5954 (mm-30) REVERT: c 11 THR cc_start: 0.8451 (t) cc_final: 0.8205 (m) REVERT: c 49 GLN cc_start: 0.7582 (tp-100) cc_final: 0.7057 (pm20) REVERT: c 53 ASN cc_start: 0.8559 (m-40) cc_final: 0.8120 (m110) REVERT: c 68 GLN cc_start: 0.7359 (mt0) cc_final: 0.7120 (mt0) REVERT: c 69 THR cc_start: 0.8130 (p) cc_final: 0.7865 (t) REVERT: d 36 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8256 (mtmp) REVERT: d 111 ASN cc_start: 0.8316 (t0) cc_final: 0.8065 (t0) REVERT: d 134 MET cc_start: 0.8791 (mtm) cc_final: 0.8298 (mtm) REVERT: d 136 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6678 (mt-10) REVERT: d 140 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6310 (m-30) REVERT: d 159 GLU cc_start: 0.7780 (tt0) cc_final: 0.7486 (tt0) REVERT: e 23 GLU cc_start: 0.7800 (mp0) cc_final: 0.6959 (mp0) REVERT: e 42 LYS cc_start: 0.7692 (ttpt) cc_final: 0.7332 (tptp) REVERT: e 116 ASP cc_start: 0.7015 (p0) cc_final: 0.6491 (p0) REVERT: e 117 GLU cc_start: 0.7036 (mp0) cc_final: 0.6743 (mp0) REVERT: e 123 ASP cc_start: 0.7532 (t0) cc_final: 0.7158 (t0) REVERT: e 162 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.8045 (p) REVERT: f 35 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7542 (m-40) REVERT: f 62 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5045 (pm20) REVERT: f 86 MET cc_start: 0.7953 (mtp) cc_final: 0.7696 (mtp) REVERT: g 23 GLU cc_start: 0.8019 (mp0) cc_final: 0.7582 (mp0) REVERT: g 47 ASN cc_start: 0.8076 (t0) cc_final: 0.7856 (t0) REVERT: g 131 GLU cc_start: 0.7138 (tp30) cc_final: 0.6780 (tp30) REVERT: h 11 GLN cc_start: 0.7636 (mt0) cc_final: 0.7360 (mt0) REVERT: h 79 MET cc_start: 0.8812 (tpp) cc_final: 0.8431 (tpp) REVERT: i 15 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7342 (mm110) REVERT: i 42 LYS cc_start: 0.7351 (tttm) cc_final: 0.7024 (tppt) REVERT: i 70 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6991 (mm110) REVERT: j 15 ARG cc_start: 0.7024 (mtp180) cc_final: 0.6602 (mtm-85) REVERT: j 62 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: j 106 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.5998 (pm20) REVERT: k 17 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: k 255 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8002 (mmm160) REVERT: k 278 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7517 (mp) REVERT: l 41 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7451 (ttt90) REVERT: m 19 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6972 (tpm170) REVERT: m 30 GLN cc_start: 0.7113 (mm-40) cc_final: 0.6884 (mm-40) REVERT: n 55 ASN cc_start: 0.8008 (m-40) cc_final: 0.7516 (t0) REVERT: n 134 LYS cc_start: 0.7496 (mttp) cc_final: 0.7078 (mttp) outliers start: 148 outliers final: 50 residues processed: 1089 average time/residue: 1.5356 time to fit residues: 2071.3927 Evaluate side-chains 993 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 915 time to evaluate : 4.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 36 LYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain Y residue 117 GLU Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain a residue 164 LEU Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain e residue 162 SER Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 35 ASN Chi-restraints excluded: chain f residue 62 GLU Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 123 ASP Chi-restraints excluded: chain i residue 15 GLN Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 62 GLU Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain k residue 278 LEU Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 31 SER Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 47 THR Chi-restraints excluded: chain m residue 71 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 607 optimal weight: 3.9990 chunk 462 optimal weight: 6.9990 chunk 319 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 412 optimal weight: 0.9990 chunk 617 optimal weight: 4.9990 chunk 653 optimal weight: 5.9990 chunk 322 optimal weight: 0.9980 chunk 584 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 33 GLN A 140 HIS C 33 GLN D 11 GLN D 111 ASN D 132 GLN E 15 GLN E 33 GLN E 39 GLN E 47 ASN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 132 GLN M 39 GLN N 23 GLN N 132 GLN O 15 GLN P 146 ASN Q 47 ASN Q 139 ASN ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN U 15 GLN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 ASN V 146 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN Z 72 ASN a 61 ASN a 169 ASN b 132 GLN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN e 139 ASN g 39 GLN h 11 GLN h 68 GLN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 270 GLN l 142 ASN ** n 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 55108 Z= 0.235 Angle : 0.631 11.918 74959 Z= 0.304 Chirality : 0.039 0.223 8198 Planarity : 0.004 0.054 9826 Dihedral : 10.368 89.836 10012 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.36 % Favored : 98.61 % Rotamer: Outliers : 2.84 % Allowed : 13.31 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.10), residues: 6771 helix: 1.79 (0.07), residues: 5157 sheet: 0.35 (0.63), residues: 49 loop : -0.18 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP l 146 HIS 0.010 0.002 HIS M 140 PHE 0.015 0.002 PHE R 98 TYR 0.021 0.002 TYR a 90 ARG 0.028 0.001 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 958 time to evaluate : 4.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7233 (m-30) cc_final: 0.6931 (m-30) REVERT: B 115 GLU cc_start: 0.8059 (mp0) cc_final: 0.7673 (mp0) REVERT: B 133 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8089 (mttm) REVERT: B 135 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7656 (ttpt) REVERT: C 13 ASP cc_start: 0.7699 (t0) cc_final: 0.7436 (t0) REVERT: C 50 SER cc_start: 0.8234 (OUTLIER) cc_final: 0.7949 (p) REVERT: D 15 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6453 (ttm-80) REVERT: D 23 GLN cc_start: 0.7771 (tt0) cc_final: 0.7537 (tt0) REVERT: D 94 THR cc_start: 0.8609 (m) cc_final: 0.8075 (p) REVERT: E 25 GLN cc_start: 0.8391 (mt0) cc_final: 0.8085 (mt0) REVERT: E 31 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8218 (mt) REVERT: G 70 GLN cc_start: 0.7385 (mp10) cc_final: 0.7177 (mm110) REVERT: G 117 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: G 131 GLU cc_start: 0.7932 (tp30) cc_final: 0.7606 (tp30) REVERT: G 169 ASN cc_start: 0.8668 (m-40) cc_final: 0.8264 (m110) REVERT: H 11 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.6746 (mt0) REVERT: H 19 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7761 (mp) REVERT: H 68 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6263 (pp30) REVERT: H 134 MET cc_start: 0.8711 (mtm) cc_final: 0.8336 (mtm) REVERT: H 149 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8238 (t) REVERT: I 42 LYS cc_start: 0.7415 (ttmm) cc_final: 0.7152 (ttpt) REVERT: I 47 ASN cc_start: 0.7630 (t0) cc_final: 0.7389 (t0) REVERT: I 49 GLN cc_start: 0.7031 (tp-100) cc_final: 0.6425 (pm20) REVERT: I 50 SER cc_start: 0.8424 (t) cc_final: 0.7935 (p) REVERT: I 143 SER cc_start: 0.7288 (p) cc_final: 0.6868 (m) REVERT: J 15 ARG cc_start: 0.7356 (mtm-85) cc_final: 0.7076 (mtm110) REVERT: J 33 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6674 (tp30) REVERT: J 79 MET cc_start: 0.8626 (tpp) cc_final: 0.8410 (tpp) REVERT: J 115 GLU cc_start: 0.7865 (mp0) cc_final: 0.7510 (mp0) REVERT: J 159 GLU cc_start: 0.7806 (tt0) cc_final: 0.7504 (tt0) REVERT: K 53 ASN cc_start: 0.7277 (m-40) cc_final: 0.6871 (m110) REVERT: K 68 GLN cc_start: 0.6727 (mp10) cc_final: 0.6357 (mm110) REVERT: K 81 LYS cc_start: 0.8428 (mttm) cc_final: 0.8068 (mttt) REVERT: K 110 TYR cc_start: 0.8504 (m-10) cc_final: 0.8175 (m-80) REVERT: K 117 GLU cc_start: 0.6941 (mp0) cc_final: 0.6653 (mp0) REVERT: K 137 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7985 (mtmm) REVERT: L 25 ASP cc_start: 0.6944 (m-30) cc_final: 0.6398 (m-30) REVERT: L 132 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.6358 (mp-120) REVERT: M 49 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7430 (pm20) REVERT: M 68 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7271 (pt0) REVERT: M 134 LYS cc_start: 0.8582 (mttm) cc_final: 0.8348 (mttp) REVERT: N 107 ASP cc_start: 0.7744 (m-30) cc_final: 0.7372 (m-30) REVERT: N 115 GLU cc_start: 0.7124 (mp0) cc_final: 0.6835 (mp0) REVERT: P 22 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8276 (t) REVERT: P 107 ASP cc_start: 0.7363 (m-30) cc_final: 0.7100 (m-30) REVERT: Q 15 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: R 1 MET cc_start: 0.7670 (ptp) cc_final: 0.6992 (ptp) REVERT: R 165 ASP cc_start: 0.7594 (m-30) cc_final: 0.7245 (m-30) REVERT: S 35 ASN cc_start: 0.8689 (m-40) cc_final: 0.8417 (m-40) REVERT: S 116 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6869 (m-30) REVERT: U 77 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7523 (p0) REVERT: U 116 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6983 (p0) REVERT: U 117 GLU cc_start: 0.7324 (mp0) cc_final: 0.6996 (mp0) REVERT: U 125 SER cc_start: 0.8736 (m) cc_final: 0.8491 (t) REVERT: V 106 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7358 (mm-30) REVERT: V 117 TYR cc_start: 0.8708 (m-10) cc_final: 0.8237 (m-10) REVERT: V 152 ASP cc_start: 0.7366 (t0) cc_final: 0.6926 (t70) REVERT: W 1 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.5597 (ttt) REVERT: W 49 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7167 (tp-100) REVERT: W 78 GLN cc_start: 0.7854 (tp40) cc_final: 0.7642 (tp40) REVERT: W 82 ASP cc_start: 0.7782 (m-30) cc_final: 0.7561 (m-30) REVERT: X 25 ASP cc_start: 0.6612 (m-30) cc_final: 0.6342 (m-30) REVERT: X 33 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6793 (mm-30) REVERT: X 132 GLN cc_start: 0.7758 (mm110) cc_final: 0.7471 (mm110) REVERT: Y 11 THR cc_start: 0.8139 (m) cc_final: 0.7808 (p) REVERT: Y 39 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7296 (mt0) REVERT: Y 68 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.6895 (mt0) REVERT: Z 1 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7817 (ttm) REVERT: Z 17 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: a 39 GLN cc_start: 0.7084 (mm-40) cc_final: 0.6493 (mm110) REVERT: a 65 TYR cc_start: 0.8102 (p90) cc_final: 0.7767 (p90) REVERT: a 67 THR cc_start: 0.7479 (m) cc_final: 0.7221 (p) REVERT: a 81 LYS cc_start: 0.7848 (mttp) cc_final: 0.7603 (mmtp) REVERT: a 86 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8313 (tmm160) REVERT: a 109 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6900 (tm-30) REVERT: a 159 GLU cc_start: 0.6853 (tt0) cc_final: 0.6562 (mt-10) REVERT: b 11 GLN cc_start: 0.7787 (mt0) cc_final: 0.7539 (mm-40) REVERT: b 86 MET cc_start: 0.8214 (mmm) cc_final: 0.7889 (mtp) REVERT: b 106 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6023 (mm-30) REVERT: c 11 THR cc_start: 0.8413 (t) cc_final: 0.8171 (m) REVERT: c 49 GLN cc_start: 0.7616 (tp-100) cc_final: 0.7053 (pm20) REVERT: c 53 ASN cc_start: 0.8501 (m-40) cc_final: 0.8109 (m110) REVERT: c 68 GLN cc_start: 0.7363 (mt0) cc_final: 0.7111 (mt0) REVERT: c 69 THR cc_start: 0.8210 (p) cc_final: 0.7956 (t) REVERT: d 134 MET cc_start: 0.8812 (mtm) cc_final: 0.8427 (mtm) REVERT: d 136 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6669 (mt-10) REVERT: d 140 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6327 (m-30) REVERT: d 159 GLU cc_start: 0.7833 (tt0) cc_final: 0.7524 (tt0) REVERT: e 23 GLU cc_start: 0.7802 (mp0) cc_final: 0.6983 (mp0) REVERT: e 42 LYS cc_start: 0.7778 (ttpt) cc_final: 0.7382 (tptp) REVERT: e 116 ASP cc_start: 0.7280 (p0) cc_final: 0.6751 (p0) REVERT: e 123 ASP cc_start: 0.7522 (t0) cc_final: 0.7167 (t0) REVERT: f 62 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.5232 (pm20) REVERT: f 86 MET cc_start: 0.7961 (mtp) cc_final: 0.7514 (mtp) REVERT: g 23 GLU cc_start: 0.8077 (mp0) cc_final: 0.7579 (mp0) REVERT: g 117 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: g 131 GLU cc_start: 0.7167 (tp30) cc_final: 0.6767 (tp30) REVERT: h 79 MET cc_start: 0.8849 (tpp) cc_final: 0.8521 (tpp) REVERT: i 15 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7305 (mm110) REVERT: i 42 LYS cc_start: 0.7316 (tttm) cc_final: 0.7080 (tppt) REVERT: i 70 GLN cc_start: 0.7185 (mm-40) cc_final: 0.6946 (mm110) REVERT: i 111 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8375 (tt) REVERT: j 15 ARG cc_start: 0.7308 (mtp180) cc_final: 0.7002 (mtm-85) REVERT: j 36 LYS cc_start: 0.8675 (mttp) cc_final: 0.8393 (mtmp) REVERT: j 62 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7046 (tt0) REVERT: j 106 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.5779 (pm20) REVERT: k 17 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: k 255 ARG cc_start: 0.8532 (mmm-85) cc_final: 0.7958 (mmm160) REVERT: k 278 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7371 (mp) REVERT: l 41 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7508 (ttt-90) REVERT: m 19 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7074 (tpm170) REVERT: m 30 GLN cc_start: 0.7159 (mm-40) cc_final: 0.6919 (mm-40) REVERT: n 55 ASN cc_start: 0.8042 (m-40) cc_final: 0.7560 (t0) REVERT: n 121 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6694 (pt0) REVERT: n 134 LYS cc_start: 0.7620 (mttp) cc_final: 0.7188 (mttp) REVERT: n 156 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7306 (m-30) outliers start: 150 outliers final: 54 residues processed: 1028 average time/residue: 1.5804 time to fit residues: 2001.3350 Evaluate side-chains 984 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 891 time to evaluate : 4.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 137 LYS Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain a residue 86 ARG Chi-restraints excluded: chain a residue 164 LEU Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain f residue 62 GLU Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 62 LYS Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain i residue 15 GLN Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain i residue 111 LEU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 62 GLU Chi-restraints excluded: chain j residue 106 GLU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain k residue 278 LEU Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 31 SER Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 47 THR Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain n residue 44 ASN Chi-restraints excluded: chain n residue 121 GLU Chi-restraints excluded: chain n residue 156 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 544 optimal weight: 0.6980 chunk 370 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 486 optimal weight: 0.8980 chunk 269 optimal weight: 0.9980 chunk 557 optimal weight: 0.5980 chunk 451 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 333 optimal weight: 4.9990 chunk 586 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 33 GLN B 11 GLN D 11 GLN D 111 ASN D 132 GLN E 15 GLN E 33 GLN E 47 ASN F 23 GLN F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 132 GLN O 15 GLN P 132 GLN P 146 ASN Q 47 ASN Q 139 ASN ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 146 ASN ** W 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN Z 35 ASN ** Z 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN b 132 GLN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 GLN e 139 ASN g 39 GLN g 57 GLN g 61 ASN h 11 GLN h 68 GLN i 139 ASN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 55108 Z= 0.197 Angle : 0.601 12.554 74959 Z= 0.290 Chirality : 0.037 0.227 8198 Planarity : 0.004 0.054 9826 Dihedral : 10.523 173.233 10012 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.23 % Favored : 98.74 % Rotamer: Outliers : 3.08 % Allowed : 13.82 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.10), residues: 6771 helix: 1.79 (0.07), residues: 5265 sheet: 0.26 (0.63), residues: 49 loop : -0.40 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP l 146 HIS 0.008 0.002 HIS M 140 PHE 0.014 0.001 PHE R 98 TYR 0.026 0.001 TYR L 74 ARG 0.028 0.000 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 946 time to evaluate : 4.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7295 (m-30) cc_final: 0.7011 (m-30) REVERT: B 11 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: B 115 GLU cc_start: 0.8061 (mp0) cc_final: 0.7678 (mp0) REVERT: B 136 GLU cc_start: 0.7387 (pp20) cc_final: 0.7169 (pp20) REVERT: C 13 ASP cc_start: 0.7627 (t0) cc_final: 0.7322 (t0) REVERT: C 50 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7950 (p) REVERT: C 70 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6151 (tp40) REVERT: C 131 GLU cc_start: 0.7936 (tp30) cc_final: 0.7727 (tp30) REVERT: D 15 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6532 (ttm-80) REVERT: D 23 GLN cc_start: 0.7800 (tt0) cc_final: 0.7499 (tt0) REVERT: D 94 THR cc_start: 0.8605 (m) cc_final: 0.8093 (p) REVERT: E 25 GLN cc_start: 0.8380 (mt0) cc_final: 0.8082 (mt0) REVERT: E 31 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8245 (mt) REVERT: G 70 GLN cc_start: 0.7450 (mp10) cc_final: 0.7210 (mm110) REVERT: G 117 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7222 (pm20) REVERT: G 131 GLU cc_start: 0.7923 (tp30) cc_final: 0.7571 (tp30) REVERT: G 169 ASN cc_start: 0.8681 (m-40) cc_final: 0.8317 (m110) REVERT: H 11 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.6671 (mt0) REVERT: H 19 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7754 (mp) REVERT: H 134 MET cc_start: 0.8652 (mtm) cc_final: 0.8239 (mtm) REVERT: I 2 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6708 (tttp) REVERT: I 47 ASN cc_start: 0.7600 (t0) cc_final: 0.7379 (t0) REVERT: I 49 GLN cc_start: 0.6955 (tp-100) cc_final: 0.6418 (pm20) REVERT: I 50 SER cc_start: 0.8445 (t) cc_final: 0.7941 (p) REVERT: I 143 SER cc_start: 0.7310 (p) cc_final: 0.6867 (m) REVERT: J 15 ARG cc_start: 0.7377 (mtm-85) cc_final: 0.7123 (mtm110) REVERT: J 33 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6706 (tp30) REVERT: J 36 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8035 (mttm) REVERT: J 79 MET cc_start: 0.8670 (tpp) cc_final: 0.8446 (tpp) REVERT: J 115 GLU cc_start: 0.7862 (mp0) cc_final: 0.7524 (mp0) REVERT: J 150 ARG cc_start: 0.6640 (mmt90) cc_final: 0.6217 (mmt-90) REVERT: J 159 GLU cc_start: 0.7802 (tt0) cc_final: 0.7503 (tt0) REVERT: K 68 GLN cc_start: 0.6725 (mp10) cc_final: 0.6304 (mm110) REVERT: K 81 LYS cc_start: 0.8431 (mttm) cc_final: 0.8197 (mttt) REVERT: K 110 TYR cc_start: 0.8516 (m-10) cc_final: 0.8265 (m-80) REVERT: K 117 GLU cc_start: 0.6813 (mp0) cc_final: 0.6548 (mp0) REVERT: K 137 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7947 (mtmm) REVERT: L 25 ASP cc_start: 0.6923 (m-30) cc_final: 0.6384 (m-30) REVERT: M 49 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7445 (pm20) REVERT: M 68 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7174 (pt0) REVERT: M 134 LYS cc_start: 0.8644 (mttm) cc_final: 0.8423 (mttp) REVERT: N 107 ASP cc_start: 0.7750 (m-30) cc_final: 0.7380 (m-30) REVERT: N 115 GLU cc_start: 0.7108 (mp0) cc_final: 0.6818 (mp0) REVERT: P 22 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8290 (t) REVERT: P 94 THR cc_start: 0.9012 (m) cc_final: 0.8619 (p) REVERT: P 107 ASP cc_start: 0.7367 (m-30) cc_final: 0.7108 (m-30) REVERT: Q 15 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8050 (mt0) REVERT: R 1 MET cc_start: 0.7696 (ptp) cc_final: 0.7059 (ptp) REVERT: S 35 ASN cc_start: 0.8680 (m-40) cc_final: 0.8330 (m110) REVERT: S 116 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6836 (m-30) REVERT: S 117 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: T 8 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8239 (m) REVERT: U 77 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7598 (p0) REVERT: U 116 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6899 (p0) REVERT: U 125 SER cc_start: 0.8748 (m) cc_final: 0.8544 (t) REVERT: V 106 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7381 (mm-30) REVERT: V 117 TYR cc_start: 0.8727 (m-10) cc_final: 0.8231 (m-10) REVERT: V 152 ASP cc_start: 0.7394 (t0) cc_final: 0.6953 (t70) REVERT: W 1 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.5574 (ttt) REVERT: W 49 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.7114 (tp-100) REVERT: W 78 GLN cc_start: 0.7890 (tp40) cc_final: 0.7653 (tp40) REVERT: W 82 ASP cc_start: 0.7784 (m-30) cc_final: 0.7553 (m-30) REVERT: X 25 ASP cc_start: 0.6667 (m-30) cc_final: 0.6401 (m-30) REVERT: X 77 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7693 (ptp90) REVERT: X 132 GLN cc_start: 0.7723 (mm110) cc_final: 0.7454 (mm-40) REVERT: Y 11 THR cc_start: 0.8140 (m) cc_final: 0.7808 (p) REVERT: Y 39 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7353 (mt0) REVERT: Y 68 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.6850 (mt0) REVERT: Z 1 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7836 (ptp) REVERT: Z 17 GLU cc_start: 0.7143 (pm20) cc_final: 0.6859 (tm-30) REVERT: a 39 GLN cc_start: 0.7118 (mm-40) cc_final: 0.6523 (mm110) REVERT: a 65 TYR cc_start: 0.8099 (p90) cc_final: 0.7758 (p90) REVERT: a 109 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6885 (tm-30) REVERT: a 159 GLU cc_start: 0.6802 (tt0) cc_final: 0.6512 (mt-10) REVERT: b 11 GLN cc_start: 0.7763 (mt0) cc_final: 0.7440 (mm-40) REVERT: b 86 MET cc_start: 0.8162 (mmm) cc_final: 0.7918 (mtp) REVERT: b 106 GLU cc_start: 0.6642 (mm-30) cc_final: 0.6010 (mm-30) REVERT: c 11 THR cc_start: 0.8444 (t) cc_final: 0.8213 (m) REVERT: c 49 GLN cc_start: 0.7610 (tp-100) cc_final: 0.7071 (pm20) REVERT: c 53 ASN cc_start: 0.8495 (m-40) cc_final: 0.8111 (m110) REVERT: c 68 GLN cc_start: 0.7271 (mt0) cc_final: 0.7025 (mt0) REVERT: c 69 THR cc_start: 0.8238 (p) cc_final: 0.7992 (t) REVERT: d 133 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8373 (mttp) REVERT: d 135 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8134 (ttmt) REVERT: d 136 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6682 (mt-10) REVERT: d 140 ASP cc_start: 0.6712 (OUTLIER) cc_final: 0.6326 (m-30) REVERT: e 23 GLU cc_start: 0.7787 (mp0) cc_final: 0.6947 (mp0) REVERT: e 42 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7395 (tptp) REVERT: e 116 ASP cc_start: 0.7338 (p0) cc_final: 0.7099 (p0) REVERT: e 123 ASP cc_start: 0.7508 (t0) cc_final: 0.7151 (t0) REVERT: f 106 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6549 (mm-30) REVERT: g 23 GLU cc_start: 0.8056 (mp0) cc_final: 0.7600 (mp0) REVERT: g 117 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: g 131 GLU cc_start: 0.7214 (tp30) cc_final: 0.6854 (tp30) REVERT: g 147 ARG cc_start: 0.7405 (ttp-170) cc_final: 0.7100 (ttp-170) REVERT: h 79 MET cc_start: 0.8889 (tpp) cc_final: 0.8546 (tpp) REVERT: i 1 MET cc_start: 0.6785 (mmt) cc_final: 0.6131 (mmt) REVERT: i 15 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7284 (mm110) REVERT: i 42 LYS cc_start: 0.7296 (tttm) cc_final: 0.7079 (tppt) REVERT: i 70 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6980 (mm110) REVERT: j 15 ARG cc_start: 0.7230 (mtp180) cc_final: 0.7029 (mtm-85) REVERT: j 36 LYS cc_start: 0.8681 (mttp) cc_final: 0.8436 (mtmp) REVERT: j 62 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7071 (tt0) REVERT: k 17 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: k 19 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6914 (mmt90) REVERT: k 255 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8258 (mmm-85) REVERT: l 41 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7503 (ttt-90) REVERT: m 19 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6999 (tpm170) REVERT: m 30 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6908 (mm-40) REVERT: m 31 SER cc_start: 0.7190 (OUTLIER) cc_final: 0.6869 (p) REVERT: n 55 ASN cc_start: 0.8039 (m-40) cc_final: 0.7584 (t0) REVERT: n 121 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6687 (pt0) REVERT: n 134 LYS cc_start: 0.7593 (mttp) cc_final: 0.7160 (mttp) REVERT: n 156 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7273 (m-30) outliers start: 163 outliers final: 49 residues processed: 1021 average time/residue: 1.5776 time to fit residues: 1981.5363 Evaluate side-chains 996 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 908 time to evaluate : 4.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 36 LYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 17 GLU Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 106 GLU Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain d residue 133 LYS Chi-restraints excluded: chain d residue 135 LYS Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain e residue 162 SER Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain i residue 15 GLN Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 62 GLU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 19 ARG Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 31 SER Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 47 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 44 ASN Chi-restraints excluded: chain n residue 121 GLU Chi-restraints excluded: chain n residue 156 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 219 optimal weight: 0.9990 chunk 588 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 383 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 654 optimal weight: 3.9990 chunk 542 optimal weight: 9.9990 chunk 302 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 343 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 11 GLN D 11 GLN D 111 ASN D 132 GLN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 53 ASN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 132 GLN L 146 ASN O 15 GLN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 146 ASN Q 47 ASN Q 139 ASN R 68 GLN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 ASN V 146 ASN W 140 HIS ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 140 HIS ** Z 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN a 169 ASN b 132 GLN c 140 HIS e 15 GLN e 139 ASN g 39 GLN g 57 GLN g 61 ASN h 68 GLN i 139 ASN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 55108 Z= 0.225 Angle : 0.620 13.358 74959 Z= 0.299 Chirality : 0.038 0.258 8198 Planarity : 0.004 0.143 9826 Dihedral : 10.413 89.528 10012 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.39 % Favored : 98.58 % Rotamer: Outliers : 2.95 % Allowed : 14.46 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.10), residues: 6771 helix: 1.80 (0.07), residues: 5301 sheet: 0.31 (0.63), residues: 48 loop : -0.40 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP l 146 HIS 0.010 0.002 HIS M 140 PHE 0.015 0.002 PHE R 98 TYR 0.018 0.001 TYR a 90 ARG 0.036 0.001 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 957 time to evaluate : 4.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7281 (m-30) cc_final: 0.6988 (m-30) REVERT: B 115 GLU cc_start: 0.8061 (mp0) cc_final: 0.7701 (mp0) REVERT: B 146 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.7010 (m-40) REVERT: C 13 ASP cc_start: 0.7572 (t0) cc_final: 0.7256 (t0) REVERT: C 50 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7955 (p) REVERT: D 15 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6588 (ttm-80) REVERT: D 23 GLN cc_start: 0.7856 (tt0) cc_final: 0.7588 (tt0) REVERT: D 94 THR cc_start: 0.8605 (m) cc_final: 0.8095 (p) REVERT: E 15 GLN cc_start: 0.7620 (mt0) cc_final: 0.7325 (mt0) REVERT: E 25 GLN cc_start: 0.8382 (mt0) cc_final: 0.8088 (mt0) REVERT: E 31 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8251 (mt) REVERT: E 120 ARG cc_start: 0.7321 (mtm-85) cc_final: 0.7049 (ttm110) REVERT: F 159 GLU cc_start: 0.7514 (tt0) cc_final: 0.7192 (tt0) REVERT: G 117 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7221 (pm20) REVERT: G 131 GLU cc_start: 0.7966 (tp30) cc_final: 0.7622 (tp30) REVERT: G 169 ASN cc_start: 0.8656 (m-40) cc_final: 0.8307 (m110) REVERT: H 11 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.6699 (mt0) REVERT: H 19 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7710 (mp) REVERT: H 134 MET cc_start: 0.8691 (mtm) cc_final: 0.8278 (mtm) REVERT: I 2 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6708 (tttp) REVERT: I 47 ASN cc_start: 0.7623 (t0) cc_final: 0.7390 (t0) REVERT: I 49 GLN cc_start: 0.6987 (tp-100) cc_final: 0.6413 (pm20) REVERT: I 50 SER cc_start: 0.8419 (t) cc_final: 0.7927 (p) REVERT: I 143 SER cc_start: 0.7333 (p) cc_final: 0.6940 (m) REVERT: J 15 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7184 (mtm110) REVERT: J 33 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6684 (tp30) REVERT: J 36 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8039 (mttm) REVERT: J 79 MET cc_start: 0.8666 (tpp) cc_final: 0.8396 (tpp) REVERT: J 115 GLU cc_start: 0.7876 (mp0) cc_final: 0.7537 (mp0) REVERT: J 150 ARG cc_start: 0.6734 (mmt90) cc_final: 0.6249 (mmt-90) REVERT: J 159 GLU cc_start: 0.7802 (tt0) cc_final: 0.7526 (tt0) REVERT: K 67 THR cc_start: 0.8347 (m) cc_final: 0.7924 (p) REVERT: K 68 GLN cc_start: 0.6803 (mp10) cc_final: 0.6408 (mm110) REVERT: K 81 LYS cc_start: 0.8436 (mttm) cc_final: 0.8197 (mttt) REVERT: K 109 GLU cc_start: 0.6972 (mp0) cc_final: 0.6015 (mp0) REVERT: K 110 TYR cc_start: 0.8627 (m-10) cc_final: 0.8359 (m-80) REVERT: K 117 GLU cc_start: 0.6814 (mp0) cc_final: 0.6571 (mp0) REVERT: K 118 ILE cc_start: 0.8478 (mm) cc_final: 0.8211 (mt) REVERT: K 137 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7956 (mtmm) REVERT: L 25 ASP cc_start: 0.6981 (m-30) cc_final: 0.6454 (m-30) REVERT: L 136 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6712 (mm-30) REVERT: M 49 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7425 (pm20) REVERT: M 68 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7177 (pt0) REVERT: M 134 LYS cc_start: 0.8605 (mttm) cc_final: 0.8381 (mttp) REVERT: N 107 ASP cc_start: 0.7803 (m-30) cc_final: 0.7438 (m-30) REVERT: N 115 GLU cc_start: 0.7097 (mp0) cc_final: 0.6814 (mp0) REVERT: P 22 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8310 (t) REVERT: P 94 THR cc_start: 0.9028 (m) cc_final: 0.8619 (p) REVERT: P 107 ASP cc_start: 0.7329 (m-30) cc_final: 0.7055 (m-30) REVERT: Q 15 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8060 (mt0) REVERT: R 1 MET cc_start: 0.7792 (ptp) cc_final: 0.7117 (ptp) REVERT: R 68 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6145 (mp-120) REVERT: S 35 ASN cc_start: 0.8764 (m-40) cc_final: 0.8515 (m-40) REVERT: S 116 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6774 (m-30) REVERT: S 117 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: T 8 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8316 (m) REVERT: U 77 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7647 (p0) REVERT: U 116 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6877 (p0) REVERT: U 117 GLU cc_start: 0.7320 (mp0) cc_final: 0.6811 (mp0) REVERT: V 106 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7291 (mm-30) REVERT: V 152 ASP cc_start: 0.7424 (t0) cc_final: 0.6978 (t70) REVERT: W 1 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.5664 (ttt) REVERT: W 49 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7118 (tp-100) REVERT: X 25 ASP cc_start: 0.6716 (m-30) cc_final: 0.6454 (m-30) REVERT: X 77 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7654 (ptp90) REVERT: X 132 GLN cc_start: 0.7739 (mm110) cc_final: 0.6928 (mm-40) REVERT: Y 11 THR cc_start: 0.8149 (m) cc_final: 0.7823 (p) REVERT: Y 39 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7346 (mt0) REVERT: Y 68 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.6854 (mt0) REVERT: Z 17 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6828 (tm-30) REVERT: a 65 TYR cc_start: 0.8121 (p90) cc_final: 0.7775 (p90) REVERT: a 109 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6950 (tm-30) REVERT: a 159 GLU cc_start: 0.6837 (tt0) cc_final: 0.6522 (mt-10) REVERT: b 11 GLN cc_start: 0.7752 (mt0) cc_final: 0.7450 (mm-40) REVERT: b 22 SER cc_start: 0.7923 (p) cc_final: 0.7671 (t) REVERT: b 106 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6076 (mm-30) REVERT: c 49 GLN cc_start: 0.7639 (tp-100) cc_final: 0.7059 (pm20) REVERT: c 53 ASN cc_start: 0.8343 (m-40) cc_final: 0.7945 (m110) REVERT: c 68 GLN cc_start: 0.7262 (mt0) cc_final: 0.7004 (mt0) REVERT: c 69 THR cc_start: 0.8145 (p) cc_final: 0.7915 (t) REVERT: c 159 GLU cc_start: 0.7846 (tt0) cc_final: 0.7609 (tt0) REVERT: d 136 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6724 (mt-10) REVERT: d 140 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.6350 (m-30) REVERT: e 23 GLU cc_start: 0.7788 (mp0) cc_final: 0.6940 (mp0) REVERT: e 42 LYS cc_start: 0.7844 (ttpt) cc_final: 0.7421 (tptp) REVERT: e 78 GLN cc_start: 0.7259 (tp40) cc_final: 0.6930 (tp-100) REVERT: e 123 ASP cc_start: 0.7515 (t0) cc_final: 0.7153 (t0) REVERT: f 86 MET cc_start: 0.8291 (mtp) cc_final: 0.8075 (mtp) REVERT: g 23 GLU cc_start: 0.8102 (mp0) cc_final: 0.7641 (mp0) REVERT: g 117 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: g 131 GLU cc_start: 0.7261 (tp30) cc_final: 0.6886 (tp30) REVERT: g 147 ARG cc_start: 0.7424 (ttp-170) cc_final: 0.7132 (ttp-170) REVERT: h 79 MET cc_start: 0.8896 (tpp) cc_final: 0.8545 (tpp) REVERT: i 42 LYS cc_start: 0.7393 (tttm) cc_final: 0.7151 (tptt) REVERT: i 70 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6805 (mm110) REVERT: i 111 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8351 (tt) REVERT: j 15 ARG cc_start: 0.7276 (mtp180) cc_final: 0.6931 (mtm-85) REVERT: j 25 ASP cc_start: 0.6486 (m-30) cc_final: 0.6219 (m-30) REVERT: j 36 LYS cc_start: 0.8659 (mttp) cc_final: 0.8424 (mtmp) REVERT: j 62 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: j 106 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6621 (mm-30) REVERT: k 237 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.7045 (ttpt) REVERT: k 255 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7845 (mmm160) REVERT: l 41 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7534 (ttt-90) REVERT: l 206 SER cc_start: 0.7675 (OUTLIER) cc_final: 0.7300 (t) REVERT: m 19 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6920 (tpm170) REVERT: m 25 VAL cc_start: 0.8399 (m) cc_final: 0.8143 (t) REVERT: n 55 ASN cc_start: 0.8044 (m-40) cc_final: 0.7574 (t0) REVERT: n 134 LYS cc_start: 0.7578 (mttp) cc_final: 0.7175 (mttp) REVERT: n 156 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7327 (m-30) outliers start: 156 outliers final: 62 residues processed: 1029 average time/residue: 1.5736 time to fit residues: 1998.5765 Evaluate side-chains 989 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 892 time to evaluate : 4.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 36 LYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 145 ASP Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain S residue 137 LYS Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain e residue 162 SER Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 62 LYS Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain h residue 111 ASN Chi-restraints excluded: chain i residue 111 LEU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 62 GLU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 47 ASP Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain k residue 237 LYS Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain l residue 245 GLU Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 31 SER Chi-restraints excluded: chain m residue 33 MET Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 47 THR Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain n residue 44 ASN Chi-restraints excluded: chain n residue 156 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 630 optimal weight: 4.9990 chunk 73 optimal weight: 0.1980 chunk 372 optimal weight: 3.9990 chunk 477 optimal weight: 0.7980 chunk 370 optimal weight: 2.9990 chunk 550 optimal weight: 5.9990 chunk 365 optimal weight: 0.5980 chunk 651 optimal weight: 8.9990 chunk 407 optimal weight: 0.6980 chunk 397 optimal weight: 1.9990 chunk 300 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN D 11 GLN D 111 ASN D 132 GLN E 33 GLN E 169 ASN F 23 GLN F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 53 ASN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 146 ASN M 78 GLN N 132 GLN O 15 GLN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 146 ASN Q 47 ASN Q 139 ASN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN U 15 GLN U 47 ASN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 146 ASN ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN ** Z 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN a 68 GLN e 15 GLN e 139 ASN g 39 GLN g 57 GLN g 61 ASN h 68 GLN i 139 ASN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 55108 Z= 0.181 Angle : 0.591 13.181 74959 Z= 0.286 Chirality : 0.037 0.268 8198 Planarity : 0.005 0.235 9826 Dihedral : 10.398 89.802 10012 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.30 % Favored : 98.69 % Rotamer: Outliers : 2.40 % Allowed : 15.50 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.10), residues: 6771 helix: 1.94 (0.07), residues: 5266 sheet: 0.14 (0.62), residues: 49 loop : -0.35 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP l 146 HIS 0.007 0.002 HIS C 140 PHE 0.013 0.001 PHE I 28 TYR 0.025 0.001 TYR L 74 ARG 0.036 0.000 ARG m 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 954 time to evaluate : 4.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7308 (m-30) cc_final: 0.7012 (m-30) REVERT: B 11 GLN cc_start: 0.7846 (mt0) cc_final: 0.7512 (mt0) REVERT: B 115 GLU cc_start: 0.8044 (mp0) cc_final: 0.7680 (mp0) REVERT: B 146 ASN cc_start: 0.7468 (OUTLIER) cc_final: 0.6978 (m-40) REVERT: C 13 ASP cc_start: 0.7523 (t0) cc_final: 0.7223 (t0) REVERT: C 50 SER cc_start: 0.8172 (p) cc_final: 0.7925 (p) REVERT: C 131 GLU cc_start: 0.7973 (tp30) cc_final: 0.7711 (tp30) REVERT: D 15 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6604 (ttm-80) REVERT: D 23 GLN cc_start: 0.7798 (tt0) cc_final: 0.7555 (tt0) REVERT: D 94 THR cc_start: 0.8604 (m) cc_final: 0.8099 (p) REVERT: E 15 GLN cc_start: 0.7565 (mt0) cc_final: 0.7284 (mt0) REVERT: E 25 GLN cc_start: 0.8356 (mt0) cc_final: 0.8089 (mt0) REVERT: E 31 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8246 (mt) REVERT: F 159 GLU cc_start: 0.7491 (tt0) cc_final: 0.7190 (tt0) REVERT: G 117 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: G 131 GLU cc_start: 0.7948 (tp30) cc_final: 0.7586 (tp30) REVERT: G 169 ASN cc_start: 0.8642 (m-40) cc_final: 0.8301 (m110) REVERT: H 11 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.6647 (mt0) REVERT: H 19 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7696 (mp) REVERT: H 134 MET cc_start: 0.8639 (mtm) cc_final: 0.8168 (mtm) REVERT: I 2 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6574 (tmtp) REVERT: I 49 GLN cc_start: 0.6979 (tp-100) cc_final: 0.6398 (pm20) REVERT: I 50 SER cc_start: 0.8412 (t) cc_final: 0.7908 (p) REVERT: I 143 SER cc_start: 0.7363 (p) cc_final: 0.6917 (m) REVERT: J 15 ARG cc_start: 0.7390 (mtm-85) cc_final: 0.7134 (mtm110) REVERT: J 33 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6694 (tp30) REVERT: J 36 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8024 (mttm) REVERT: J 79 MET cc_start: 0.8677 (tpp) cc_final: 0.8442 (tpp) REVERT: J 115 GLU cc_start: 0.7848 (mp0) cc_final: 0.7507 (mp0) REVERT: J 150 ARG cc_start: 0.6698 (mmt90) cc_final: 0.6222 (mmt-90) REVERT: J 159 GLU cc_start: 0.7784 (tt0) cc_final: 0.7524 (tt0) REVERT: K 23 GLU cc_start: 0.8144 (mp0) cc_final: 0.7847 (mp0) REVERT: K 67 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.7970 (p) REVERT: K 68 GLN cc_start: 0.6846 (mp10) cc_final: 0.6477 (mm110) REVERT: K 81 LYS cc_start: 0.8421 (mttm) cc_final: 0.8152 (mttp) REVERT: K 110 TYR cc_start: 0.8578 (m-10) cc_final: 0.8310 (m-80) REVERT: K 117 GLU cc_start: 0.6858 (mp0) cc_final: 0.6620 (mp0) REVERT: K 118 ILE cc_start: 0.8487 (mm) cc_final: 0.8261 (mt) REVERT: K 137 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7959 (mtmm) REVERT: L 25 ASP cc_start: 0.6965 (m-30) cc_final: 0.6449 (m-30) REVERT: M 49 GLN cc_start: 0.7936 (tp-100) cc_final: 0.7434 (pm20) REVERT: M 68 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7160 (pt0) REVERT: M 134 LYS cc_start: 0.8656 (mttm) cc_final: 0.8449 (mttp) REVERT: N 107 ASP cc_start: 0.7787 (m-30) cc_final: 0.7410 (m-30) REVERT: N 115 GLU cc_start: 0.7073 (mp0) cc_final: 0.6798 (mp0) REVERT: P 22 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8313 (t) REVERT: P 94 THR cc_start: 0.9007 (m) cc_final: 0.8568 (p) REVERT: P 107 ASP cc_start: 0.7308 (m-30) cc_final: 0.7042 (m-30) REVERT: R 1 MET cc_start: 0.7682 (ptp) cc_final: 0.7126 (ptp) REVERT: S 35 ASN cc_start: 0.8737 (m-40) cc_final: 0.8426 (m110) REVERT: S 116 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6819 (m-30) REVERT: S 117 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: T 8 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8252 (m) REVERT: U 77 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7644 (p0) REVERT: U 116 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6792 (p0) REVERT: U 117 GLU cc_start: 0.7271 (mp0) cc_final: 0.6194 (mp0) REVERT: V 106 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7306 (mm-30) REVERT: V 152 ASP cc_start: 0.7439 (t0) cc_final: 0.6993 (t70) REVERT: W 1 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.5498 (ttt) REVERT: X 25 ASP cc_start: 0.6736 (m-30) cc_final: 0.6471 (m-30) REVERT: X 77 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7697 (ptp90) REVERT: X 132 GLN cc_start: 0.7743 (mm110) cc_final: 0.6923 (mm-40) REVERT: Y 11 THR cc_start: 0.8135 (m) cc_final: 0.7621 (p) REVERT: Y 39 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7280 (mt0) REVERT: Y 68 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.6836 (mt0) REVERT: a 39 GLN cc_start: 0.7022 (mm-40) cc_final: 0.6523 (mm110) REVERT: a 65 TYR cc_start: 0.8122 (p90) cc_final: 0.7758 (p90) REVERT: a 68 GLN cc_start: 0.7178 (mt0) cc_final: 0.6713 (pt0) REVERT: a 159 GLU cc_start: 0.6803 (tt0) cc_final: 0.6497 (mt-10) REVERT: b 11 GLN cc_start: 0.7715 (mt0) cc_final: 0.7433 (mm-40) REVERT: b 106 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6078 (mm-30) REVERT: c 49 GLN cc_start: 0.7669 (tp-100) cc_final: 0.7104 (pm20) REVERT: c 53 ASN cc_start: 0.8467 (m-40) cc_final: 0.8073 (m110) REVERT: c 68 GLN cc_start: 0.7246 (mt0) cc_final: 0.6971 (mt0) REVERT: c 69 THR cc_start: 0.8131 (p) cc_final: 0.7907 (t) REVERT: d 136 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6721 (mt-10) REVERT: d 140 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.6330 (m-30) REVERT: e 23 GLU cc_start: 0.7770 (mp0) cc_final: 0.6924 (mp0) REVERT: e 42 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7429 (tptp) REVERT: e 78 GLN cc_start: 0.7267 (tp40) cc_final: 0.6953 (tp-100) REVERT: e 116 ASP cc_start: 0.7211 (p0) cc_final: 0.6870 (m-30) REVERT: e 123 ASP cc_start: 0.7520 (t0) cc_final: 0.7149 (t0) REVERT: f 86 MET cc_start: 0.8188 (mtp) cc_final: 0.7892 (mtp) REVERT: g 23 GLU cc_start: 0.8098 (mp0) cc_final: 0.7836 (mp0) REVERT: g 117 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6920 (mt-10) REVERT: g 131 GLU cc_start: 0.7250 (tp30) cc_final: 0.6929 (tp30) REVERT: g 147 ARG cc_start: 0.7426 (ttp-170) cc_final: 0.7106 (ttp-170) REVERT: h 79 MET cc_start: 0.8859 (tpp) cc_final: 0.8547 (tpp) REVERT: h 87 GLU cc_start: 0.7551 (tt0) cc_final: 0.7071 (tt0) REVERT: i 70 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6871 (mm110) REVERT: j 15 ARG cc_start: 0.7289 (mtp180) cc_final: 0.7027 (mtm110) REVERT: j 25 ASP cc_start: 0.6478 (m-30) cc_final: 0.6192 (m-30) REVERT: j 133 LYS cc_start: 0.8260 (mttp) cc_final: 0.8046 (mttp) REVERT: j 135 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7528 (ttmt) REVERT: k 19 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6849 (mmt90) REVERT: k 255 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.7842 (mmm160) REVERT: l 41 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7544 (ttt-90) REVERT: l 206 SER cc_start: 0.7653 (OUTLIER) cc_final: 0.7304 (t) REVERT: m 19 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6954 (tpm170) REVERT: m 25 VAL cc_start: 0.8405 (m) cc_final: 0.8112 (t) REVERT: m 31 SER cc_start: 0.7208 (OUTLIER) cc_final: 0.6980 (p) REVERT: n 55 ASN cc_start: 0.8020 (m-40) cc_final: 0.7581 (t0) REVERT: n 134 LYS cc_start: 0.7568 (mttp) cc_final: 0.7161 (mttp) REVERT: n 156 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7310 (m-30) outliers start: 127 outliers final: 52 residues processed: 1021 average time/residue: 1.5138 time to fit residues: 1905.7288 Evaluate side-chains 968 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 885 time to evaluate : 4.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 36 LYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain S residue 137 LYS Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain e residue 134 LYS Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 62 LYS Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 135 LYS Chi-restraints excluded: chain k residue 19 ARG Chi-restraints excluded: chain k residue 47 ASP Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 31 SER Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain n residue 44 ASN Chi-restraints excluded: chain n residue 156 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 403 optimal weight: 0.6980 chunk 260 optimal weight: 2.9990 chunk 389 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 414 optimal weight: 4.9990 chunk 443 optimal weight: 2.9990 chunk 322 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 512 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 11 GLN D 11 GLN D 111 ASN D 132 GLN E 33 GLN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 53 ASN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 132 GLN L 146 ASN M 39 GLN O 15 GLN O 68 GLN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 146 ASN Q 47 ASN Q 139 ASN R 68 GLN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 139 ASN V 111 ASN V 146 ASN ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN a 169 ASN b 132 GLN d 132 GLN e 15 GLN e 139 ASN g 57 GLN g 61 ASN h 68 GLN i 139 ASN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 259 GLN ** n 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 55108 Z= 0.323 Angle : 0.683 12.730 74959 Z= 0.332 Chirality : 0.042 0.302 8198 Planarity : 0.006 0.393 9826 Dihedral : 10.593 89.582 10012 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.72 % Allowed : 15.45 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.10), residues: 6771 helix: 1.77 (0.07), residues: 5266 sheet: 0.24 (0.62), residues: 48 loop : -0.35 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 128 HIS 0.009 0.003 HIS E 140 PHE 0.019 0.002 PHE B 98 TYR 0.021 0.002 TYR b 92 ARG 0.047 0.001 ARG m 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 937 time to evaluate : 4.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7338 (m-30) cc_final: 0.7049 (m-30) REVERT: B 11 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7613 (mt0) REVERT: B 115 GLU cc_start: 0.8079 (mp0) cc_final: 0.7712 (mp0) REVERT: C 13 ASP cc_start: 0.7649 (t0) cc_final: 0.7373 (t0) REVERT: C 50 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.7972 (p) REVERT: C 70 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6249 (tp40) REVERT: D 15 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7200 (ttm-80) REVERT: D 94 THR cc_start: 0.8621 (m) cc_final: 0.8108 (p) REVERT: D 139 LEU cc_start: 0.7872 (mt) cc_final: 0.7583 (mt) REVERT: E 15 GLN cc_start: 0.7634 (mt0) cc_final: 0.7361 (mt0) REVERT: E 31 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8234 (mt) REVERT: F 159 GLU cc_start: 0.7528 (tt0) cc_final: 0.7239 (tt0) REVERT: G 23 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7309 (mm-30) REVERT: G 117 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7392 (pm20) REVERT: G 131 GLU cc_start: 0.7999 (tp30) cc_final: 0.7641 (tp30) REVERT: G 169 ASN cc_start: 0.8647 (m-40) cc_final: 0.8300 (m110) REVERT: H 11 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.6830 (mt0) REVERT: H 19 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7742 (mp) REVERT: H 134 MET cc_start: 0.8731 (mtm) cc_final: 0.8292 (mtm) REVERT: I 23 GLU cc_start: 0.7938 (mp0) cc_final: 0.7500 (mp0) REVERT: I 49 GLN cc_start: 0.7096 (tp-100) cc_final: 0.6435 (pm20) REVERT: I 50 SER cc_start: 0.8384 (t) cc_final: 0.7865 (p) REVERT: I 143 SER cc_start: 0.7355 (p) cc_final: 0.6958 (m) REVERT: J 33 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6633 (tp30) REVERT: J 79 MET cc_start: 0.8656 (tpp) cc_final: 0.8385 (tpp) REVERT: J 115 GLU cc_start: 0.7883 (mp0) cc_final: 0.7543 (mp0) REVERT: J 150 ARG cc_start: 0.6745 (mmt90) cc_final: 0.6233 (mmt-90) REVERT: J 159 GLU cc_start: 0.7805 (tt0) cc_final: 0.7528 (tt0) REVERT: K 23 GLU cc_start: 0.8167 (mp0) cc_final: 0.7932 (mp0) REVERT: K 67 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8099 (p) REVERT: K 68 GLN cc_start: 0.6985 (mp10) cc_final: 0.6652 (mm110) REVERT: K 81 LYS cc_start: 0.8425 (mttm) cc_final: 0.8173 (mttt) REVERT: K 110 TYR cc_start: 0.8725 (m-10) cc_final: 0.8457 (m-80) REVERT: K 117 GLU cc_start: 0.6879 (mp0) cc_final: 0.6608 (mp0) REVERT: K 137 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7928 (mtmm) REVERT: L 25 ASP cc_start: 0.7002 (m-30) cc_final: 0.6487 (m-30) REVERT: M 49 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7399 (pm20) REVERT: M 68 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7254 (pt0) REVERT: M 70 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7101 (mm-40) REVERT: M 134 LYS cc_start: 0.8510 (mttm) cc_final: 0.8285 (mttp) REVERT: N 33 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7221 (mm-30) REVERT: N 115 GLU cc_start: 0.7109 (mp0) cc_final: 0.6852 (mp0) REVERT: N 134 MET cc_start: 0.8871 (mtm) cc_final: 0.8369 (mtm) REVERT: N 166 ARG cc_start: 0.7620 (ptm160) cc_final: 0.7008 (tpt170) REVERT: O 17 ARG cc_start: 0.7901 (ptm160) cc_final: 0.7625 (ptm160) REVERT: P 22 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8363 (t) REVERT: P 107 ASP cc_start: 0.7356 (m-30) cc_final: 0.7103 (m-30) REVERT: Q 33 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7174 (mm-40) REVERT: R 1 MET cc_start: 0.7699 (ptp) cc_final: 0.7228 (ptp) REVERT: R 68 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.6325 (mp-120) REVERT: S 35 ASN cc_start: 0.8803 (m-40) cc_final: 0.8512 (m-40) REVERT: S 47 ASN cc_start: 0.8105 (t0) cc_final: 0.7890 (t0) REVERT: S 116 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6732 (m-30) REVERT: U 77 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7679 (p0) REVERT: U 116 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6929 (p0) REVERT: U 117 GLU cc_start: 0.7289 (mp0) cc_final: 0.6882 (mp0) REVERT: V 106 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7297 (mm-30) REVERT: V 152 ASP cc_start: 0.7491 (t0) cc_final: 0.7083 (t70) REVERT: W 1 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.5789 (ttt) REVERT: X 25 ASP cc_start: 0.7003 (m-30) cc_final: 0.6745 (m-30) REVERT: X 77 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7701 (ptp-170) REVERT: X 132 GLN cc_start: 0.7771 (mm110) cc_final: 0.7503 (mm-40) REVERT: Y 68 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.6880 (mt0) REVERT: a 68 GLN cc_start: 0.7347 (mt0) cc_final: 0.6902 (pt0) REVERT: a 109 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7020 (tm-30) REVERT: a 159 GLU cc_start: 0.6874 (tt0) cc_final: 0.6475 (mt-10) REVERT: b 23 GLN cc_start: 0.8122 (mt0) cc_final: 0.7881 (mt0) REVERT: b 106 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6245 (mm-30) REVERT: c 49 GLN cc_start: 0.7816 (tp-100) cc_final: 0.7088 (pm20) REVERT: c 53 ASN cc_start: 0.8348 (m-40) cc_final: 0.7957 (m110) REVERT: c 68 GLN cc_start: 0.7236 (mt0) cc_final: 0.6978 (mt0) REVERT: c 69 THR cc_start: 0.8313 (p) cc_final: 0.8090 (t) REVERT: d 136 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6704 (mt-10) REVERT: d 140 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6390 (m-30) REVERT: e 23 GLU cc_start: 0.7813 (mp0) cc_final: 0.6944 (mp0) REVERT: e 42 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7469 (tttp) REVERT: e 57 GLN cc_start: 0.7545 (tp-100) cc_final: 0.7256 (mm-40) REVERT: e 78 GLN cc_start: 0.7263 (tp40) cc_final: 0.7009 (tp-100) REVERT: e 116 ASP cc_start: 0.7311 (p0) cc_final: 0.6974 (m-30) REVERT: e 123 ASP cc_start: 0.7530 (t0) cc_final: 0.7156 (t0) REVERT: f 86 MET cc_start: 0.8229 (mtp) cc_final: 0.7901 (mtp) REVERT: g 23 GLU cc_start: 0.8042 (mp0) cc_final: 0.7562 (mp0) REVERT: g 47 ASN cc_start: 0.8152 (t0) cc_final: 0.7803 (t0) REVERT: g 117 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6921 (mt-10) REVERT: g 131 GLU cc_start: 0.7321 (tp30) cc_final: 0.6996 (tp30) REVERT: g 147 ARG cc_start: 0.7427 (ttp-170) cc_final: 0.7129 (ttp-170) REVERT: h 79 MET cc_start: 0.8916 (tpp) cc_final: 0.8615 (tpp) REVERT: i 15 GLN cc_start: 0.7666 (mp10) cc_final: 0.7226 (mp10) REVERT: i 70 GLN cc_start: 0.7103 (mm-40) cc_final: 0.6762 (mm110) REVERT: i 111 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8389 (tt) REVERT: j 15 ARG cc_start: 0.7548 (mtp180) cc_final: 0.7282 (mtm110) REVERT: j 25 ASP cc_start: 0.6607 (m-30) cc_final: 0.6274 (m-30) REVERT: j 135 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7642 (ttmt) REVERT: k 80 GLU cc_start: 0.6992 (tp30) cc_final: 0.6787 (tp30) REVERT: k 255 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.7917 (mmm160) REVERT: l 41 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7633 (ttm-80) REVERT: l 206 SER cc_start: 0.7719 (OUTLIER) cc_final: 0.7365 (t) REVERT: m 19 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6920 (tpm170) REVERT: m 25 VAL cc_start: 0.8470 (m) cc_final: 0.8206 (t) REVERT: m 69 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.6929 (tmtm) REVERT: n 55 ASN cc_start: 0.8118 (m-40) cc_final: 0.7694 (t0) REVERT: n 134 LYS cc_start: 0.7651 (mttp) cc_final: 0.7279 (mttp) outliers start: 144 outliers final: 59 residues processed: 1013 average time/residue: 1.5485 time to fit residues: 1932.2866 Evaluate side-chains 977 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 888 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain G residue 23 GLU Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain Q residue 145 ASP Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 116 ASP Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain e residue 134 LYS Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 62 LYS Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain h residue 111 ASN Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain i residue 111 LEU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 135 LYS Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 47 ASP Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 31 SER Chi-restraints excluded: chain m residue 33 MET Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 47 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 69 LYS Chi-restraints excluded: chain n residue 44 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 592 optimal weight: 0.0370 chunk 624 optimal weight: 2.9990 chunk 569 optimal weight: 0.8980 chunk 607 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 chunk 476 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 548 optimal weight: 0.7980 chunk 574 optimal weight: 0.0470 chunk 605 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 132 GLN D 11 GLN D 111 ASN D 132 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN F 23 GLN F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 53 ASN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 146 ASN N 132 GLN O 15 GLN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 ASN Q 139 ASN R 47 ASN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 ASN V 146 ASN W 68 GLN ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN b 132 GLN d 132 GLN e 15 GLN e 139 ASN g 57 GLN g 61 ASN h 68 GLN i 139 ASN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 270 GLN l 259 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 55108 Z= 0.204 Angle : 0.628 14.678 74959 Z= 0.305 Chirality : 0.038 0.263 8198 Planarity : 0.004 0.098 9826 Dihedral : 10.513 89.973 10012 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.39 % Favored : 98.60 % Rotamer: Outliers : 2.12 % Allowed : 16.28 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.10), residues: 6771 helix: 1.85 (0.07), residues: 5272 sheet: 0.15 (0.62), residues: 48 loop : -0.35 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP l 146 HIS 0.008 0.002 HIS M 140 PHE 0.014 0.001 PHE R 98 TYR 0.032 0.001 TYR g 135 ARG 0.019 0.000 ARG m 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 918 time to evaluate : 4.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7348 (m-30) cc_final: 0.7047 (m-30) REVERT: B 115 GLU cc_start: 0.8065 (mp0) cc_final: 0.7686 (mp0) REVERT: C 13 ASP cc_start: 0.7521 (t0) cc_final: 0.7231 (t0) REVERT: C 50 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7959 (p) REVERT: C 70 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6211 (tp40) REVERT: D 15 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7120 (ttm-80) REVERT: D 94 THR cc_start: 0.8603 (m) cc_final: 0.8104 (p) REVERT: D 139 LEU cc_start: 0.7869 (mt) cc_final: 0.7622 (mt) REVERT: E 15 GLN cc_start: 0.7625 (mt0) cc_final: 0.7355 (mt0) REVERT: F 159 GLU cc_start: 0.7478 (tt0) cc_final: 0.7254 (tt0) REVERT: G 17 ARG cc_start: 0.8474 (ptm160) cc_final: 0.8223 (ptm160) REVERT: G 117 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7166 (pm20) REVERT: G 131 GLU cc_start: 0.7967 (tp30) cc_final: 0.7602 (tp30) REVERT: G 169 ASN cc_start: 0.8625 (m-40) cc_final: 0.8283 (m110) REVERT: H 11 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.6707 (mt0) REVERT: H 19 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7708 (mp) REVERT: H 134 MET cc_start: 0.8663 (mtm) cc_final: 0.8251 (mtm) REVERT: I 23 GLU cc_start: 0.7929 (mp0) cc_final: 0.7456 (mp0) REVERT: I 49 GLN cc_start: 0.7127 (tp-100) cc_final: 0.6458 (pm20) REVERT: I 50 SER cc_start: 0.8416 (t) cc_final: 0.7913 (p) REVERT: I 143 SER cc_start: 0.7334 (p) cc_final: 0.6944 (m) REVERT: J 33 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6683 (tp30) REVERT: J 79 MET cc_start: 0.8622 (tpp) cc_final: 0.8366 (tpp) REVERT: J 115 GLU cc_start: 0.7866 (mp0) cc_final: 0.7522 (mp0) REVERT: J 150 ARG cc_start: 0.6702 (mmt90) cc_final: 0.6215 (mmt-90) REVERT: J 159 GLU cc_start: 0.7782 (tt0) cc_final: 0.7513 (tt0) REVERT: K 23 GLU cc_start: 0.8164 (mp0) cc_final: 0.7909 (mp0) REVERT: K 67 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8134 (p) REVERT: K 68 GLN cc_start: 0.6971 (mp10) cc_final: 0.6628 (mm110) REVERT: K 110 TYR cc_start: 0.8665 (m-10) cc_final: 0.8402 (m-80) REVERT: K 117 GLU cc_start: 0.6857 (mp0) cc_final: 0.6617 (mp0) REVERT: K 137 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7945 (mtmm) REVERT: L 25 ASP cc_start: 0.6995 (m-30) cc_final: 0.6489 (m-30) REVERT: M 49 GLN cc_start: 0.7962 (tp-100) cc_final: 0.7434 (pm20) REVERT: M 68 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7235 (pt0) REVERT: M 70 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7097 (mm-40) REVERT: M 134 LYS cc_start: 0.8553 (mttm) cc_final: 0.8334 (mttp) REVERT: N 33 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7099 (mm-30) REVERT: N 115 GLU cc_start: 0.7089 (mp0) cc_final: 0.6794 (mp0) REVERT: N 166 ARG cc_start: 0.7675 (ptm160) cc_final: 0.6928 (tpt90) REVERT: P 22 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8361 (t) REVERT: P 107 ASP cc_start: 0.7323 (m-30) cc_final: 0.7051 (m-30) REVERT: P 166 ARG cc_start: 0.7704 (mtp85) cc_final: 0.6754 (mmp80) REVERT: Q 33 GLN cc_start: 0.7437 (mm-40) cc_final: 0.6967 (mm-40) REVERT: R 1 MET cc_start: 0.7720 (ptp) cc_final: 0.7101 (ptp) REVERT: S 35 ASN cc_start: 0.8770 (m-40) cc_final: 0.8509 (m-40) REVERT: S 47 ASN cc_start: 0.8111 (t0) cc_final: 0.7883 (t0) REVERT: S 116 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: T 8 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8356 (m) REVERT: T 62 GLU cc_start: 0.7497 (pt0) cc_final: 0.7187 (pt0) REVERT: T 107 ASP cc_start: 0.8087 (m-30) cc_final: 0.7759 (m-30) REVERT: U 77 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7676 (p0) REVERT: U 116 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.6818 (p0) REVERT: U 117 GLU cc_start: 0.7291 (mp0) cc_final: 0.6208 (mp0) REVERT: V 106 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7278 (mm-30) REVERT: V 150 ARG cc_start: 0.7316 (mmm-85) cc_final: 0.7011 (tpt-90) REVERT: V 152 ASP cc_start: 0.7454 (t0) cc_final: 0.7029 (t70) REVERT: W 1 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.5665 (ttt) REVERT: W 42 LYS cc_start: 0.8211 (tmtp) cc_final: 0.7922 (tmtt) REVERT: X 25 ASP cc_start: 0.6970 (m-30) cc_final: 0.6721 (m-30) REVERT: X 77 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7692 (ptp-170) REVERT: X 132 GLN cc_start: 0.7769 (mm110) cc_final: 0.6926 (mm-40) REVERT: Y 11 THR cc_start: 0.8008 (m) cc_final: 0.7686 (p) REVERT: Y 68 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.6828 (mt0) REVERT: Y 166 TYR cc_start: 0.8441 (t80) cc_final: 0.8217 (t80) REVERT: Z 17 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6772 (mm-30) REVERT: a 68 GLN cc_start: 0.7322 (mt0) cc_final: 0.6893 (pt0) REVERT: a 109 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6898 (tm-30) REVERT: a 134 LYS cc_start: 0.8485 (mmtp) cc_final: 0.8206 (mttt) REVERT: a 159 GLU cc_start: 0.6817 (tt0) cc_final: 0.6424 (mt-10) REVERT: b 106 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6262 (mm-30) REVERT: c 49 GLN cc_start: 0.7730 (tp-100) cc_final: 0.7093 (pm20) REVERT: c 53 ASN cc_start: 0.8346 (m-40) cc_final: 0.7961 (m110) REVERT: c 68 GLN cc_start: 0.7212 (mt0) cc_final: 0.7005 (mt0) REVERT: c 69 THR cc_start: 0.8201 (p) cc_final: 0.7979 (t) REVERT: d 136 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6638 (mt-10) REVERT: d 140 ASP cc_start: 0.6752 (OUTLIER) cc_final: 0.6357 (m-30) REVERT: e 23 GLU cc_start: 0.7768 (mp0) cc_final: 0.6922 (mp0) REVERT: e 42 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7455 (tttp) REVERT: e 78 GLN cc_start: 0.7221 (tp40) cc_final: 0.6860 (tp-100) REVERT: e 116 ASP cc_start: 0.7339 (p0) cc_final: 0.6938 (m-30) REVERT: e 123 ASP cc_start: 0.7534 (t0) cc_final: 0.7158 (t0) REVERT: f 86 MET cc_start: 0.8239 (mtp) cc_final: 0.7935 (mtp) REVERT: g 23 GLU cc_start: 0.8015 (mp0) cc_final: 0.7557 (mp0) REVERT: g 117 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: g 131 GLU cc_start: 0.7310 (tp30) cc_final: 0.6962 (tp30) REVERT: g 147 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.7134 (ttp-170) REVERT: h 79 MET cc_start: 0.8884 (tpp) cc_final: 0.8549 (tpp) REVERT: h 150 ARG cc_start: 0.7224 (tpp-160) cc_final: 0.6601 (tpp-160) REVERT: i 70 GLN cc_start: 0.7153 (mm-40) cc_final: 0.6795 (mm110) REVERT: i 111 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8351 (tt) REVERT: j 15 ARG cc_start: 0.7535 (mtp180) cc_final: 0.7289 (mtm110) REVERT: j 25 ASP cc_start: 0.6596 (m-30) cc_final: 0.6253 (m-30) REVERT: j 135 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7715 (ttpt) REVERT: k 17 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7011 (pt0) REVERT: k 19 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6845 (mmt90) REVERT: k 80 GLU cc_start: 0.6942 (tp30) cc_final: 0.6736 (tp30) REVERT: k 161 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8450 (m) REVERT: k 255 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.7885 (mmm160) REVERT: l 41 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7555 (ttt-90) REVERT: m 19 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6907 (tpm170) REVERT: m 25 VAL cc_start: 0.8429 (m) cc_final: 0.8127 (t) REVERT: m 31 SER cc_start: 0.7143 (OUTLIER) cc_final: 0.6905 (p) REVERT: n 55 ASN cc_start: 0.8093 (m-40) cc_final: 0.7658 (t0) REVERT: n 134 LYS cc_start: 0.7526 (mttp) cc_final: 0.7112 (mttp) outliers start: 112 outliers final: 54 residues processed: 979 average time/residue: 1.5909 time to fit residues: 1912.0723 Evaluate side-chains 952 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 869 time to evaluate : 4.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain Q residue 145 ASP Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 50 SER Chi-restraints excluded: chain g residue 57 GLN Chi-restraints excluded: chain g residue 62 LYS Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain i residue 111 LEU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 135 LYS Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 19 ARG Chi-restraints excluded: chain k residue 47 ASP Chi-restraints excluded: chain k residue 161 THR Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain l residue 245 GLU Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 31 SER Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 47 THR Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 44 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 398 optimal weight: 0.7980 chunk 642 optimal weight: 0.0870 chunk 391 optimal weight: 0.5980 chunk 304 optimal weight: 5.9990 chunk 446 optimal weight: 0.9980 chunk 673 optimal weight: 0.9990 chunk 619 optimal weight: 3.9990 chunk 536 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 414 optimal weight: 0.9980 chunk 328 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN D 11 GLN D 111 ASN D 132 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN E 78 GLN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 53 ASN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 132 GLN L 146 ASN O 15 GLN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 ASN Q 139 ASN ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN U 15 GLN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 ASN V 146 ASN ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 140 HIS ** Z 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 132 GLN e 15 GLN e 139 ASN g 57 GLN g 61 ASN h 68 GLN i 139 ASN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 259 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 55108 Z= 0.183 Angle : 0.606 13.682 74959 Z= 0.295 Chirality : 0.037 0.240 8198 Planarity : 0.004 0.201 9826 Dihedral : 10.465 89.912 10012 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.48 % Favored : 98.51 % Rotamer: Outliers : 1.83 % Allowed : 16.75 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.10), residues: 6771 helix: 1.92 (0.07), residues: 5291 sheet: -0.09 (0.60), residues: 49 loop : -0.40 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP l 146 HIS 0.007 0.002 HIS C 140 PHE 0.012 0.001 PHE R 98 TYR 0.025 0.001 TYR g 135 ARG 0.048 0.000 ARG m 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13542 Ramachandran restraints generated. 6771 Oldfield, 0 Emsley, 6771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 922 time to evaluate : 4.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7345 (m-30) cc_final: 0.7046 (m-30) REVERT: B 115 GLU cc_start: 0.8047 (mp0) cc_final: 0.7657 (mp0) REVERT: C 13 ASP cc_start: 0.7484 (t0) cc_final: 0.7210 (t0) REVERT: C 50 SER cc_start: 0.8205 (p) cc_final: 0.7962 (p) REVERT: D 15 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6868 (ttm-80) REVERT: D 94 THR cc_start: 0.8576 (m) cc_final: 0.8063 (p) REVERT: D 139 LEU cc_start: 0.7887 (mt) cc_final: 0.7601 (mt) REVERT: E 15 GLN cc_start: 0.7591 (mt0) cc_final: 0.7373 (mt0) REVERT: F 15 ARG cc_start: 0.7221 (mtm180) cc_final: 0.6872 (mtp85) REVERT: F 159 GLU cc_start: 0.7532 (tt0) cc_final: 0.7305 (tt0) REVERT: G 117 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: G 131 GLU cc_start: 0.7955 (tp30) cc_final: 0.7581 (tp30) REVERT: G 169 ASN cc_start: 0.8642 (m-40) cc_final: 0.8298 (m110) REVERT: H 11 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.6651 (mt0) REVERT: H 19 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7594 (mp) REVERT: H 134 MET cc_start: 0.8641 (mtm) cc_final: 0.8216 (mtm) REVERT: I 23 GLU cc_start: 0.7963 (mp0) cc_final: 0.7486 (mp0) REVERT: I 49 GLN cc_start: 0.7049 (tp-100) cc_final: 0.6430 (pm20) REVERT: I 50 SER cc_start: 0.8443 (t) cc_final: 0.7944 (p) REVERT: I 109 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6690 (tp30) REVERT: I 143 SER cc_start: 0.7405 (p) cc_final: 0.6955 (m) REVERT: J 33 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6779 (tp30) REVERT: J 115 GLU cc_start: 0.7846 (mp0) cc_final: 0.7512 (mp0) REVERT: J 159 GLU cc_start: 0.7777 (tt0) cc_final: 0.7510 (tt0) REVERT: K 23 GLU cc_start: 0.8161 (mp0) cc_final: 0.7933 (mp0) REVERT: K 67 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8083 (p) REVERT: K 117 GLU cc_start: 0.6895 (mp0) cc_final: 0.6573 (mp0) REVERT: K 137 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7983 (mtmm) REVERT: L 25 ASP cc_start: 0.6980 (m-30) cc_final: 0.6452 (m-30) REVERT: M 49 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7405 (pm20) REVERT: M 68 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7193 (pt0) REVERT: M 70 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7094 (mm-40) REVERT: N 107 ASP cc_start: 0.7819 (m-30) cc_final: 0.7459 (m-30) REVERT: N 115 GLU cc_start: 0.6996 (mp0) cc_final: 0.6733 (mp0) REVERT: N 166 ARG cc_start: 0.7754 (ptm160) cc_final: 0.6987 (tpt90) REVERT: P 22 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8338 (t) REVERT: P 94 THR cc_start: 0.9004 (m) cc_final: 0.8532 (p) REVERT: P 106 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7268 (mm-30) REVERT: P 107 ASP cc_start: 0.7357 (m-30) cc_final: 0.7069 (m-30) REVERT: Q 33 GLN cc_start: 0.7370 (mm-40) cc_final: 0.6990 (mm-40) REVERT: Q 77 ASP cc_start: 0.7890 (p0) cc_final: 0.7368 (p0) REVERT: R 1 MET cc_start: 0.7750 (ptp) cc_final: 0.7282 (ptp) REVERT: S 35 ASN cc_start: 0.8711 (m-40) cc_final: 0.8445 (m-40) REVERT: S 47 ASN cc_start: 0.8117 (t0) cc_final: 0.7898 (t0) REVERT: S 116 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6764 (m-30) REVERT: T 8 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8322 (m) REVERT: U 33 GLN cc_start: 0.8432 (tp40) cc_final: 0.7972 (tp40) REVERT: U 77 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7675 (p0) REVERT: U 116 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6815 (p0) REVERT: U 117 GLU cc_start: 0.7302 (mp0) cc_final: 0.6241 (mp0) REVERT: U 159 GLU cc_start: 0.7747 (tt0) cc_final: 0.7538 (tt0) REVERT: V 33 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6555 (mp0) REVERT: V 106 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7291 (mm-30) REVERT: V 150 ARG cc_start: 0.7281 (mmm-85) cc_final: 0.7010 (tpt-90) REVERT: V 152 ASP cc_start: 0.7431 (t0) cc_final: 0.7024 (t70) REVERT: W 1 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.5586 (ttt) REVERT: X 25 ASP cc_start: 0.6887 (m-30) cc_final: 0.6630 (m-30) REVERT: X 77 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7636 (ptp90) REVERT: X 132 GLN cc_start: 0.7751 (mm110) cc_final: 0.6891 (mm-40) REVERT: Y 11 THR cc_start: 0.7990 (m) cc_final: 0.7533 (p) REVERT: Y 68 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.6815 (mt0) REVERT: Z 17 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6693 (mm-30) REVERT: a 68 GLN cc_start: 0.7254 (mt0) cc_final: 0.6843 (pt0) REVERT: a 159 GLU cc_start: 0.6799 (tt0) cc_final: 0.6450 (mt-10) REVERT: b 11 GLN cc_start: 0.7659 (mt0) cc_final: 0.7370 (mm-40) REVERT: b 106 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6164 (mm-30) REVERT: c 49 GLN cc_start: 0.7633 (tp-100) cc_final: 0.7073 (pm20) REVERT: c 53 ASN cc_start: 0.8334 (m-40) cc_final: 0.7953 (m110) REVERT: c 69 THR cc_start: 0.8165 (p) cc_final: 0.7948 (t) REVERT: d 136 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6633 (mt-10) REVERT: d 140 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6322 (m-30) REVERT: e 23 GLU cc_start: 0.7727 (mp0) cc_final: 0.6909 (mp0) REVERT: e 42 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7454 (tttp) REVERT: e 78 GLN cc_start: 0.7233 (tp40) cc_final: 0.6964 (tp-100) REVERT: e 116 ASP cc_start: 0.7344 (p0) cc_final: 0.6973 (m-30) REVERT: e 123 ASP cc_start: 0.7546 (t0) cc_final: 0.7168 (t0) REVERT: f 86 MET cc_start: 0.8253 (mtp) cc_final: 0.7919 (mtp) REVERT: g 23 GLU cc_start: 0.8061 (mp0) cc_final: 0.7818 (mp0) REVERT: g 47 ASN cc_start: 0.8052 (t0) cc_final: 0.7721 (t0) REVERT: g 117 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6982 (mt-10) REVERT: g 131 GLU cc_start: 0.7288 (tp30) cc_final: 0.6963 (tp30) REVERT: g 147 ARG cc_start: 0.7432 (ttp-170) cc_final: 0.7138 (ttp-170) REVERT: h 79 MET cc_start: 0.8864 (tpp) cc_final: 0.8586 (tpp) REVERT: h 87 GLU cc_start: 0.7480 (tt0) cc_final: 0.7000 (tt0) REVERT: h 150 ARG cc_start: 0.7250 (tpp-160) cc_final: 0.6608 (tpp-160) REVERT: i 70 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6774 (mm110) REVERT: j 25 ASP cc_start: 0.6572 (m-30) cc_final: 0.6232 (m-30) REVERT: k 255 ARG cc_start: 0.8373 (mmm-85) cc_final: 0.7853 (mmm160) REVERT: l 41 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7546 (ttt-90) REVERT: m 19 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6898 (tpm170) REVERT: m 25 VAL cc_start: 0.8332 (m) cc_final: 0.7963 (t) REVERT: m 31 SER cc_start: 0.7255 (OUTLIER) cc_final: 0.7013 (p) REVERT: n 55 ASN cc_start: 0.8027 (m-40) cc_final: 0.7602 (t0) REVERT: n 134 LYS cc_start: 0.7508 (mttp) cc_final: 0.7088 (mttp) outliers start: 97 outliers final: 49 residues processed: 977 average time/residue: 1.5912 time to fit residues: 1908.3219 Evaluate side-chains 952 residues out of total 5289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 881 time to evaluate : 4.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 137 LYS Chi-restraints excluded: chain M residue 50 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 154 SER Chi-restraints excluded: chain Q residue 145 ASP Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain S residue 32 ARG Chi-restraints excluded: chain S residue 116 ASP Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 116 ASP Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 136 GLU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 116 ASP Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 68 GLN Chi-restraints excluded: chain c residue 117 GLU Chi-restraints excluded: chain d residue 136 GLU Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain f residue 115 GLU Chi-restraints excluded: chain f residue 166 ARG Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 117 GLU Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain i residue 31 LEU Chi-restraints excluded: chain j residue 4 VAL Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 149 THR Chi-restraints excluded: chain k residue 47 ASP Chi-restraints excluded: chain k residue 207 SER Chi-restraints excluded: chain l residue 41 ARG Chi-restraints excluded: chain l residue 206 SER Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain m residue 31 SER Chi-restraints excluded: chain m residue 41 ILE Chi-restraints excluded: chain m residue 46 SER Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 44 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 425 optimal weight: 0.9980 chunk 571 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 494 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 537 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 551 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN D 11 GLN D 111 ASN D 132 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 15 GLN K 53 ASN ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 146 ASN M 78 GLN O 15 GLN ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 ASN Q 68 GLN Q 139 ASN R 68 GLN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 139 ASN V 111 ASN V 146 ASN ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 132 GLN c 68 GLN d 132 GLN e 15 GLN e 139 ASN h 68 GLN i 139 ASN j 132 GLN ** k 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 259 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.104076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094369 restraints weight = 75547.569| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 0.86 r_work: 0.3013 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 55108 Z= 0.269 Angle : 0.678 19.128 74959 Z= 0.328 Chirality : 0.040 0.284 8198 Planarity : 0.006 0.417 9826 Dihedral : 10.553 89.864 10012 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.87 % Allowed : 16.92 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.10), residues: 6771 helix: 1.85 (0.07), residues: 5285 sheet: 0.16 (0.62), residues: 48 loop : -0.38 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP l 146 HIS 0.008 0.002 HIS E 140 PHE 0.016 0.002 PHE R 98 TYR 0.033 0.002 TYR g 135 ARG 0.049 0.001 ARG m 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26210.55 seconds wall clock time: 446 minutes 17.51 seconds (26777.51 seconds total)