Starting phenix.real_space_refine on Fri Mar 1 12:17:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9j_43074/03_2024/8v9j_43074_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9j_43074/03_2024/8v9j_43074.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9j_43074/03_2024/8v9j_43074_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9j_43074/03_2024/8v9j_43074_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9j_43074/03_2024/8v9j_43074_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9j_43074/03_2024/8v9j_43074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9j_43074/03_2024/8v9j_43074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9j_43074/03_2024/8v9j_43074_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9j_43074/03_2024/8v9j_43074_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4778 5.49 5 S 114 5.16 5 C 77162 2.51 5 N 28593 2.21 5 O 42406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d GLU 72": "OE1" <-> "OE2" Residue "e TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "e GLU 113": "OE1" <-> "OE2" Residue "e GLU 141": "OE1" <-> "OE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "h TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 82": "OD1" <-> "OD2" Residue "k PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 63": "OD1" <-> "OD2" Residue "t PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 143": "OD1" <-> "OD2" Residue "z GLU 186": "OE1" <-> "OE2" Residue "z ASP 280": "OD1" <-> "OD2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "E PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E ASP 181": "OD1" <-> "OD2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F ASP 149": "OD1" <-> "OD2" Residue "F ASP 151": "OD1" <-> "OD2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "I TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 19": "OD1" <-> "OD2" Residue "L ASP 52": "OD1" <-> "OD2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M ASP 37": "OD1" <-> "OD2" Residue "N GLU 51": "OE1" <-> "OE2" Residue "N TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 123": "OD1" <-> "OD2" Residue "O PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "P ASP 74": "OD1" <-> "OD2" Residue "Q PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 33": "OE1" <-> "OE2" Residue "S TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 44": "OD1" <-> "OD2" Residue "U GLU 38": "OE1" <-> "OE2" Residue "U GLU 69": "OE1" <-> "OE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ASP 51": "OD1" <-> "OD2" Residue "X ASP 30": "OD1" <-> "OD2" Residue "1 GLU 9": "OE1" <-> "OE2" Residue "1 TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 10": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153055 Number of models: 1 Model: "" Number of chains: 61 Chain: "a" Number of atoms: 32439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1511, 32439 Classifications: {'RNA': 1511} Modifications used: {'rna2p_pur': 113, 'rna2p_pyr': 85, 'rna3p_pur': 736, 'rna3p_pyr': 577} Link IDs: {'rna2p': 198, 'rna3p': 1312} Chain: "b" 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: "c" 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: "d" 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: "e" 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: "f" 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: "g" 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: "h" 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: "i" 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: "j" 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: "k" 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: "l" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "m" 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: "n" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" 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: "p" 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: "q" 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: "r" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 513 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "s" 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: "t" 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: "u" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 280 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "v" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "y" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1581 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p': 5, 'rna3p_pur': 33, 'rna3p_pyr': 27} Link IDs: {'rna2p': 9, 'rna3p': 64} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "z" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2812 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 349} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 65997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3073, 65997 Classifications: {'RNA': 3073} Modifications used: {'rna2p_pur': 294, 'rna2p_pyr': 149, 'rna3p_pur': 1465, 'rna3p_pyr': 1165} Link IDs: {'rna2p': 443, 'rna3p': 2629} Chain breaks: 1 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': 7, 'rna3p_pur': 57, 'rna3p_pyr': 47} Link IDs: {'rna2p': 14, 'rna3p': 103} 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: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1439 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 173} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1018 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 147} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 68 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: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 531 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 Chain: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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 breaks: 1 Chain: "X" 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: "Y" 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: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "1" 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: "2" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 474 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "3" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 436 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "4" 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: "5" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "6" 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: "7" 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: "8" 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: "9" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A11SA SG CYS Z 5 180.278 113.724 194.664 1.00 35.78 S ATOM A11SW SG CYS Z 8 179.410 115.866 197.619 1.00 39.36 S ATOM A122E SG CYS Z 52 180.125 117.491 194.196 1.00 39.68 S ATOM A122X SG CYS Z 55 182.933 116.200 196.124 1.00 42.65 S ATOM A13ML SG CYS 5 15 148.989 180.270 190.284 1.00 43.36 S ATOM A13N7 SG CYS 5 18 150.276 177.994 193.091 1.00 44.96 S ATOM A13T6 SG CYS 5 42 146.681 178.798 192.949 1.00 39.40 S ATOM A13TR SG CYS 5 45 149.118 181.429 194.042 1.00 42.60 S Time building chain proxies: 57.03, per 1000 atoms: 0.37 Number of scatterers: 153055 At special positions: 0 Unit cell: (247.35, 239.7, 288.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 114 16.00 P 4778 15.00 O 42406 8.00 N 28593 7.00 C 77162 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: 54.76 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 42 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 18 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 45 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 15 " pdb=" ZN Z 101 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 52 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 55 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 8 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 5 " Number of angles added : 12 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11952 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 194 helices and 80 sheets defined 38.7% alpha, 19.0% beta 1595 base pairs and 2462 stacking pairs defined. Time for finding SS restraints: 77.09 Creating SS restraints... Processing helix chain 'b' and resid 5 through 13 Processing helix chain 'b' and resid 24 through 29 removed outlier: 4.857A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG b 29 " --> pdb=" O PRO b 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 29' Processing helix chain 'b' and resid 42 through 64 Processing helix chain 'b' and resid 73 through 88 removed outlier: 4.391A pdb=" N GLU b 78 " --> pdb=" O LYS b 74 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER b 79 " --> pdb=" O GLN b 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 124 removed outlier: 4.448A pdb=" N VAL b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS b 108 " --> pdb=" O PHE b 104 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS b 109 " --> pdb=" O SER b 105 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY b 124 " --> pdb=" O MET b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 149 removed outlier: 4.543A pdb=" N ARG b 146 " --> pdb=" O ASN b 142 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER b 147 " --> pdb=" O LYS b 143 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 155 removed outlier: 3.980A pdb=" N GLN b 155 " --> pdb=" O ILE b 151 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 228 removed outlier: 4.203A pdb=" N ALA b 210 " --> pdb=" O ALA b 206 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.627A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU c 12 " --> pdb=" O HIS c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 3.666A pdb=" N LEU c 46 " --> pdb=" O LEU c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 76 removed outlier: 4.348A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 94 removed outlier: 3.519A pdb=" N ASP c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 3.541A pdb=" N GLN c 111 " --> pdb=" O ASN c 107 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 removed outlier: 3.762A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 143 removed outlier: 3.962A pdb=" N GLN c 143 " --> pdb=" O SER c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.976A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER d 12 " --> pdb=" O ALA d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 30 removed outlier: 5.490A pdb=" N GLU d 27 " --> pdb=" O ASP d 23 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS d 28 " --> pdb=" O GLN d 24 " (cutoff:3.500A) Proline residue: d 30 - end of helix Processing helix chain 'd' and resid 44 through 61 removed outlier: 3.958A pdb=" N TYR d 60 " --> pdb=" O ALA d 56 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY d 61 " --> pdb=" O ARG d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 78 Proline residue: d 78 - end of helix Processing helix chain 'd' and resid 80 through 92 removed outlier: 4.148A pdb=" N ARG d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 removed outlier: 3.662A pdb=" N GLY d 101 " --> pdb=" O VAL d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 116 removed outlier: 3.546A pdb=" N HIS d 115 " --> pdb=" O GLN d 111 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY d 116 " --> pdb=" O LEU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 141 through 148 removed outlier: 3.843A pdb=" N LEU d 145 " --> pdb=" O LYS d 141 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASN d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR d 147 " --> pdb=" O LYS d 143 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU d 148 " --> pdb=" O SER d 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 141 through 148' Processing helix chain 'd' and resid 149 through 157 Processing helix chain 'd' and resid 182 through 187 removed outlier: 4.329A pdb=" N ASP d 187 " --> pdb=" O ARG d 183 " (cutoff:3.500A) Processing helix chain 'd' and resid 192 through 201 removed outlier: 3.695A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 80 through 96 removed outlier: 3.678A pdb=" N LYS e 94 " --> pdb=" O GLU e 90 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN e 95 " --> pdb=" O GLU e 91 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE e 96 " --> pdb=" O ALA e 92 " (cutoff:3.500A) Processing helix chain 'e' and resid 134 through 144 Processing helix chain 'e' and resid 157 through 172 removed outlier: 3.536A pdb=" N LEU e 171 " --> pdb=" O ALA e 167 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU e 172 " --> pdb=" O ALA e 168 " (cutoff:3.500A) Processing helix chain 'e' and resid 174 through 183 Processing helix chain 'e' and resid 185 through 190 removed outlier: 3.516A pdb=" N VAL e 189 " --> pdb=" O PRO e 185 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 214 Processing helix chain 'f' and resid 15 through 32 removed outlier: 3.962A pdb=" N VAL f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix removed outlier: 3.688A pdb=" N GLU f 24 " --> pdb=" O ALA f 20 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL f 29 " --> pdb=" O THR f 25 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 82 removed outlier: 3.569A pdb=" N LEU f 81 " --> pdb=" O ARG f 77 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN f 82 " --> pdb=" O GLN f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.096A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.544A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.840A pdb=" N ARG g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN g 110 " --> pdb=" O ASN g 106 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG g 111 " --> pdb=" O PHE g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 149 removed outlier: 4.254A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 114 through 122 Processing helix chain 'i' and resid 54 through 59 removed outlier: 4.690A pdb=" N PHE i 59 " --> pdb=" O LEU i 55 " (cutoff:3.500A) Processing helix chain 'i' and resid 61 through 76 Proline residue: i 71 - end of helix Processing helix chain 'i' and resid 91 through 112 Proline residue: i 112 - end of helix Processing helix chain 'i' and resid 113 through 122 removed outlier: 4.838A pdb=" N ALA i 117 " --> pdb=" O GLU i 113 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS i 120 " --> pdb=" O PRO i 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.234A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 60 removed outlier: 3.598A pdb=" N VAL k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLY k 60 " --> pdb=" O SER k 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 55 through 60' Processing helix chain 'k' and resid 68 through 87 removed outlier: 3.819A pdb=" N HIS k 86 " --> pdb=" O LYS k 82 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 101 through 113 removed outlier: 4.244A pdb=" N GLY k 113 " --> pdb=" O LEU k 109 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.080A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.399A pdb=" N THR m 20 " --> pdb=" O GLU m 16 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 4.474A pdb=" N SER m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 64 Processing helix chain 'm' and resid 67 through 85 removed outlier: 4.142A pdb=" N ILE m 84 " --> pdb=" O ARG m 80 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY m 85 " --> pdb=" O LYS m 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 Processing helix chain 'm' and resid 107 through 112 Processing helix chain 'n' and resid 3 through 13 removed outlier: 5.290A pdb=" N LYS n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.540A pdb=" N LYS o 8 " --> pdb=" O THR o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.046A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS o 47 " --> pdb=" O LEU o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 52 through 63 Processing helix chain 'p' and resid 67 through 78 Processing helix chain 'p' and resid 79 through 85 Processing helix chain 'p' and resid 101 through 114 removed outlier: 3.740A pdb=" N GLU p 114 " --> pdb=" O LEU p 110 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 25 removed outlier: 3.534A pdb=" N SER r 24 " --> pdb=" O CYS r 20 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LYS r 25 " --> pdb=" O VAL r 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 20 through 25' Processing helix chain 'r' and resid 34 through 43 removed outlier: 3.843A pdb=" N LEU r 38 " --> pdb=" O ASP r 34 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR r 41 " --> pdb=" O LEU r 37 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER r 43 " --> pdb=" O ARG r 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 55 Processing helix chain 'r' and resid 57 through 75 Processing helix chain 's' and resid 12 through 26 removed outlier: 3.609A pdb=" N LEU s 16 " --> pdb=" O ASP s 12 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN s 26 " --> pdb=" O GLN s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 46 removed outlier: 4.072A pdb=" N ILE s 45 " --> pdb=" O ILE s 41 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLY s 46 " --> pdb=" O PRO s 42 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 41 through 46' Processing helix chain 's' and resid 70 through 76 removed outlier: 4.367A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 removed outlier: 3.551A pdb=" N GLY t 42 " --> pdb=" O ALA t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 removed outlier: 3.621A pdb=" N ALA t 53 " --> pdb=" O GLU t 49 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 86 removed outlier: 3.685A pdb=" N LEU t 86 " --> pdb=" O ALA t 82 " (cutoff:3.500A) Processing helix chain 'u' and resid 3 through 25 removed outlier: 4.763A pdb=" N LYS u 7 " --> pdb=" O SER u 3 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG u 25 " --> pdb=" O LEU u 21 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 33 Processing helix chain 'z' and resid 8 through 18 removed outlier: 4.186A pdb=" N ARG z 18 " --> pdb=" O ASP z 14 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 58 removed outlier: 4.420A pdb=" N ASP z 58 " --> pdb=" O ARG z 54 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 83 removed outlier: 3.723A pdb=" N ARG z 74 " --> pdb=" O LEU z 70 " (cutoff:3.500A) Proline residue: z 75 - end of helix removed outlier: 4.131A pdb=" N GLU z 78 " --> pdb=" O ARG z 74 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR z 82 " --> pdb=" O GLU z 78 " (cutoff:3.500A) Processing helix chain 'z' and resid 122 through 133 removed outlier: 3.765A pdb=" N ARG z 133 " --> pdb=" O LEU z 129 " (cutoff:3.500A) Processing helix chain 'z' and resid 176 through 207 Processing helix chain 'z' and resid 219 through 227 removed outlier: 3.894A pdb=" N ALA z 223 " --> pdb=" O TRP z 219 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE z 227 " --> pdb=" O ALA z 223 " (cutoff:3.500A) Processing helix chain 'z' and resid 245 through 276 Processing helix chain 'z' and resid 284 through 295 removed outlier: 3.642A pdb=" N ALA z 294 " --> pdb=" O ALA z 290 " (cutoff:3.500A) Processing helix chain 'z' and resid 336 through 349 removed outlier: 4.114A pdb=" N ARG z 340 " --> pdb=" O ARG z 336 " (cutoff:3.500A) Processing helix chain 'z' and resid 357 through 362 removed outlier: 4.642A pdb=" N ALA z 361 " --> pdb=" O GLY z 357 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL z 362 " --> pdb=" O ALA z 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 357 through 362' Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.649A 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: 4.213A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.160A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.328A 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 264 through 269 removed outlier: 3.952A pdb=" N ILE C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.904A pdb=" N VAL D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE D 63 " --> pdb=" O PRO D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 63' Processing helix chain 'D' and resid 64 through 74 removed outlier: 3.548A pdb=" N GLN D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 96 removed outlier: 4.107A pdb=" N VAL D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TYR D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU D 96 " --> pdb=" O VAL D 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 96' Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'E' and resid 21 through 26 removed outlier: 3.560A pdb=" N ASP E 26 " --> pdb=" O ALA E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 47 removed outlier: 3.620A pdb=" N GLN E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLN E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 122 removed outlier: 3.586A pdb=" N ALA E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 149 Processing helix chain 'E' and resid 162 through 171 removed outlier: 3.880A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ASN E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 192 removed outlier: 3.699A pdb=" N VAL E 188 " --> pdb=" O ASN E 184 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 210 removed outlier: 3.832A pdb=" N ALA E 203 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN E 208 " --> pdb=" O TYR E 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 removed outlier: 4.124A pdb=" N GLU F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 19 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 removed outlier: 5.045A pdb=" N ARG F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 4.297A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA F 65 " --> pdb=" O ILE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 118 removed outlier: 3.820A pdb=" N TRP F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 4.754A 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 149 through 154 removed outlier: 3.707A pdb=" N ILE F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP F 154 " --> pdb=" O VAL F 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 149 through 154' Processing helix chain 'F' and resid 169 through 181 removed outlier: 3.507A pdb=" N GLY F 173 " --> pdb=" O ASN F 169 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 removed outlier: 4.636A pdb=" N GLN G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.682A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 152 removed outlier: 3.905A pdb=" N LEU G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 42 through 60 removed outlier: 3.746A pdb=" N GLN H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE H 50 " --> pdb=" O GLN H 46 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL H 58 " --> pdb=" O ARG H 54 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 75 removed outlier: 4.132A pdb=" N GLU H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 108 Processing helix chain 'H' and resid 113 through 118 removed outlier: 4.267A pdb=" N VAL H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 5.682A 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: 3.678A pdb=" N ALA I 19 " --> pdb=" O GLU I 15 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER I 20 " --> pdb=" O GLN I 16 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N THR I 21 " --> pdb=" O PHE I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 44 Processing helix chain 'I' and resid 53 through 65 removed outlier: 3.883A pdb=" N GLU I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLY I 65 " --> pdb=" O ALA I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 101 removed outlier: 5.527A pdb=" N ALA I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP I 99 " --> pdb=" O LYS I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 126 removed outlier: 4.072A pdb=" N ILE I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA I 124 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP I 125 " --> pdb=" O GLU I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 32 removed outlier: 3.675A pdb=" N GLY J 31 " --> pdb=" O GLY J 27 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN J 32 " --> pdb=" O PRO J 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 27 through 32' Processing helix chain 'J' and resid 36 through 49 removed outlier: 4.061A pdb=" N PHE J 40 " --> pdb=" O ASN J 36 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS J 42 " --> pdb=" O MET J 38 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA J 43 " --> pdb=" O GLU J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 86 removed outlier: 3.512A pdb=" N LEU J 81 " --> pdb=" O ALA J 77 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 115 removed outlier: 3.519A pdb=" N ARG J 108 " --> pdb=" O TRP J 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU J 109 " --> pdb=" O ASP J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 138 removed outlier: 3.776A pdb=" N ALA J 126 " --> pdb=" O ASP J 122 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR J 133 " --> pdb=" O ILE J 129 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET J 137 " --> pdb=" O THR J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 200 removed outlier: 3.937A pdb=" N GLU K 187 " --> pdb=" O THR K 183 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN K 188 " --> pdb=" O LYS K 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 38 removed outlier: 3.709A pdb=" N ARG L 37 " --> pdb=" O ALA L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 96 removed outlier: 3.671A pdb=" N GLU L 94 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 110 removed outlier: 4.193A pdb=" N VAL L 101 " --> pdb=" O PRO L 97 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA L 104 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU L 109 " --> pdb=" O ILE L 105 " (cutoff:3.500A) Proline residue: L 110 - end of helix Processing helix chain 'L' and resid 112 through 122 removed outlier: 3.625A pdb=" N GLN L 117 " --> pdb=" O LYS L 113 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN L 119 " --> pdb=" O GLY L 115 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS L 120 " --> pdb=" O ARG L 116 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS L 121 " --> pdb=" O GLN L 117 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU L 122 " --> pdb=" O ILE L 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 110 removed outlier: 4.258A pdb=" N GLU M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 118 Processing helix chain 'N' and resid 39 through 44 removed outlier: 3.979A pdb=" N ARG N 43 " --> pdb=" O GLY N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 3.958A pdb=" N LEU N 61 " --> pdb=" O ILE N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 87 removed outlier: 3.816A pdb=" N ILE N 83 " --> pdb=" O ASN N 79 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN N 84 " --> pdb=" O VAL N 80 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS N 85 " --> pdb=" O GLY N 81 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA N 86 " --> pdb=" O ASP N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 102 Processing helix chain 'N' and resid 130 through 141 removed outlier: 3.586A pdb=" N GLU N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA N 140 " --> pdb=" O ALA N 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY N 141 " --> pdb=" O ILE N 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 59 removed outlier: 3.564A pdb=" N GLU O 48 " --> pdb=" O ASN O 44 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA O 53 " --> pdb=" O SER O 49 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE O 54 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 3.558A pdb=" N ALA O 114 " --> pdb=" O ASP O 110 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS O 123 " --> pdb=" O THR O 119 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS O 124 " --> pdb=" O ARG O 120 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Proline residue: O 126 - end of helix Processing helix chain 'P' and resid 13 through 32 removed outlier: 3.727A pdb=" N SER P 18 " --> pdb=" O SER P 14 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA P 19 " --> pdb=" O SER P 15 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA P 22 " --> pdb=" O SER P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 58 removed outlier: 3.561A pdb=" N ARG P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) Proline residue: P 46 - end of helix removed outlier: 3.549A pdb=" N LYS P 50 " --> pdb=" O PRO P 46 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS P 54 " --> pdb=" O LYS P 50 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY P 58 " --> pdb=" O HIS P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 71 removed outlier: 3.922A pdb=" N LYS P 68 " --> pdb=" O ARG P 64 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS P 69 " --> pdb=" O GLU P 65 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG P 71 " --> pdb=" O MET P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 89 removed outlier: 3.755A pdb=" N HIS P 77 " --> pdb=" O LYS P 73 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR P 78 " --> pdb=" O ASP P 74 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY P 84 " --> pdb=" O PHE P 80 " (cutoff:3.500A) Proline residue: P 85 - end of helix removed outlier: 3.811A pdb=" N ALA P 88 " --> pdb=" O GLY P 84 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASP P 89 " --> pdb=" O PRO P 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 29 removed outlier: 3.597A pdb=" N ARG Q 24 " --> pdb=" O ARG Q 20 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU Q 25 " --> pdb=" O ARG Q 21 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS Q 27 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LYS Q 28 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL Q 29 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 73 removed outlier: 4.133A pdb=" N ILE Q 73 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 96 removed outlier: 3.667A pdb=" N ALA Q 89 " --> pdb=" O GLY Q 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG Q 91 " --> pdb=" O LEU Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 124 removed outlier: 3.540A pdb=" N GLU Q 122 " --> pdb=" O ASP Q 118 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA Q 123 " --> pdb=" O ALA Q 119 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY Q 124 " --> pdb=" O ALA Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 12 removed outlier: 3.861A pdb=" N ASP R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ALA R 10 " --> pdb=" O PHE R 6 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER R 11 " --> pdb=" O VAL R 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 103 removed outlier: 4.829A pdb=" N ARG R 100 " --> pdb=" O LEU R 96 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU R 101 " --> pdb=" O TYR R 97 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ARG R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 96 through 103' Processing helix chain 'S' and resid 8 through 22 removed outlier: 4.107A pdb=" N LYS S 12 " --> pdb=" O LEU S 8 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS S 13 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG S 14 " --> pdb=" O ALA S 10 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR S 16 " --> pdb=" O LYS S 12 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS S 22 " --> pdb=" O LEU S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 31 removed outlier: 4.041A pdb=" N ARG S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 73 removed outlier: 3.572A pdb=" N LEU S 40 " --> pdb=" O LYS S 36 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR S 47 " --> pdb=" O LEU S 43 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU S 60 " --> pdb=" O GLU S 56 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA S 67 " --> pdb=" O SER S 63 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN S 72 " --> pdb=" O ALA S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 Processing helix chain 'S' and resid 91 through 101 removed outlier: 3.708A pdb=" N GLU S 97 " --> pdb=" O LYS S 93 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL S 100 " --> pdb=" O ALA S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 118 removed outlier: 3.821A pdb=" N VAL S 112 " --> pdb=" O ALA S 108 " (cutoff:3.500A) Proline residue: S 118 - end of helix Processing helix chain 'T' and resid 51 through 59 removed outlier: 4.506A pdb=" N LYS T 57 " --> pdb=" O ASP T 53 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL T 58 " --> pdb=" O ASP T 54 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ALA T 59 " --> pdb=" O LEU T 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 32 removed outlier: 3.723A pdb=" N ARG U 26 " --> pdb=" O THR U 22 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL U 27 " --> pdb=" O LYS U 23 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU U 30 " --> pdb=" O ARG U 26 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 46 removed outlier: 3.645A pdb=" N ASP U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG U 44 " --> pdb=" O LEU U 40 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP U 45 " --> pdb=" O ASP U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 50 through 68 removed outlier: 3.683A pdb=" N VAL U 54 " --> pdb=" O ALA U 50 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL U 57 " --> pdb=" O PRO U 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 12 removed outlier: 4.735A pdb=" N ILE V 10 " --> pdb=" O ASP V 6 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE V 11 " --> pdb=" O PRO V 7 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU V 12 " --> pdb=" O ARG V 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 6 through 12' Processing helix chain 'V' and resid 17 through 27 removed outlier: 3.547A pdb=" N GLU V 25 " --> pdb=" O TYR V 21 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP V 26 " --> pdb=" O GLY V 22 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 51 removed outlier: 3.657A pdb=" N ASP V 51 " --> pdb=" O GLU V 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 72 removed outlier: 4.341A pdb=" N VAL W 71 " --> pdb=" O HIS W 67 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N MET W 72 " --> pdb=" O VAL W 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 67 through 72' Processing helix chain 'X' and resid 20 through 31 removed outlier: 3.505A pdb=" N GLN X 26 " --> pdb=" O GLY X 22 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 61 removed outlier: 3.534A pdb=" N SER X 60 " --> pdb=" O ALA X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 194 removed outlier: 3.502A pdb=" N GLU X 191 " --> pdb=" O ALA X 187 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU X 192 " --> pdb=" O GLU X 188 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU X 193 " --> pdb=" O ALA X 189 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLY X 194 " --> pdb=" O LEU X 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 59 Processing helix chain '1' and resid 6 through 13 removed outlier: 3.570A pdb=" N ARG 1 11 " --> pdb=" O PRO 1 7 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU 1 12 " --> pdb=" O GLY 1 8 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU 1 13 " --> pdb=" O GLU 1 9 " (cutoff:3.500A) Processing helix chain '1' and resid 14 through 39 removed outlier: 3.992A pdb=" N LYS 1 19 " --> pdb=" O ASP 1 15 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS 1 26 " --> pdb=" O LEU 1 22 " (cutoff:3.500A) Processing helix chain '1' and resid 44 through 67 removed outlier: 4.255A pdb=" N ARG 1 48 " --> pdb=" O ASN 1 44 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA 1 55 " --> pdb=" O ARG 1 51 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU 1 65 " --> pdb=" O LEU 1 61 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 removed outlier: 3.583A pdb=" N SER 2 22 " --> pdb=" O LYS 2 18 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU 2 23 " --> pdb=" O GLN 2 19 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG 2 24 " --> pdb=" O ARG 2 20 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU 2 26 " --> pdb=" O SER 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 51 removed outlier: 3.624A pdb=" N THR 2 49 " --> pdb=" O GLY 2 45 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL 2 50 " --> pdb=" O LEU 2 46 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 47 Processing helix chain '3' and resid 56 through 64 removed outlier: 3.681A pdb=" N PHE 3 61 " --> pdb=" O ARG 3 57 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU 3 62 " --> pdb=" O VAL 3 58 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 21 removed outlier: 4.067A pdb=" N ARG 4 16 " --> pdb=" O ASN 4 12 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLN 4 19 " --> pdb=" O SER 4 15 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP 4 20 " --> pdb=" O ARG 4 16 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LYS 4 21 " --> pdb=" O ARG 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 40 through 50 removed outlier: 5.016A pdb=" N LYS 4 45 " --> pdb=" O ARG 4 41 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA 4 46 " --> pdb=" O ARG 4 42 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG 4 48 " --> pdb=" O LEU 4 44 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU 4 49 " --> pdb=" O LYS 4 45 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY 4 50 " --> pdb=" O ALA 4 46 " (cutoff:3.500A) Processing helix chain '5' and resid 28 through 33 Proline residue: 5 33 - end of helix Processing helix chain '6' and resid 11 through 19 Processing helix chain '6' and resid 20 through 28 removed outlier: 3.779A pdb=" N ARG 6 26 " --> pdb=" O ARG 6 22 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR 6 27 " --> pdb=" O LEU 6 23 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG 6 28 " --> pdb=" O ARG 6 24 " (cutoff:3.500A) Processing helix chain '6' and resid 29 through 41 Processing helix chain '7' and resid 7 through 14 removed outlier: 3.579A pdb=" N LYS 7 12 " --> pdb=" O SER 7 8 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 45 removed outlier: 3.617A pdb=" N LEU 7 44 " --> pdb=" O ARG 7 40 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP 7 45 " --> pdb=" O THR 7 41 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 64 removed outlier: 4.469A pdb=" N SER 7 56 " --> pdb=" O ALA 7 52 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ARG 7 57 " --> pdb=" O ALA 7 53 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE 7 58 " --> pdb=" O ASP 7 54 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS 7 60 " --> pdb=" O SER 7 56 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU 7 61 " --> pdb=" O ARG 7 57 " (cutoff:3.500A) Processing helix chain '9' and resid 2 through 13 removed outlier: 4.458A pdb=" N LYS 9 12 " --> pdb=" O LYS 9 8 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N HIS 9 13 " --> pdb=" O ARG 9 9 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 67 through 71 removed outlier: 3.525A pdb=" N VAL b 161 " --> pdb=" O PRO b 182 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA b 185 " --> pdb=" O TYR b 198 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.906A pdb=" N VAL c 65 " --> pdb=" O GLN c 99 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 164 through 171 removed outlier: 4.659A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'd' and resid 136 through 139 removed outlier: 6.616A pdb=" N ARG d 174 " --> pdb=" O VAL d 169 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL d 169 " --> pdb=" O ARG d 174 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'e' and resid 37 through 41 removed outlier: 6.781A pdb=" N LEU e 61 " --> pdb=" O VAL e 41 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 109 through 113 removed outlier: 5.648A pdb=" N VAL e 118 " --> pdb=" O LEU e 153 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA e 124 " --> pdb=" O ASP e 147 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP e 147 " --> pdb=" O ALA e 124 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 58 through 65 Processing sheet with id= 8, first strand: chain 'f' and resid 37 through 44 removed outlier: 4.003A pdb=" N VAL f 37 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR f 93 " --> pdb=" O PRO f 3 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 45 through 48 removed outlier: 7.029A pdb=" N ALA f 56 " --> pdb=" O LEU f 48 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.633A pdb=" N ALA g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'h' and resid 23 through 28 removed outlier: 6.488A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.698A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'i' and resid 26 through 31 removed outlier: 4.508A pdb=" N ILE i 26 " --> pdb=" O LEU i 41 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU i 41 " --> pdb=" O ILE i 26 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN i 47 " --> pdb=" O PHE i 81 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.554A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'k' and resid 39 through 44 removed outlier: 6.965A pdb=" N VAL k 93 " --> pdb=" O GLY k 117 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'k' and resid 92 through 96 Processing sheet with id= 17, first strand: chain 'l' and resid 29 through 33 Processing sheet with id= 18, first strand: chain 'l' and resid 35 through 41 removed outlier: 5.156A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'p' and resid 5 through 11 Processing sheet with id= 20, first strand: chain 'q' and resid 21 through 26 removed outlier: 5.035A pdb=" N LYS q 21 " --> pdb=" O GLU q 78 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N SER q 75 " --> pdb=" O VAL q 91 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ARG q 87 " --> pdb=" O THR q 79 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'q' and resid 34 through 45 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 's' and resid 31 through 34 removed outlier: 3.530A pdb=" N ILE s 31 " --> pdb=" O THR s 48 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'z' and resid 1 through 4 removed outlier: 3.701A pdb=" N ASP z 2 " --> pdb=" O THR z 101 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLU z 105 " --> pdb=" O LEU z 4 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TRP z 100 " --> pdb=" O GLY z 95 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ARG z 88 " --> pdb=" O ALA z 31 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASN z 30 " --> pdb=" O THR z 111 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR z 111 " --> pdb=" O ASN z 30 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'z' and resid 158 through 162 removed outlier: 4.400A pdb=" N GLY z 215 " --> pdb=" O ASP z 238 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'z' and resid 317 through 320 removed outlier: 4.589A pdb=" N SER z 317 " --> pdb=" O GLY z 313 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'z' and resid 350 through 355 removed outlier: 3.855A pdb=" N TYR z 302 " --> pdb=" O SER z 353 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS z 299 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP z 303 " --> pdb=" O GLY z 368 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLY z 368 " --> pdb=" O ASP z 303 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 2 through 6 removed outlier: 5.337A pdb=" N ALA C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 28 Processing sheet with id= 29, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.749A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C 94 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL C 75 " --> pdb=" O SER C 119 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER C 119 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 117 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP C 115 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 163 through 166 removed outlier: 3.669A pdb=" N GLN C 164 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA C 174 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C' and resid 91 through 97 removed outlier: 5.287A pdb=" N ASN C 91 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 80 through 86 removed outlier: 5.261A pdb=" N SER D 48 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN D 51 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLN D 99 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 172 through 178 removed outlier: 4.499A pdb=" N ASP D 173 " --> pdb=" O SER D 118 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR D 117 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU D 205 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 11.983A pdb=" N LYS D 119 " --> pdb=" O GLY D 203 " (cutoff:3.500A) removed outlier: 13.877A pdb=" N GLY D 203 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY D 204 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 28 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 184 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.732A pdb=" N LEU E 3 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY E 16 " --> pdb=" O VAL E 7 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'E' and resid 123 through 126 Processing sheet with id= 36, first strand: chain 'F' and resid 72 through 76 removed outlier: 4.232A pdb=" N ARG F 95 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY F 93 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE F 92 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS F 40 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N GLY F 46 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N GLY F 158 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET F 159 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'F' and resid 79 through 82 removed outlier: 6.995A pdb=" N LYS F 79 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU F 88 " --> pdb=" O LYS F 79 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 39, first strand: chain 'G' and resid 41 through 46 removed outlier: 3.835A pdb=" N ALA G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'G' and resid 83 through 90 removed outlier: 3.540A pdb=" N ILE G 90 " --> pdb=" O THR G 130 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR G 130 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.686A pdb=" N LEU G 104 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE G 116 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'H' and resid 17 through 21 removed outlier: 4.625A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'H' and resid 77 through 83 removed outlier: 3.985A pdb=" N VAL H 78 " --> pdb=" O SER H 145 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'I' and resid 46 through 51 removed outlier: 8.121A pdb=" N SER I 46 " --> pdb=" O LYS I 83 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS I 83 " --> pdb=" O SER I 46 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA I 22 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR I 23 " --> pdb=" O TYR I 109 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'J' and resid 10 through 16 removed outlier: 3.625A pdb=" N ILE J 11 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE J 15 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE J 56 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL J 55 " --> pdb=" O PRO J 75 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR J 61 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER J 67 " --> pdb=" O TYR J 63 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'K' and resid 59 through 62 removed outlier: 6.334A pdb=" N VAL K 59 " --> pdb=" O VAL K 165 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'K' and resid 170 through 174 removed outlier: 3.660A pdb=" N VAL K 44 " --> pdb=" O PHE K 173 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU K 43 " --> pdb=" O SER K 215 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N SER K 215 " --> pdb=" O GLU K 43 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS K 211 " --> pdb=" O ARG K 47 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'L' and resid 52 through 57 removed outlier: 4.953A pdb=" N ASP L 19 " --> pdb=" O PHE L 140 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'L' and resid 74 through 78 removed outlier: 7.355A pdb=" N GLY L 83 " --> pdb=" O SER L 78 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'M' and resid 18 through 21 removed outlier: 4.329A pdb=" N SER M 6 " --> pdb=" O CYS M 21 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN M 82 " --> pdb=" O ARG M 7 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU M 81 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL M 66 " --> pdb=" O GLU M 81 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'M' and resid 39 through 42 Processing sheet with id= 52, first strand: chain 'M' and resid 68 through 71 removed outlier: 3.610A pdb=" N ILE M 77 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'N' and resid 75 through 78 Processing sheet with id= 54, first strand: chain 'O' and resid 62 through 67 removed outlier: 6.851A pdb=" N LEU O 103 " --> pdb=" O ASN O 67 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE O 104 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASP O 31 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS O 128 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'O' and resid 72 through 75 removed outlier: 3.506A pdb=" N TRP O 92 " --> pdb=" O LEU O 74 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'P' and resid 33 through 37 removed outlier: 4.428A pdb=" N MET P 110 " --> pdb=" O VAL P 100 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N TYR P 94 " --> pdb=" O VAL P 116 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Q' and resid 36 through 42 removed outlier: 6.630A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'Q' and resid 47 through 51 removed outlier: 6.566A pdb=" N ILE Q 47 " --> pdb=" O SER Q 65 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA Q 61 " --> pdb=" O LEU Q 51 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'R' and resid 37 through 44 removed outlier: 6.759A pdb=" N THR R 24 " --> pdb=" O LEU R 86 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS R 82 " --> pdb=" O HIS R 28 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'R' and resid 48 through 51 removed outlier: 4.011A pdb=" N ARG R 48 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR R 59 " --> pdb=" O ARG R 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR R 57 " --> pdb=" O GLN R 50 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLU R 56 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'T' and resid 13 through 16 removed outlier: 3.665A pdb=" N LEU T 41 " --> pdb=" O ILE T 6 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN T 47 " --> pdb=" O ASP T 44 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'T' and resid 19 through 22 removed outlier: 4.166A pdb=" N ASP T 20 " --> pdb=" O VAL T 99 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL T 96 " --> pdb=" O LEU T 65 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR T 61 " --> pdb=" O THR T 100 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA T 33 " --> pdb=" O VAL T 64 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'T' and resid 66 through 70 removed outlier: 3.717A pdb=" N GLU T 66 " --> pdb=" O VAL T 96 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN T 92 " --> pdb=" O GLY T 70 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'U' and resid 8 through 15 removed outlier: 6.776A pdb=" N ILE U 113 " --> pdb=" O ALA U 79 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N THR U 75 " --> pdb=" O ARG U 117 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'U' and resid 85 through 95 removed outlier: 5.181A pdb=" N GLU U 85 " --> pdb=" O HIS U 109 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N HIS U 109 " --> pdb=" O GLU U 85 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR U 107 " --> pdb=" O PRO U 87 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG U 99 " --> pdb=" O ARG U 95 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 28 through 33 removed outlier: 4.363A pdb=" N LYS V 80 " --> pdb=" O VAL V 33 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS V 65 " --> pdb=" O ARG V 76 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER V 78 " --> pdb=" O GLN V 63 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLN V 63 " --> pdb=" O SER V 78 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS V 80 " --> pdb=" O ASN V 61 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN V 61 " --> pdb=" O LYS V 80 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA V 82 " --> pdb=" O THR V 59 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR V 59 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL V 84 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL V 57 " --> pdb=" O VAL V 84 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'W' and resid 39 through 44 removed outlier: 5.378A pdb=" N ASN W 39 " --> pdb=" O ALA W 64 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'X' and resid 8 through 12 removed outlier: 3.589A pdb=" N ASN X 9 " --> pdb=" O ILE X 66 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'X' and resid 44 through 49 removed outlier: 3.712A pdb=" N HIS X 94 " --> pdb=" O ASP X 84 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP X 84 " --> pdb=" O HIS X 94 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA X 82 " --> pdb=" O ASP X 96 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'X' and resid 121 through 127 removed outlier: 7.981A pdb=" N GLY X 121 " --> pdb=" O ALA X 184 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL X 178 " --> pdb=" O ASP X 127 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'X' and resid 143 through 149 removed outlier: 7.096A pdb=" N GLU X 132 " --> pdb=" O ILE X 171 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'Y' and resid 65 through 70 Processing sheet with id= 73, first strand: chain 'Z' and resid 12 through 19 removed outlier: 3.761A pdb=" N THR Z 25 " --> pdb=" O SER Z 17 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER Z 19 " --> pdb=" O ARG Z 23 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain '2' and resid 32 through 38 removed outlier: 4.343A pdb=" N GLN 2 33 " --> pdb=" O GLN 2 8 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU 2 3 " --> pdb=" O VAL 2 59 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU 2 53 " --> pdb=" O VAL 2 9 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain '3' and resid 21 through 25 removed outlier: 3.730A pdb=" N VAL 3 14 " --> pdb=" O PHE 3 22 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLY 3 31 " --> pdb=" O ASP 3 11 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain '4' and resid 28 through 31 Processing sheet with id= 77, first strand: chain '5' and resid 10 through 13 removed outlier: 3.549A pdb=" N TYR 5 23 " --> pdb=" O LEU 5 13 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain '5' and resid 36 through 40 removed outlier: 6.100A pdb=" N LEU 5 36 " --> pdb=" O GLU 5 53 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '7' and resid 22 through 25 removed outlier: 6.321A pdb=" N ILE 7 22 " --> pdb=" O VAL 7 50 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain '8' and resid 14 through 18 removed outlier: 5.466A pdb=" N VAL 8 23 " --> pdb=" O GLN 8 36 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N CYS 8 27 " --> pdb=" O HIS 8 32 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS 8 32 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) 2065 hydrogen bonds defined for protein. 6117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4101 hydrogen bonds 6558 hydrogen bond angles 0 basepair planarities 1595 basepair parallelities 2462 stacking parallelities Total time for adding SS restraints: 255.22 Time building geometry restraints manager: 59.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 20685 1.33 - 1.45: 68782 1.45 - 1.57: 66835 1.57 - 1.69: 9552 1.69 - 1.81: 191 Bond restraints: 166045 Sorted by residual: bond pdb=" C4 5MU y 54 " pdb=" C5 5MU y 54 " ideal model delta sigma weight residual 1.802 1.479 0.323 2.00e-02 2.50e+03 2.60e+02 bond pdb=" N1 5MU y 54 " pdb=" C6 5MU y 54 " ideal model delta sigma weight residual 1.635 1.336 0.299 2.00e-02 2.50e+03 2.24e+02 bond pdb=" C5 5MU y 54 " pdb=" C6 5MU y 54 " ideal model delta sigma weight residual 1.155 1.384 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C2 4SU y 8 " pdb=" N3 4SU y 8 " ideal model delta sigma weight residual 1.499 1.332 0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" N3 5MU y 54 " pdb=" C4 5MU y 54 " ideal model delta sigma weight residual 1.182 1.335 -0.153 2.00e-02 2.50e+03 5.84e+01 ... (remaining 166040 not shown) Histogram of bond angle deviations from ideal: 95.94 - 104.42: 20572 104.42 - 112.89: 101098 112.89 - 121.36: 83550 121.36 - 129.84: 40075 129.84 - 138.31: 2813 Bond angle restraints: 248108 Sorted by residual: angle pdb=" C6 5MU y 54 " pdb=" C5 5MU y 54 " pdb=" C5M 5MU y 54 " ideal model delta sigma weight residual 106.09 120.85 -14.76 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C8 7MG y 46 " pdb=" N7 7MG y 46 " pdb=" CM7 7MG y 46 " ideal model delta sigma weight residual 126.72 112.95 13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" CA PRO d 32 " pdb=" N PRO d 32 " pdb=" CD PRO d 32 " ideal model delta sigma weight residual 112.00 105.71 6.29 1.40e+00 5.10e-01 2.02e+01 angle pdb=" N3 5MU y 54 " pdb=" C4 5MU y 54 " pdb=" O4 5MU y 54 " ideal model delta sigma weight residual 107.56 120.79 -13.23 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C ALA f 67 " pdb=" N GLU f 68 " pdb=" CA GLU f 68 " ideal model delta sigma weight residual 120.68 126.62 -5.94 1.52e+00 4.33e-01 1.53e+01 ... (remaining 248103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 94725 35.97 - 71.94: 10708 71.94 - 107.91: 1288 107.91 - 143.88: 24 143.88 - 179.85: 50 Dihedral angle restraints: 106795 sinusoidal: 88209 harmonic: 18586 Sorted by residual: dihedral pdb=" O4' U a 328 " pdb=" C1' U a 328 " pdb=" N1 U a 328 " pdb=" C2 U a 328 " ideal model delta sinusoidal sigma weight residual -160.00 18.07 -178.07 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 139 " pdb=" C1' U A 139 " pdb=" N1 U A 139 " pdb=" C2 U A 139 " ideal model delta sinusoidal sigma weight residual 200.00 28.52 171.48 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' C A3046 " pdb=" C1' C A3046 " pdb=" N1 C A3046 " pdb=" C2 C A3046 " ideal model delta sinusoidal sigma weight residual -160.00 9.30 -169.30 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 106792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 28505 0.056 - 0.111: 2673 0.111 - 0.167: 423 0.167 - 0.223: 59 0.223 - 0.278: 11 Chirality restraints: 31671 Sorted by residual: chirality pdb=" C3' U a1482 " pdb=" C4' U a1482 " pdb=" O3' U a1482 " pdb=" C2' U a1482 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB VAL b 157 " pdb=" CA VAL b 157 " pdb=" CG1 VAL b 157 " pdb=" CG2 VAL b 157 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1' C a 791 " pdb=" O4' C a 791 " pdb=" C2' C a 791 " pdb=" N1 C a 791 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 31668 not shown) Planarity restraints: 13764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG y 46 " -0.788 2.00e-02 2.50e+03 5.56e-01 6.97e+03 pdb=" C4' 7MG y 46 " 0.230 2.00e-02 2.50e+03 pdb=" O4' 7MG y 46 " 0.568 2.00e-02 2.50e+03 pdb=" C3' 7MG y 46 " -0.206 2.00e-02 2.50e+03 pdb=" O3' 7MG y 46 " 0.933 2.00e-02 2.50e+03 pdb=" C2' 7MG y 46 " -0.619 2.00e-02 2.50e+03 pdb=" O2' 7MG y 46 " -0.570 2.00e-02 2.50e+03 pdb=" C1' 7MG y 46 " 0.409 2.00e-02 2.50e+03 pdb=" N9 7MG y 46 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU y 54 " 0.031 2.00e-02 2.50e+03 5.46e-01 6.71e+03 pdb=" C4' 5MU y 54 " 0.428 2.00e-02 2.50e+03 pdb=" O4' 5MU y 54 " 0.566 2.00e-02 2.50e+03 pdb=" C3' 5MU y 54 " -0.584 2.00e-02 2.50e+03 pdb=" O3' 5MU y 54 " -0.541 2.00e-02 2.50e+03 pdb=" C2' 5MU y 54 " -0.216 2.00e-02 2.50e+03 pdb=" O2' 5MU y 54 " 0.889 2.00e-02 2.50e+03 pdb=" C1' 5MU y 54 " 0.237 2.00e-02 2.50e+03 pdb=" N1 5MU y 54 " -0.809 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR d 31 " -0.071 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO d 32 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO d 32 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO d 32 " -0.055 5.00e-02 4.00e+02 ... (remaining 13761 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 5111 2.65 - 3.21: 121757 3.21 - 3.78: 282444 3.78 - 4.34: 396323 4.34 - 4.90: 542348 Nonbonded interactions: 1347983 Sorted by model distance: nonbonded pdb=" O2' U a 438 " pdb=" O2 U a 439 " model vdw 2.090 2.440 nonbonded pdb=" OP2 C a1207 " pdb=" OG1 THR m 103 " model vdw 2.120 2.440 nonbonded pdb=" O4 U A1540 " pdb=" O6 G A1632 " model vdw 2.125 2.432 nonbonded pdb=" O2' G A1867 " pdb=" OD2 ASP P 106 " model vdw 2.130 2.440 nonbonded pdb=" O2' A a 728 " pdb=" N7 A a 729 " model vdw 2.141 2.520 ... (remaining 1347978 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: 7.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 30.970 Check model and map are aligned: 1.630 Set scattering table: 1.040 Process input model: 570.140 Find NCS groups from input model: 3.070 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: 0.030 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 617.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 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 : 0.004 0.323 166045 Z= 0.239 Angle : 0.559 14.760 248108 Z= 0.288 Chirality : 0.035 0.278 31671 Planarity : 0.008 0.556 13764 Dihedral : 22.951 179.850 94843 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % 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: -0.82 (0.10), residues: 6433 helix: -0.14 (0.12), residues: 2063 sheet: -0.18 (0.14), residues: 1327 loop : -0.91 (0.11), residues: 3043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP O 92 HIS 0.006 0.001 HIS 7 31 PHE 0.025 0.001 PHE R 6 TYR 0.012 0.001 TYR R 97 ARG 0.021 0.000 ARG R 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1666 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1666 time to evaluate : 6.470 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: c 113 GLN cc_start: 0.8250 (tp-100) cc_final: 0.7762 (tp40) REVERT: c 117 GLN cc_start: 0.8581 (mt0) cc_final: 0.8224 (mt0) REVERT: d 68 ARG cc_start: 0.8424 (mmm160) cc_final: 0.8212 (mmm160) REVERT: d 72 GLU cc_start: 0.8029 (mp0) cc_final: 0.7774 (mp0) REVERT: d 126 ASP cc_start: 0.8571 (p0) cc_final: 0.8371 (p0) REVERT: e 147 ASP cc_start: 0.8307 (m-30) cc_final: 0.8078 (m-30) REVERT: e 186 ILE cc_start: 0.9168 (tp) cc_final: 0.8911 (tp) REVERT: g 36 LYS cc_start: 0.8268 (mtpt) cc_final: 0.8000 (mtpp) REVERT: g 52 GLU cc_start: 0.7834 (pp20) cc_final: 0.7059 (pp20) REVERT: g 107 PHE cc_start: 0.8238 (m-80) cc_final: 0.7735 (m-10) REVERT: i 61 ASN cc_start: 0.8374 (t0) cc_final: 0.8074 (t0) REVERT: i 136 TYR cc_start: 0.9292 (p90) cc_final: 0.8869 (p90) REVERT: i 149 LYS cc_start: 0.9164 (ttmt) cc_final: 0.8872 (ttpt) REVERT: j 96 VAL cc_start: 0.8691 (t) cc_final: 0.8388 (p) REVERT: l 47 SER cc_start: 0.9227 (t) cc_final: 0.8965 (t) REVERT: p 15 ASN cc_start: 0.8348 (p0) cc_final: 0.8057 (p0) REVERT: s 10 PHE cc_start: 0.8122 (t80) cc_final: 0.7233 (t80) REVERT: s 37 ARG cc_start: 0.8141 (mtm110) cc_final: 0.7640 (mtm110) REVERT: s 70 LYS cc_start: 0.8535 (mmtp) cc_final: 0.7870 (mmtp) REVERT: F 105 GLU cc_start: 0.8703 (mp0) cc_final: 0.7911 (mp0) REVERT: F 142 GLN cc_start: 0.9119 (pm20) cc_final: 0.8460 (pm20) REVERT: G 144 GLN cc_start: 0.9138 (tp40) cc_final: 0.8923 (tp40) REVERT: H 106 LYS cc_start: 0.8565 (tttt) cc_final: 0.7851 (mmtt) REVERT: H 121 LYS cc_start: 0.8406 (mttm) cc_final: 0.8169 (mttt) REVERT: I 122 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8687 (mmmt) REVERT: Q 118 ASP cc_start: 0.8350 (m-30) cc_final: 0.7289 (m-30) REVERT: 4 31 SER cc_start: 0.8680 (m) cc_final: 0.8299 (m) outliers start: 0 outliers final: 0 residues processed: 1666 average time/residue: 1.4324 time to fit residues: 4053.4101 Evaluate side-chains 1368 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1368 time to evaluate : 6.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 933 optimal weight: 0.0000 chunk 838 optimal weight: 1.9990 chunk 465 optimal weight: 10.0000 chunk 286 optimal weight: 6.9990 chunk 565 optimal weight: 10.0000 chunk 447 optimal weight: 10.0000 chunk 866 optimal weight: 4.9990 chunk 335 optimal weight: 5.9990 chunk 527 optimal weight: 10.0000 chunk 645 optimal weight: 8.9990 chunk 1004 optimal weight: 5.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 101 ASN c 122 GLN d 115 HIS d 146 ASN d 185 GLN e 108 HIS g 28 ASN g 142 HIS i 146 GLN j 56 HIS k 27 HIS k 31 HIS k 37 ASN k 49 ASN k 110 GLN l 72 HIS ** m 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 52 GLN m 88 GLN ** m 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN o 37 GLN o 72 GLN p 65 GLN p 107 ASN q 33 GLN s 47 HIS t 21 ASN t 71 GLN z 17 GLN z 112 ASN z 179 GLN z 217 GLN C 53 HIS C 109 GLN C 113 GLN C 129 ASN C 135 ASN C 164 GLN C 227 ASN D 15 GLN D 21 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 179 ASN E 76 GLN E 151 ASN E 202 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN H 11 HIS H 111 ASN J 19 GLN J 21 ASN K 57 GLN L 77 HIS L 103 ASN L 119 GLN L 132 HIS N 58 HIS N 76 GLN N 107 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 62 ASN ** Q 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 ASN Q 48 HIS S 41 HIS S 72 ASN S 122 ASN T 67 HIS T 76 HIS T 92 GLN U 66 GLN V 34 HIS W 67 HIS W 70 ASN X 6 ASN X 9 ASN X 46 HIS X 61 HIS X 64 ASN X 94 HIS Y 19 GLN Y 29 GLN Y 79 ASN 4 12 ASN 4 19 GLN 5 22 ASN 5 31 ASN 5 48 HIS 7 31 HIS 8 4 ASN Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 166045 Z= 0.265 Angle : 0.576 14.607 248108 Z= 0.300 Chirality : 0.036 0.287 31671 Planarity : 0.005 0.120 13764 Dihedral : 23.369 179.697 82447 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 1.91 % Allowed : 11.40 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % 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: -0.38 (0.10), residues: 6433 helix: 0.60 (0.11), residues: 2113 sheet: -0.06 (0.14), residues: 1351 loop : -0.91 (0.11), residues: 2969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP d 165 HIS 0.008 0.001 HIS Q 48 PHE 0.033 0.001 PHE g 107 TYR 0.027 0.001 TYR m 21 ARG 0.011 0.001 ARG c 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1500 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1400 time to evaluate : 6.651 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: c 6 ASN cc_start: 0.9214 (t0) cc_final: 0.8923 (t0) REVERT: c 133 MET cc_start: 0.8785 (mtt) cc_final: 0.8283 (mtt) REVERT: c 168 TYR cc_start: 0.7427 (m-80) cc_final: 0.6563 (m-80) REVERT: d 98 TYR cc_start: 0.8833 (t80) cc_final: 0.8554 (t80) REVERT: e 147 ASP cc_start: 0.8178 (m-30) cc_final: 0.7964 (m-30) REVERT: g 118 GLU cc_start: 0.8454 (pm20) cc_final: 0.7856 (pp20) REVERT: g 140 ASP cc_start: 0.9310 (m-30) cc_final: 0.9097 (m-30) REVERT: h 43 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8027 (mm-30) REVERT: i 33 LYS cc_start: 0.8810 (ptpt) cc_final: 0.7939 (ptmm) REVERT: i 61 ASN cc_start: 0.8315 (t0) cc_final: 0.7983 (t0) REVERT: i 136 TYR cc_start: 0.9268 (p90) cc_final: 0.8895 (p90) REVERT: i 149 LYS cc_start: 0.9225 (ttmt) cc_final: 0.8942 (ttpt) REVERT: j 72 ARG cc_start: 0.8448 (mpp80) cc_final: 0.8241 (mpp80) REVERT: j 96 VAL cc_start: 0.8681 (t) cc_final: 0.8414 (p) REVERT: l 47 SER cc_start: 0.9238 (t) cc_final: 0.8969 (t) REVERT: m 20 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8661 (p) REVERT: n 52 GLU cc_start: 0.7729 (mp0) cc_final: 0.7507 (mp0) REVERT: o 36 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9162 (mp) REVERT: p 15 ASN cc_start: 0.8344 (p0) cc_final: 0.7985 (p0) REVERT: p 44 GLU cc_start: 0.7895 (pp20) cc_final: 0.7506 (pp20) REVERT: q 41 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: q 92 GLU cc_start: 0.8178 (pm20) cc_final: 0.7854 (pm20) REVERT: r 19 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8465 (mmtm) REVERT: s 10 PHE cc_start: 0.7921 (t80) cc_final: 0.7035 (t80) REVERT: s 37 ARG cc_start: 0.8172 (mtm110) cc_final: 0.7670 (mtm110) REVERT: D 19 GLU cc_start: 0.7932 (pm20) cc_final: 0.7689 (pm20) REVERT: F 25 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8472 (mp10) REVERT: F 58 ASN cc_start: 0.9207 (m110) cc_final: 0.8777 (m-40) REVERT: F 142 GLN cc_start: 0.9054 (pm20) cc_final: 0.8493 (pm20) REVERT: H 106 LYS cc_start: 0.8322 (tttt) cc_final: 0.7666 (mmtt) REVERT: H 121 LYS cc_start: 0.8411 (mttm) cc_final: 0.8137 (mttt) REVERT: J 16 GLN cc_start: 0.8263 (tp40) cc_final: 0.8058 (tp40) REVERT: J 123 ILE cc_start: 0.9144 (tp) cc_final: 0.8883 (tp) REVERT: Q 113 ILE cc_start: 0.9335 (mm) cc_final: 0.9111 (mm) REVERT: V 96 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: X 143 GLN cc_start: 0.8324 (pp30) cc_final: 0.8054 (pp30) REVERT: 1 9 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7644 (mt-10) outliers start: 100 outliers final: 67 residues processed: 1440 average time/residue: 1.3449 time to fit residues: 3314.5610 Evaluate side-chains 1413 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1341 time to evaluate : 6.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 89 MET Chi-restraints excluded: chain c residue 4 LYS Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 73 SER Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain o residue 80 SER Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 83 SER Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain z residue 118 ASP Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain J residue 41 CYS Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain T residue 54 ASP Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 77 LYS Chi-restraints excluded: chain V residue 96 PHE Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 5 residue 54 SER Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 9 residue 14 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 558 optimal weight: 9.9990 chunk 311 optimal weight: 9.9990 chunk 835 optimal weight: 6.9990 chunk 683 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 1006 optimal weight: 5.9990 chunk 1086 optimal weight: 5.9990 chunk 896 optimal weight: 0.0070 chunk 997 optimal weight: 2.9990 chunk 343 optimal weight: 9.9990 chunk 807 optimal weight: 4.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 122 GLN e 160 ASN ** i 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 146 GLN j 56 HIS k 84 GLN k 110 GLN k 125 GLN ** m 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 GLN ** n 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 GLN s 47 HIS t 21 ASN E 76 GLN F 70 GLN F 187 ASN G 75 ASN N 107 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 HIS Q 16 ASN Q 41 ASN X 64 ASN X 161 GLN ** 3 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 4 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 166045 Z= 0.261 Angle : 0.560 13.007 248108 Z= 0.292 Chirality : 0.036 0.287 31671 Planarity : 0.005 0.122 13764 Dihedral : 23.324 179.872 82447 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.10 % Favored : 95.87 % Rotamer: Outliers : 2.85 % Allowed : 13.36 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.10), residues: 6433 helix: 1.05 (0.11), residues: 2143 sheet: 0.03 (0.14), residues: 1344 loop : -0.86 (0.11), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP d 165 HIS 0.010 0.001 HIS P 16 PHE 0.020 0.001 PHE i 48 TYR 0.026 0.001 TYR d 4 ARG 0.008 0.000 ARG r 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1520 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1371 time to evaluate : 6.617 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: d 162 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8356 (mm) REVERT: e 147 ASP cc_start: 0.8208 (m-30) cc_final: 0.8006 (m-30) REVERT: f 24 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8014 (mm-30) REVERT: f 31 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7721 (mtm-85) REVERT: g 142 HIS cc_start: 0.8507 (m170) cc_final: 0.8098 (m-70) REVERT: h 43 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8061 (mm-30) REVERT: i 61 ASN cc_start: 0.8287 (t0) cc_final: 0.7937 (t0) REVERT: i 81 PHE cc_start: 0.8850 (m-80) cc_final: 0.8622 (m-80) REVERT: i 111 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7973 (tm-30) REVERT: i 119 LYS cc_start: 0.8832 (tttm) cc_final: 0.8511 (tttt) REVERT: i 136 TYR cc_start: 0.9270 (p90) cc_final: 0.8918 (p90) REVERT: i 149 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8976 (ttpt) REVERT: j 10 LEU cc_start: 0.8921 (pp) cc_final: 0.8590 (mm) REVERT: j 24 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8805 (tmmt) REVERT: j 96 VAL cc_start: 0.8606 (t) cc_final: 0.8239 (p) REVERT: l 47 SER cc_start: 0.9246 (t) cc_final: 0.8971 (t) REVERT: m 75 GLN cc_start: 0.8926 (mp10) cc_final: 0.8567 (mp10) REVERT: n 52 GLU cc_start: 0.7787 (mp0) cc_final: 0.7475 (mp0) REVERT: o 36 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9204 (mp) REVERT: p 15 ASN cc_start: 0.8467 (p0) cc_final: 0.8052 (p0) REVERT: p 17 GLN cc_start: 0.8927 (mt0) cc_final: 0.8718 (mt0) REVERT: q 92 GLU cc_start: 0.8328 (pm20) cc_final: 0.7871 (pm20) REVERT: r 19 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8458 (mmtm) REVERT: s 10 PHE cc_start: 0.7840 (t80) cc_final: 0.6995 (t80) REVERT: s 37 ARG cc_start: 0.8155 (mtm110) cc_final: 0.7689 (mtm110) REVERT: t 21 ASN cc_start: 0.9195 (m-40) cc_final: 0.8972 (m-40) REVERT: t 46 LYS cc_start: 0.9041 (tttp) cc_final: 0.8737 (tptm) REVERT: z 338 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8600 (m) REVERT: F 17 GLU cc_start: 0.8790 (pm20) cc_final: 0.8383 (pm20) REVERT: F 25 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8443 (mp10) REVERT: F 142 GLN cc_start: 0.9029 (pm20) cc_final: 0.8441 (pm20) REVERT: H 106 LYS cc_start: 0.8345 (tttt) cc_final: 0.7690 (mmtt) REVERT: H 121 LYS cc_start: 0.8437 (mttm) cc_final: 0.8164 (mttt) REVERT: J 16 GLN cc_start: 0.8205 (tp40) cc_final: 0.7962 (tp40) REVERT: J 140 THR cc_start: 0.9264 (m) cc_final: 0.8941 (p) REVERT: Q 113 ILE cc_start: 0.9357 (mm) cc_final: 0.9130 (mm) REVERT: Q 126 LYS cc_start: 0.8389 (ptpp) cc_final: 0.8164 (ptpp) REVERT: V 96 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: X 89 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8262 (mtm-85) REVERT: 1 66 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8889 (mp) REVERT: 5 6 ASP cc_start: 0.7346 (t0) cc_final: 0.7134 (t0) outliers start: 149 outliers final: 104 residues processed: 1431 average time/residue: 1.3616 time to fit residues: 3337.6537 Evaluate side-chains 1435 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1325 time to evaluate : 6.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain c residue 4 LYS Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 177 THR Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain d residue 105 THR Chi-restraints excluded: chain d residue 162 ILE Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 146 GLN Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 110 GLN Chi-restraints excluded: chain l residue 14 ASP Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain o residue 80 SER Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain q residue 32 MET Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 83 SER Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain z residue 101 THR Chi-restraints excluded: chain z residue 118 ASP Chi-restraints excluded: chain z residue 176 MET Chi-restraints excluded: chain z residue 338 THR Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain J residue 41 CYS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 77 LYS Chi-restraints excluded: chain V residue 96 PHE Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain 1 residue 66 LEU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 4 residue 21 LYS Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 4 residue 32 VAL Chi-restraints excluded: chain 5 residue 25 THR Chi-restraints excluded: chain 5 residue 54 SER Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 7 residue 48 THR Chi-restraints excluded: chain 9 residue 14 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 994 optimal weight: 0.0170 chunk 756 optimal weight: 2.9990 chunk 522 optimal weight: 10.0000 chunk 111 optimal weight: 40.0000 chunk 480 optimal weight: 7.9990 chunk 675 optimal weight: 10.0000 chunk 1009 optimal weight: 0.9990 chunk 1069 optimal weight: 5.9990 chunk 527 optimal weight: 10.0000 chunk 957 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 122 GLN ** i 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 146 GLN j 56 HIS k 125 GLN m 88 GLN ** m 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 8 HIS o 37 GLN p 41 HIS q 33 GLN s 47 HIS E 47 GLN F 58 ASN G 75 ASN H 11 HIS ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN Q 16 ASN Q 41 ASN ** X 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 166045 Z= 0.238 Angle : 0.548 12.388 248108 Z= 0.286 Chirality : 0.035 0.291 31671 Planarity : 0.004 0.119 13764 Dihedral : 23.301 179.835 82447 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.24 % Favored : 95.73 % Rotamer: Outliers : 3.02 % Allowed : 14.98 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.10), residues: 6433 helix: 1.30 (0.12), residues: 2137 sheet: 0.10 (0.14), residues: 1344 loop : -0.81 (0.11), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP s 34 HIS 0.008 0.001 HIS P 16 PHE 0.024 0.001 PHE F 121 TYR 0.026 0.001 TYR d 4 ARG 0.009 0.000 ARG j 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1519 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1361 time to evaluate : 6.467 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: c 170 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7278 (tm-30) REVERT: d 126 ASP cc_start: 0.8689 (p0) cc_final: 0.8426 (p0) REVERT: f 24 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8092 (mm-30) REVERT: f 31 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7723 (mtm-85) REVERT: h 43 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8097 (mm-30) REVERT: i 61 ASN cc_start: 0.8240 (t0) cc_final: 0.7894 (t0) REVERT: i 81 PHE cc_start: 0.8747 (m-80) cc_final: 0.8484 (m-80) REVERT: i 111 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7991 (tm-30) REVERT: i 136 TYR cc_start: 0.9271 (p90) cc_final: 0.8942 (p90) REVERT: j 10 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8595 (mm) REVERT: j 72 ARG cc_start: 0.8366 (mpp80) cc_final: 0.8133 (mpp80) REVERT: j 96 VAL cc_start: 0.8622 (t) cc_final: 0.8228 (p) REVERT: l 47 SER cc_start: 0.9238 (t) cc_final: 0.8971 (t) REVERT: n 8 HIS cc_start: 0.8923 (OUTLIER) cc_final: 0.8439 (t-170) REVERT: n 52 GLU cc_start: 0.7820 (mp0) cc_final: 0.7540 (mp0) REVERT: o 36 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9180 (mp) REVERT: p 15 ASN cc_start: 0.8477 (p0) cc_final: 0.8067 (p0) REVERT: q 92 GLU cc_start: 0.8381 (pm20) cc_final: 0.7872 (pm20) REVERT: r 19 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8504 (mmtm) REVERT: s 10 PHE cc_start: 0.7713 (t80) cc_final: 0.6984 (t80) REVERT: s 37 ARG cc_start: 0.8137 (mtm110) cc_final: 0.7647 (mtm110) REVERT: s 53 ASP cc_start: 0.8663 (t0) cc_final: 0.8106 (p0) REVERT: z 43 ASP cc_start: 0.8841 (t0) cc_final: 0.8595 (t0) REVERT: z 338 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8463 (m) REVERT: D 18 ASP cc_start: 0.7482 (t0) cc_final: 0.7115 (t0) REVERT: D 19 GLU cc_start: 0.7880 (pm20) cc_final: 0.7618 (pm20) REVERT: F 25 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8415 (mp10) REVERT: F 105 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7774 (mt-10) REVERT: F 142 GLN cc_start: 0.9027 (pm20) cc_final: 0.8436 (pm20) REVERT: H 106 LYS cc_start: 0.8328 (tttt) cc_final: 0.7637 (mmtt) REVERT: H 121 LYS cc_start: 0.8448 (mttm) cc_final: 0.8198 (mttt) REVERT: J 112 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8696 (mm-30) REVERT: J 140 THR cc_start: 0.9235 (m) cc_final: 0.8895 (p) REVERT: Q 113 ILE cc_start: 0.9364 (mm) cc_final: 0.9117 (mm) REVERT: V 96 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: X 143 GLN cc_start: 0.8524 (pp30) cc_final: 0.7993 (pp30) REVERT: 1 66 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8851 (mp) REVERT: 3 25 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8695 (mtp-110) outliers start: 158 outliers final: 114 residues processed: 1419 average time/residue: 1.3446 time to fit residues: 3273.0177 Evaluate side-chains 1446 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1325 time to evaluate : 6.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain c residue 4 LYS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 143 LYS Chi-restraints excluded: chain i residue 146 GLN Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 106 ILE Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 8 HIS Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 80 SER Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain q residue 32 MET Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 83 SER Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain z residue 118 ASP Chi-restraints excluded: chain z residue 176 MET Chi-restraints excluded: chain z residue 338 THR Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain J residue 41 CYS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 104 TRP Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 136 GLU Chi-restraints excluded: chain Q residue 48 HIS Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain T residue 54 ASP Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 77 LYS Chi-restraints excluded: chain V residue 96 PHE Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain 1 residue 40 GLN Chi-restraints excluded: chain 1 residue 66 LEU Chi-restraints excluded: chain 3 residue 21 SER Chi-restraints excluded: chain 4 residue 21 LYS Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 4 residue 32 VAL Chi-restraints excluded: chain 5 residue 25 THR Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 7 residue 48 THR Chi-restraints excluded: chain 9 residue 14 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 890 optimal weight: 0.0060 chunk 606 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 795 optimal weight: 5.9990 chunk 441 optimal weight: 10.0000 chunk 912 optimal weight: 3.9990 chunk 738 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 545 optimal weight: 10.0000 chunk 959 optimal weight: 4.9990 chunk 269 optimal weight: 10.0000 overall best weight: 4.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 122 GLN g 25 GLN ** i 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 146 GLN j 47 ASN j 56 HIS k 125 GLN m 88 GLN ** m 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 GLN s 47 HIS t 21 ASN t 71 GLN F 58 ASN G 75 ASN J 16 GLN J 36 ASN N 107 ASN Q 41 ASN R 50 GLN ** X 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 129 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 166045 Z= 0.323 Angle : 0.581 12.503 248108 Z= 0.301 Chirality : 0.037 0.302 31671 Planarity : 0.005 0.119 13764 Dihedral : 23.270 179.650 82447 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 3.62 % Allowed : 15.96 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.11), residues: 6433 helix: 1.39 (0.12), residues: 2133 sheet: 0.12 (0.14), residues: 1342 loop : -0.84 (0.11), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP s 34 HIS 0.029 0.001 HIS n 8 PHE 0.024 0.001 PHE e 97 TYR 0.027 0.001 TYR d 4 ARG 0.010 0.000 ARG r 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1526 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1337 time to evaluate : 6.516 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: c 170 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7416 (tm-30) REVERT: d 126 ASP cc_start: 0.8789 (p0) cc_final: 0.8397 (p0) REVERT: f 24 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8167 (mm-30) REVERT: g 142 HIS cc_start: 0.8512 (m170) cc_final: 0.7991 (m-70) REVERT: h 43 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8143 (mm-30) REVERT: i 47 GLN cc_start: 0.8222 (mp10) cc_final: 0.8004 (mp10) REVERT: i 61 ASN cc_start: 0.8287 (t0) cc_final: 0.7933 (t0) REVERT: i 81 PHE cc_start: 0.8713 (m-80) cc_final: 0.8482 (m-80) REVERT: i 111 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8010 (tm-30) REVERT: i 136 TYR cc_start: 0.9266 (p90) cc_final: 0.8968 (p90) REVERT: j 10 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8619 (mm) REVERT: j 67 MET cc_start: 0.8448 (ttm) cc_final: 0.8116 (ttt) REVERT: j 96 VAL cc_start: 0.8666 (t) cc_final: 0.8263 (p) REVERT: l 47 SER cc_start: 0.9253 (t) cc_final: 0.8985 (t) REVERT: m 75 GLN cc_start: 0.8947 (mp10) cc_final: 0.8723 (mp10) REVERT: n 52 GLU cc_start: 0.7894 (mp0) cc_final: 0.7594 (mp0) REVERT: o 36 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9212 (mp) REVERT: p 15 ASN cc_start: 0.8510 (p0) cc_final: 0.8086 (p0) REVERT: q 92 GLU cc_start: 0.8470 (pm20) cc_final: 0.7988 (pm20) REVERT: r 19 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8533 (mmtm) REVERT: s 10 PHE cc_start: 0.7784 (t80) cc_final: 0.7074 (t80) REVERT: s 37 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7682 (mtm110) REVERT: s 53 ASP cc_start: 0.8612 (t0) cc_final: 0.8136 (p0) REVERT: z 43 ASP cc_start: 0.8862 (t0) cc_final: 0.8612 (t0) REVERT: F 25 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8430 (mp10) REVERT: F 105 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7804 (mt-10) REVERT: F 142 GLN cc_start: 0.9027 (pm20) cc_final: 0.8436 (pm20) REVERT: H 106 LYS cc_start: 0.8319 (tttt) cc_final: 0.7623 (mmtt) REVERT: J 112 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8683 (mm-30) REVERT: J 140 THR cc_start: 0.9244 (m) cc_final: 0.8936 (p) REVERT: Q 113 ILE cc_start: 0.9372 (mm) cc_final: 0.9107 (mm) REVERT: V 96 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: 1 66 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8867 (mp) REVERT: 3 25 ARG cc_start: 0.8973 (mtp85) cc_final: 0.8756 (mtp-110) outliers start: 189 outliers final: 147 residues processed: 1420 average time/residue: 1.4556 time to fit residues: 3588.1255 Evaluate side-chains 1470 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1318 time to evaluate : 5.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain c residue 4 LYS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 66 ASP Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain f residue 91 LEU Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 117 VAL Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 146 GLN Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain o residue 21 ASP Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 80 SER Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 32 MET Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 83 SER Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain z residue 101 THR Chi-restraints excluded: chain z residue 118 ASP Chi-restraints excluded: chain z residue 176 MET Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain J residue 41 CYS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 104 TRP Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 136 GLU Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 48 HIS Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 77 LYS Chi-restraints excluded: chain V residue 96 PHE Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain 1 residue 40 GLN Chi-restraints excluded: chain 1 residue 66 LEU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 4 residue 21 LYS Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 4 residue 32 VAL Chi-restraints excluded: chain 5 residue 25 THR Chi-restraints excluded: chain 5 residue 54 SER Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 7 residue 48 THR Chi-restraints excluded: chain 7 residue 59 ASN Chi-restraints excluded: chain 9 residue 14 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 359 optimal weight: 0.9990 chunk 962 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 627 optimal weight: 10.0000 chunk 263 optimal weight: 7.9990 chunk 1070 optimal weight: 0.9990 chunk 888 optimal weight: 50.0000 chunk 495 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 353 optimal weight: 5.9990 chunk 561 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 122 GLN c 125 ASN ** d 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 146 HIS e 160 ASN g 25 GLN ** i 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 146 GLN j 56 HIS k 125 GLN ** m 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 GLN o 37 GLN ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 HIS t 21 ASN t 71 GLN E 47 GLN N 107 ASN Q 41 ASN ** X 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 166045 Z= 0.309 Angle : 0.579 12.642 248108 Z= 0.301 Chirality : 0.037 0.298 31671 Planarity : 0.005 0.118 13764 Dihedral : 23.275 179.533 82447 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 3.48 % Allowed : 17.49 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 6433 helix: 1.43 (0.12), residues: 2130 sheet: 0.12 (0.14), residues: 1361 loop : -0.85 (0.11), residues: 2942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP d 165 HIS 0.008 0.001 HIS P 16 PHE 0.021 0.001 PHE e 97 TYR 0.031 0.001 TYR d 4 ARG 0.011 0.000 ARG r 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1524 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1342 time to evaluate : 6.590 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: c 170 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7392 (tm-30) REVERT: d 98 TYR cc_start: 0.8842 (t80) cc_final: 0.8616 (t80) REVERT: d 126 ASP cc_start: 0.8784 (p0) cc_final: 0.8385 (p0) REVERT: f 17 ARG cc_start: 0.8161 (ptp-170) cc_final: 0.7897 (ptp-170) REVERT: g 40 GLU cc_start: 0.8340 (pp20) cc_final: 0.7625 (tm-30) REVERT: g 142 HIS cc_start: 0.8539 (m170) cc_final: 0.7966 (m-70) REVERT: h 43 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8109 (mm-30) REVERT: i 61 ASN cc_start: 0.8295 (t0) cc_final: 0.7938 (t0) REVERT: i 81 PHE cc_start: 0.8715 (m-80) cc_final: 0.8425 (m-80) REVERT: i 111 GLN cc_start: 0.8358 (tm-30) cc_final: 0.8049 (tm-30) REVERT: i 136 TYR cc_start: 0.9263 (p90) cc_final: 0.8976 (p90) REVERT: j 67 MET cc_start: 0.8455 (ttm) cc_final: 0.8131 (ttt) REVERT: j 88 MET cc_start: 0.7820 (pmm) cc_final: 0.7242 (ppp) REVERT: j 96 VAL cc_start: 0.8657 (t) cc_final: 0.8390 (p) REVERT: l 47 SER cc_start: 0.9240 (t) cc_final: 0.8967 (t) REVERT: m 75 GLN cc_start: 0.8901 (mp10) cc_final: 0.8581 (mp10) REVERT: n 52 GLU cc_start: 0.7886 (mp0) cc_final: 0.7589 (mp0) REVERT: o 36 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9218 (mp) REVERT: p 15 ASN cc_start: 0.8551 (p0) cc_final: 0.8131 (p0) REVERT: q 92 GLU cc_start: 0.8501 (pm20) cc_final: 0.8001 (pm20) REVERT: r 19 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8536 (mmtm) REVERT: s 5 LEU cc_start: 0.8120 (pt) cc_final: 0.6971 (mt) REVERT: s 10 PHE cc_start: 0.7700 (t80) cc_final: 0.6926 (t80) REVERT: s 37 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7683 (mtm110) REVERT: s 53 ASP cc_start: 0.8658 (t0) cc_final: 0.8217 (p0) REVERT: z 43 ASP cc_start: 0.8866 (t0) cc_final: 0.8629 (t0) REVERT: F 142 GLN cc_start: 0.9037 (pm20) cc_final: 0.8459 (pm20) REVERT: J 140 THR cc_start: 0.9240 (m) cc_final: 0.8936 (p) REVERT: Q 113 ILE cc_start: 0.9352 (mm) cc_final: 0.9064 (mm) REVERT: V 96 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: X 143 GLN cc_start: 0.8591 (pp30) cc_final: 0.8118 (pp30) REVERT: 1 66 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8901 (mp) outliers start: 182 outliers final: 146 residues processed: 1422 average time/residue: 1.3431 time to fit residues: 3282.7195 Evaluate side-chains 1475 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1325 time to evaluate : 6.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain e residue 176 GLU Chi-restraints excluded: chain e residue 186 ILE Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 91 LEU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 143 LYS Chi-restraints excluded: chain i residue 146 GLN Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 80 SER Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 32 MET Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 83 SER Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain z residue 118 ASP Chi-restraints excluded: chain z residue 176 MET Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain J residue 41 CYS Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 104 TRP Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 136 GLU Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 48 HIS Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 77 LYS Chi-restraints excluded: chain V residue 96 PHE Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain 1 residue 40 GLN Chi-restraints excluded: chain 1 residue 66 LEU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 4 residue 21 LYS Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 4 residue 32 VAL Chi-restraints excluded: chain 5 residue 25 THR Chi-restraints excluded: chain 5 residue 54 SER Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 7 residue 48 THR Chi-restraints excluded: chain 9 residue 14 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 1031 optimal weight: 0.8980 chunk 120 optimal weight: 20.0000 chunk 609 optimal weight: 7.9990 chunk 781 optimal weight: 4.9990 chunk 605 optimal weight: 7.9990 chunk 900 optimal weight: 0.9980 chunk 597 optimal weight: 10.0000 chunk 1066 optimal weight: 0.0980 chunk 667 optimal weight: 7.9990 chunk 649 optimal weight: 6.9990 chunk 492 optimal weight: 6.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 122 GLN ** d 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 GLN ** i 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 56 HIS k 125 GLN ** m 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 GLN ** m 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 GLN s 47 HIS t 21 ASN t 71 GLN E 47 GLN N 107 ASN Q 41 ASN R 50 GLN ** X 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 166045 Z= 0.205 Angle : 0.546 14.090 248108 Z= 0.285 Chirality : 0.034 0.273 31671 Planarity : 0.004 0.118 13764 Dihedral : 23.287 179.628 82447 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.24 % Favored : 95.74 % Rotamer: Outliers : 3.02 % Allowed : 18.37 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.11), residues: 6433 helix: 1.52 (0.12), residues: 2135 sheet: 0.17 (0.14), residues: 1357 loop : -0.79 (0.11), residues: 2941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP d 165 HIS 0.008 0.001 HIS H 11 PHE 0.021 0.001 PHE I 81 TYR 0.033 0.001 TYR d 4 ARG 0.010 0.000 ARG d 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1510 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1352 time to evaluate : 6.530 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: c 170 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7490 (tm-30) REVERT: d 98 TYR cc_start: 0.8802 (t80) cc_final: 0.8547 (t80) REVERT: d 126 ASP cc_start: 0.8751 (p0) cc_final: 0.8305 (p0) REVERT: g 142 HIS cc_start: 0.8595 (m170) cc_final: 0.8112 (m-70) REVERT: h 43 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8104 (mm-30) REVERT: i 61 ASN cc_start: 0.8246 (t0) cc_final: 0.7902 (t0) REVERT: i 81 PHE cc_start: 0.8680 (m-80) cc_final: 0.8355 (m-80) REVERT: i 111 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8107 (tm-30) REVERT: i 136 TYR cc_start: 0.9265 (p90) cc_final: 0.8989 (p90) REVERT: j 67 MET cc_start: 0.8435 (ttm) cc_final: 0.8111 (ttt) REVERT: j 72 ARG cc_start: 0.8440 (mpp80) cc_final: 0.8222 (mpp80) REVERT: j 88 MET cc_start: 0.7827 (pmm) cc_final: 0.7332 (ppp) REVERT: j 96 VAL cc_start: 0.8637 (t) cc_final: 0.8372 (p) REVERT: l 47 SER cc_start: 0.9206 (t) cc_final: 0.8929 (t) REVERT: m 59 TYR cc_start: 0.7864 (t80) cc_final: 0.7659 (t80) REVERT: n 52 GLU cc_start: 0.7930 (mp0) cc_final: 0.7614 (mp0) REVERT: o 36 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9163 (mp) REVERT: p 15 ASN cc_start: 0.8529 (p0) cc_final: 0.8119 (p0) REVERT: q 92 GLU cc_start: 0.8474 (pm20) cc_final: 0.7947 (pm20) REVERT: r 19 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8487 (mmtm) REVERT: s 5 LEU cc_start: 0.8186 (pt) cc_final: 0.7067 (mt) REVERT: s 10 PHE cc_start: 0.7642 (t80) cc_final: 0.6848 (t80) REVERT: s 37 ARG cc_start: 0.8133 (mtm110) cc_final: 0.7660 (mtm110) REVERT: s 53 ASP cc_start: 0.8577 (t0) cc_final: 0.8120 (p0) REVERT: z 43 ASP cc_start: 0.8811 (t0) cc_final: 0.8599 (t0) REVERT: F 105 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7873 (mt-10) REVERT: F 142 GLN cc_start: 0.9024 (pm20) cc_final: 0.8431 (pm20) REVERT: J 140 THR cc_start: 0.9226 (m) cc_final: 0.8938 (p) REVERT: Q 113 ILE cc_start: 0.9329 (mm) cc_final: 0.9040 (mm) REVERT: Q 126 LYS cc_start: 0.8424 (ptpp) cc_final: 0.8068 (ptpp) REVERT: U 66 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8412 (tm-30) REVERT: V 96 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: X 143 GLN cc_start: 0.8544 (pp30) cc_final: 0.8171 (pp30) REVERT: 1 66 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8875 (mp) REVERT: 3 25 ARG cc_start: 0.8952 (mtp85) cc_final: 0.8733 (mtp-110) REVERT: 5 6 ASP cc_start: 0.7347 (t0) cc_final: 0.7142 (t0) outliers start: 158 outliers final: 131 residues processed: 1421 average time/residue: 1.3470 time to fit residues: 3296.5231 Evaluate side-chains 1458 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1323 time to evaluate : 6.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 143 LYS Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain q residue 32 MET Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 83 SER Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain z residue 101 THR Chi-restraints excluded: chain z residue 118 ASP Chi-restraints excluded: chain z residue 176 MET Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain J residue 41 CYS Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 104 TRP Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 136 GLU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 48 HIS Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain T residue 63 GLU Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 77 LYS Chi-restraints excluded: chain V residue 96 PHE Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain 1 residue 40 GLN Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 1 residue 66 LEU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 4 residue 21 LYS Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 4 residue 32 VAL Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 7 residue 48 THR Chi-restraints excluded: chain 9 residue 14 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 659 optimal weight: 30.0000 chunk 425 optimal weight: 10.0000 chunk 636 optimal weight: 10.0000 chunk 321 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 206 optimal weight: 9.9990 chunk 677 optimal weight: 10.0000 chunk 726 optimal weight: 10.0000 chunk 527 optimal weight: 10.0000 chunk 99 optimal weight: 40.0000 chunk 837 optimal weight: 9.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 GLN g 68 ASN ** i 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 146 GLN j 56 HIS k 47 GLN k 125 GLN m 88 GLN o 37 GLN s 47 HIS t 21 ASN t 52 HIS t 71 GLN C 109 GLN C 203 ASN E 47 GLN F 70 GLN F 83 GLN G 75 ASN N 107 ASN ** P 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 ASN U 48 GLN ** X 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 166045 Z= 0.502 Angle : 0.665 12.771 248108 Z= 0.342 Chirality : 0.043 0.343 31671 Planarity : 0.005 0.120 13764 Dihedral : 23.261 179.331 82447 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 3.60 % Allowed : 18.52 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.10), residues: 6433 helix: 1.31 (0.11), residues: 2146 sheet: 0.11 (0.14), residues: 1370 loop : -0.92 (0.11), residues: 2917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP d 165 HIS 0.011 0.001 HIS P 16 PHE 0.020 0.002 PHE F 84 TYR 0.032 0.002 TYR d 4 ARG 0.014 0.001 ARG r 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1500 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1312 time to evaluate : 6.531 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: c 168 TYR cc_start: 0.7414 (m-80) cc_final: 0.7103 (m-80) REVERT: c 170 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7595 (tm-30) REVERT: d 126 ASP cc_start: 0.8796 (p0) cc_final: 0.8314 (p0) REVERT: g 142 HIS cc_start: 0.8641 (m170) cc_final: 0.8173 (m-70) REVERT: h 43 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8140 (mm-30) REVERT: i 61 ASN cc_start: 0.8237 (t0) cc_final: 0.7870 (t0) REVERT: i 81 PHE cc_start: 0.8713 (m-80) cc_final: 0.8372 (m-80) REVERT: i 111 GLN cc_start: 0.8276 (tm-30) cc_final: 0.8046 (tm-30) REVERT: i 136 TYR cc_start: 0.9258 (p90) cc_final: 0.8975 (p90) REVERT: j 67 MET cc_start: 0.8474 (ttm) cc_final: 0.8148 (ttt) REVERT: j 88 MET cc_start: 0.7860 (pmm) cc_final: 0.7353 (ppp) REVERT: j 96 VAL cc_start: 0.8662 (t) cc_final: 0.8433 (p) REVERT: l 47 SER cc_start: 0.9253 (t) cc_final: 0.8980 (t) REVERT: m 59 TYR cc_start: 0.7946 (t80) cc_final: 0.7724 (t80) REVERT: n 52 GLU cc_start: 0.7988 (mp0) cc_final: 0.7712 (mp0) REVERT: o 36 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9245 (mp) REVERT: p 15 ASN cc_start: 0.8616 (p0) cc_final: 0.8154 (p0) REVERT: q 92 GLU cc_start: 0.8558 (pm20) cc_final: 0.7991 (pm20) REVERT: r 19 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8550 (mmtm) REVERT: s 5 LEU cc_start: 0.8207 (pt) cc_final: 0.7126 (mt) REVERT: s 10 PHE cc_start: 0.7764 (t80) cc_final: 0.7049 (t80) REVERT: s 37 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7761 (mtm110) REVERT: s 53 ASP cc_start: 0.8582 (t0) cc_final: 0.8128 (p0) REVERT: z 43 ASP cc_start: 0.8919 (t0) cc_final: 0.8658 (t0) REVERT: C 68 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7924 (ttt90) REVERT: F 142 GLN cc_start: 0.9025 (pm20) cc_final: 0.8443 (pm20) REVERT: I 35 ASN cc_start: 0.9423 (m110) cc_final: 0.8775 (m110) REVERT: J 140 THR cc_start: 0.9288 (m) cc_final: 0.9000 (p) REVERT: Q 113 ILE cc_start: 0.9375 (mm) cc_final: 0.9093 (mm) REVERT: U 66 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8442 (tm-30) REVERT: V 96 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8134 (m-80) REVERT: X 143 GLN cc_start: 0.8594 (pp30) cc_final: 0.8052 (pp30) REVERT: 1 66 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8925 (mp) REVERT: 3 28 LYS cc_start: 0.8773 (tptp) cc_final: 0.8452 (tptm) REVERT: 5 6 ASP cc_start: 0.7468 (t0) cc_final: 0.7245 (t0) outliers start: 188 outliers final: 160 residues processed: 1391 average time/residue: 1.4505 time to fit residues: 3505.7051 Evaluate side-chains 1460 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1295 time to evaluate : 6.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 110 SER Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 105 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 42 SER Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 117 VAL Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 146 GLN Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 24 ASN Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 72 GLN Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 32 MET Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 83 SER Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 28 LEU Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain z residue 101 THR Chi-restraints excluded: chain z residue 118 ASP Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain J residue 41 CYS Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 104 TRP Chi-restraints excluded: chain J residue 121 ASN Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 136 GLU Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 48 HIS Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 77 LYS Chi-restraints excluded: chain V residue 96 PHE Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 188 GLU Chi-restraints excluded: chain Z residue 21 SER Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain 1 residue 40 GLN Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 1 residue 66 LEU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 4 residue 21 LYS Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 4 residue 32 VAL Chi-restraints excluded: chain 5 residue 25 THR Chi-restraints excluded: chain 5 residue 37 GLU Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 7 residue 48 THR Chi-restraints excluded: chain 7 residue 59 ASN Chi-restraints excluded: chain 9 residue 14 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 969 optimal weight: 1.9990 chunk 1021 optimal weight: 6.9990 chunk 931 optimal weight: 0.7980 chunk 993 optimal weight: 2.9990 chunk 1020 optimal weight: 1.9990 chunk 597 optimal weight: 8.9990 chunk 432 optimal weight: 7.9990 chunk 780 optimal weight: 2.9990 chunk 304 optimal weight: 40.0000 chunk 897 optimal weight: 0.9980 chunk 939 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 122 GLN g 25 GLN ** i 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 146 GLN j 56 HIS k 47 GLN ** k 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 125 GLN ** m 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 GLN m 106 ASN o 37 GLN o 46 HIS ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 HIS t 21 ASN t 71 GLN C 109 GLN C 245 HIS D 145 HIS E 47 GLN J 21 ASN N 107 ASN Q 41 ASN ** X 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 166045 Z= 0.150 Angle : 0.545 13.087 248108 Z= 0.284 Chirality : 0.033 0.271 31671 Planarity : 0.004 0.117 13764 Dihedral : 23.316 179.536 82447 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.72 % Favored : 96.25 % Rotamer: Outliers : 2.39 % Allowed : 19.65 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.11), residues: 6433 helix: 1.56 (0.12), residues: 2127 sheet: 0.22 (0.14), residues: 1314 loop : -0.78 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP d 165 HIS 0.008 0.001 HIS H 11 PHE 0.021 0.001 PHE F 121 TYR 0.042 0.001 TYR d 4 ARG 0.015 0.000 ARG r 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1335 time to evaluate : 6.737 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: c 170 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7586 (tm-30) REVERT: g 52 GLU cc_start: 0.7868 (pp20) cc_final: 0.7437 (pp20) REVERT: g 142 HIS cc_start: 0.8631 (m170) cc_final: 0.8013 (m-70) REVERT: h 43 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8080 (mm-30) REVERT: i 57 ASN cc_start: 0.8726 (t0) cc_final: 0.8355 (p0) REVERT: i 61 ASN cc_start: 0.8264 (t0) cc_final: 0.7926 (t0) REVERT: i 81 PHE cc_start: 0.8583 (m-80) cc_final: 0.8263 (m-80) REVERT: i 111 GLN cc_start: 0.8341 (tm-30) cc_final: 0.8098 (tm-30) REVERT: i 136 TYR cc_start: 0.9268 (p90) cc_final: 0.8930 (p90) REVERT: j 67 MET cc_start: 0.8407 (ttm) cc_final: 0.8108 (ttt) REVERT: j 72 ARG cc_start: 0.8248 (mpp80) cc_final: 0.8028 (mpp80) REVERT: j 88 MET cc_start: 0.7887 (pmm) cc_final: 0.7451 (ppp) REVERT: j 96 VAL cc_start: 0.8621 (t) cc_final: 0.8385 (p) REVERT: l 47 SER cc_start: 0.9187 (t) cc_final: 0.8902 (t) REVERT: m 59 TYR cc_start: 0.8006 (t80) cc_final: 0.7789 (t80) REVERT: n 52 GLU cc_start: 0.7988 (mp0) cc_final: 0.7700 (mp0) REVERT: o 36 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9162 (mp) REVERT: p 15 ASN cc_start: 0.8529 (p0) cc_final: 0.8112 (p0) REVERT: p 39 ARG cc_start: 0.8219 (ptp90) cc_final: 0.7697 (ptp90) REVERT: q 54 ARG cc_start: 0.8620 (ttt-90) cc_final: 0.8355 (ttt-90) REVERT: q 92 GLU cc_start: 0.8465 (pm20) cc_final: 0.7867 (pm20) REVERT: r 19 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8582 (mmtm) REVERT: s 5 LEU cc_start: 0.8194 (pt) cc_final: 0.7091 (mt) REVERT: s 10 PHE cc_start: 0.7633 (t80) cc_final: 0.7364 (t80) REVERT: s 37 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7637 (ptp90) REVERT: s 53 ASP cc_start: 0.8575 (t0) cc_final: 0.8155 (p0) REVERT: t 46 LYS cc_start: 0.8943 (tttp) cc_final: 0.8649 (tptp) REVERT: F 90 MET cc_start: 0.8398 (ptp) cc_final: 0.8177 (ptp) REVERT: F 105 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7663 (mt-10) REVERT: F 142 GLN cc_start: 0.9005 (pm20) cc_final: 0.8422 (pm20) REVERT: J 140 THR cc_start: 0.9223 (m) cc_final: 0.8963 (p) REVERT: Q 113 ILE cc_start: 0.9318 (mm) cc_final: 0.9034 (mm) REVERT: U 66 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8424 (tm-30) REVERT: V 96 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: X 143 GLN cc_start: 0.8514 (pp30) cc_final: 0.7854 (pp30) REVERT: 1 66 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8855 (mp) REVERT: 3 25 ARG cc_start: 0.8822 (mtp-110) cc_final: 0.8330 (mtp-110) outliers start: 125 outliers final: 102 residues processed: 1386 average time/residue: 1.3496 time to fit residues: 3209.5281 Evaluate side-chains 1420 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1314 time to evaluate : 6.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 105 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 42 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 117 VAL Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 143 LYS Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 80 SER Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain q residue 32 MET Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain z residue 118 ASP Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain J residue 41 CYS Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 136 GLU Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 48 HIS Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain V residue 96 PHE Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain 1 residue 66 LEU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 5 residue 25 THR Chi-restraints excluded: chain 5 residue 54 SER Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 9 residue 14 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 989 optimal weight: 2.9990 chunk 652 optimal weight: 10.0000 chunk 1050 optimal weight: 20.0000 chunk 641 optimal weight: 8.9990 chunk 498 optimal weight: 10.0000 chunk 730 optimal weight: 10.0000 chunk 1101 optimal weight: 0.9980 chunk 1014 optimal weight: 2.9990 chunk 877 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 677 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 146 GLN j 56 HIS k 47 GLN k 125 GLN l 73 ASN l 105 GLN m 88 GLN o 37 GLN ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 81 GLN s 47 HIS t 21 ASN t 71 GLN G 75 ASN N 107 ASN ** P 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 166045 Z= 0.290 Angle : 0.574 12.824 248108 Z= 0.298 Chirality : 0.036 0.293 31671 Planarity : 0.005 0.118 13764 Dihedral : 23.248 179.692 82447 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 2.20 % Allowed : 20.32 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.11), residues: 6433 helix: 1.56 (0.12), residues: 2129 sheet: 0.23 (0.14), residues: 1336 loop : -0.81 (0.11), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP d 165 HIS 0.008 0.001 HIS H 11 PHE 0.018 0.001 PHE i 59 TYR 0.037 0.001 TYR d 4 ARG 0.015 0.000 ARG r 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12866 Ramachandran restraints generated. 6433 Oldfield, 0 Emsley, 6433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1299 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 revert: symmetry clash REVERT: c 170 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7655 (tm-30) REVERT: d 68 ARG cc_start: 0.8609 (mmm160) cc_final: 0.8387 (mmm160) REVERT: d 126 ASP cc_start: 0.8803 (p0) cc_final: 0.8349 (p0) REVERT: e 70 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7820 (mmp) REVERT: g 52 GLU cc_start: 0.7883 (pp20) cc_final: 0.7450 (pp20) REVERT: g 142 HIS cc_start: 0.8686 (m170) cc_final: 0.8209 (m-70) REVERT: h 43 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8081 (mm-30) REVERT: i 61 ASN cc_start: 0.8199 (t0) cc_final: 0.7860 (t0) REVERT: i 81 PHE cc_start: 0.8541 (m-80) cc_final: 0.8209 (m-80) REVERT: i 111 GLN cc_start: 0.8275 (tm-30) cc_final: 0.8030 (tm-30) REVERT: i 136 TYR cc_start: 0.9271 (p90) cc_final: 0.9006 (p90) REVERT: j 67 MET cc_start: 0.8444 (ttm) cc_final: 0.8142 (ttt) REVERT: j 88 MET cc_start: 0.7918 (pmm) cc_final: 0.7470 (ppp) REVERT: j 96 VAL cc_start: 0.8659 (t) cc_final: 0.8418 (p) REVERT: l 47 SER cc_start: 0.9193 (t) cc_final: 0.8900 (t) REVERT: m 59 TYR cc_start: 0.8038 (t80) cc_final: 0.7819 (t80) REVERT: n 52 GLU cc_start: 0.7985 (mp0) cc_final: 0.7717 (mp0) REVERT: o 36 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9200 (mp) REVERT: p 15 ASN cc_start: 0.8595 (p0) cc_final: 0.8172 (p0) REVERT: q 92 GLU cc_start: 0.8491 (pm20) cc_final: 0.7905 (pm20) REVERT: r 19 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8539 (mmtm) REVERT: s 5 LEU cc_start: 0.8219 (pt) cc_final: 0.7131 (mt) REVERT: s 10 PHE cc_start: 0.7702 (t80) cc_final: 0.7422 (t80) REVERT: s 37 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7708 (ptp90) REVERT: s 53 ASP cc_start: 0.8586 (t0) cc_final: 0.8150 (p0) REVERT: t 46 LYS cc_start: 0.8975 (tttp) cc_final: 0.8662 (tptp) REVERT: F 53 ASP cc_start: 0.8558 (t0) cc_final: 0.8354 (t70) REVERT: F 90 MET cc_start: 0.8412 (ptp) cc_final: 0.8207 (ptp) REVERT: F 105 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7710 (mt-10) REVERT: F 142 GLN cc_start: 0.9006 (pm20) cc_final: 0.8414 (pm20) REVERT: I 17 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.7810 (t80) REVERT: I 39 LEU cc_start: 0.9545 (tp) cc_final: 0.9246 (tp) REVERT: J 140 THR cc_start: 0.9196 (m) cc_final: 0.8856 (p) REVERT: Q 113 ILE cc_start: 0.9343 (mm) cc_final: 0.9046 (mm) REVERT: U 66 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8440 (tm-30) REVERT: V 96 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8041 (m-80) REVERT: X 143 GLN cc_start: 0.8549 (pp30) cc_final: 0.7800 (pp30) REVERT: 1 66 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8866 (mp) REVERT: 3 25 ARG cc_start: 0.8899 (mtp-110) cc_final: 0.8420 (mtp-110) REVERT: 3 28 LYS cc_start: 0.8703 (tptp) cc_final: 0.8418 (tptm) outliers start: 115 outliers final: 107 residues processed: 1350 average time/residue: 1.3424 time to fit residues: 3122.2261 Evaluate side-chains 1406 residues out of total 5340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1293 time to evaluate : 6.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 42 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 81 VAL Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 117 VAL Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 143 LYS Chi-restraints excluded: chain i residue 146 GLN Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain q residue 32 MET Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 21 VAL Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain z residue 118 ASP Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 63 LYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 17 PHE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain J residue 41 CYS Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 130 SER Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 136 GLU Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 48 HIS Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain T residue 47 ASN Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain V residue 96 PHE Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 1 residue 66 LEU Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 5 residue 25 THR Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 9 residue 14 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 538 optimal weight: 10.0000 chunk 696 optimal weight: 10.0000 chunk 934 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 809 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 chunk 243 optimal weight: 5.9990 chunk 878 optimal weight: 20.0000 chunk 367 optimal weight: 9.9990 chunk 902 optimal weight: 10.0000 chunk 111 optimal weight: 40.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 155 GLN c 122 GLN ** d 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN ** i 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 56 HIS k 47 GLN k 125 GLN l 73 ASN l 105 GLN m 88 GLN o 37 GLN ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 HIS t 21 ASN t 71 GLN C 109 GLN E 47 GLN J 16 GLN J 21 ASN N 107 ASN O 17 GLN ** P 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.060021 restraints weight = 321564.938| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 1.47 r_work: 0.2495 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2400 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 166045 Z= 0.412 Angle : 0.637 12.596 248108 Z= 0.330 Chirality : 0.040 0.326 31671 Planarity : 0.005 0.120 13764 Dihedral : 23.253 179.439 82447 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.09 % Rotamer: Outliers : 2.37 % Allowed : 20.13 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.11), residues: 6433 helix: 1.40 (0.11), residues: 2144 sheet: 0.17 (0.14), residues: 1365 loop : -0.90 (0.11), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP d 165 HIS 0.010 0.001 HIS P 16 PHE 0.028 0.002 PHE F 121 TYR 0.051 0.002 TYR i 147 ARG 0.015 0.001 ARG r 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47782.63 seconds wall clock time: 830 minutes 26.13 seconds (49826.13 seconds total)