Starting phenix.real_space_refine on Wed Mar 27 01:35:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzi_8932/03_2024/6dzi_8932.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzi_8932/03_2024/6dzi_8932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzi_8932/03_2024/6dzi_8932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzi_8932/03_2024/6dzi_8932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzi_8932/03_2024/6dzi_8932.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzi_8932/03_2024/6dzi_8932.pdb" } resolution = 3.46 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4748 5.49 5 S 93 5.16 5 C 75920 2.51 5 N 28228 2.21 5 O 41879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "m ARG 198": "NH1" <-> "NH2" Residue "8 ARG 35": "NH1" <-> "NH2" Residue "8 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 177": "NH1" <-> "NH2" Residue "Y PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "T TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 2": "NH1" <-> "NH2" Residue "c ARG 6": "NH1" <-> "NH2" Residue "c ARG 12": "NH1" <-> "NH2" Residue "c ARG 24": "NH1" <-> "NH2" Residue "c ARG 37": "NH1" <-> "NH2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "c ARG 45": "NH1" <-> "NH2" Residue "d ARG 17": "NH1" <-> "NH2" Residue "y ARG 26": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150868 Number of models: 1 Model: "" Number of chains: 56 Chain: "h" Number of atoms: 32439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1511, 32439 Classifications: {'RNA': 1511} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 86, 'rna3p_pur': 737, 'rna3p_pyr': 576} Link IDs: {'rna2p': 198, 'rna3p': 1312} Chain: "j" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 280 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "k" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1660 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain: "l" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1641 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "m" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1296 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 8, 'TRANS': 171} Chain: "n" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "p" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "q" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "4" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "s" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 788 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "t" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 855 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "u" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "v" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "x" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "z" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "5" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 748 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "6" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 662 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "7" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 660 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "8" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1793 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "r" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 659 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Y" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 861 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "9" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 819 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "A" Number of atoms: 66981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3119, 66981 Classifications: {'RNA': 3119} Modifications used: {'rna2p_pur': 301, 'rna2p_pyr': 150, 'rna3p_pur': 1482, 'rna3p_pyr': 1186} Link IDs: {'rna2p': 451, 'rna3p': 2667} Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2522 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 46} Link IDs: {'rna2p': 15, 'rna3p': 102} Chain: "C" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2110 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 19, 'TRANS': 255} Chain: "D" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 205} Chain: "E" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1569 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1445 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1348 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "H" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1119 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 918 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "J" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 990 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "K" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "L" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "M" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "N" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "O" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "P" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Q" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "R" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "S" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "T" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 732 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "W" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1428 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain: "X" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 586 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "Z" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "a" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 474 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "b" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "c" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 456 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "f" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "g" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 593 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "y" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 617 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "3" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Time building chain proxies: 57.30, per 1000 atoms: 0.38 Number of scatterers: 150868 At special positions: 0 Unit cell: (272.85, 258.94, 241.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 93 16.00 P 4748 15.00 O 41879 8.00 N 28228 7.00 C 75920 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 64.83 Conformation dependent library (CDL) restraints added in 7.7 seconds 12346 Ramachandran restraints generated. 6173 Oldfield, 0 Emsley, 6173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11480 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 0 sheets defined 38.1% alpha, 0.0% beta 1337 base pairs and 2458 stacking pairs defined. Time for finding SS restraints: 51.18 Creating SS restraints... Processing helix chain 'j' and resid 3 through 33 removed outlier: 5.318A pdb=" N LYS j 7 " --> pdb=" O SER j 3 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL j 26 " --> pdb=" O ARG j 22 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN j 27 " --> pdb=" O ARG j 23 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG j 29 " --> pdb=" O ARG j 25 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS j 33 " --> pdb=" O ARG j 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 6 through 12 Processing helix chain 'k' and resid 27 through 47 removed outlier: 4.339A pdb=" N GLU k 47 " --> pdb=" O ALA k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 71 through 76 removed outlier: 3.649A pdb=" N VAL k 75 " --> pdb=" O ARG k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 80 through 94 Processing helix chain 'k' and resid 111 through 126 removed outlier: 4.021A pdb=" N ARG k 126 " --> pdb=" O GLN k 122 " (cutoff:3.500A) Processing helix chain 'k' and resid 128 through 144 removed outlier: 4.919A pdb=" N ALA k 132 " --> pdb=" O ALA k 128 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN k 143 " --> pdb=" O SER k 139 " (cutoff:3.500A) Proline residue: k 144 - end of helix Processing helix chain 'l' and resid 7 through 16 removed outlier: 4.078A pdb=" N LYS l 11 " --> pdb=" O PRO l 7 " (cutoff:3.500A) Processing helix chain 'l' and resid 23 through 30 Proline residue: l 30 - end of helix Processing helix chain 'l' and resid 44 through 61 removed outlier: 3.787A pdb=" N GLN l 48 " --> pdb=" O SER l 44 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS l 53 " --> pdb=" O GLN l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 63 through 78 Proline residue: l 78 - end of helix Processing helix chain 'l' and resid 80 through 101 removed outlier: 4.089A pdb=" N ARG l 92 " --> pdb=" O ILE l 88 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU l 93 " --> pdb=" O LEU l 89 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASP l 94 " --> pdb=" O GLU l 90 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN l 95 " --> pdb=" O SER l 91 " (cutoff:3.500A) Processing helix chain 'l' and resid 105 through 116 removed outlier: 3.645A pdb=" N GLY l 116 " --> pdb=" O LEU l 112 " (cutoff:3.500A) Processing helix chain 'l' and resid 141 through 157 removed outlier: 5.727A pdb=" N LEU l 145 " --> pdb=" O LYS l 141 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASN l 146 " --> pdb=" O GLU l 142 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR l 147 " --> pdb=" O LYS l 143 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU l 148 " --> pdb=" O SER l 144 " (cutoff:3.500A) Proline residue: l 149 - end of helix Processing helix chain 'l' and resid 182 through 187 removed outlier: 3.629A pdb=" N ASP l 187 " --> pdb=" O ARG l 183 " (cutoff:3.500A) Processing helix chain 'l' and resid 191 through 201 removed outlier: 5.036A pdb=" N ILE l 195 " --> pdb=" O THR l 191 " (cutoff:3.500A) Processing helix chain 'm' and resid 80 through 96 removed outlier: 3.712A pdb=" N PHE m 96 " --> pdb=" O ALA m 92 " (cutoff:3.500A) Processing helix chain 'm' and resid 134 through 144 Processing helix chain 'm' and resid 157 through 183 removed outlier: 5.824A pdb=" N GLN m 173 " --> pdb=" O LEU m 169 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ARG m 174 " --> pdb=" O LYS m 170 " (cutoff:3.500A) Proline residue: m 175 - end of helix Processing helix chain 'm' and resid 185 through 214 Proline residue: m 191 - end of helix removed outlier: 7.257A pdb=" N MET m 194 " --> pdb=" O ALA m 190 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU m 195 " --> pdb=" O PRO m 191 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA m 214 " --> pdb=" O ARG m 210 " (cutoff:3.500A) Processing helix chain 'n' and resid 15 through 32 removed outlier: 4.654A pdb=" N ALA n 20 " --> pdb=" O GLU n 16 " (cutoff:3.500A) Proline residue: n 21 - end of helix removed outlier: 3.943A pdb=" N PHE n 26 " --> pdb=" O SER n 22 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL n 29 " --> pdb=" O THR n 25 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE n 30 " --> pdb=" O PHE n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 68 through 83 removed outlier: 5.400A pdb=" N GLU n 83 " --> pdb=" O LEU n 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 20 through 31 removed outlier: 4.216A pdb=" N THR p 24 " --> pdb=" O SER p 20 " (cutoff:3.500A) Processing helix chain 'p' and resid 35 through 55 Processing helix chain 'p' and resid 57 through 70 removed outlier: 3.724A pdb=" N THR p 61 " --> pdb=" O ASP p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 92 through 111 removed outlier: 4.066A pdb=" N GLN p 110 " --> pdb=" O ASN p 106 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG p 111 " --> pdb=" O PHE p 107 " (cutoff:3.500A) Processing helix chain 'p' and resid 115 through 130 Processing helix chain 'p' and resid 132 through 149 Processing helix chain 'q' and resid 5 through 21 Processing helix chain 'q' and resid 30 through 44 Processing helix chain 'q' and resid 114 through 122 Processing helix chain '4' and resid 54 through 59 removed outlier: 4.558A pdb=" N PHE 4 59 " --> pdb=" O LEU 4 55 " (cutoff:3.500A) Processing helix chain '4' and resid 61 through 76 Proline residue: 4 71 - end of helix Processing helix chain '4' and resid 91 through 112 Proline residue: 4 112 - end of helix Processing helix chain 's' and resid 14 through 33 removed outlier: 4.410A pdb=" N THR s 32 " --> pdb=" O THR s 28 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY s 33 " --> pdb=" O VAL s 29 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 90 removed outlier: 3.989A pdb=" N ARG s 89 " --> pdb=" O ASP s 85 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE s 90 " --> pdb=" O ALA s 86 " (cutoff:3.500A) Processing helix chain 't' and resid 55 through 60 removed outlier: 3.850A pdb=" N GLY t 60 " --> pdb=" O SER t 56 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 removed outlier: 3.710A pdb=" N ALA t 72 " --> pdb=" O THR t 68 " (cutoff:3.500A) Processing helix chain 't' and resid 101 through 113 removed outlier: 3.699A pdb=" N GLY t 113 " --> pdb=" O LEU t 109 " (cutoff:3.500A) Processing helix chain 'u' and resid 3 through 11 Processing helix chain 'u' and resid 113 through 118 removed outlier: 4.317A pdb=" N TYR u 117 " --> pdb=" O ALA u 113 " (cutoff:3.500A) Processing helix chain 'v' and resid 14 through 21 removed outlier: 4.097A pdb=" N THR v 20 " --> pdb=" O GLU v 16 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR v 21 " --> pdb=" O ILE v 17 " (cutoff:3.500A) Processing helix chain 'v' and resid 26 through 38 Processing helix chain 'v' and resid 49 through 64 Processing helix chain 'v' and resid 67 through 95 removed outlier: 3.793A pdb=" N GLY v 85 " --> pdb=" O LYS v 81 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N CYS v 86 " --> pdb=" O ILE v 82 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N TYR v 87 " --> pdb=" O GLU v 83 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N GLN v 88 " --> pdb=" O ILE v 84 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLY v 89 " --> pdb=" O GLY v 85 " (cutoff:3.500A) Processing helix chain 'v' and resid 107 through 112 Processing helix chain 'x' and resid 4 through 15 Processing helix chain 'x' and resid 24 through 47 removed outlier: 3.901A pdb=" N VAL x 45 " --> pdb=" O GLU x 41 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS x 47 " --> pdb=" O LEU x 43 " (cutoff:3.500A) Processing helix chain 'x' and resid 49 through 86 removed outlier: 3.867A pdb=" N GLY x 55 " --> pdb=" O HIS x 51 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL x 75 " --> pdb=" O ALA x 71 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ALA x 76 " --> pdb=" O GLN x 72 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ARG x 77 " --> pdb=" O VAL x 73 " (cutoff:3.500A) Processing helix chain 'z' and resid 52 through 63 removed outlier: 3.605A pdb=" N GLY z 63 " --> pdb=" O TRP z 59 " (cutoff:3.500A) Processing helix chain 'z' and resid 67 through 85 removed outlier: 5.250A pdb=" N ASP z 79 " --> pdb=" O LYS z 75 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N TRP z 80 " --> pdb=" O ILE z 76 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN z 81 " --> pdb=" O THR z 77 " (cutoff:3.500A) Processing helix chain 'z' and resid 101 through 114 Processing helix chain '6' and resid 12 through 26 Processing helix chain '6' and resid 70 through 76 removed outlier: 4.588A pdb=" N PHE 6 74 " --> pdb=" O LYS 6 70 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA 6 75 " --> pdb=" O LEU 6 71 " (cutoff:3.500A) Proline residue: 6 76 - end of helix No H-bonds generated for 'chain '6' and resid 70 through 76' Processing helix chain '7' and resid 4 through 42 Processing helix chain '7' and resid 44 through 65 removed outlier: 4.379A pdb=" N ALA 7 53 " --> pdb=" O GLU 7 49 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY 7 65 " --> pdb=" O ALA 7 61 " (cutoff:3.500A) Processing helix chain '7' and resid 68 through 86 Processing helix chain '8' and resid 5 through 13 removed outlier: 6.807A pdb=" N SER 8 12 " --> pdb=" O GLN 8 8 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY 8 13 " --> pdb=" O LEU 8 9 " (cutoff:3.500A) Processing helix chain '8' and resid 27 through 32 removed outlier: 5.454A pdb=" N PHE 8 32 " --> pdb=" O LYS 8 28 " (cutoff:3.500A) Processing helix chain '8' and resid 42 through 64 Processing helix chain '8' and resid 73 through 88 removed outlier: 5.849A pdb=" N GLU 8 78 " --> pdb=" O LYS 8 74 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER 8 79 " --> pdb=" O GLN 8 75 " (cutoff:3.500A) Processing helix chain '8' and resid 103 through 155 removed outlier: 3.950A pdb=" N VAL 8 107 " --> pdb=" O ASN 8 103 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS 8 109 " --> pdb=" O SER 8 105 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLY 8 125 " --> pdb=" O GLU 8 121 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N PHE 8 126 " --> pdb=" O GLN 8 122 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N GLU 8 127 " --> pdb=" O THR 8 123 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY 8 128 " --> pdb=" O GLY 8 124 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ARG 8 129 " --> pdb=" O GLY 8 125 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR 8 130 " --> pdb=" O PHE 8 126 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS 8 131 " --> pdb=" O GLU 8 127 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N LYS 8 132 " --> pdb=" O GLY 8 128 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU 8 133 " --> pdb=" O ARG 8 129 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLY 8 149 " --> pdb=" O GLU 8 145 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N GLY 8 150 " --> pdb=" O ARG 8 146 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE 8 151 " --> pdb=" O SER 8 147 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG 8 152 " --> pdb=" O LEU 8 148 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASP 8 153 " --> pdb=" O GLY 8 149 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLN 8 155 " --> pdb=" O ILE 8 151 " (cutoff:3.500A) Processing helix chain '8' and resid 165 through 170 Processing helix chain '8' and resid 192 through 197 removed outlier: 6.473A pdb=" N VAL 8 196 " --> pdb=" O ASP 8 192 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASP 8 197 " --> pdb=" O PRO 8 193 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 192 through 197' Processing helix chain '8' and resid 206 through 228 Processing helix chain 'r' and resid 36 through 45 removed outlier: 3.673A pdb=" N LEU r 40 " --> pdb=" O ASP r 36 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR r 42 " --> pdb=" O ALA r 38 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE r 43 " --> pdb=" O VAL r 39 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU r 44 " --> pdb=" O LEU r 40 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER r 45 " --> pdb=" O ARG r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 57 Processing helix chain 'r' and resid 59 through 77 Processing helix chain 'Y' and resid 17 through 35 removed outlier: 4.980A pdb=" N ARG Y 21 " --> pdb=" O PRO Y 17 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR Y 22 " --> pdb=" O ASP Y 18 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU Y 31 " --> pdb=" O LYS Y 27 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N PHE Y 34 " --> pdb=" O ARG Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 103 removed outlier: 3.946A pdb=" N ALA Y 83 " --> pdb=" O SER Y 79 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LYS Y 103 " --> pdb=" O LYS Y 99 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 33 removed outlier: 4.221A pdb=" N GLU 9 22 " --> pdb=" O GLN 9 18 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG 9 23 " --> pdb=" O ARG 9 19 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA 9 25 " --> pdb=" O ALA 9 21 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU 9 26 " --> pdb=" O GLU 9 22 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS 9 28 " --> pdb=" O ARG 9 24 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ARG 9 29 " --> pdb=" O ALA 9 25 " (cutoff:3.500A) Processing helix chain '9' and resid 43 through 57 removed outlier: 3.594A pdb=" N ARG 9 50 " --> pdb=" O SER 9 46 " (cutoff:3.500A) Proline residue: 9 52 - end of helix removed outlier: 6.268A pdb=" N SER 9 55 " --> pdb=" O LEU 9 51 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER 9 56 " --> pdb=" O PRO 9 52 " (cutoff:3.500A) Proline residue: 9 57 - end of helix Processing helix chain '9' and resid 80 through 91 Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.843A pdb=" N ILE C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix No H-bonds generated for 'chain 'C' and resid 132 through 137' Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.203A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.772A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 262 through 269 removed outlier: 4.758A pdb=" N LYS C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 267 " --> pdb=" O PRO C 263 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.726A pdb=" N GLY D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 74 removed outlier: 4.009A pdb=" N ALA D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 95 removed outlier: 4.288A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TYR D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'E' and resid 21 through 26 removed outlier: 4.390A pdb=" N PHE E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 47 removed outlier: 5.135A pdb=" N GLN E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 122 removed outlier: 3.911A pdb=" N ASN E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 149 removed outlier: 3.657A pdb=" N ALA E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 170 removed outlier: 3.980A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 192 removed outlier: 4.268A pdb=" N VAL E 188 " --> pdb=" O ASN E 184 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASP E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 210 removed outlier: 4.836A pdb=" N LYS E 210 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 removed outlier: 3.647A pdb=" N ILE F 19 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 69 removed outlier: 7.807A pdb=" N ALA F 51 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N LYS F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU F 56 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASN F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 118 removed outlier: 3.557A pdb=" N ALA F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU F 115 " --> pdb=" O ILE F 111 " (cutoff:3.500A) Proline residue: F 116 - end of helix Processing helix chain 'F' and resid 169 through 181 Processing helix chain 'G' and resid 2 through 7 removed outlier: 4.369A pdb=" N GLN G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 4.421A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.724A pdb=" N LEU G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 42 through 60 removed outlier: 4.454A pdb=" N ARG H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 74 removed outlier: 3.940A pdb=" N ALA H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLY H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 108 removed outlier: 3.935A pdb=" N VAL H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 removed outlier: 4.084A pdb=" N VAL H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLN H 118 " --> pdb=" O LYS H 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 113 through 118' Processing helix chain 'I' and resid 2 through 21 removed outlier: 3.715A pdb=" N ALA I 19 " --> pdb=" O GLU I 15 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N THR I 21 " --> pdb=" O PHE I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 43 Processing helix chain 'I' and resid 53 through 65 removed outlier: 4.050A pdb=" N ARG I 59 " --> pdb=" O THR I 55 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N SER I 62 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLY I 65 " --> pdb=" O ALA I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 101 removed outlier: 4.560A pdb=" N ALA I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 126 Processing helix chain 'J' and resid 24 through 32 Proline residue: J 28 - end of helix removed outlier: 4.644A pdb=" N GLN J 32 " --> pdb=" O PRO J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 52 removed outlier: 4.479A pdb=" N PHE J 40 " --> pdb=" O ASN J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 85 Processing helix chain 'J' and resid 103 through 118 Processing helix chain 'J' and resid 122 through 138 Processing helix chain 'K' and resid 24 through 38 Processing helix chain 'K' and resid 67 through 72 removed outlier: 3.768A pdb=" N LYS K 72 " --> pdb=" O LYS K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 110 removed outlier: 3.905A pdb=" N LEU K 92 " --> pdb=" O THR K 88 " (cutoff:3.500A) Proline residue: K 97 - end of helix removed outlier: 4.740A pdb=" N VAL K 100 " --> pdb=" O HIS K 96 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU K 109 " --> pdb=" O ILE K 105 " (cutoff:3.500A) Proline residue: K 110 - end of helix Processing helix chain 'K' and resid 112 through 123 removed outlier: 3.792A pdb=" N LYS K 120 " --> pdb=" O ARG K 116 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS K 121 " --> pdb=" O GLN K 117 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU K 122 " --> pdb=" O ILE K 118 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS K 123 " --> pdb=" O GLN K 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 118 removed outlier: 4.990A pdb=" N ARG L 107 " --> pdb=" O GLY L 103 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU L 108 " --> pdb=" O ARG L 104 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE L 111 " --> pdb=" O ARG L 107 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N MET L 112 " --> pdb=" O GLU L 108 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N LYS L 113 " --> pdb=" O LYS L 109 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE L 114 " --> pdb=" O LYS L 110 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL L 115 " --> pdb=" O PHE L 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 44 removed outlier: 3.540A pdb=" N LYS M 44 " --> pdb=" O THR M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 Processing helix chain 'M' and resid 79 through 87 removed outlier: 3.578A pdb=" N ILE M 83 " --> pdb=" O ASN M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 102 removed outlier: 3.620A pdb=" N LYS M 101 " --> pdb=" O GLU M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 141 Processing helix chain 'N' and resid 43 through 59 removed outlier: 3.787A pdb=" N ILE N 47 " --> pdb=" O THR N 43 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS N 57 " --> pdb=" O ALA N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 126 removed outlier: 3.914A pdb=" N LYS N 124 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU N 125 " --> pdb=" O ALA N 121 " (cutoff:3.500A) Proline residue: N 126 - end of helix Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 38 through 89 Proline residue: O 46 - end of helix removed outlier: 3.833A pdb=" N GLY O 58 " --> pdb=" O HIS O 54 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ALA O 59 " --> pdb=" O ALA O 55 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N LEU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N HIS O 61 " --> pdb=" O LYS O 57 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASN O 62 " --> pdb=" O GLY O 58 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS O 69 " --> pdb=" O GLU O 65 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE O 70 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG O 71 " --> pdb=" O MET O 67 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N ASP O 72 " --> pdb=" O LYS O 68 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N LYS O 73 " --> pdb=" O LYS O 69 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ASP O 74 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL O 75 " --> pdb=" O ARG O 71 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) Proline residue: O 85 - end of helix removed outlier: 3.596A pdb=" N ALA O 88 " --> pdb=" O GLY O 84 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ASP O 89 " --> pdb=" O PRO O 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 30 removed outlier: 4.496A pdb=" N LYS P 27 " --> pdb=" O ALA P 23 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LYS P 28 " --> pdb=" O ARG P 24 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL P 29 " --> pdb=" O LEU P 25 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA P 30 " --> pdb=" O ARG P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 74 removed outlier: 4.733A pdb=" N ILE P 73 " --> pdb=" O ASP P 69 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASP P 74 " --> pdb=" O VAL P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 96 Processing helix chain 'P' and resid 111 through 124 Processing helix chain 'Q' and resid 4 through 12 removed outlier: 4.977A pdb=" N ALA Q 10 " --> pdb=" O PHE Q 6 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 109 removed outlier: 5.203A pdb=" N ARG Q 100 " --> pdb=" O LEU Q 96 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU Q 101 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU Q 102 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ARG Q 103 " --> pdb=" O LEU Q 99 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N GLY Q 104 " --> pdb=" O ARG Q 100 " (cutoff:3.500A) removed outlier: 10.168A pdb=" N LYS Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LYS Q 106 " --> pdb=" O LEU Q 102 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS Q 108 " --> pdb=" O GLY Q 104 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE Q 109 " --> pdb=" O LYS Q 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 96 through 109' Processing helix chain 'R' and resid 8 through 22 removed outlier: 5.113A pdb=" N LYS R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 31 removed outlier: 4.062A pdb=" N ARG R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU R 31 " --> pdb=" O GLN R 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 26 through 31' Processing helix chain 'R' and resid 36 through 72 removed outlier: 4.845A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 87 Processing helix chain 'R' and resid 91 through 117 Proline residue: R 103 - end of helix removed outlier: 3.674A pdb=" N PHE R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 59 removed outlier: 4.876A pdb=" N ALA S 59 " --> pdb=" O LEU S 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 32 removed outlier: 4.316A pdb=" N VAL T 27 " --> pdb=" O LYS T 23 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU T 30 " --> pdb=" O ARG T 26 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL T 31 " --> pdb=" O VAL T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 46 Processing helix chain 'T' and resid 50 through 68 removed outlier: 4.065A pdb=" N VAL T 54 " --> pdb=" O ALA T 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 6 through 12 removed outlier: 4.682A pdb=" N ILE U 10 " --> pdb=" O ASP U 6 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE U 11 " --> pdb=" O PRO U 7 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU U 12 " --> pdb=" O ARG U 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 6 through 12' Processing helix chain 'U' and resid 17 through 27 removed outlier: 3.963A pdb=" N ASP U 26 " --> pdb=" O GLY U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 51 removed outlier: 4.100A pdb=" N ASP U 51 " --> pdb=" O GLU U 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 31 Processing helix chain 'W' and resid 50 through 62 Processing helix chain 'W' and resid 186 through 193 removed outlier: 4.258A pdb=" N GLU W 191 " --> pdb=" O ALA W 187 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU W 193 " --> pdb=" O ALA W 189 " (cutoff:3.500A) Processing helix chain 'Z' and resid 6 through 39 removed outlier: 3.708A pdb=" N GLU Z 12 " --> pdb=" O GLY Z 8 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU Z 13 " --> pdb=" O GLU Z 9 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N THR Z 14 " --> pdb=" O LEU Z 10 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP Z 15 " --> pdb=" O ARG Z 11 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASP Z 16 " --> pdb=" O GLU Z 12 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU Z 17 " --> pdb=" O LEU Z 13 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 67 removed outlier: 4.954A pdb=" N LEU Z 47 " --> pdb=" O ASN Z 43 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG Z 48 " --> pdb=" O ASN Z 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 27 Processing helix chain 'a' and resid 40 through 51 Processing helix chain 'b' and resid 9 through 21 removed outlier: 3.908A pdb=" N GLN b 19 " --> pdb=" O SER b 15 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TRP b 20 " --> pdb=" O ARG b 16 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS b 21 " --> pdb=" O ARG b 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 50 removed outlier: 3.999A pdb=" N LEU b 44 " --> pdb=" O PRO b 40 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS b 45 " --> pdb=" O ARG b 41 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA b 46 " --> pdb=" O ARG b 42 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 28 removed outlier: 4.033A pdb=" N ARG d 15 " --> pdb=" O ASN d 11 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE d 21 " --> pdb=" O ARG d 17 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ARG d 22 " --> pdb=" O VAL d 18 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU d 23 " --> pdb=" O HIS d 19 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR d 27 " --> pdb=" O LEU d 23 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG d 28 " --> pdb=" O ARG d 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 32 through 46 removed outlier: 4.727A pdb=" N LYS e 36 " --> pdb=" O LEU e 32 " (cutoff:3.500A) Proline residue: e 37 - end of helix removed outlier: 6.169A pdb=" N ARG e 40 " --> pdb=" O LYS e 36 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU e 44 " --> pdb=" O ARG e 40 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP e 45 " --> pdb=" O THR e 41 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLY e 46 " --> pdb=" O ARG e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 64 removed outlier: 3.769A pdb=" N ASN e 55 " --> pdb=" O SER e 51 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER e 56 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY e 64 " --> pdb=" O LYS e 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 59 Proline residue: g 59 - end of helix Processing helix chain 'y' and resid 51 through 74 removed outlier: 7.860A pdb=" N ILE y 63 " --> pdb=" O ASP y 59 " (cutoff:3.500A) removed outlier: 10.617A pdb=" N GLU y 64 " --> pdb=" O ARG y 60 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA y 65 " --> pdb=" O ASP y 61 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL y 66 " --> pdb=" O GLY y 62 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG y 73 " --> pdb=" O ARG y 69 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 14 removed outlier: 4.668A pdb=" N HIS 3 13 " --> pdb=" O ARG 3 9 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER 3 14 " --> pdb=" O ASP 3 10 " (cutoff:3.500A) 1434 hydrogen bonds defined for protein. 4302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3411 hydrogen bonds 5696 hydrogen bond angles 0 basepair planarities 1337 basepair parallelities 2458 stacking parallelities Total time for adding SS restraints: 243.66 Time building geometry restraints manager: 70.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.39: 61909 1.39 - 1.58: 92838 1.58 - 1.78: 8884 1.78 - 1.97: 147 1.97 - 2.16: 1 Bond restraints: 163779 Sorted by residual: bond pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 1.332 2.163 -0.831 1.31e-02 5.83e+03 4.03e+03 bond pdb=" CA GLN Q 50 " pdb=" CB GLN Q 50 " ideal model delta sigma weight residual 1.527 1.349 0.177 1.75e-02 3.27e+03 1.03e+02 bond pdb=" CA ALA C 45 " pdb=" C ALA C 45 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.41e-02 5.03e+03 3.03e+01 bond pdb=" C GLN d 9 " pdb=" N PRO d 10 " ideal model delta sigma weight residual 1.329 1.386 -0.056 1.25e-02 6.40e+03 2.03e+01 bond pdb=" C ARG c 6 " pdb=" N PRO c 7 " ideal model delta sigma weight residual 1.335 1.392 -0.057 1.30e-02 5.92e+03 1.92e+01 ... (remaining 163774 not shown) Histogram of bond angle deviations from ideal: 84.25 - 97.27: 3 97.27 - 110.30: 81387 110.30 - 123.32: 137502 123.32 - 136.35: 25958 136.35 - 149.37: 14 Bond angle restraints: 244864 Sorted by residual: angle pdb=" CA VAL V 47 " pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 116.60 84.25 32.35 1.45e+00 4.76e-01 4.98e+02 angle pdb=" O VAL V 47 " pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 122.57 102.43 20.14 1.25e+00 6.40e-01 2.60e+02 angle pdb=" C LEU 8 187 " pdb=" N ASP 8 188 " pdb=" CA ASP 8 188 " ideal model delta sigma weight residual 121.42 144.38 -22.96 1.43e+00 4.89e-01 2.58e+02 angle pdb=" N ARG g 90 " pdb=" CA ARG g 90 " pdb=" C ARG g 90 " ideal model delta sigma weight residual 112.72 97.28 15.44 1.28e+00 6.10e-01 1.45e+02 angle pdb=" C HIS 8 18 " pdb=" N GLN 8 19 " pdb=" CA GLN 8 19 " ideal model delta sigma weight residual 122.02 141.60 -19.58 1.89e+00 2.80e-01 1.07e+02 ... (remaining 244859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 92929 35.94 - 71.87: 11193 71.87 - 107.81: 1271 107.81 - 143.74: 61 143.74 - 179.68: 42 Dihedral angle restraints: 105496 sinusoidal: 87648 harmonic: 17848 Sorted by residual: dihedral pdb=" CA VAL V 47 " pdb=" C VAL V 47 " pdb=" N SER V 56 " pdb=" CA SER V 56 " ideal model delta harmonic sigma weight residual 180.00 103.49 76.51 0 5.00e+00 4.00e-02 2.34e+02 dihedral pdb=" C5' U A 316 " pdb=" C4' U A 316 " pdb=" C3' U A 316 " pdb=" O3' U A 316 " ideal model delta sinusoidal sigma weight residual 147.00 77.15 69.85 1 8.00e+00 1.56e-02 9.83e+01 dihedral pdb=" C4' U A 316 " pdb=" C3' U A 316 " pdb=" C2' U A 316 " pdb=" C1' U A 316 " ideal model delta sinusoidal sigma weight residual -35.00 34.49 -69.49 1 8.00e+00 1.56e-02 9.74e+01 ... (remaining 105493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.370: 31188 0.370 - 0.740: 26 0.740 - 1.111: 12 1.111 - 1.481: 13 1.481 - 1.851: 8 Chirality restraints: 31247 Sorted by residual: chirality pdb=" CB ILE 8 50 " pdb=" CA ILE 8 50 " pdb=" CG1 ILE 8 50 " pdb=" CG2 ILE 8 50 " both_signs ideal model delta sigma weight residual False 2.64 0.79 1.85 2.00e-01 2.50e+01 8.57e+01 chirality pdb=" CB THR 8 214 " pdb=" CA THR 8 214 " pdb=" OG1 THR 8 214 " pdb=" CG2 THR 8 214 " both_signs ideal model delta sigma weight residual False 2.55 0.79 1.76 2.00e-01 2.50e+01 7.77e+01 chirality pdb=" CG LEU u 7 " pdb=" CB LEU u 7 " pdb=" CD1 LEU u 7 " pdb=" CD2 LEU u 7 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 ... (remaining 31244 not shown) Planarity restraints: 13450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL V 47 " -0.156 2.00e-02 2.50e+03 2.57e-01 6.61e+02 pdb=" C VAL V 47 " 0.430 2.00e-02 2.50e+03 pdb=" O VAL V 47 " -0.231 2.00e-02 2.50e+03 pdb=" N SER V 56 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN 8 24 " -0.089 5.00e-02 4.00e+02 1.39e-01 3.08e+01 pdb=" N PRO 8 25 " 0.240 5.00e-02 4.00e+02 pdb=" CA PRO 8 25 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO 8 25 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C A1747 " 0.059 2.00e-02 2.50e+03 3.15e-02 2.23e+01 pdb=" N1 C A1747 " -0.061 2.00e-02 2.50e+03 pdb=" C2 C A1747 " 0.021 2.00e-02 2.50e+03 pdb=" O2 C A1747 " -0.022 2.00e-02 2.50e+03 pdb=" N3 C A1747 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C A1747 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C A1747 " 0.023 2.00e-02 2.50e+03 pdb=" C5 C A1747 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C A1747 " -0.016 2.00e-02 2.50e+03 ... (remaining 13447 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 17 1.80 - 2.58: 2783 2.58 - 3.35: 174538 3.35 - 4.13: 454967 4.13 - 4.90: 695406 Nonbonded interactions: 1327711 Sorted by model distance: nonbonded pdb=" OP1 G A1379 " pdb=" NH2 ARG b 16 " model vdw 1.028 2.520 nonbonded pdb=" NH2 ARG q 78 " pdb=" CD2 TYR q 130 " model vdw 1.246 3.420 nonbonded pdb=" NZ LYS H 57 " pdb=" NH2 ARG H 60 " model vdw 1.281 3.200 nonbonded pdb=" O2 C h 806 " pdb=" ND2 ASN q 16 " model vdw 1.320 2.520 nonbonded pdb=" CE1 PHE 8 16 " pdb=" CD1 ILE 8 41 " model vdw 1.385 3.760 ... (remaining 1327706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.370 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: 0.140 Extract box with map and model: 23.240 Check model and map are aligned: 1.630 Set scattering table: 1.050 Process input model: 525.550 Find NCS groups from input model: 3.140 Set up NCS constraints: 0.380 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 562.330 ------------------------------------------------------------------------------- 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 : 0.011 0.831 163779 Z= 0.674 Angle : 1.051 33.069 244864 Z= 0.536 Chirality : 0.072 1.851 31247 Planarity : 0.007 0.257 13450 Dihedral : 23.506 179.675 94016 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.75 % Favored : 89.49 % Rotamer: Outliers : 0.62 % Allowed : 2.28 % Favored : 97.10 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.15 % 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: -4.46 (0.09), residues: 6173 helix: -2.13 (0.09), residues: 2024 sheet: -3.02 (0.13), residues: 1088 loop : -3.56 (0.09), residues: 3061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP N 93 HIS 0.025 0.003 HIS O 16 PHE 0.039 0.004 PHE d 8 TYR 0.048 0.004 TYR N 41 ARG 0.020 0.002 ARG 7 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12346 Ramachandran restraints generated. 6173 Oldfield, 0 Emsley, 6173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12346 Ramachandran restraints generated. 6173 Oldfield, 0 Emsley, 6173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1449 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1417 time to evaluate : 6.488 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: 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 TARDY: cannot create tardy model for: "MET g 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: j 19 LYS cc_start: 0.8636 (tttt) cc_final: 0.8359 (mttt) REVERT: k 19 LYS cc_start: 0.7660 (mttt) cc_final: 0.6850 (tptt) REVERT: k 60 ARG cc_start: 0.5285 (mpt180) cc_final: 0.4763 (mtm-85) REVERT: k 106 LYS cc_start: 0.4877 (mttt) cc_final: 0.4287 (mmmt) REVERT: k 135 LYS cc_start: 0.6960 (tttt) cc_final: 0.6584 (ptpt) REVERT: k 167 PHE cc_start: 0.7578 (p90) cc_final: 0.7341 (p90) REVERT: k 177 THR cc_start: 0.6400 (m) cc_final: 0.6197 (m) REVERT: l 60 TYR cc_start: 0.7211 (m-10) cc_final: 0.6937 (m-10) REVERT: l 108 MET cc_start: 0.6961 (ttt) cc_final: 0.6675 (ttm) REVERT: l 124 LYS cc_start: 0.5568 (tttt) cc_final: 0.5295 (ttmt) REVERT: m 63 ILE cc_start: 0.8564 (mp) cc_final: 0.8263 (pt) REVERT: m 91 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6992 (mm-30) REVERT: m 97 PHE cc_start: 0.6035 (t80) cc_final: 0.5809 (t80) REVERT: m 111 GLN cc_start: 0.6888 (mm110) cc_final: 0.6647 (tp40) REVERT: m 130 VAL cc_start: 0.5838 (t) cc_final: 0.5563 (p) REVERT: n 5 GLU cc_start: 0.7309 (tt0) cc_final: 0.6144 (mt-10) REVERT: p 32 LEU cc_start: 0.6007 (tp) cc_final: 0.5632 (mt) REVERT: q 3 MET cc_start: 0.5444 (tpp) cc_final: 0.3975 (tmm) REVERT: q 93 ASN cc_start: 0.7398 (m-40) cc_final: 0.7161 (m-40) REVERT: 4 142 ARG cc_start: 0.6698 (mtt180) cc_final: 0.6482 (mtm-85) REVERT: 4 149 LYS cc_start: 0.4728 (ptpt) cc_final: 0.4147 (tptm) REVERT: t 82 LYS cc_start: 0.6122 (mttt) cc_final: 0.5881 (mttt) REVERT: t 86 HIS cc_start: 0.7969 (m-70) cc_final: 0.7586 (m90) REVERT: t 137 ARG cc_start: 0.5929 (OUTLIER) cc_final: 0.5150 (ptt90) REVERT: u 29 GLN cc_start: 0.7491 (mp10) cc_final: 0.6776 (mp10) REVERT: u 56 LYS cc_start: 0.8333 (tptt) cc_final: 0.7826 (tmtt) REVERT: u 117 TYR cc_start: 0.7402 (m-80) cc_final: 0.7165 (m-80) REVERT: u 123 LYS cc_start: 0.6344 (mttt) cc_final: 0.5448 (mmtm) REVERT: v 96 LEU cc_start: 0.6252 (mt) cc_final: 0.5814 (mt) REVERT: v 115 ARG cc_start: 0.4413 (ptt180) cc_final: 0.3918 (mmm160) REVERT: x 9 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8117 (mmtm) REVERT: z 20 ILE cc_start: 0.8248 (mt) cc_final: 0.8041 (mm) REVERT: z 47 SER cc_start: 0.6831 (m) cc_final: 0.6624 (t) REVERT: z 71 LEU cc_start: 0.7592 (tp) cc_final: 0.7187 (mt) REVERT: z 102 LYS cc_start: 0.6775 (ttmt) cc_final: 0.6571 (tptt) REVERT: 5 26 TYR cc_start: 0.7779 (m-10) cc_final: 0.7570 (m-10) REVERT: 5 33 GLN cc_start: 0.7914 (mt0) cc_final: 0.7645 (mt0) REVERT: 5 52 ILE cc_start: 0.8112 (mm) cc_final: 0.7789 (tt) REVERT: 6 10 PHE cc_start: 0.5596 (t80) cc_final: 0.5331 (t80) REVERT: 7 18 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7174 (ttm110) REVERT: 7 29 ARG cc_start: 0.7039 (ttm170) cc_final: 0.6615 (mtt90) REVERT: 8 22 ARG cc_start: 0.7234 (mtt180) cc_final: 0.6950 (mmm160) REVERT: 8 39 TYR cc_start: 0.1047 (OUTLIER) cc_final: 0.0254 (t80) REVERT: 8 228 ARG cc_start: 0.4048 (ttt180) cc_final: 0.3748 (ttm-80) REVERT: Y 94 ARG cc_start: 0.5196 (mmt-90) cc_final: 0.4799 (mmm160) REVERT: Y 102 ARG cc_start: 0.6521 (ttm170) cc_final: 0.5643 (ttp80) REVERT: C 10 THR cc_start: 0.8980 (t) cc_final: 0.8684 (m) REVERT: C 217 LYS cc_start: 0.8559 (mttt) cc_final: 0.8286 (tttp) REVERT: E 63 LYS cc_start: 0.8146 (tmtp) cc_final: 0.7783 (pttm) REVERT: E 152 LYS cc_start: 0.8605 (mttt) cc_final: 0.8305 (mppt) REVERT: E 193 ASP cc_start: 0.6422 (m-30) cc_final: 0.6085 (m-30) REVERT: F 90 MET cc_start: 0.5991 (mtp) cc_final: 0.5711 (tpt) REVERT: F 142 GLN cc_start: 0.4797 (pm20) cc_final: 0.4334 (pm20) REVERT: F 147 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7849 (mp0) REVERT: F 149 ASP cc_start: 0.7509 (m-30) cc_final: 0.7074 (t0) REVERT: F 154 ASP cc_start: 0.5801 (p0) cc_final: 0.5367 (m-30) REVERT: G 165 TYR cc_start: 0.6790 (m-80) cc_final: 0.6506 (m-80) REVERT: J 42 LYS cc_start: 0.5250 (mmtm) cc_final: 0.4584 (ptmt) REVERT: J 89 LYS cc_start: 0.5915 (mttt) cc_final: 0.5710 (mmtt) REVERT: K 5 THR cc_start: 0.9121 (m) cc_final: 0.8903 (p) REVERT: K 21 SER cc_start: 0.8197 (t) cc_final: 0.7942 (p) REVERT: K 89 ILE cc_start: 0.8876 (mm) cc_final: 0.8539 (mt) REVERT: L 17 LYS cc_start: 0.7776 (mttp) cc_final: 0.7528 (mtpp) REVERT: L 99 PHE cc_start: 0.8625 (m-10) cc_final: 0.8101 (m-80) REVERT: N 27 VAL cc_start: 0.8864 (t) cc_final: 0.8495 (p) REVERT: N 28 SER cc_start: 0.8594 (m) cc_final: 0.8302 (p) REVERT: N 32 TYR cc_start: 0.8237 (m-80) cc_final: 0.7984 (m-80) REVERT: N 67 ASN cc_start: 0.7707 (m-40) cc_final: 0.7239 (t0) REVERT: P 43 SER cc_start: 0.7798 (t) cc_final: 0.6896 (p) REVERT: P 118 ASP cc_start: 0.8030 (m-30) cc_final: 0.7646 (m-30) REVERT: R 22 LYS cc_start: 0.8343 (mttt) cc_final: 0.8112 (mmmt) REVERT: R 66 ASN cc_start: 0.8432 (t0) cc_final: 0.8208 (t0) REVERT: S 49 THR cc_start: 0.6736 (m) cc_final: 0.6426 (p) REVERT: T 102 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7869 (ttm170) REVERT: V 17 LYS cc_start: 0.8316 (tttt) cc_final: 0.8021 (pttm) REVERT: W 84 ASP cc_start: 0.7208 (m-30) cc_final: 0.6997 (t0) REVERT: W 86 HIS cc_start: 0.8149 (t-90) cc_final: 0.7548 (t-90) REVERT: W 131 ILE cc_start: 0.7668 (mt) cc_final: 0.7255 (mt) REVERT: W 192 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8355 (mt-10) REVERT: X 56 ASP cc_start: 0.8110 (p0) cc_final: 0.7868 (p0) REVERT: X 57 ASP cc_start: 0.7413 (m-30) cc_final: 0.7181 (m-30) REVERT: a 56 VAL cc_start: 0.8747 (t) cc_final: 0.8368 (m) REVERT: c 24 ARG cc_start: 0.5866 (ttt180) cc_final: 0.5648 (ptm160) REVERT: c 33 ARG cc_start: 0.2146 (OUTLIER) cc_final: 0.1727 (mmm-85) REVERT: y 21 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.6874 (m170) REVERT: y 53 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6289 (mtpt) outliers start: 32 outliers final: 7 residues processed: 1445 average time/residue: 1.5202 time to fit residues: 3599.5403 Evaluate side-chains 951 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 938 time to evaluate : 5.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain 4 residue 126 ARG Chi-restraints excluded: chain t residue 137 ARG Chi-restraints excluded: chain 7 residue 18 ARG Chi-restraints excluded: chain 8 residue 16 PHE Chi-restraints excluded: chain 8 residue 18 HIS Chi-restraints excluded: chain 8 residue 39 TYR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 33 ARG Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain y residue 21 HIS Chi-restraints excluded: chain y residue 53 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1077 random chunks: chunk 909 optimal weight: 0.8980 chunk 816 optimal weight: 4.9990 chunk 452 optimal weight: 0.7980 chunk 278 optimal weight: 0.8980 chunk 550 optimal weight: 10.0000 chunk 436 optimal weight: 6.9990 chunk 844 optimal weight: 0.7980 chunk 326 optimal weight: 3.9990 chunk 513 optimal weight: 10.0000 chunk 628 optimal weight: 3.9990 chunk 978 optimal weight: 30.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 27 GLN k 122 GLN l 66 GLN l 178 HIS l 179 GLN m 95 ASN ** m 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 163 HIS p 142 HIS q 63 GLN s 70 HIS t 84 GLN u 112 GLN x 14 GLN x 28 GLN ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 69 HIS ** 7 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 84 ASN 8 94 GLN ** r 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 10 ASN C 113 GLN C 143 HIS C 227 ASN H 11 HIS ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN M 84 ASN ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 ASN Q 82 HIS ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 ASN ** S 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN U 61 ASN V 4 HIS ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN X 29 GLN X 50 ASN a 42 GLN b 12 ASN ** c 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 36 GLN g 15 GLN 3 13 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 163779 Z= 0.190 Angle : 0.662 10.840 244864 Z= 0.330 Chirality : 0.036 0.314 31247 Planarity : 0.005 0.087 13450 Dihedral : 24.371 179.772 81775 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.23 % Favored : 93.60 % Rotamer: Outliers : 2.12 % Allowed : 8.98 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.81 (0.10), residues: 6175 helix: -0.28 (0.11), residues: 2062 sheet: -2.26 (0.14), residues: 1101 loop : -2.91 (0.10), residues: 3012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP p 103 HIS 0.009 0.001 HIS 4 64 PHE 0.019 0.002 PHE l 67 TYR 0.020 0.002 TYR u 117 ARG 0.014 0.001 ARG l 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1097 time to evaluate : 5.832 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: symmetry clash TARDY: cannot create tardy model for: "MET g 1 " (corrupted residue). Skipping it. REVERT: j 19 LYS cc_start: 0.8595 (tttt) cc_final: 0.8369 (mttt) REVERT: j 24 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7624 (p) REVERT: k 19 LYS cc_start: 0.7356 (mttt) cc_final: 0.6801 (tptt) REVERT: k 60 ARG cc_start: 0.5447 (mpt180) cc_final: 0.4791 (mtm-85) REVERT: k 106 LYS cc_start: 0.4829 (mttt) cc_final: 0.4251 (mmmt) REVERT: k 167 PHE cc_start: 0.7651 (p90) cc_final: 0.7433 (p90) REVERT: k 177 THR cc_start: 0.6390 (m) cc_final: 0.6149 (m) REVERT: l 55 LYS cc_start: 0.6225 (mttt) cc_final: 0.6004 (mttp) REVERT: l 66 GLN cc_start: 0.8129 (tt0) cc_final: 0.7784 (mm-40) REVERT: l 108 MET cc_start: 0.6902 (ttt) cc_final: 0.6612 (ttm) REVERT: l 124 LYS cc_start: 0.5620 (tttt) cc_final: 0.5247 (ttmt) REVERT: l 179 GLN cc_start: 0.6214 (OUTLIER) cc_final: 0.5979 (tm130) REVERT: m 97 PHE cc_start: 0.5920 (t80) cc_final: 0.5441 (t80) REVERT: m 130 VAL cc_start: 0.5878 (t) cc_final: 0.5550 (p) REVERT: n 5 GLU cc_start: 0.7272 (tt0) cc_final: 0.6042 (mt-10) REVERT: n 23 LEU cc_start: 0.6719 (mp) cc_final: 0.6447 (pp) REVERT: n 31 ARG cc_start: 0.6204 (mtp85) cc_final: 0.5885 (ptp-110) REVERT: p 32 LEU cc_start: 0.5825 (tp) cc_final: 0.5480 (mt) REVERT: p 148 ASN cc_start: 0.7798 (m-40) cc_final: 0.7449 (m-40) REVERT: q 3 MET cc_start: 0.5493 (tpp) cc_final: 0.3921 (tmm) REVERT: q 43 GLU cc_start: 0.6442 (mm-30) cc_final: 0.6075 (mp0) REVERT: 4 33 LYS cc_start: 0.3750 (pttt) cc_final: 0.3487 (ttpt) REVERT: 4 69 LYS cc_start: 0.7245 (mttt) cc_final: 0.6911 (mtmt) REVERT: 4 142 ARG cc_start: 0.6616 (mtt180) cc_final: 0.6330 (mtm-85) REVERT: 4 146 GLN cc_start: 0.6810 (mt0) cc_final: 0.6499 (mm-40) REVERT: 4 149 LYS cc_start: 0.4404 (ptpt) cc_final: 0.3935 (tptm) REVERT: t 53 TRP cc_start: 0.7807 (p-90) cc_final: 0.7513 (p-90) REVERT: u 56 LYS cc_start: 0.8369 (tptt) cc_final: 0.7903 (tmtt) REVERT: u 123 LYS cc_start: 0.6284 (mttt) cc_final: 0.5424 (mmtm) REVERT: v 115 ARG cc_start: 0.4486 (ptt180) cc_final: 0.4036 (mmm160) REVERT: x 9 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8200 (mptt) REVERT: x 44 LYS cc_start: 0.8503 (mtpp) cc_final: 0.8270 (mtpp) REVERT: z 47 SER cc_start: 0.6761 (m) cc_final: 0.6346 (t) REVERT: z 71 LEU cc_start: 0.7571 (tp) cc_final: 0.7329 (mt) REVERT: z 102 LYS cc_start: 0.6646 (ttmt) cc_final: 0.6339 (tptm) REVERT: 5 89 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6270 (ppt-90) REVERT: 7 9 LYS cc_start: 0.7012 (tptp) cc_final: 0.6803 (tptp) REVERT: 7 29 ARG cc_start: 0.6967 (ttm170) cc_final: 0.6702 (mtt90) REVERT: 7 56 ARG cc_start: 0.4276 (ptm160) cc_final: 0.3861 (ptt90) REVERT: 8 22 ARG cc_start: 0.7274 (mtt180) cc_final: 0.7035 (mmm160) REVERT: 8 35 ARG cc_start: 0.2081 (OUTLIER) cc_final: 0.1606 (ptm-80) REVERT: 8 41 ILE cc_start: 0.1492 (OUTLIER) cc_final: 0.1161 (pt) REVERT: 8 89 MET cc_start: 0.3358 (mmm) cc_final: 0.3059 (mmt) REVERT: 8 143 LYS cc_start: 0.5740 (ttmt) cc_final: 0.4817 (mtmm) REVERT: r 79 LEU cc_start: 0.6710 (tt) cc_final: 0.6449 (mp) REVERT: 9 23 ARG cc_start: 0.7275 (ttp-170) cc_final: 0.6502 (tpp-160) REVERT: 9 92 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6757 (tm-30) REVERT: C 10 THR cc_start: 0.9001 (t) cc_final: 0.8761 (m) REVERT: C 146 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7450 (mm-30) REVERT: C 182 ILE cc_start: 0.9169 (mm) cc_final: 0.8920 (mm) REVERT: C 217 LYS cc_start: 0.8814 (mttt) cc_final: 0.8452 (mtpp) REVERT: D 57 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8141 (mm) REVERT: D 108 ASP cc_start: 0.7092 (m-30) cc_final: 0.6842 (m-30) REVERT: E 63 LYS cc_start: 0.8118 (tmtp) cc_final: 0.7794 (pttm) REVERT: E 98 TYR cc_start: 0.8176 (m-80) cc_final: 0.7952 (m-80) REVERT: E 143 THR cc_start: 0.8624 (p) cc_final: 0.8302 (t) REVERT: F 58 ASN cc_start: 0.7797 (t0) cc_final: 0.7333 (t0) REVERT: F 90 MET cc_start: 0.6072 (mtp) cc_final: 0.5865 (tpt) REVERT: F 149 ASP cc_start: 0.7540 (m-30) cc_final: 0.7018 (t70) REVERT: H 2 LYS cc_start: 0.7417 (mtmt) cc_final: 0.7005 (tttm) REVERT: I 1 MET cc_start: 0.4361 (tmm) cc_final: 0.3666 (tpt) REVERT: J 38 MET cc_start: 0.4769 (ptm) cc_final: 0.4155 (ptp) REVERT: J 42 LYS cc_start: 0.5281 (mmtm) cc_final: 0.4829 (ptpt) REVERT: K 76 ARG cc_start: 0.8206 (mtt180) cc_final: 0.7793 (mtm-85) REVERT: K 89 ILE cc_start: 0.8900 (mm) cc_final: 0.8457 (mt) REVERT: L 1 MET cc_start: 0.6351 (ttm) cc_final: 0.5935 (ttm) REVERT: L 69 ARG cc_start: 0.7238 (ttm170) cc_final: 0.6949 (ttt90) REVERT: L 70 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8209 (ttt180) REVERT: L 110 LYS cc_start: 0.7905 (mppt) cc_final: 0.7637 (mppt) REVERT: L 113 LYS cc_start: 0.7691 (mmmm) cc_final: 0.7440 (mmmt) REVERT: N 18 ARG cc_start: 0.7961 (ptm160) cc_final: 0.7755 (ptm160) REVERT: N 27 VAL cc_start: 0.8585 (t) cc_final: 0.8359 (p) REVERT: N 66 ILE cc_start: 0.8867 (mt) cc_final: 0.8630 (pt) REVERT: N 67 ASN cc_start: 0.7785 (m-40) cc_final: 0.7353 (t0) REVERT: N 107 SER cc_start: 0.9057 (t) cc_final: 0.8600 (t) REVERT: P 19 LEU cc_start: 0.9083 (mm) cc_final: 0.8839 (mm) REVERT: P 43 SER cc_start: 0.7766 (t) cc_final: 0.6896 (p) REVERT: P 64 SER cc_start: 0.7253 (p) cc_final: 0.6956 (m) REVERT: P 118 ASP cc_start: 0.8174 (m-30) cc_final: 0.7871 (m-30) REVERT: Q 82 HIS cc_start: 0.6960 (OUTLIER) cc_final: 0.6674 (m-70) REVERT: Q 102 LEU cc_start: 0.8796 (mp) cc_final: 0.8423 (mp) REVERT: Q 103 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7505 (mtm110) REVERT: R 34 LYS cc_start: 0.8806 (mptm) cc_final: 0.8589 (mmtt) REVERT: R 97 GLU cc_start: 0.7345 (tp30) cc_final: 0.7099 (tp30) REVERT: U 62 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7331 (mmt180) REVERT: U 68 ARG cc_start: 0.7345 (ttm170) cc_final: 0.7119 (ttm-80) REVERT: V 17 LYS cc_start: 0.8202 (tttt) cc_final: 0.7911 (pttm) REVERT: W 84 ASP cc_start: 0.7239 (m-30) cc_final: 0.7038 (t0) REVERT: W 138 LEU cc_start: 0.6887 (mt) cc_final: 0.6573 (mt) REVERT: X 56 ASP cc_start: 0.8375 (p0) cc_final: 0.8168 (p0) REVERT: c 28 ARG cc_start: 0.5988 (mtm180) cc_final: 0.5320 (tpt90) REVERT: e 58 ILE cc_start: 0.9253 (mt) cc_final: 0.9036 (mp) REVERT: e 62 LEU cc_start: 0.8978 (mt) cc_final: 0.8750 (mt) outliers start: 109 outliers final: 71 residues processed: 1156 average time/residue: 1.4554 time to fit residues: 2851.4422 Evaluate side-chains 1026 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 947 time to evaluate : 6.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 179 GLN Chi-restraints excluded: chain m residue 66 ASP Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain p residue 96 SER Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 63 GLN Chi-restraints excluded: chain q residue 108 THR Chi-restraints excluded: chain t residue 43 ILE Chi-restraints excluded: chain t residue 122 VAL Chi-restraints excluded: chain t residue 137 ARG Chi-restraints excluded: chain u residue 98 ILE Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 82 ILE Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain 5 residue 89 ARG Chi-restraints excluded: chain 6 residue 11 VAL Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 74 PHE Chi-restraints excluded: chain 8 residue 35 ARG Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 8 residue 123 THR Chi-restraints excluded: chain 8 residue 159 SER Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain 9 residue 17 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 70 ARG Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain P residue 46 HIS Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain a residue 42 GLN Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 26 ASN Chi-restraints excluded: chain g residue 53 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1077 random chunks: chunk 543 optimal weight: 7.9990 chunk 303 optimal weight: 20.0000 chunk 814 optimal weight: 2.9990 chunk 665 optimal weight: 6.9990 chunk 269 optimal weight: 7.9990 chunk 979 optimal weight: 0.9990 chunk 1058 optimal weight: 4.9990 chunk 872 optimal weight: 2.9990 chunk 971 optimal weight: 6.9990 chunk 334 optimal weight: 7.9990 chunk 786 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 111 GLN ** l 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 80 ASN p 142 HIS p 148 ASN q 63 GLN t 84 GLN x 7 GLN ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 69 HIS 7 21 ASN ** r 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 62 ASN ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN R 94 ASN S 67 HIS ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 ASN c 26 ASN c 46 HIS g 15 GLN 3 13 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 163779 Z= 0.274 Angle : 0.650 10.932 244864 Z= 0.328 Chirality : 0.037 0.301 31247 Planarity : 0.005 0.076 13450 Dihedral : 24.192 179.980 81747 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.63 % Favored : 92.31 % Rotamer: Outliers : 3.47 % Allowed : 11.51 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.18 (0.10), residues: 6175 helix: 0.24 (0.11), residues: 2069 sheet: -1.84 (0.15), residues: 1066 loop : -2.58 (0.10), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 92 HIS 0.028 0.001 HIS Q 82 PHE 0.020 0.002 PHE X 69 TYR 0.016 0.002 TYR 8 49 ARG 0.010 0.001 ARG u 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1044 time to evaluate : 6.471 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET g 1 " (corrupted residue). Skipping it. REVERT: j 19 LYS cc_start: 0.8608 (tttt) cc_final: 0.8202 (mttt) REVERT: j 24 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7492 (p) REVERT: k 19 LYS cc_start: 0.7389 (mttt) cc_final: 0.6724 (tptt) REVERT: k 60 ARG cc_start: 0.5606 (mpt180) cc_final: 0.4867 (mtm-85) REVERT: k 106 LYS cc_start: 0.5121 (mttt) cc_final: 0.4558 (mmmt) REVERT: k 133 MET cc_start: 0.6134 (mtp) cc_final: 0.5636 (ttp) REVERT: l 108 MET cc_start: 0.6918 (ttt) cc_final: 0.6643 (ttm) REVERT: l 124 LYS cc_start: 0.5592 (tttt) cc_final: 0.5199 (ttmt) REVERT: l 136 ASP cc_start: 0.6549 (m-30) cc_final: 0.6337 (m-30) REVERT: m 56 PHE cc_start: 0.6108 (m-80) cc_final: 0.5831 (m-80) REVERT: m 97 PHE cc_start: 0.6080 (t80) cc_final: 0.5627 (t80) REVERT: m 130 VAL cc_start: 0.6037 (t) cc_final: 0.5737 (p) REVERT: n 5 GLU cc_start: 0.7390 (tt0) cc_final: 0.6160 (mt-10) REVERT: n 23 LEU cc_start: 0.6691 (mp) cc_final: 0.6489 (pp) REVERT: n 26 PHE cc_start: 0.6261 (m-80) cc_final: 0.6058 (m-80) REVERT: n 31 ARG cc_start: 0.6192 (mtp85) cc_final: 0.5812 (ptp-110) REVERT: n 93 THR cc_start: 0.5631 (m) cc_final: 0.5332 (m) REVERT: p 32 LEU cc_start: 0.5892 (tp) cc_final: 0.5519 (mt) REVERT: p 148 ASN cc_start: 0.7692 (m110) cc_final: 0.7329 (m-40) REVERT: q 3 MET cc_start: 0.5509 (tpp) cc_final: 0.3937 (tmm) REVERT: 4 34 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5668 (mp0) REVERT: t 137 ARG cc_start: 0.6142 (OUTLIER) cc_final: 0.4994 (ptt90) REVERT: u 56 LYS cc_start: 0.8326 (tptt) cc_final: 0.7893 (tmtt) REVERT: u 89 ASP cc_start: 0.6941 (m-30) cc_final: 0.6561 (m-30) REVERT: u 123 LYS cc_start: 0.6413 (mttt) cc_final: 0.5547 (mmtm) REVERT: v 23 TYR cc_start: 0.5470 (t80) cc_final: 0.5106 (t80) REVERT: v 92 HIS cc_start: 0.6347 (m-70) cc_final: 0.5968 (m90) REVERT: v 115 ARG cc_start: 0.4373 (ptt180) cc_final: 0.3981 (mmm160) REVERT: x 9 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8299 (mptt) REVERT: x 44 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8260 (mtpp) REVERT: z 17 GLN cc_start: 0.7339 (mt0) cc_final: 0.6992 (mm-40) REVERT: z 39 ARG cc_start: 0.7231 (ptt-90) cc_final: 0.6994 (ptp-170) REVERT: z 71 LEU cc_start: 0.7602 (tp) cc_final: 0.7162 (mt) REVERT: z 82 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7235 (mtpp) REVERT: z 102 LYS cc_start: 0.6690 (ttmt) cc_final: 0.6362 (tptm) REVERT: 5 19 ARG cc_start: 0.7169 (ptt-90) cc_final: 0.6829 (ptp90) REVERT: 5 89 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6325 (ppt-90) REVERT: 7 29 ARG cc_start: 0.6892 (ttm170) cc_final: 0.6521 (mtt90) REVERT: 8 22 ARG cc_start: 0.7443 (mtt180) cc_final: 0.7134 (mmm160) REVERT: 8 35 ARG cc_start: 0.2023 (OUTLIER) cc_final: 0.1625 (ptm-80) REVERT: 8 41 ILE cc_start: 0.2102 (OUTLIER) cc_final: 0.1689 (pt) REVERT: 8 89 MET cc_start: 0.3466 (mmm) cc_final: 0.2821 (mmt) REVERT: r 79 LEU cc_start: 0.6797 (tt) cc_final: 0.6559 (mp) REVERT: Y 21 ARG cc_start: 0.6073 (mtt180) cc_final: 0.5711 (mmp-170) REVERT: Y 80 PHE cc_start: 0.7324 (p90) cc_final: 0.6796 (t80) REVERT: 9 23 ARG cc_start: 0.7385 (ttp-170) cc_final: 0.6955 (tpm170) REVERT: 9 62 ASN cc_start: 0.7795 (m110) cc_final: 0.7384 (m110) REVERT: C 146 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7586 (mm-30) REVERT: C 217 LYS cc_start: 0.8942 (mttt) cc_final: 0.8584 (mtpp) REVERT: D 108 ASP cc_start: 0.7149 (m-30) cc_final: 0.6842 (m-30) REVERT: E 55 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8007 (ttm-80) REVERT: E 143 THR cc_start: 0.8686 (p) cc_final: 0.8465 (t) REVERT: F 13 GLN cc_start: 0.8187 (pp30) cc_final: 0.7818 (pp30) REVERT: F 71 LYS cc_start: 0.7188 (ttpt) cc_final: 0.6815 (tppt) REVERT: F 90 MET cc_start: 0.6351 (mtp) cc_final: 0.5839 (tpt) REVERT: F 149 ASP cc_start: 0.7487 (m-30) cc_final: 0.7054 (t0) REVERT: G 158 TYR cc_start: 0.8216 (m-80) cc_final: 0.7897 (m-80) REVERT: H 2 LYS cc_start: 0.7662 (mtmt) cc_final: 0.7065 (tttm) REVERT: I 1 MET cc_start: 0.4341 (tmm) cc_final: 0.2185 (ptt) REVERT: J 38 MET cc_start: 0.4579 (ptm) cc_final: 0.4199 (ptm) REVERT: J 42 LYS cc_start: 0.5098 (mmtm) cc_final: 0.4896 (ptpt) REVERT: K 52 ASP cc_start: 0.7887 (m-30) cc_final: 0.7607 (m-30) REVERT: K 89 ILE cc_start: 0.9042 (mm) cc_final: 0.8653 (mt) REVERT: L 69 ARG cc_start: 0.7388 (ttm170) cc_final: 0.7153 (ttt90) REVERT: L 70 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8228 (ttt180) REVERT: M 26 GLU cc_start: 0.6933 (tp30) cc_final: 0.6242 (tp30) REVERT: N 66 ILE cc_start: 0.8993 (mt) cc_final: 0.8786 (pt) REVERT: N 67 ASN cc_start: 0.8205 (m-40) cc_final: 0.7540 (t0) REVERT: O 37 THR cc_start: 0.8337 (p) cc_final: 0.7967 (m) REVERT: P 19 LEU cc_start: 0.9139 (mm) cc_final: 0.8755 (mm) REVERT: P 43 SER cc_start: 0.8112 (t) cc_final: 0.7429 (p) REVERT: P 52 VAL cc_start: 0.9102 (t) cc_final: 0.8872 (m) REVERT: P 113 ILE cc_start: 0.8968 (mm) cc_final: 0.8652 (mm) REVERT: P 118 ASP cc_start: 0.8306 (m-30) cc_final: 0.7957 (m-30) REVERT: Q 1 MET cc_start: 0.6508 (mmm) cc_final: 0.6259 (mmp) REVERT: Q 98 TYR cc_start: 0.9128 (p90) cc_final: 0.8758 (p90) REVERT: R 42 SER cc_start: 0.9196 (t) cc_final: 0.8874 (m) REVERT: U 24 ILE cc_start: 0.8790 (mt) cc_final: 0.8542 (pt) REVERT: U 68 ARG cc_start: 0.7417 (ttm170) cc_final: 0.7162 (ttm-80) REVERT: V 17 LYS cc_start: 0.8441 (tttt) cc_final: 0.8232 (pttm) REVERT: V 97 ILE cc_start: 0.6947 (mt) cc_final: 0.6731 (mm) REVERT: W 84 ASP cc_start: 0.7381 (m-30) cc_final: 0.6981 (t0) REVERT: W 132 GLU cc_start: 0.6656 (tt0) cc_final: 0.6449 (tt0) REVERT: X 56 ASP cc_start: 0.8414 (p0) cc_final: 0.8202 (p0) REVERT: b 36 GLN cc_start: 0.7326 (mp10) cc_final: 0.6807 (mp10) REVERT: c 8 ILE cc_start: 0.5291 (OUTLIER) cc_final: 0.4982 (mp) REVERT: c 28 ARG cc_start: 0.6595 (mtm180) cc_final: 0.5646 (tpm170) REVERT: c 45 ARG cc_start: 0.7581 (mmt180) cc_final: 0.7367 (mmt180) outliers start: 178 outliers final: 116 residues processed: 1146 average time/residue: 1.4893 time to fit residues: 2927.2225 Evaluate side-chains 1076 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 950 time to evaluate : 6.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 151 VAL Chi-restraints excluded: chain k residue 162 MET Chi-restraints excluded: chain l residue 9 THR Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 123 VAL Chi-restraints excluded: chain l residue 147 THR Chi-restraints excluded: chain m residue 37 ILE Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 66 ASP Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain m residue 113 GLU Chi-restraints excluded: chain m residue 186 ILE Chi-restraints excluded: chain n residue 88 THR Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 96 SER Chi-restraints excluded: chain q residue 108 THR Chi-restraints excluded: chain 4 residue 34 GLU Chi-restraints excluded: chain t residue 122 VAL Chi-restraints excluded: chain t residue 137 ARG Chi-restraints excluded: chain u residue 98 ILE Chi-restraints excluded: chain v residue 30 SER Chi-restraints excluded: chain v residue 45 THR Chi-restraints excluded: chain v residue 82 ILE Chi-restraints excluded: chain x residue 7 GLN Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 82 LYS Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 89 ARG Chi-restraints excluded: chain 6 residue 11 VAL Chi-restraints excluded: chain 6 residue 74 PHE Chi-restraints excluded: chain 7 residue 23 SER Chi-restraints excluded: chain 8 residue 4 VAL Chi-restraints excluded: chain 8 residue 35 ARG Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 8 residue 111 LEU Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain 9 residue 17 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 70 ARG Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 97 GLN Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain a residue 13 ILE Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 28 THR Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 53 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1077 random chunks: chunk 968 optimal weight: 0.4980 chunk 736 optimal weight: 9.9990 chunk 508 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 467 optimal weight: 8.9990 chunk 657 optimal weight: 6.9990 chunk 983 optimal weight: 0.7980 chunk 1041 optimal weight: 2.9990 chunk 513 optimal weight: 10.0000 chunk 931 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 142 HIS q 63 GLN ** 4 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 6 GLN x 14 GLN 6 14 HIS 6 69 HIS 7 22 GLN 8 142 ASN r 72 ASN 9 10 ASN ** 9 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 ASN L 4 GLN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 HIS ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 143 GLN X 50 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 163779 Z= 0.233 Angle : 0.605 11.223 244864 Z= 0.305 Chirality : 0.035 0.300 31247 Planarity : 0.005 0.090 13450 Dihedral : 24.119 179.657 81747 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.40 % Favored : 93.54 % Rotamer: Outliers : 3.74 % Allowed : 13.90 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % 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: -1.74 (0.10), residues: 6175 helix: 0.60 (0.11), residues: 2070 sheet: -1.54 (0.16), residues: 1033 loop : -2.32 (0.10), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 92 HIS 0.006 0.001 HIS 6 14 PHE 0.029 0.002 PHE g 60 TYR 0.022 0.002 TYR x 78 ARG 0.010 0.001 ARG Z 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1023 time to evaluate : 6.452 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET g 1 " (corrupted residue). Skipping it. REVERT: j 19 LYS cc_start: 0.8597 (tttt) cc_final: 0.8177 (mttt) REVERT: j 24 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7486 (p) REVERT: k 19 LYS cc_start: 0.7350 (mttt) cc_final: 0.6686 (tptt) REVERT: k 60 ARG cc_start: 0.5640 (mpt180) cc_final: 0.4903 (mtm-85) REVERT: k 64 ARG cc_start: 0.4167 (ttt180) cc_final: 0.3372 (mmm160) REVERT: k 99 GLN cc_start: 0.7494 (mt0) cc_final: 0.7190 (mt0) REVERT: k 106 LYS cc_start: 0.5154 (mttt) cc_final: 0.4712 (mmmt) REVERT: k 133 MET cc_start: 0.6197 (mtp) cc_final: 0.5706 (ttp) REVERT: k 177 THR cc_start: 0.6541 (m) cc_final: 0.6157 (p) REVERT: l 55 LYS cc_start: 0.6140 (mttt) cc_final: 0.5769 (mmtp) REVERT: l 124 LYS cc_start: 0.5788 (tttt) cc_final: 0.5445 (ttmt) REVERT: m 56 PHE cc_start: 0.6167 (m-80) cc_final: 0.5925 (m-80) REVERT: m 70 MET cc_start: 0.6850 (mpp) cc_final: 0.6533 (mpp) REVERT: m 97 PHE cc_start: 0.6026 (t80) cc_final: 0.5475 (t80) REVERT: m 130 VAL cc_start: 0.6012 (t) cc_final: 0.5678 (p) REVERT: n 5 GLU cc_start: 0.7377 (tt0) cc_final: 0.6132 (mt-10) REVERT: n 31 ARG cc_start: 0.6252 (mtp85) cc_final: 0.5774 (ptp-110) REVERT: n 93 THR cc_start: 0.5739 (m) cc_final: 0.5394 (m) REVERT: p 21 GLN cc_start: 0.5909 (pt0) cc_final: 0.5687 (mt0) REVERT: p 32 LEU cc_start: 0.6418 (tp) cc_final: 0.5923 (mt) REVERT: p 148 ASN cc_start: 0.7548 (m110) cc_final: 0.7281 (m-40) REVERT: q 3 MET cc_start: 0.5452 (tpp) cc_final: 0.3971 (tmm) REVERT: q 31 LYS cc_start: 0.7699 (pttt) cc_final: 0.7417 (tmmt) REVERT: q 58 LYS cc_start: 0.7816 (mtmm) cc_final: 0.7014 (mtmm) REVERT: 4 69 LYS cc_start: 0.7093 (mttt) cc_final: 0.6796 (mtmt) REVERT: 4 146 GLN cc_start: 0.6842 (mt0) cc_final: 0.6433 (mm-40) REVERT: 4 149 LYS cc_start: 0.4957 (ptpt) cc_final: 0.4567 (tptm) REVERT: s 14 ASP cc_start: 0.6064 (OUTLIER) cc_final: 0.5669 (p0) REVERT: u 56 LYS cc_start: 0.8294 (tptt) cc_final: 0.7858 (tmtt) REVERT: u 89 ASP cc_start: 0.7087 (m-30) cc_final: 0.6759 (m-30) REVERT: u 123 LYS cc_start: 0.6416 (mttt) cc_final: 0.5612 (mmmt) REVERT: v 23 TYR cc_start: 0.5637 (t80) cc_final: 0.5290 (t80) REVERT: v 115 ARG cc_start: 0.4481 (ptt180) cc_final: 0.3871 (mmm160) REVERT: x 9 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8262 (mptt) REVERT: z 7 LEU cc_start: 0.7909 (tp) cc_final: 0.7708 (tp) REVERT: z 17 GLN cc_start: 0.7275 (mt0) cc_final: 0.7008 (mm-40) REVERT: z 71 LEU cc_start: 0.7680 (tp) cc_final: 0.7413 (mt) REVERT: z 102 LYS cc_start: 0.6404 (ttmt) cc_final: 0.6109 (tptm) REVERT: 5 19 ARG cc_start: 0.7195 (ptt-90) cc_final: 0.6955 (ptp90) REVERT: 5 33 GLN cc_start: 0.7913 (mt0) cc_final: 0.7696 (mt0) REVERT: 5 89 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6139 (ppt-90) REVERT: 7 18 ARG cc_start: 0.7320 (ttp-110) cc_final: 0.7115 (ttp-110) REVERT: 7 29 ARG cc_start: 0.6845 (ttm170) cc_final: 0.6515 (mtt90) REVERT: 8 16 PHE cc_start: 0.1667 (OUTLIER) cc_final: 0.1351 (p90) REVERT: 8 22 ARG cc_start: 0.7351 (mtt180) cc_final: 0.6994 (mmm160) REVERT: 8 89 MET cc_start: 0.3635 (mmm) cc_final: 0.3182 (mmt) REVERT: r 33 ASP cc_start: 0.6693 (t0) cc_final: 0.6283 (t0) REVERT: r 53 ARG cc_start: 0.7375 (ttt180) cc_final: 0.6704 (ttt180) REVERT: r 79 LEU cc_start: 0.6771 (tt) cc_final: 0.6571 (mp) REVERT: Y 44 GLU cc_start: 0.5545 (mp0) cc_final: 0.5177 (mp0) REVERT: Y 80 PHE cc_start: 0.7263 (p90) cc_final: 0.6800 (t80) REVERT: C 10 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8731 (m) REVERT: C 146 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7568 (mm-30) REVERT: C 217 LYS cc_start: 0.8952 (mttt) cc_final: 0.8608 (mtpp) REVERT: D 108 ASP cc_start: 0.7186 (m-30) cc_final: 0.6882 (m-30) REVERT: D 111 TYR cc_start: 0.9004 (m-80) cc_final: 0.8774 (m-80) REVERT: D 175 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8896 (m) REVERT: E 55 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8032 (ttm-80) REVERT: F 13 GLN cc_start: 0.8204 (pp30) cc_final: 0.7757 (pp30) REVERT: F 58 ASN cc_start: 0.7774 (t0) cc_final: 0.7470 (t0) REVERT: F 90 MET cc_start: 0.6346 (mtp) cc_final: 0.5736 (tpt) REVERT: F 144 MET cc_start: 0.7689 (pmm) cc_final: 0.7423 (pmm) REVERT: F 149 ASP cc_start: 0.7508 (m-30) cc_final: 0.7048 (t0) REVERT: G 158 TYR cc_start: 0.8327 (m-80) cc_final: 0.8000 (m-80) REVERT: H 2 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7051 (tttm) REVERT: I 1 MET cc_start: 0.4522 (tmm) cc_final: 0.3038 (ptt) REVERT: J 38 MET cc_start: 0.4498 (ptm) cc_final: 0.4142 (ptm) REVERT: K 89 ILE cc_start: 0.8986 (mm) cc_final: 0.8663 (mt) REVERT: L 1 MET cc_start: 0.7354 (ttm) cc_final: 0.6820 (ttm) REVERT: L 2 ILE cc_start: 0.8841 (mm) cc_final: 0.8495 (tp) REVERT: L 69 ARG cc_start: 0.7404 (ttm170) cc_final: 0.7171 (ttt90) REVERT: L 70 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8191 (ttt180) REVERT: M 26 GLU cc_start: 0.6972 (tp30) cc_final: 0.6415 (tp30) REVERT: M 69 ASN cc_start: 0.8469 (t0) cc_final: 0.8235 (t0) REVERT: N 67 ASN cc_start: 0.8186 (m-40) cc_final: 0.7527 (t0) REVERT: N 135 GLU cc_start: 0.8274 (mp0) cc_final: 0.8026 (mp0) REVERT: O 37 THR cc_start: 0.8399 (p) cc_final: 0.8048 (m) REVERT: P 19 LEU cc_start: 0.9144 (mm) cc_final: 0.8733 (mm) REVERT: P 43 SER cc_start: 0.8146 (t) cc_final: 0.7488 (p) REVERT: P 113 ILE cc_start: 0.8998 (mm) cc_final: 0.8674 (mm) REVERT: P 118 ASP cc_start: 0.8271 (m-30) cc_final: 0.7938 (m-30) REVERT: Q 1 MET cc_start: 0.6484 (mmm) cc_final: 0.6272 (mmp) REVERT: Q 103 ARG cc_start: 0.7069 (mtm110) cc_final: 0.6852 (mtm110) REVERT: R 42 SER cc_start: 0.9152 (t) cc_final: 0.8838 (p) REVERT: U 24 ILE cc_start: 0.8884 (mt) cc_final: 0.8598 (pt) REVERT: U 73 PHE cc_start: 0.7045 (m-80) cc_final: 0.6816 (m-80) REVERT: V 17 LYS cc_start: 0.8496 (tttt) cc_final: 0.8293 (pttm) REVERT: V 97 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.7000 (mm) REVERT: W 84 ASP cc_start: 0.7390 (m-30) cc_final: 0.6962 (t0) REVERT: X 56 ASP cc_start: 0.8434 (p0) cc_final: 0.8207 (p0) REVERT: Z 53 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7542 (mm-30) REVERT: a 17 TRP cc_start: 0.8686 (t-100) cc_final: 0.8402 (t-100) REVERT: c 8 ILE cc_start: 0.5152 (OUTLIER) cc_final: 0.4932 (mp) REVERT: c 45 ARG cc_start: 0.7612 (mmt180) cc_final: 0.7379 (mmt180) outliers start: 192 outliers final: 128 residues processed: 1126 average time/residue: 1.3950 time to fit residues: 2682.1072 Evaluate side-chains 1076 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 938 time to evaluate : 6.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 151 VAL Chi-restraints excluded: chain k residue 162 MET Chi-restraints excluded: chain l residue 9 THR Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 123 VAL Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 147 THR Chi-restraints excluded: chain l residue 156 THR Chi-restraints excluded: chain m residue 37 ILE Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 66 ASP Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain m residue 113 GLU Chi-restraints excluded: chain m residue 186 ILE Chi-restraints excluded: chain p residue 57 ASP Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 96 SER Chi-restraints excluded: chain q residue 63 GLN Chi-restraints excluded: chain q residue 108 THR Chi-restraints excluded: chain s residue 14 ASP Chi-restraints excluded: chain t residue 49 ASN Chi-restraints excluded: chain t residue 122 VAL Chi-restraints excluded: chain t residue 137 ARG Chi-restraints excluded: chain u residue 81 LEU Chi-restraints excluded: chain u residue 98 ILE Chi-restraints excluded: chain v residue 66 VAL Chi-restraints excluded: chain v residue 82 ILE Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain 5 residue 52 ILE Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain 5 residue 89 ARG Chi-restraints excluded: chain 6 residue 11 VAL Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 74 PHE Chi-restraints excluded: chain 7 residue 23 SER Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 8 residue 16 PHE Chi-restraints excluded: chain 8 residue 123 THR Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain 9 residue 17 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 91 PHE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 70 ARG Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 108 SER Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 83 ILE Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain S residue 66 GLU Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 97 GLN Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 170 LEU Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 28 THR Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 53 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1077 random chunks: chunk 867 optimal weight: 0.8980 chunk 590 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 775 optimal weight: 8.9990 chunk 429 optimal weight: 10.0000 chunk 888 optimal weight: 6.9990 chunk 719 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 531 optimal weight: 7.9990 chunk 934 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 49 GLN l 75 ASN ** l 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 GLN p 142 HIS ** q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 7 GLN ** z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 22 GLN 8 24 ASN 9 10 ASN 9 89 HIS ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN H 66 ASN J 88 GLN L 4 GLN N 12 GLN N 67 ASN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 ASN Q 50 GLN R 72 ASN T 67 ASN ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 44 HIS X 50 ASN ** g 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 163779 Z= 0.366 Angle : 0.707 13.600 244864 Z= 0.354 Chirality : 0.040 0.324 31247 Planarity : 0.006 0.099 13450 Dihedral : 24.155 179.376 81747 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.53 % Favored : 91.40 % Rotamer: Outliers : 4.34 % Allowed : 15.40 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % 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: -1.85 (0.10), residues: 6175 helix: 0.48 (0.11), residues: 2075 sheet: -1.64 (0.16), residues: 1040 loop : -2.35 (0.10), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 92 HIS 0.039 0.002 HIS 6 14 PHE 0.020 0.002 PHE l 58 TYR 0.025 0.002 TYR l 71 ARG 0.008 0.001 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1009 time to evaluate : 6.560 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: symmetry clash TARDY: cannot create tardy model for: "MET g 1 " (corrupted residue). Skipping it. REVERT: j 8 ARG cc_start: 0.8519 (mtp85) cc_final: 0.7892 (mmm160) REVERT: j 19 LYS cc_start: 0.8643 (tttt) cc_final: 0.8072 (mttt) REVERT: j 24 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7437 (p) REVERT: k 19 LYS cc_start: 0.7344 (mttt) cc_final: 0.6704 (tppt) REVERT: k 60 ARG cc_start: 0.5739 (mpt180) cc_final: 0.4909 (mtm-85) REVERT: k 64 ARG cc_start: 0.4013 (ttt180) cc_final: 0.3385 (mmm160) REVERT: k 99 GLN cc_start: 0.7939 (mt0) cc_final: 0.7412 (mt0) REVERT: k 133 MET cc_start: 0.6206 (mtp) cc_final: 0.5600 (ttp) REVERT: k 177 THR cc_start: 0.6527 (m) cc_final: 0.6015 (p) REVERT: l 58 PHE cc_start: 0.7866 (m-80) cc_final: 0.7627 (m-80) REVERT: m 56 PHE cc_start: 0.6216 (m-80) cc_final: 0.6007 (m-80) REVERT: m 94 LYS cc_start: 0.8083 (ttmm) cc_final: 0.7834 (ttpp) REVERT: m 97 PHE cc_start: 0.6143 (t80) cc_final: 0.5752 (t80) REVERT: m 111 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7472 (tp40) REVERT: m 130 VAL cc_start: 0.6104 (t) cc_final: 0.5760 (p) REVERT: n 5 GLU cc_start: 0.7467 (tt0) cc_final: 0.6207 (mt-10) REVERT: n 31 ARG cc_start: 0.6275 (mtp85) cc_final: 0.5883 (ptp-110) REVERT: n 93 THR cc_start: 0.5515 (m) cc_final: 0.5108 (m) REVERT: p 32 LEU cc_start: 0.6563 (tp) cc_final: 0.5951 (mt) REVERT: p 148 ASN cc_start: 0.7469 (m110) cc_final: 0.7141 (m-40) REVERT: q 3 MET cc_start: 0.5653 (tpp) cc_final: 0.4506 (tmm) REVERT: q 31 LYS cc_start: 0.7606 (pttt) cc_final: 0.7392 (tmmt) REVERT: 4 69 LYS cc_start: 0.7091 (mttt) cc_final: 0.6750 (mtmt) REVERT: 4 149 LYS cc_start: 0.5333 (ptpt) cc_final: 0.4955 (tptm) REVERT: s 14 ASP cc_start: 0.5787 (p0) cc_final: 0.5376 (p0) REVERT: s 62 ARG cc_start: 0.5544 (mtt-85) cc_final: 0.5226 (mtt180) REVERT: t 137 ARG cc_start: 0.6233 (OUTLIER) cc_final: 0.5165 (ptt90) REVERT: u 56 LYS cc_start: 0.8401 (tptt) cc_final: 0.7979 (tmtt) REVERT: u 75 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6616 (pt0) REVERT: u 123 LYS cc_start: 0.6421 (mttt) cc_final: 0.5721 (mmmt) REVERT: v 115 ARG cc_start: 0.4592 (ptt180) cc_final: 0.3896 (mmm160) REVERT: x 9 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8290 (mptt) REVERT: z 17 GLN cc_start: 0.7230 (mt0) cc_final: 0.6889 (mm-40) REVERT: z 39 ARG cc_start: 0.7153 (ptp-170) cc_final: 0.6925 (ptp90) REVERT: z 102 LYS cc_start: 0.6471 (ttmt) cc_final: 0.6077 (tptm) REVERT: 5 19 ARG cc_start: 0.7168 (ptt-90) cc_final: 0.6921 (ptp90) REVERT: 5 33 GLN cc_start: 0.7886 (mt0) cc_final: 0.7663 (mt0) REVERT: 5 89 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6765 (ptm-80) REVERT: 7 29 ARG cc_start: 0.6910 (ttm170) cc_final: 0.6531 (mtt90) REVERT: 8 4 VAL cc_start: 0.1407 (OUTLIER) cc_final: 0.1110 (t) REVERT: 8 16 PHE cc_start: 0.2030 (OUTLIER) cc_final: 0.1187 (p90) REVERT: 8 21 ARG cc_start: 0.6797 (mtt180) cc_final: 0.6142 (ttp-170) REVERT: 8 22 ARG cc_start: 0.7506 (mtt180) cc_final: 0.7177 (mmm160) REVERT: 8 89 MET cc_start: 0.3698 (mmm) cc_final: 0.3203 (mmt) REVERT: 8 146 ARG cc_start: 0.5244 (ptt180) cc_final: 0.3680 (mtm-85) REVERT: 8 154 MET cc_start: 0.4296 (OUTLIER) cc_final: 0.3101 (ppp) REVERT: r 79 LEU cc_start: 0.6811 (tt) cc_final: 0.6562 (mp) REVERT: Y 80 PHE cc_start: 0.7316 (p90) cc_final: 0.6806 (t80) REVERT: C 10 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8763 (m) REVERT: C 146 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7572 (mm-30) REVERT: C 186 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8012 (t0) REVERT: C 217 LYS cc_start: 0.9021 (mttt) cc_final: 0.8683 (mtpp) REVERT: E 55 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8068 (ttm-80) REVERT: E 128 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8055 (t) REVERT: F 58 ASN cc_start: 0.7866 (t0) cc_final: 0.7616 (t0) REVERT: F 149 ASP cc_start: 0.7626 (m-30) cc_final: 0.7133 (t0) REVERT: G 158 TYR cc_start: 0.8410 (m-80) cc_final: 0.8159 (m-80) REVERT: H 2 LYS cc_start: 0.7711 (mtmt) cc_final: 0.7132 (tttm) REVERT: I 1 MET cc_start: 0.4222 (tmm) cc_final: 0.3092 (ptt) REVERT: K 89 ILE cc_start: 0.9102 (mm) cc_final: 0.8862 (mt) REVERT: K 95 LYS cc_start: 0.8267 (mttt) cc_final: 0.7920 (mmtp) REVERT: K 101 VAL cc_start: 0.7780 (t) cc_final: 0.7438 (p) REVERT: K 112 ASN cc_start: 0.8750 (p0) cc_final: 0.8510 (p0) REVERT: L 2 ILE cc_start: 0.8947 (mm) cc_final: 0.8639 (tp) REVERT: L 5 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7297 (tp30) REVERT: L 54 ARG cc_start: 0.7474 (ttm170) cc_final: 0.6852 (ttm170) REVERT: L 69 ARG cc_start: 0.7508 (ttm170) cc_final: 0.7209 (ttt90) REVERT: L 117 LEU cc_start: 0.8812 (mp) cc_final: 0.8572 (mp) REVERT: M 26 GLU cc_start: 0.6972 (tp30) cc_final: 0.6469 (tp30) REVERT: N 67 ASN cc_start: 0.8234 (m110) cc_final: 0.7559 (t0) REVERT: P 43 SER cc_start: 0.8265 (t) cc_final: 0.7615 (p) REVERT: P 86 GLN cc_start: 0.8235 (mt0) cc_final: 0.8023 (mt0) REVERT: R 42 SER cc_start: 0.9228 (t) cc_final: 0.8936 (p) REVERT: R 100 VAL cc_start: 0.8021 (t) cc_final: 0.7789 (t) REVERT: U 24 ILE cc_start: 0.9012 (mt) cc_final: 0.8765 (pt) REVERT: V 97 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7226 (mm) REVERT: W 32 LYS cc_start: 0.7872 (mttm) cc_final: 0.7532 (mttt) REVERT: W 84 ASP cc_start: 0.7467 (m-30) cc_final: 0.6932 (t70) REVERT: Z 9 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6591 (pt0) REVERT: Z 24 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7118 (mm-30) REVERT: c 8 ILE cc_start: 0.5705 (OUTLIER) cc_final: 0.5434 (mp) REVERT: c 52 GLU cc_start: 0.7278 (tp30) cc_final: 0.7041 (tp30) outliers start: 223 outliers final: 160 residues processed: 1143 average time/residue: 1.3923 time to fit residues: 2718.3503 Evaluate side-chains 1124 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 951 time to evaluate : 6.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 13 SER Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain k residue 114 LEU Chi-restraints excluded: chain l residue 9 THR Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 123 VAL Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 147 THR Chi-restraints excluded: chain l residue 156 THR Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 66 ASP Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain m residue 104 SER Chi-restraints excluded: chain m residue 110 VAL Chi-restraints excluded: chain m residue 113 GLU Chi-restraints excluded: chain m residue 186 ILE Chi-restraints excluded: chain n residue 88 THR Chi-restraints excluded: chain p residue 57 ASP Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 96 SER Chi-restraints excluded: chain p residue 128 SER Chi-restraints excluded: chain q residue 108 THR Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 43 ILE Chi-restraints excluded: chain t residue 49 ASN Chi-restraints excluded: chain t residue 116 VAL Chi-restraints excluded: chain t residue 122 VAL Chi-restraints excluded: chain t residue 137 ARG Chi-restraints excluded: chain u residue 75 GLN Chi-restraints excluded: chain u residue 98 ILE Chi-restraints excluded: chain v residue 66 VAL Chi-restraints excluded: chain v residue 82 ILE Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 52 ILE Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 89 ARG Chi-restraints excluded: chain 6 residue 11 VAL Chi-restraints excluded: chain 6 residue 74 PHE Chi-restraints excluded: chain 7 residue 23 SER Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 8 residue 4 VAL Chi-restraints excluded: chain 8 residue 16 PHE Chi-restraints excluded: chain 8 residue 50 ILE Chi-restraints excluded: chain 8 residue 123 THR Chi-restraints excluded: chain 8 residue 154 MET Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 65 GLN Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 72 ASN Chi-restraints excluded: chain 9 residue 17 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 91 PHE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 71 PHE Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain Q residue 26 ASN Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 97 GLN Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 170 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 62 LEU Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 28 THR Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain y residue 67 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1077 random chunks: chunk 350 optimal weight: 3.9990 chunk 937 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 611 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 chunk 1042 optimal weight: 2.9990 chunk 865 optimal weight: 3.9990 chunk 482 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 344 optimal weight: 7.9990 chunk 547 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 75 ASN ** l 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 142 HIS ** 4 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 112 GLN ** z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 22 GLN 7 84 ASN 9 10 ASN ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 ASN K 147 GLN L 4 GLN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN R 72 ASN ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 143 GLN X 50 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 163779 Z= 0.255 Angle : 0.619 12.000 244864 Z= 0.313 Chirality : 0.036 0.339 31247 Planarity : 0.005 0.093 13450 Dihedral : 24.108 179.387 81747 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.88 % Favored : 93.09 % Rotamer: Outliers : 4.36 % Allowed : 16.57 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % 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: -1.62 (0.10), residues: 6175 helix: 0.65 (0.11), residues: 2090 sheet: -1.55 (0.16), residues: 1039 loop : -2.20 (0.10), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP a 17 HIS 0.013 0.001 HIS Q 28 PHE 0.028 0.002 PHE g 60 TYR 0.026 0.002 TYR x 78 ARG 0.007 0.001 ARG e 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1002 time to evaluate : 6.591 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 TARDY: cannot create tardy model for: "MET g 1 " (corrupted residue). Skipping it. REVERT: j 19 LYS cc_start: 0.8630 (tttt) cc_final: 0.8020 (mttt) REVERT: j 24 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7379 (p) REVERT: k 60 ARG cc_start: 0.5724 (mpt180) cc_final: 0.4910 (mtm-85) REVERT: k 64 ARG cc_start: 0.3922 (ttt180) cc_final: 0.3383 (mmm160) REVERT: k 133 MET cc_start: 0.6172 (mtp) cc_final: 0.5669 (ttp) REVERT: k 177 THR cc_start: 0.6623 (m) cc_final: 0.6176 (p) REVERT: m 56 PHE cc_start: 0.6241 (m-80) cc_final: 0.6040 (m-80) REVERT: m 94 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7781 (ttpp) REVERT: m 97 PHE cc_start: 0.5959 (t80) cc_final: 0.5436 (t80) REVERT: m 130 VAL cc_start: 0.6094 (t) cc_final: 0.5740 (p) REVERT: n 5 GLU cc_start: 0.7407 (tt0) cc_final: 0.6101 (mt-10) REVERT: n 31 ARG cc_start: 0.6431 (mtp85) cc_final: 0.6039 (ptp-110) REVERT: n 93 THR cc_start: 0.5497 (m) cc_final: 0.5045 (m) REVERT: p 148 ASN cc_start: 0.7437 (m110) cc_final: 0.7162 (m-40) REVERT: q 3 MET cc_start: 0.5642 (tpp) cc_final: 0.4134 (tmm) REVERT: q 31 LYS cc_start: 0.7621 (pttt) cc_final: 0.7420 (tmmt) REVERT: q 77 LEU cc_start: 0.8357 (mt) cc_final: 0.8136 (mt) REVERT: 4 69 LYS cc_start: 0.7110 (mttt) cc_final: 0.6784 (mtmt) REVERT: s 14 ASP cc_start: 0.5775 (OUTLIER) cc_final: 0.5451 (p0) REVERT: s 62 ARG cc_start: 0.5633 (mtt-85) cc_final: 0.5352 (mtt180) REVERT: t 137 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5358 (ptt90) REVERT: u 56 LYS cc_start: 0.8406 (tptt) cc_final: 0.7992 (tmtt) REVERT: u 75 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6585 (pt0) REVERT: u 123 LYS cc_start: 0.6356 (mttt) cc_final: 0.5689 (mmmt) REVERT: v 92 HIS cc_start: 0.6428 (m-70) cc_final: 0.5716 (m-70) REVERT: v 114 LYS cc_start: 0.5973 (ttmt) cc_final: 0.5677 (ttpt) REVERT: v 115 ARG cc_start: 0.4625 (ptt180) cc_final: 0.3900 (mmm160) REVERT: x 9 LYS cc_start: 0.8564 (mmtt) cc_final: 0.7920 (mmmt) REVERT: z 17 GLN cc_start: 0.7123 (mt0) cc_final: 0.6485 (mm-40) REVERT: z 102 LYS cc_start: 0.6405 (ttmt) cc_final: 0.6071 (tptm) REVERT: 5 19 ARG cc_start: 0.7162 (ptt-90) cc_final: 0.6956 (ptp90) REVERT: 5 33 GLN cc_start: 0.7884 (mt0) cc_final: 0.7656 (mt0) REVERT: 7 29 ARG cc_start: 0.6935 (ttm170) cc_final: 0.6493 (mtt90) REVERT: 8 16 PHE cc_start: 0.1835 (OUTLIER) cc_final: 0.0570 (p90) REVERT: 8 21 ARG cc_start: 0.6747 (mtt180) cc_final: 0.6495 (ttm170) REVERT: 8 22 ARG cc_start: 0.7305 (mtt180) cc_final: 0.7018 (mmm160) REVERT: 8 89 MET cc_start: 0.3744 (mmm) cc_final: 0.3208 (mmt) REVERT: r 79 LEU cc_start: 0.6809 (tt) cc_final: 0.6558 (mp) REVERT: Y 80 PHE cc_start: 0.7119 (p90) cc_final: 0.6594 (t80) REVERT: C 10 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8769 (m) REVERT: C 146 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7639 (mm-30) REVERT: C 181 GLU cc_start: 0.8253 (pt0) cc_final: 0.7982 (pt0) REVERT: C 217 LYS cc_start: 0.8962 (mttt) cc_final: 0.8654 (mtpp) REVERT: D 108 ASP cc_start: 0.6776 (m-30) cc_final: 0.6359 (m-30) REVERT: E 55 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8023 (ttm-80) REVERT: E 128 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8068 (t) REVERT: F 13 GLN cc_start: 0.8228 (pp30) cc_final: 0.7742 (pp30) REVERT: F 58 ASN cc_start: 0.7886 (t0) cc_final: 0.7567 (t0) REVERT: F 149 ASP cc_start: 0.7605 (m-30) cc_final: 0.7121 (t0) REVERT: G 158 TYR cc_start: 0.8417 (m-80) cc_final: 0.8201 (m-80) REVERT: H 2 LYS cc_start: 0.7690 (mtmt) cc_final: 0.7130 (tttp) REVERT: I 1 MET cc_start: 0.4411 (tmm) cc_final: 0.3370 (ptt) REVERT: K 52 ASP cc_start: 0.7852 (m-30) cc_final: 0.7643 (m-30) REVERT: K 89 ILE cc_start: 0.9016 (mm) cc_final: 0.8739 (mt) REVERT: K 95 LYS cc_start: 0.8267 (mttt) cc_final: 0.7968 (mmtp) REVERT: L 2 ILE cc_start: 0.8991 (mm) cc_final: 0.8703 (tp) REVERT: L 5 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7275 (tp30) REVERT: M 69 ASN cc_start: 0.8534 (t0) cc_final: 0.8312 (t0) REVERT: N 67 ASN cc_start: 0.8157 (m110) cc_final: 0.7399 (t0) REVERT: O 37 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8202 (m) REVERT: O 106 ASP cc_start: 0.8861 (p0) cc_final: 0.8571 (p0) REVERT: P 19 LEU cc_start: 0.9178 (mm) cc_final: 0.8779 (mm) REVERT: P 43 SER cc_start: 0.8258 (t) cc_final: 0.7614 (p) REVERT: P 86 GLN cc_start: 0.8330 (mt0) cc_final: 0.7812 (mt0) REVERT: P 118 ASP cc_start: 0.8172 (m-30) cc_final: 0.7967 (m-30) REVERT: Q 23 ASP cc_start: 0.8254 (m-30) cc_final: 0.7875 (m-30) REVERT: Q 26 ASN cc_start: 0.7539 (OUTLIER) cc_final: 0.7157 (m-40) REVERT: Q 63 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7575 (tm-30) REVERT: R 42 SER cc_start: 0.9185 (t) cc_final: 0.8891 (p) REVERT: R 111 ASP cc_start: 0.8171 (p0) cc_final: 0.7243 (m-30) REVERT: S 81 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8076 (mttp) REVERT: T 97 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8613 (mt0) REVERT: U 24 ILE cc_start: 0.9012 (mt) cc_final: 0.8753 (pt) REVERT: W 26 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7608 (tm-30) REVERT: W 32 LYS cc_start: 0.7889 (mttm) cc_final: 0.7571 (mttt) REVERT: W 52 ARG cc_start: 0.7355 (mmm160) cc_final: 0.7041 (mmm160) REVERT: W 84 ASP cc_start: 0.7459 (m-30) cc_final: 0.6988 (t70) REVERT: W 169 ASN cc_start: 0.8074 (t0) cc_final: 0.7704 (m-40) REVERT: Z 9 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6572 (pt0) REVERT: Z 66 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7958 (mp) REVERT: c 21 TYR cc_start: 0.6581 (m-10) cc_final: 0.6343 (m-10) REVERT: c 48 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6967 (mm-30) REVERT: c 52 GLU cc_start: 0.7285 (tp30) cc_final: 0.6739 (tp30) REVERT: f 1 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7334 (ttt) outliers start: 224 outliers final: 162 residues processed: 1137 average time/residue: 1.3506 time to fit residues: 2631.9827 Evaluate side-chains 1129 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 953 time to evaluate : 6.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain k residue 21 ARG Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain k residue 114 LEU Chi-restraints excluded: chain k residue 151 VAL Chi-restraints excluded: chain k residue 162 MET Chi-restraints excluded: chain l residue 9 THR Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 123 VAL Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 147 THR Chi-restraints excluded: chain l residue 156 THR Chi-restraints excluded: chain l residue 169 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 66 ASP Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain m residue 104 SER Chi-restraints excluded: chain m residue 113 GLU Chi-restraints excluded: chain m residue 165 THR Chi-restraints excluded: chain m residue 186 ILE Chi-restraints excluded: chain p residue 64 ARG Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 96 SER Chi-restraints excluded: chain p residue 128 SER Chi-restraints excluded: chain q residue 108 THR Chi-restraints excluded: chain s residue 14 ASP Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 43 ILE Chi-restraints excluded: chain t residue 49 ASN Chi-restraints excluded: chain t residue 116 VAL Chi-restraints excluded: chain t residue 122 VAL Chi-restraints excluded: chain t residue 137 ARG Chi-restraints excluded: chain u residue 75 GLN Chi-restraints excluded: chain v residue 66 VAL Chi-restraints excluded: chain v residue 82 ILE Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 27 THR Chi-restraints excluded: chain z residue 47 SER Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 52 ILE Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain 5 residue 82 LEU Chi-restraints excluded: chain 6 residue 11 VAL Chi-restraints excluded: chain 6 residue 74 PHE Chi-restraints excluded: chain 7 residue 23 SER Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 50 LEU Chi-restraints excluded: chain 8 residue 16 PHE Chi-restraints excluded: chain 8 residue 50 ILE Chi-restraints excluded: chain 8 residue 123 THR Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain 9 residue 17 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 91 PHE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 71 PHE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 108 SER Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 26 ASN Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 81 LYS Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 97 GLN Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 170 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 62 LEU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 28 THR Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain y residue 58 ILE Chi-restraints excluded: chain y residue 67 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1077 random chunks: chunk 1004 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 chunk 593 optimal weight: 10.0000 chunk 760 optimal weight: 1.9990 chunk 589 optimal weight: 6.9990 chunk 877 optimal weight: 5.9990 chunk 581 optimal weight: 6.9990 chunk 1038 optimal weight: 0.7980 chunk 649 optimal weight: 7.9990 chunk 632 optimal weight: 30.0000 chunk 479 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 142 HIS ** q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 14 HIS 7 21 ASN 7 22 GLN 7 84 ASN 8 75 GLN Y 47 HIS 9 10 ASN C 227 ASN ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN L 4 GLN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 ASN Q 50 GLN ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 143 GLN X 50 ASN ** Z 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 9 GLN ** g 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 163779 Z= 0.373 Angle : 0.702 12.422 244864 Z= 0.351 Chirality : 0.040 0.331 31247 Planarity : 0.006 0.090 13450 Dihedral : 24.142 178.968 81745 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.83 % Favored : 91.13 % Rotamer: Outliers : 4.99 % Allowed : 16.85 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % 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: -1.76 (0.10), residues: 6175 helix: 0.49 (0.11), residues: 2092 sheet: -1.64 (0.16), residues: 1070 loop : -2.24 (0.10), residues: 3013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 17 HIS 0.007 0.001 HIS G 66 PHE 0.019 0.002 PHE 8 30 TYR 0.024 0.002 TYR x 78 ARG 0.008 0.001 ARG Q 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 961 time to evaluate : 6.705 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 TARDY: cannot create tardy model for: "MET g 1 " (corrupted residue). Skipping it. REVERT: j 19 LYS cc_start: 0.8641 (tttt) cc_final: 0.8028 (mttt) REVERT: j 24 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7394 (p) REVERT: k 23 TYR cc_start: 0.6780 (t80) cc_final: 0.6473 (t80) REVERT: k 60 ARG cc_start: 0.5488 (mpt180) cc_final: 0.4500 (mtm110) REVERT: k 133 MET cc_start: 0.6087 (mtp) cc_final: 0.5527 (ttp) REVERT: k 177 THR cc_start: 0.6663 (m) cc_final: 0.6166 (p) REVERT: l 58 PHE cc_start: 0.7977 (m-80) cc_final: 0.7753 (m-80) REVERT: m 94 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7736 (ttpp) REVERT: m 130 VAL cc_start: 0.6215 (OUTLIER) cc_final: 0.5856 (p) REVERT: p 32 LEU cc_start: 0.6658 (tp) cc_final: 0.6043 (mt) REVERT: p 41 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6290 (mmt180) REVERT: p 148 ASN cc_start: 0.7414 (m110) cc_final: 0.7100 (m-40) REVERT: q 3 MET cc_start: 0.5778 (tpp) cc_final: 0.4230 (tmm) REVERT: q 31 LYS cc_start: 0.7743 (pttt) cc_final: 0.7523 (tppp) REVERT: 4 69 LYS cc_start: 0.7072 (mttt) cc_final: 0.6720 (mtmt) REVERT: s 14 ASP cc_start: 0.5830 (OUTLIER) cc_final: 0.5532 (p0) REVERT: s 62 ARG cc_start: 0.5588 (mtt-85) cc_final: 0.5253 (mtt180) REVERT: t 137 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.5394 (ptt90) REVERT: u 56 LYS cc_start: 0.8385 (tptt) cc_final: 0.7992 (tmtt) REVERT: u 75 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6594 (pt0) REVERT: u 123 LYS cc_start: 0.6324 (mttt) cc_final: 0.5745 (mmmt) REVERT: v 115 ARG cc_start: 0.4511 (ptt180) cc_final: 0.3799 (mmm160) REVERT: x 9 LYS cc_start: 0.8578 (mmtt) cc_final: 0.7932 (mmmt) REVERT: z 17 GLN cc_start: 0.7190 (mt0) cc_final: 0.6802 (mm-40) REVERT: z 102 LYS cc_start: 0.6462 (ttmt) cc_final: 0.6004 (tptm) REVERT: 5 19 ARG cc_start: 0.7148 (ptt-90) cc_final: 0.6793 (ptp90) REVERT: 5 92 GLU cc_start: 0.8028 (tt0) cc_final: 0.7238 (pm20) REVERT: 7 29 ARG cc_start: 0.6979 (ttm170) cc_final: 0.6541 (mtt90) REVERT: 8 16 PHE cc_start: 0.2000 (OUTLIER) cc_final: 0.0261 (p90) REVERT: 8 21 ARG cc_start: 0.6824 (mtt180) cc_final: 0.6382 (ttm170) REVERT: 8 89 MET cc_start: 0.3720 (mmm) cc_final: 0.3178 (mmt) REVERT: r 79 LEU cc_start: 0.6887 (tt) cc_final: 0.6598 (mp) REVERT: Y 80 PHE cc_start: 0.7188 (p90) cc_final: 0.6578 (t80) REVERT: C 10 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8777 (m) REVERT: C 146 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7621 (mm-30) REVERT: C 186 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7968 (t0) REVERT: C 217 LYS cc_start: 0.8995 (mttt) cc_final: 0.8690 (mtpp) REVERT: D 108 ASP cc_start: 0.6938 (m-30) cc_final: 0.6516 (m-30) REVERT: E 55 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8021 (ttm-80) REVERT: E 128 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8101 (t) REVERT: F 58 ASN cc_start: 0.7883 (t0) cc_final: 0.7636 (t0) REVERT: F 149 ASP cc_start: 0.7737 (m-30) cc_final: 0.7182 (t0) REVERT: G 4 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7284 (mp) REVERT: H 2 LYS cc_start: 0.7728 (mtmt) cc_final: 0.7149 (tttm) REVERT: I 1 MET cc_start: 0.4312 (tmm) cc_final: 0.3358 (ptt) REVERT: K 89 ILE cc_start: 0.9112 (mm) cc_final: 0.8864 (mt) REVERT: K 95 LYS cc_start: 0.8276 (mttt) cc_final: 0.7976 (mmtp) REVERT: K 112 ASN cc_start: 0.8810 (p0) cc_final: 0.8580 (p0) REVERT: K 136 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7742 (mt0) REVERT: L 2 ILE cc_start: 0.9023 (mm) cc_final: 0.8703 (tp) REVERT: L 5 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7324 (tp30) REVERT: L 54 ARG cc_start: 0.7619 (ttm170) cc_final: 0.6977 (ttm170) REVERT: M 120 VAL cc_start: 0.7199 (OUTLIER) cc_final: 0.6992 (m) REVERT: N 67 ASN cc_start: 0.8253 (m110) cc_final: 0.7369 (t0) REVERT: P 43 SER cc_start: 0.8291 (t) cc_final: 0.7633 (p) REVERT: P 113 ILE cc_start: 0.9057 (mm) cc_final: 0.8852 (mm) REVERT: Q 20 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.7849 (p) REVERT: Q 23 ASP cc_start: 0.8132 (m-30) cc_final: 0.7708 (m-30) REVERT: Q 63 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7629 (tm-30) REVERT: R 42 SER cc_start: 0.9230 (t) cc_final: 0.8947 (p) REVERT: S 81 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8102 (mttp) REVERT: U 24 ILE cc_start: 0.9036 (mt) cc_final: 0.8827 (pt) REVERT: W 32 LYS cc_start: 0.7909 (mttm) cc_final: 0.7607 (mttt) REVERT: W 52 ARG cc_start: 0.7489 (mmm160) cc_final: 0.7141 (mmm160) REVERT: W 84 ASP cc_start: 0.7516 (m-30) cc_final: 0.7005 (t70) REVERT: W 169 ASN cc_start: 0.8089 (t0) cc_final: 0.7648 (m-40) REVERT: Z 9 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6651 (pt0) REVERT: Z 66 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8314 (mp) REVERT: c 21 TYR cc_start: 0.6623 (m-10) cc_final: 0.6289 (m-10) REVERT: c 48 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6994 (mm-30) REVERT: c 52 GLU cc_start: 0.7408 (tp30) cc_final: 0.6923 (tp30) REVERT: y 45 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7972 (mtm110) outliers start: 256 outliers final: 202 residues processed: 1119 average time/residue: 1.4263 time to fit residues: 2754.6481 Evaluate side-chains 1159 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 940 time to evaluate : 6.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain k residue 21 ARG Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain k residue 114 LEU Chi-restraints excluded: chain l residue 9 THR Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 123 VAL Chi-restraints excluded: chain l residue 126 ASP Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 147 THR Chi-restraints excluded: chain l residue 156 THR Chi-restraints excluded: chain l residue 169 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 51 LYS Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 66 ASP Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain m residue 104 SER Chi-restraints excluded: chain m residue 110 VAL Chi-restraints excluded: chain m residue 113 GLU Chi-restraints excluded: chain m residue 130 VAL Chi-restraints excluded: chain m residue 165 THR Chi-restraints excluded: chain m residue 186 ILE Chi-restraints excluded: chain n residue 10 LEU Chi-restraints excluded: chain p residue 41 ARG Chi-restraints excluded: chain p residue 64 ARG Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 96 SER Chi-restraints excluded: chain p residue 128 SER Chi-restraints excluded: chain q residue 108 THR Chi-restraints excluded: chain s residue 14 ASP Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 41 VAL Chi-restraints excluded: chain t residue 43 ILE Chi-restraints excluded: chain t residue 49 ASN Chi-restraints excluded: chain t residue 116 VAL Chi-restraints excluded: chain t residue 122 VAL Chi-restraints excluded: chain t residue 137 ARG Chi-restraints excluded: chain u residue 75 GLN Chi-restraints excluded: chain v residue 45 THR Chi-restraints excluded: chain v residue 66 VAL Chi-restraints excluded: chain v residue 82 ILE Chi-restraints excluded: chain x residue 4 THR Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 27 THR Chi-restraints excluded: chain z residue 47 SER Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 27 VAL Chi-restraints excluded: chain 5 residue 52 ILE Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 82 LEU Chi-restraints excluded: chain 6 residue 11 VAL Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 74 PHE Chi-restraints excluded: chain 7 residue 23 SER Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 50 LEU Chi-restraints excluded: chain 7 residue 77 SER Chi-restraints excluded: chain 8 residue 16 PHE Chi-restraints excluded: chain 8 residue 50 ILE Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 190 ASN Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 65 GLN Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 68 THR Chi-restraints excluded: chain r residue 72 ASN Chi-restraints excluded: chain 9 residue 17 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 91 PHE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 71 PHE Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 108 SER Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 26 ASN Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain S residue 81 LYS Chi-restraints excluded: chain S residue 84 TYR Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 97 GLN Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain W residue 143 GLN Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 62 LEU Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 24 LEU Chi-restraints excluded: chain g residue 28 THR Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain y residue 58 ILE Chi-restraints excluded: chain y residue 67 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1077 random chunks: chunk 642 optimal weight: 7.9990 chunk 414 optimal weight: 10.0000 chunk 619 optimal weight: 4.9990 chunk 312 optimal weight: 9.9990 chunk 203 optimal weight: 0.8980 chunk 201 optimal weight: 6.9990 chunk 659 optimal weight: 6.9990 chunk 707 optimal weight: 5.9990 chunk 513 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 815 optimal weight: 3.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 106 ASN p 142 HIS ** q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 33 GLN 7 3 ASN 7 22 GLN 7 84 ASN Y 19 HIS 9 10 ASN ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN O 16 HIS ** Q 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 163779 Z= 0.370 Angle : 0.708 12.918 244864 Z= 0.354 Chirality : 0.040 0.331 31247 Planarity : 0.006 0.087 13450 Dihedral : 24.167 179.465 81745 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.31 % Favored : 91.63 % Rotamer: Outliers : 5.04 % Allowed : 17.22 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % 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: -1.84 (0.10), residues: 6175 helix: 0.43 (0.11), residues: 2095 sheet: -1.75 (0.15), residues: 1106 loop : -2.27 (0.10), residues: 2974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP t 53 HIS 0.023 0.001 HIS 6 14 PHE 0.029 0.002 PHE g 60 TYR 0.024 0.002 TYR x 78 ARG 0.009 0.001 ARG 4 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 995 time to evaluate : 6.257 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 TARDY: cannot create tardy model for: "MET g 1 " (corrupted residue). Skipping it. REVERT: j 19 LYS cc_start: 0.8614 (tttt) cc_final: 0.8020 (mttt) REVERT: j 24 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7382 (p) REVERT: k 23 TYR cc_start: 0.6918 (t80) cc_final: 0.6679 (t80) REVERT: k 60 ARG cc_start: 0.5612 (mpt180) cc_final: 0.4565 (mtm110) REVERT: k 133 MET cc_start: 0.6105 (mtp) cc_final: 0.5503 (ttp) REVERT: k 143 GLN cc_start: 0.4226 (mt0) cc_final: 0.3902 (tm-30) REVERT: k 177 THR cc_start: 0.6834 (m) cc_final: 0.6353 (p) REVERT: l 58 PHE cc_start: 0.7896 (m-80) cc_final: 0.7623 (m-80) REVERT: m 94 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7757 (ttpp) REVERT: m 130 VAL cc_start: 0.6224 (OUTLIER) cc_final: 0.5875 (p) REVERT: n 31 ARG cc_start: 0.6399 (ttm110) cc_final: 0.5799 (mtt-85) REVERT: p 32 LEU cc_start: 0.6648 (tp) cc_final: 0.6015 (mt) REVERT: p 41 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6251 (mmt180) REVERT: p 136 LYS cc_start: 0.5559 (tttt) cc_final: 0.5221 (tptp) REVERT: p 148 ASN cc_start: 0.7317 (m110) cc_final: 0.6973 (m-40) REVERT: q 3 MET cc_start: 0.5791 (tpp) cc_final: 0.4250 (tmm) REVERT: q 31 LYS cc_start: 0.7780 (pttt) cc_final: 0.7559 (tppp) REVERT: 4 69 LYS cc_start: 0.7072 (mttt) cc_final: 0.6717 (mtmt) REVERT: s 14 ASP cc_start: 0.5858 (OUTLIER) cc_final: 0.5553 (p0) REVERT: s 66 GLU cc_start: 0.6080 (tt0) cc_final: 0.5239 (mp0) REVERT: t 137 ARG cc_start: 0.6436 (OUTLIER) cc_final: 0.5540 (ptt90) REVERT: u 56 LYS cc_start: 0.8382 (tptt) cc_final: 0.7933 (tptp) REVERT: u 75 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6601 (pt0) REVERT: u 123 LYS cc_start: 0.6374 (mttt) cc_final: 0.5611 (mmmt) REVERT: v 92 HIS cc_start: 0.6406 (m-70) cc_final: 0.5687 (m-70) REVERT: v 114 LYS cc_start: 0.5893 (ttmt) cc_final: 0.4241 (tptp) REVERT: v 115 ARG cc_start: 0.4566 (ptt180) cc_final: 0.3849 (mmm160) REVERT: x 9 LYS cc_start: 0.8584 (mmtt) cc_final: 0.7931 (mmmt) REVERT: x 60 VAL cc_start: 0.8258 (t) cc_final: 0.7964 (m) REVERT: z 17 GLN cc_start: 0.7213 (mt0) cc_final: 0.6639 (mm-40) REVERT: z 29 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.5315 (ttm-80) REVERT: z 102 LYS cc_start: 0.6369 (ttmt) cc_final: 0.5922 (tptm) REVERT: 5 19 ARG cc_start: 0.7093 (ptt-90) cc_final: 0.6753 (ptp90) REVERT: 5 92 GLU cc_start: 0.8026 (tt0) cc_final: 0.7216 (pm20) REVERT: 7 25 LYS cc_start: 0.7203 (mttt) cc_final: 0.6963 (mttm) REVERT: 8 16 PHE cc_start: 0.1993 (OUTLIER) cc_final: 0.0234 (p90) REVERT: 8 21 ARG cc_start: 0.6652 (mtt180) cc_final: 0.6375 (ttm170) REVERT: 8 89 MET cc_start: 0.3792 (mmm) cc_final: 0.3212 (mmt) REVERT: r 79 LEU cc_start: 0.6992 (tt) cc_final: 0.6719 (mp) REVERT: Y 80 PHE cc_start: 0.7253 (p90) cc_final: 0.6669 (t80) REVERT: C 10 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8843 (m) REVERT: C 23 GLU cc_start: 0.8209 (mp0) cc_final: 0.7891 (mp0) REVERT: C 146 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7598 (mm-30) REVERT: C 186 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7862 (t0) REVERT: C 217 LYS cc_start: 0.9008 (mttt) cc_final: 0.8692 (mtpp) REVERT: D 108 ASP cc_start: 0.6894 (m-30) cc_final: 0.6463 (m-30) REVERT: E 55 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8028 (ttm-80) REVERT: F 58 ASN cc_start: 0.7843 (t0) cc_final: 0.7620 (t0) REVERT: F 149 ASP cc_start: 0.7730 (m-30) cc_final: 0.7158 (t0) REVERT: F 157 ARG cc_start: 0.5993 (ptp-170) cc_final: 0.5602 (ptp90) REVERT: G 4 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7291 (mp) REVERT: H 2 LYS cc_start: 0.7749 (mtmt) cc_final: 0.7153 (tttm) REVERT: I 1 MET cc_start: 0.4380 (tmm) cc_final: 0.3420 (ptt) REVERT: K 89 ILE cc_start: 0.9099 (mm) cc_final: 0.8786 (mt) REVERT: K 95 LYS cc_start: 0.8278 (mttt) cc_final: 0.7979 (mmtp) REVERT: K 112 ASN cc_start: 0.8844 (p0) cc_final: 0.8608 (p0) REVERT: K 136 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: L 2 ILE cc_start: 0.9031 (mm) cc_final: 0.8719 (tp) REVERT: M 120 VAL cc_start: 0.7169 (OUTLIER) cc_final: 0.6965 (m) REVERT: N 67 ASN cc_start: 0.8270 (m110) cc_final: 0.7397 (t0) REVERT: O 106 ASP cc_start: 0.8862 (p0) cc_final: 0.8510 (p0) REVERT: P 43 SER cc_start: 0.8299 (t) cc_final: 0.7641 (p) REVERT: P 118 ASP cc_start: 0.8220 (m-30) cc_final: 0.8016 (m-30) REVERT: Q 20 SER cc_start: 0.8896 (OUTLIER) cc_final: 0.8476 (p) REVERT: Q 63 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7595 (tm-30) REVERT: R 42 SER cc_start: 0.9233 (t) cc_final: 0.8941 (p) REVERT: S 81 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8036 (mttp) REVERT: T 97 GLN cc_start: 0.9402 (OUTLIER) cc_final: 0.8702 (mt0) REVERT: W 32 LYS cc_start: 0.7967 (mttm) cc_final: 0.7652 (mttt) REVERT: W 52 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7121 (mmm160) REVERT: W 84 ASP cc_start: 0.7533 (m-30) cc_final: 0.6991 (t70) REVERT: W 169 ASN cc_start: 0.8044 (t0) cc_final: 0.7587 (m-40) REVERT: Z 9 GLU cc_start: 0.7485 (tm-30) cc_final: 0.6707 (pt0) REVERT: Z 66 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8450 (mp) REVERT: a 40 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.8040 (p0) REVERT: c 48 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6996 (mm-30) REVERT: c 52 GLU cc_start: 0.7468 (tp30) cc_final: 0.6949 (tp30) REVERT: y 45 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7986 (mtm110) outliers start: 259 outliers final: 199 residues processed: 1150 average time/residue: 1.4265 time to fit residues: 2846.7092 Evaluate side-chains 1180 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 961 time to evaluate : 6.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain k residue 21 ARG Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain k residue 114 LEU Chi-restraints excluded: chain k residue 162 MET Chi-restraints excluded: chain l residue 9 THR Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 123 VAL Chi-restraints excluded: chain l residue 126 ASP Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain l residue 147 THR Chi-restraints excluded: chain l residue 169 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 51 LYS Chi-restraints excluded: chain m residue 59 THR Chi-restraints excluded: chain m residue 66 ASP Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain m residue 104 SER Chi-restraints excluded: chain m residue 110 VAL Chi-restraints excluded: chain m residue 113 GLU Chi-restraints excluded: chain m residue 130 VAL Chi-restraints excluded: chain m residue 165 THR Chi-restraints excluded: chain m residue 186 ILE Chi-restraints excluded: chain n residue 10 LEU Chi-restraints excluded: chain p residue 41 ARG Chi-restraints excluded: chain p residue 64 ARG Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 96 SER Chi-restraints excluded: chain p residue 128 SER Chi-restraints excluded: chain q residue 108 THR Chi-restraints excluded: chain q residue 131 VAL Chi-restraints excluded: chain s residue 14 ASP Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 41 VAL Chi-restraints excluded: chain t residue 43 ILE Chi-restraints excluded: chain t residue 49 ASN Chi-restraints excluded: chain t residue 116 VAL Chi-restraints excluded: chain t residue 122 VAL Chi-restraints excluded: chain t residue 137 ARG Chi-restraints excluded: chain u residue 75 GLN Chi-restraints excluded: chain v residue 45 THR Chi-restraints excluded: chain v residue 66 VAL Chi-restraints excluded: chain v residue 82 ILE Chi-restraints excluded: chain x residue 4 THR Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 27 THR Chi-restraints excluded: chain z residue 29 ARG Chi-restraints excluded: chain z residue 47 SER Chi-restraints excluded: chain z residue 79 ASP Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 52 ILE Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 82 LEU Chi-restraints excluded: chain 6 residue 11 VAL Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 74 PHE Chi-restraints excluded: chain 7 residue 23 SER Chi-restraints excluded: chain 7 residue 30 THR Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 77 SER Chi-restraints excluded: chain 8 residue 16 PHE Chi-restraints excluded: chain 8 residue 33 THR Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 190 ASN Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 65 GLN Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 68 THR Chi-restraints excluded: chain r residue 72 ASN Chi-restraints excluded: chain 9 residue 17 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain J residue 45 ASN Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 108 SER Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain S residue 66 GLU Chi-restraints excluded: chain S residue 81 LYS Chi-restraints excluded: chain S residue 84 TYR Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 97 GLN Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 170 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 62 LEU Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 28 THR Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain y residue 58 ILE Chi-restraints excluded: chain y residue 67 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1077 random chunks: chunk 944 optimal weight: 2.9990 chunk 994 optimal weight: 0.9980 chunk 907 optimal weight: 2.9990 chunk 967 optimal weight: 3.9990 chunk 582 optimal weight: 5.9990 chunk 421 optimal weight: 6.9990 chunk 759 optimal weight: 0.8980 chunk 296 optimal weight: 6.9990 chunk 874 optimal weight: 3.9990 chunk 914 optimal weight: 0.8980 chunk 963 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 142 HIS ** 4 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 41 HIS 7 3 ASN 7 21 ASN 7 22 GLN 7 84 ASN 9 10 ASN C 109 GLN D 20 ASN ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN L 4 GLN ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 143 GLN X 50 ASN ** Z 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 163779 Z= 0.177 Angle : 0.576 12.803 244864 Z= 0.292 Chirality : 0.034 0.355 31247 Planarity : 0.005 0.082 13450 Dihedral : 24.081 179.784 81745 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.38 % Favored : 93.57 % Rotamer: Outliers : 2.94 % Allowed : 19.67 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % 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: -1.40 (0.11), residues: 6175 helix: 0.79 (0.11), residues: 2095 sheet: -1.47 (0.16), residues: 1067 loop : -2.01 (0.11), residues: 3013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP a 17 HIS 0.005 0.001 HIS 6 14 PHE 0.019 0.002 PHE 4 123 TYR 0.024 0.001 TYR 5 9 ARG 0.014 0.001 ARG L 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1029 time to evaluate : 6.618 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 TARDY: cannot create tardy model for: "MET g 1 " (corrupted residue). Skipping it. REVERT: j 19 LYS cc_start: 0.8559 (tttt) cc_final: 0.7951 (mttt) REVERT: j 24 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.7283 (p) REVERT: k 23 TYR cc_start: 0.6920 (t80) cc_final: 0.6665 (t80) REVERT: k 60 ARG cc_start: 0.5510 (mpt180) cc_final: 0.4496 (mtm110) REVERT: k 133 MET cc_start: 0.6048 (mtp) cc_final: 0.5716 (ttm) REVERT: k 143 GLN cc_start: 0.4039 (mt0) cc_final: 0.3744 (tm-30) REVERT: k 177 THR cc_start: 0.6818 (m) cc_final: 0.6346 (p) REVERT: l 57 ARG cc_start: 0.5742 (ptt90) cc_final: 0.4834 (mtm110) REVERT: m 94 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7759 (ttpp) REVERT: m 97 PHE cc_start: 0.6002 (t80) cc_final: 0.5444 (t80) REVERT: m 130 VAL cc_start: 0.6047 (OUTLIER) cc_final: 0.5683 (p) REVERT: m 170 LYS cc_start: 0.7323 (mtpt) cc_final: 0.7103 (mtmm) REVERT: n 31 ARG cc_start: 0.6360 (ttm110) cc_final: 0.5764 (mtt-85) REVERT: p 41 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6251 (mmt180) REVERT: p 116 MET cc_start: 0.5648 (tpt) cc_final: 0.5217 (ttt) REVERT: q 3 MET cc_start: 0.5648 (tpp) cc_final: 0.4207 (tmm) REVERT: q 31 LYS cc_start: 0.7675 (pttt) cc_final: 0.7462 (tppp) REVERT: 4 69 LYS cc_start: 0.7108 (mttt) cc_final: 0.6798 (mtmt) REVERT: s 14 ASP cc_start: 0.5764 (OUTLIER) cc_final: 0.5481 (p0) REVERT: s 63 GLU cc_start: 0.7485 (tt0) cc_final: 0.7114 (mt-10) REVERT: s 88 MET cc_start: 0.6400 (mmt) cc_final: 0.6149 (mmt) REVERT: t 137 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5576 (ptt90) REVERT: u 56 LYS cc_start: 0.8312 (tptt) cc_final: 0.7905 (tmtt) REVERT: u 75 GLN cc_start: 0.6765 (OUTLIER) cc_final: 0.6507 (pt0) REVERT: u 123 LYS cc_start: 0.6211 (mttt) cc_final: 0.5587 (mmmt) REVERT: v 92 HIS cc_start: 0.6427 (m-70) cc_final: 0.5699 (m-70) REVERT: v 114 LYS cc_start: 0.5826 (ttmt) cc_final: 0.5573 (ttpt) REVERT: v 115 ARG cc_start: 0.4617 (ptt180) cc_final: 0.3908 (mmm160) REVERT: x 9 LYS cc_start: 0.8550 (mmtt) cc_final: 0.7914 (mmmt) REVERT: z 17 GLN cc_start: 0.6986 (mt0) cc_final: 0.6651 (mm-40) REVERT: z 102 LYS cc_start: 0.6210 (ttmt) cc_final: 0.5757 (tptm) REVERT: 5 21 LYS cc_start: 0.8297 (mmtp) cc_final: 0.7930 (mppt) REVERT: 7 29 ARG cc_start: 0.6824 (ttm-80) cc_final: 0.6360 (mtt90) REVERT: 8 1 MET cc_start: 0.4495 (OUTLIER) cc_final: 0.4206 (ptp) REVERT: 8 16 PHE cc_start: 0.1778 (OUTLIER) cc_final: 0.0128 (p90) REVERT: 8 21 ARG cc_start: 0.6590 (mtt180) cc_final: 0.6278 (ttm170) REVERT: 8 89 MET cc_start: 0.3661 (mmm) cc_final: 0.0219 (mtp) REVERT: r 79 LEU cc_start: 0.7015 (tt) cc_final: 0.6777 (mp) REVERT: Y 80 PHE cc_start: 0.7107 (p90) cc_final: 0.6715 (t80) REVERT: C 146 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7561 (mm-30) REVERT: C 186 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7730 (t0) REVERT: C 217 LYS cc_start: 0.8940 (mttt) cc_final: 0.8616 (mtpp) REVERT: D 108 ASP cc_start: 0.6751 (m-30) cc_final: 0.6349 (m-30) REVERT: F 13 GLN cc_start: 0.8229 (pp30) cc_final: 0.7700 (pp30) REVERT: F 149 ASP cc_start: 0.7734 (m-30) cc_final: 0.7107 (t0) REVERT: K 89 ILE cc_start: 0.9047 (mm) cc_final: 0.8709 (mt) REVERT: K 95 LYS cc_start: 0.8197 (mttt) cc_final: 0.7918 (mmtp) REVERT: K 136 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7677 (mt0) REVERT: L 2 ILE cc_start: 0.9006 (mm) cc_final: 0.8691 (tp) REVERT: M 69 ASN cc_start: 0.8346 (t0) cc_final: 0.8101 (t0) REVERT: M 120 VAL cc_start: 0.7055 (OUTLIER) cc_final: 0.6849 (m) REVERT: N 16 GLU cc_start: 0.7366 (tp30) cc_final: 0.7040 (tp30) REVERT: N 67 ASN cc_start: 0.8255 (m110) cc_final: 0.7375 (t0) REVERT: O 37 THR cc_start: 0.8474 (p) cc_final: 0.8231 (m) REVERT: O 106 ASP cc_start: 0.8925 (p0) cc_final: 0.8634 (p0) REVERT: P 19 LEU cc_start: 0.9160 (mm) cc_final: 0.8758 (mm) REVERT: P 43 SER cc_start: 0.8105 (t) cc_final: 0.7439 (p) REVERT: P 93 LYS cc_start: 0.7789 (mmmt) cc_final: 0.7188 (mmtt) REVERT: P 118 ASP cc_start: 0.8175 (m-30) cc_final: 0.7933 (m-30) REVERT: Q 63 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7511 (tm-30) REVERT: Q 111 GLU cc_start: 0.8213 (mp0) cc_final: 0.7706 (tm-30) REVERT: R 42 SER cc_start: 0.9158 (t) cc_final: 0.8852 (p) REVERT: R 111 ASP cc_start: 0.7992 (p0) cc_final: 0.7224 (m-30) REVERT: S 81 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8076 (mttp) REVERT: T 97 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.8722 (mt0) REVERT: W 32 LYS cc_start: 0.7850 (mttm) cc_final: 0.7531 (mttt) REVERT: W 84 ASP cc_start: 0.7510 (m-30) cc_final: 0.7125 (t0) REVERT: W 169 ASN cc_start: 0.7965 (t0) cc_final: 0.7594 (m-40) REVERT: Z 9 GLU cc_start: 0.7490 (tm-30) cc_final: 0.6684 (pt0) REVERT: Z 20 ASP cc_start: 0.8128 (m-30) cc_final: 0.7800 (m-30) REVERT: Z 24 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7199 (mm-30) REVERT: Z 66 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8377 (mp) REVERT: c 26 ASN cc_start: 0.8270 (p0) cc_final: 0.8008 (p0) REVERT: c 52 GLU cc_start: 0.7178 (tp30) cc_final: 0.6681 (tp30) outliers start: 151 outliers final: 115 residues processed: 1108 average time/residue: 1.3308 time to fit residues: 2528.1286 Evaluate side-chains 1106 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 977 time to evaluate : 5.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain k residue 21 ARG Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 114 LEU Chi-restraints excluded: chain k residue 162 MET Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 66 ASP Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain m residue 104 SER Chi-restraints excluded: chain m residue 113 GLU Chi-restraints excluded: chain m residue 130 VAL Chi-restraints excluded: chain m residue 186 ILE Chi-restraints excluded: chain p residue 41 ARG Chi-restraints excluded: chain p residue 64 ARG Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 96 SER Chi-restraints excluded: chain q residue 108 THR Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain s residue 14 ASP Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 43 ILE Chi-restraints excluded: chain t residue 122 VAL Chi-restraints excluded: chain t residue 137 ARG Chi-restraints excluded: chain u residue 75 GLN Chi-restraints excluded: chain v residue 66 VAL Chi-restraints excluded: chain v residue 82 ILE Chi-restraints excluded: chain x residue 4 THR Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 27 THR Chi-restraints excluded: chain 5 residue 52 ILE Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain 6 residue 11 VAL Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 74 PHE Chi-restraints excluded: chain 7 residue 23 SER Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 8 residue 16 PHE Chi-restraints excluded: chain 8 residue 33 THR Chi-restraints excluded: chain 8 residue 183 VAL Chi-restraints excluded: chain 8 residue 190 ASN Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 65 GLN Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 68 THR Chi-restraints excluded: chain 9 residue 17 VAL Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 108 SER Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain S residue 81 LYS Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 97 GLN Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain W residue 143 GLN Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 170 LEU Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 28 THR Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain y residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1077 random chunks: chunk 635 optimal weight: 30.0000 chunk 1022 optimal weight: 4.9990 chunk 624 optimal weight: 6.9990 chunk 485 optimal weight: 5.9990 chunk 711 optimal weight: 10.0000 chunk 1072 optimal weight: 8.9990 chunk 987 optimal weight: 1.9990 chunk 854 optimal weight: 0.0970 chunk 88 optimal weight: 10.0000 chunk 659 optimal weight: 8.9990 chunk 523 optimal weight: 7.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 54 GLN ** l 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 142 HIS ** q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 3 ASN 7 21 ASN 7 22 GLN 7 84 ASN 9 10 ASN ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN G 22 GLN H 147 ASN ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN L 4 GLN Q 26 ASN R 72 ASN ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 143 GLN X 50 ASN ** Z 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 163779 Z= 0.333 Angle : 0.671 11.997 244864 Z= 0.337 Chirality : 0.039 0.327 31247 Planarity : 0.005 0.081 13450 Dihedral : 24.085 179.620 81745 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.16 % Favored : 91.81 % Rotamer: Outliers : 3.23 % Allowed : 19.96 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % 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: -1.57 (0.10), residues: 6175 helix: 0.62 (0.11), residues: 2093 sheet: -1.55 (0.16), residues: 1107 loop : -2.10 (0.11), residues: 2975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP a 17 HIS 0.008 0.001 HIS G 66 PHE 0.023 0.002 PHE 6 10 TYR 0.025 0.002 TYR x 78 ARG 0.014 0.001 ARG L 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12350 Ramachandran restraints generated. 6175 Oldfield, 0 Emsley, 6175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 968 time to evaluate : 6.618 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 TARDY: cannot create tardy model for: "MET g 1 " (corrupted residue). Skipping it. REVERT: j 19 LYS cc_start: 0.8603 (tttt) cc_final: 0.7995 (mttt) REVERT: j 24 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7392 (p) REVERT: k 23 TYR cc_start: 0.6961 (t80) cc_final: 0.6654 (t80) REVERT: k 60 ARG cc_start: 0.5565 (mpt180) cc_final: 0.4562 (mtm110) REVERT: k 133 MET cc_start: 0.6037 (mtp) cc_final: 0.5475 (ttp) REVERT: k 143 GLN cc_start: 0.4118 (mt0) cc_final: 0.3807 (tm-30) REVERT: k 177 THR cc_start: 0.6831 (m) cc_final: 0.6350 (p) REVERT: l 57 ARG cc_start: 0.5731 (ptt90) cc_final: 0.4704 (mtm110) REVERT: m 94 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7750 (ttpp) REVERT: m 130 VAL cc_start: 0.6124 (OUTLIER) cc_final: 0.5768 (p) REVERT: n 31 ARG cc_start: 0.6318 (ttm110) cc_final: 0.5693 (mtt-85) REVERT: p 41 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6272 (mmt180) REVERT: p 136 LYS cc_start: 0.5541 (tttt) cc_final: 0.5226 (tptp) REVERT: q 3 MET cc_start: 0.5731 (tpp) cc_final: 0.4242 (tmm) REVERT: q 31 LYS cc_start: 0.7767 (pttt) cc_final: 0.7542 (tppp) REVERT: 4 69 LYS cc_start: 0.7106 (mttt) cc_final: 0.6765 (mtmt) REVERT: s 14 ASP cc_start: 0.5794 (OUTLIER) cc_final: 0.5489 (p0) REVERT: s 63 GLU cc_start: 0.7169 (tt0) cc_final: 0.6732 (mt-10) REVERT: t 137 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.5668 (ptt90) REVERT: u 56 LYS cc_start: 0.8268 (tptt) cc_final: 0.7879 (tmtt) REVERT: u 75 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6564 (pt0) REVERT: v 92 HIS cc_start: 0.6495 (m-70) cc_final: 0.5764 (m-70) REVERT: v 114 LYS cc_start: 0.5948 (ttmt) cc_final: 0.5593 (ttpt) REVERT: v 115 ARG cc_start: 0.4452 (ptt180) cc_final: 0.3731 (mmm160) REVERT: x 9 LYS cc_start: 0.8533 (mmtt) cc_final: 0.7906 (mmmt) REVERT: x 60 VAL cc_start: 0.8257 (t) cc_final: 0.7978 (m) REVERT: z 17 GLN cc_start: 0.7141 (mt0) cc_final: 0.6672 (mm-40) REVERT: z 29 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.5247 (ttm-80) REVERT: z 102 LYS cc_start: 0.6201 (ttmt) cc_final: 0.5785 (tptm) REVERT: 5 92 GLU cc_start: 0.8094 (tt0) cc_final: 0.6905 (mm-30) REVERT: 7 29 ARG cc_start: 0.6901 (ttm-80) cc_final: 0.6419 (mtt90) REVERT: 8 1 MET cc_start: 0.4503 (OUTLIER) cc_final: 0.4226 (ptp) REVERT: 8 16 PHE cc_start: 0.1889 (OUTLIER) cc_final: 0.0132 (p90) REVERT: 8 21 ARG cc_start: 0.6675 (mtt180) cc_final: 0.6325 (ttm170) REVERT: 8 89 MET cc_start: 0.3996 (mmm) cc_final: 0.0480 (mtp) REVERT: r 79 LEU cc_start: 0.7025 (tt) cc_final: 0.6634 (mp) REVERT: Y 80 PHE cc_start: 0.7113 (p90) cc_final: 0.6660 (t80) REVERT: C 146 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7584 (mm-30) REVERT: C 186 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7907 (t0) REVERT: C 217 LYS cc_start: 0.9002 (mttt) cc_final: 0.8680 (mtpp) REVERT: D 60 ARG cc_start: 0.7789 (tmm-80) cc_final: 0.7507 (tmm-80) REVERT: D 108 ASP cc_start: 0.6804 (m-30) cc_final: 0.6373 (m-30) REVERT: F 149 ASP cc_start: 0.7749 (m-30) cc_final: 0.7093 (t0) REVERT: G 104 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7706 (tt) REVERT: K 52 ASP cc_start: 0.7854 (m-30) cc_final: 0.7605 (m-30) REVERT: K 89 ILE cc_start: 0.9173 (mm) cc_final: 0.8819 (mt) REVERT: K 112 ASN cc_start: 0.8793 (p0) cc_final: 0.8569 (p0) REVERT: K 136 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: L 2 ILE cc_start: 0.9032 (mm) cc_final: 0.8717 (tp) REVERT: N 67 ASN cc_start: 0.8288 (m110) cc_final: 0.7360 (t0) REVERT: O 37 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8218 (m) REVERT: O 106 ASP cc_start: 0.8852 (p0) cc_final: 0.8552 (p0) REVERT: P 43 SER cc_start: 0.8238 (t) cc_final: 0.7553 (p) REVERT: P 118 ASP cc_start: 0.8209 (m-30) cc_final: 0.7966 (m-30) REVERT: Q 63 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7578 (tm-30) REVERT: Q 111 GLU cc_start: 0.8251 (mp0) cc_final: 0.7765 (tm-30) REVERT: R 42 SER cc_start: 0.9225 (t) cc_final: 0.8943 (p) REVERT: R 111 ASP cc_start: 0.8061 (p0) cc_final: 0.7246 (m-30) REVERT: S 81 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8169 (mttp) REVERT: T 97 GLN cc_start: 0.9400 (OUTLIER) cc_final: 0.8736 (mt0) REVERT: W 32 LYS cc_start: 0.7902 (mttm) cc_final: 0.7577 (mttt) REVERT: W 52 ARG cc_start: 0.7217 (mmm160) cc_final: 0.6877 (mmm160) REVERT: W 84 ASP cc_start: 0.7518 (m-30) cc_final: 0.7079 (t0) REVERT: W 169 ASN cc_start: 0.8062 (t0) cc_final: 0.7706 (m-40) REVERT: Z 9 GLU cc_start: 0.7537 (tm-30) cc_final: 0.6697 (pt0) REVERT: Z 66 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8427 (mp) REVERT: c 52 GLU cc_start: 0.7331 (tp30) cc_final: 0.6832 (tp30) REVERT: y 21 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7058 (m170) outliers start: 166 outliers final: 132 residues processed: 1068 average time/residue: 1.3525 time to fit residues: 2491.9417 Evaluate side-chains 1107 residues out of total 5136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 958 time to evaluate : 6.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain k residue 21 ARG Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 114 LEU Chi-restraints excluded: chain k residue 162 MET Chi-restraints excluded: chain l residue 62 VAL Chi-restraints excluded: chain l residue 140 VAL Chi-restraints excluded: chain m residue 66 ASP Chi-restraints excluded: chain m residue 101 LEU Chi-restraints excluded: chain m residue 104 SER Chi-restraints excluded: chain m residue 113 GLU Chi-restraints excluded: chain m residue 130 VAL Chi-restraints excluded: chain m residue 186 ILE Chi-restraints excluded: chain n residue 88 THR Chi-restraints excluded: chain p residue 41 ARG Chi-restraints excluded: chain p residue 64 ARG Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 96 SER Chi-restraints excluded: chain q residue 108 THR Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 45 THR Chi-restraints excluded: chain s residue 14 ASP Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 43 ILE Chi-restraints excluded: chain t residue 49 ASN Chi-restraints excluded: chain t residue 122 VAL Chi-restraints excluded: chain t residue 137 ARG Chi-restraints excluded: chain u residue 75 GLN Chi-restraints excluded: chain v residue 66 VAL Chi-restraints excluded: chain v residue 82 ILE Chi-restraints excluded: chain x residue 4 THR Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 27 THR Chi-restraints excluded: chain z residue 29 ARG Chi-restraints excluded: chain 5 residue 52 ILE Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 6 residue 11 VAL Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 74 PHE Chi-restraints excluded: chain 7 residue 23 SER Chi-restraints excluded: chain 7 residue 30 THR Chi-restraints excluded: chain 7 residue 32 ILE Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 8 residue 16 PHE Chi-restraints excluded: chain 8 residue 33 THR Chi-restraints excluded: chain 8 residue 190 ASN Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 65 GLN Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 68 THR Chi-restraints excluded: chain 9 residue 17 VAL Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 108 SER Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain S residue 81 LYS Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 97 GLN Chi-restraints excluded: chain U residue 16 ILE Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 170 LEU Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain c residue 35 VAL Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 28 THR Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain y residue 21 HIS Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain y residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1077 random chunks: chunk 678 optimal weight: 5.9990 chunk 910 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 787 optimal weight: 0.5980 chunk 126 optimal weight: 20.0000 chunk 237 optimal weight: 1.9990 chunk 855 optimal weight: 5.9990 chunk 358 optimal weight: 1.9990 chunk 878 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 142 HIS 4 61 ASN 7 3 ASN 7 21 ASN 7 22 GLN 7 84 ASN 9 10 ASN C 109 GLN ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN L 4 GLN M 107 ASN Q 26 ASN Q 50 GLN ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 ASN ** Z 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.145046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114618 restraints weight = 305674.120| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.47 r_work: 0.3235 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 163779 Z= 0.207 Angle : 0.592 12.593 244864 Z= 0.300 Chirality : 0.035 0.330 31247 Planarity : 0.005 0.081 13450 Dihedral : 24.061 179.974 81745 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.70 % Favored : 93.26 % Rotamer: Outliers : 3.37 % Allowed : 19.94 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % 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: -1.34 (0.11), residues: 6175 helix: 0.82 (0.11), residues: 2084 sheet: -1.48 (0.16), residues: 1057 loop : -1.94 (0.11), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP a 17 HIS 0.006 0.001 HIS G 66 PHE 0.020 0.002 PHE 6 10 TYR 0.023 0.002 TYR x 78 ARG 0.013 0.001 ARG L 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40643.66 seconds wall clock time: 710 minutes 9.59 seconds (42609.59 seconds total)