Starting phenix.real_space_refine on Wed Mar 27 14:13:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o61_3751/03_2024/5o61_3751_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o61_3751/03_2024/5o61_3751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o61_3751/03_2024/5o61_3751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o61_3751/03_2024/5o61_3751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o61_3751/03_2024/5o61_3751_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o61_3751/03_2024/5o61_3751_neut.pdb" } resolution = 3.31 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= 0.002 sd= 0.034 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 4828 5.49 5 Mg 625 5.21 5 S 104 5.16 5 C 75610 2.51 5 N 28158 2.21 5 O 42132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "F PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 120": "OE1" <-> "OE2" Residue "N GLU 16": "OE1" <-> "OE2" Residue "N GLU 48": "OE1" <-> "OE2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "Q GLU 70": "OE1" <-> "OE2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "d ARG 17": "NH1" <-> "NH2" Residue "BC TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD GLU 73": "OE1" <-> "OE2" Residue "BE ARG 198": "NH1" <-> "NH2" Residue "BG GLU 74": "OE1" <-> "OE2" Residue "BG GLU 90": "OE1" <-> "OE2" Residue "BK PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BL GLU 70": "OE1" <-> "OE2" Residue "BM GLU 32": "OE1" <-> "OE2" Residue "BN TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP GLU 90": "OE1" <-> "OE2" Residue "BR PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BV PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BV GLU 169": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 151463 Number of models: 1 Model: "" Number of chains: 73 Chain: "3" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "A" Number of atoms: 66981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3119, 66981 Classifications: {'RNA': 3119} Modifications used: {'rna2p_pur': 298, 'rna2p_pyr': 146, 'rna3p_pur': 1485, 'rna3p_pyr': 1190} Link IDs: {'rna2p': 444, 'rna3p': 2674} 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: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1445 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1348 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "H" Number of atoms: 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: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "L" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "M" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "N" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "O" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "P" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Q" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "R" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "S" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "T" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 732 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain breaks: 1 Chain: "W" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1428 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain: "X" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 586 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "Y" 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: "Z" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "a" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 474 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "b" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "c" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "f" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "g" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 458 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain breaks: 1 Chain: "BA" Number of atoms: 32439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1511, 32439 Classifications: {'RNA': 1511} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 85, 'rna3p_pur': 737, 'rna3p_pyr': 577} Link IDs: {'rna2p': 197, 'rna3p': 1313} Chain: "BB" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 280 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "BC" 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: "BD" 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: "BE" 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: "BF" 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: "BG" 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: "BH" 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: "BI" 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: "BJ" 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: "BK" 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: "BL" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "BM" 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: "BN" 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: "BO" 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: "BP" 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: "BQ" 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: "BR" 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: "BS" 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: "BT" 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: "BV" 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: "BW" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 65} Chain: "BX" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 390 Unusual residues: {' MG': 390} Classifications: {'undetermined': 390} Link IDs: {None: 389} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 215 Unusual residues: {' MG': 215} Classifications: {'undetermined': 215} Link IDs: {None: 214} Chain: "BF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "BR" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BW" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 93846 SG CYS Y 5 182.075 172.227 64.848 1.00 60.15 S ATOM 93868 SG CYS Y 8 182.658 176.128 65.983 1.00 67.65 S ATOM 94210 SG CYS Y 52 179.066 174.626 65.561 1.00 66.45 S ATOM 94229 SG CYS Y 55 180.962 175.350 62.411 1.00 83.67 S ATOM 95797 SG CYS c 15 138.495 215.238 103.899 1.00 60.36 S ATOM 95819 SG CYS c 18 141.880 215.876 101.986 1.00 82.46 S ATOM 96034 SG CYS c 42 141.997 216.295 105.817 1.00 70.18 S ATOM 96055 SG CYS c 45 140.260 219.081 103.563 1.00 79.61 S ATOM 97087 SG CYS f 11 146.668 143.316 195.330 1.00100.07 S ATOM 97110 SG CYS f 14 149.834 144.743 194.013 1.00 75.21 S ATOM 97219 SG CYS f 27 150.412 141.486 195.923 1.00 79.04 S ATOM 97429 SG CYS g 16 71.897 204.260 136.515 1.00106.76 S ATOM 97439 SG CYS g 18 69.925 205.480 139.774 1.00116.91 S ATOM 97587 SG CYS g 38 73.654 204.568 140.105 1.00 99.32 S ATOM 97608 SG CYS g 41 70.861 201.831 139.160 1.00 98.01 S ATOM A0X11 SG CYSBN 24 57.623 124.092 137.144 1.00 59.73 S ATOM A0X1O SG CYSBN 27 61.397 122.447 137.307 1.00 71.90 S ATOM A0X4M SG CYSBN 40 60.722 124.665 134.502 1.00 82.73 S ATOM A0X5B SG CYSBN 43 59.223 121.217 134.607 1.00 80.61 S ATOM A0Z3M SG CYSBR 20 115.052 102.290 52.147 1.00 83.25 S ATOM A0Z4A SG CYSBR 23 116.053 98.664 52.177 1.00 76.49 S ATOM A0ZBU SG CYSBR 57 117.153 100.532 55.351 1.00 71.39 S Time building chain proxies: 59.38, per 1000 atoms: 0.39 Number of scatterers: 151463 At special positions: 0 Unit cell: (282.17, 261.32, 259.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 104 16.00 P 4828 15.00 Mg 625 11.99 O 42132 8.00 N 28158 7.00 C 75610 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: 66.88 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y 101 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 52 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 55 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 8 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 5 " pdb=" ZN c 101 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 18 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 45 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 42 " pdb="ZN ZN c 101 " - pdb=" SG CYS c 15 " pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 32 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb=" ZN g 101 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 41 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 18 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 16 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 38 " pdb=" ZNBN 101 " pdb="ZN ZNBN 101 " - pdb=" SG CYSBN 27 " pdb="ZN ZNBN 101 " - pdb=" SG CYSBN 40 " pdb="ZN ZNBN 101 " - pdb=" SG CYSBN 43 " pdb="ZN ZNBN 101 " - pdb=" SG CYSBN 24 " pdb=" ZNBR 101 " pdb="ZN ZNBR 101 " - pdb=" ND1 HISBR 60 " pdb="ZN ZNBR 101 " - pdb=" SG CYSBR 23 " pdb="ZN ZNBR 101 " - pdb=" SG CYSBR 57 " pdb="ZN ZNBR 101 " - pdb=" SG CYSBR 20 " Number of angles added : 30 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11106 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 73 sheets defined 35.5% alpha, 18.3% beta 1582 base pairs and 2642 stacking pairs defined. Time for finding SS restraints: 57.50 Creating SS restraints... Processing helix chain '3' and resid 2 through 12 Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 208 through 215 removed outlier: 3.706A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.529A pdb=" N VAL C 225 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 267 Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.754A pdb=" N VAL D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 30 through 46 Processing helix chain 'E' and resid 103 through 121 Processing helix chain 'E' and resid 137 through 149 removed outlier: 3.756A pdb=" N ALA E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 171 removed outlier: 3.825A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASN E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 removed outlier: 3.532A pdb=" N LEU E 183 " --> pdb=" O PRO E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 191 removed outlier: 3.533A pdb=" N VAL E 188 " --> pdb=" O ASN E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'F' and resid 9 through 18 Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.668A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 113 Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.735A pdb=" N GLN F 128 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE F 129 " --> pdb=" O PRO F 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 125 through 129' Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.583A pdb=" N MET F 144 " --> pdb=" O GLU F 141 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE F 145 " --> pdb=" O GLN F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 145' Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 169 through 180 Processing helix chain 'G' and resid 59 through 82 removed outlier: 4.279A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 41 through 60 removed outlier: 4.320A pdb=" N ARG H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 70 Processing helix chain 'H' and resid 96 through 108 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'I' and resid 2 through 19 Processing helix chain 'I' and resid 32 through 43 Processing helix chain 'I' and resid 53 through 58 Processing helix chain 'I' and resid 65 through 69 removed outlier: 3.948A pdb=" N GLY I 68 " --> pdb=" O GLY I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 101 Processing helix chain 'I' and resid 116 through 124 Processing helix chain 'J' and resid 26 through 32 removed outlier: 3.960A pdb=" N GLN J 32 " --> pdb=" O PRO J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 52 removed outlier: 3.730A pdb=" N PHE J 40 " --> pdb=" O ASN J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 84 Processing helix chain 'J' and resid 103 through 118 Processing helix chain 'J' and resid 122 through 137 removed outlier: 3.773A pdb=" N MET J 137 " --> pdb=" O THR J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 38 Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 89 through 96 removed outlier: 3.509A pdb=" N HIS K 96 " --> pdb=" O LEU K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 107 removed outlier: 4.250A pdb=" N VAL K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 120 removed outlier: 3.939A pdb=" N LYS K 120 " --> pdb=" O ARG K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 136 removed outlier: 4.032A pdb=" N ALA K 133 " --> pdb=" O HIS K 130 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA K 134 " --> pdb=" O PRO K 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 109 removed outlier: 3.819A pdb=" N GLU L 108 " --> pdb=" O ARG L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 118 Processing helix chain 'M' and resid 39 through 44 removed outlier: 4.048A pdb=" N ARG M 43 " --> pdb=" O GLY M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.685A pdb=" N LEU M 61 " --> pdb=" O ILE M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 87 Processing helix chain 'M' and resid 94 through 102 removed outlier: 3.641A pdb=" N LEU M 98 " --> pdb=" O GLY M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 140 Processing helix chain 'N' and resid 44 through 59 removed outlier: 3.716A pdb=" N HIS N 57 " --> pdb=" O ALA N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 123 Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 38 through 57 Proline residue: O 46 - end of helix removed outlier: 4.119A pdb=" N LYS O 50 " --> pdb=" O PRO O 46 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS O 57 " --> pdb=" O THR O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 71 removed outlier: 4.040A pdb=" N LYS O 69 " --> pdb=" O GLU O 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG O 71 " --> pdb=" O MET O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 82 Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'P' and resid 9 through 26 Processing helix chain 'P' and resid 67 through 72 Processing helix chain 'P' and resid 76 through 95 Processing helix chain 'P' and resid 110 through 123 Processing helix chain 'Q' and resid 4 through 12 removed outlier: 4.461A pdb=" N ALA Q 10 " --> pdb=" O PHE Q 6 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 55 removed outlier: 3.588A pdb=" N SER Q 55 " --> pdb=" O GLY Q 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 52 through 55' Processing helix chain 'Q' and resid 96 through 102 removed outlier: 3.520A pdb=" N LEU Q 102 " --> pdb=" O LEU Q 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 108 Processing helix chain 'R' and resid 6 through 21 removed outlier: 4.273A pdb=" N LYS R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 removed outlier: 4.082A pdb=" N ARG R 28 " --> pdb=" O ARG R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 72 removed outlier: 3.696A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 116 Processing helix chain 'S' and resid 51 through 58 Processing helix chain 'T' and resid 20 through 32 removed outlier: 3.863A pdb=" N VAL T 27 " --> pdb=" O LYS T 23 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU T 30 " --> pdb=" O ARG T 26 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL T 31 " --> pdb=" O VAL T 27 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG T 32 " --> pdb=" O ILE T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 46 Processing helix chain 'T' and resid 50 through 68 Processing helix chain 'T' and resid 96 through 98 No H-bonds generated for 'chain 'T' and resid 96 through 98' Processing helix chain 'U' and resid 6 through 9 Processing helix chain 'U' and resid 17 through 25 Processing helix chain 'U' and resid 38 through 51 Processing helix chain 'W' and resid 20 through 30 Processing helix chain 'W' and resid 51 through 62 Processing helix chain 'W' and resid 160 through 162 No H-bonds generated for 'chain 'W' and resid 160 through 162' Processing helix chain 'W' and resid 186 through 191 removed outlier: 3.625A pdb=" N GLU W 191 " --> pdb=" O ALA W 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 58 Processing helix chain 'Z' and resid 6 through 11 Processing helix chain 'Z' and resid 14 through 39 removed outlier: 3.636A pdb=" N ARG Z 23 " --> pdb=" O LYS Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 67 removed outlier: 3.512A pdb=" N VAL Z 50 " --> pdb=" O ARG Z 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 27 removed outlier: 3.564A pdb=" N GLY a 27 " --> pdb=" O LEU a 23 " (cutoff:3.500A) Processing helix chain 'a' and resid 40 through 51 Processing helix chain 'b' and resid 9 through 18 Processing helix chain 'b' and resid 43 through 49 Processing helix chain 'd' and resid 11 through 20 Processing helix chain 'd' and resid 20 through 27 removed outlier: 4.002A pdb=" N THR d 27 " --> pdb=" O LEU d 23 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 40 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.529A pdb=" N LYS e 12 " --> pdb=" O SER e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 43 Processing helix chain 'e' and resid 51 through 63 removed outlier: 4.518A pdb=" N SER e 56 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ARG e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 65 removed outlier: 3.877A pdb=" N ARG g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) Processing helix chain 'BB' and resid 4 through 24 Processing helix chain 'BB' and resid 24 through 33 Processing helix chain 'BC' and resid 6 through 11 removed outlier: 3.668A pdb=" N ARGBC 11 " --> pdb=" O PROBC 7 " (cutoff:3.500A) Processing helix chain 'BC' and resid 27 through 46 removed outlier: 3.661A pdb=" N LEUBC 46 " --> pdb=" O LEUBC 42 " (cutoff:3.500A) Processing helix chain 'BC' and resid 80 through 93 Processing helix chain 'BC' and resid 111 through 125 Processing helix chain 'BC' and resid 128 through 143 removed outlier: 3.908A pdb=" N GLNBC 143 " --> pdb=" O SERBC 139 " (cutoff:3.500A) Processing helix chain 'BD' and resid 7 through 16 removed outlier: 4.398A pdb=" N LYSBD 11 " --> pdb=" O PROBD 7 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SERBD 12 " --> pdb=" O ALABD 8 " (cutoff:3.500A) Processing helix chain 'BD' and resid 23 through 29 removed outlier: 3.962A pdb=" N GLUBD 27 " --> pdb=" O ASPBD 23 " (cutoff:3.500A) Processing helix chain 'BD' and resid 44 through 61 removed outlier: 4.036A pdb=" N LEUBD 50 " --> pdb=" O TYRBD 46 " (cutoff:3.500A) Processing helix chain 'BD' and resid 63 through 77 Processing helix chain 'BD' and resid 80 through 89 Processing helix chain 'BD' and resid 92 through 100 Processing helix chain 'BD' and resid 105 through 115 Processing helix chain 'BD' and resid 147 through 156 Processing helix chain 'BD' and resid 182 through 187 removed outlier: 3.672A pdb=" N ASPBD 187 " --> pdb=" O ARGBD 183 " (cutoff:3.500A) Processing helix chain 'BD' and resid 192 through 201 Processing helix chain 'BE' and resid 80 through 95 Processing helix chain 'BE' and resid 133 through 143 Processing helix chain 'BE' and resid 157 through 172 removed outlier: 3.512A pdb=" N LEUBE 172 " --> pdb=" O ALABE 168 " (cutoff:3.500A) Processing helix chain 'BE' and resid 174 through 182 Processing helix chain 'BE' and resid 185 through 190 removed outlier: 3.837A pdb=" N VALBE 189 " --> pdb=" O PROBE 185 " (cutoff:3.500A) Processing helix chain 'BE' and resid 191 through 213 Processing helix chain 'BF' and resid 18 through 35 removed outlier: 3.787A pdb=" N VALBF 29 " --> pdb=" O THRBF 25 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILEBF 30 " --> pdb=" O PHEBF 26 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARGBF 31 " --> pdb=" O LEUBF 27 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLYBF 35 " --> pdb=" O ARGBF 31 " (cutoff:3.500A) Processing helix chain 'BF' and resid 68 through 80 removed outlier: 3.556A pdb=" N SERBF 73 " --> pdb=" O PROBF 69 " (cutoff:3.500A) Processing helix chain 'BG' and resid 20 through 30 removed outlier: 3.921A pdb=" N THRBG 24 " --> pdb=" O SERBG 20 " (cutoff:3.500A) Processing helix chain 'BG' and resid 35 through 55 removed outlier: 3.533A pdb=" N ALABG 39 " --> pdb=" O LYSBG 35 " (cutoff:3.500A) Processing helix chain 'BG' and resid 57 through 70 Processing helix chain 'BG' and resid 92 through 109 removed outlier: 3.503A pdb=" N SERBG 96 " --> pdb=" O ARGBG 92 " (cutoff:3.500A) Processing helix chain 'BG' and resid 115 through 129 removed outlier: 3.632A pdb=" N ALABG 121 " --> pdb=" O VALBG 117 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASNBG 129 " --> pdb=" O LEUBG 125 " (cutoff:3.500A) Processing helix chain 'BG' and resid 132 through 147 Processing helix chain 'BG' and resid 148 through 155 removed outlier: 3.748A pdb=" N HISBG 153 " --> pdb=" O ALABG 150 " (cutoff:3.500A) Processing helix chain 'BH' and resid 5 through 20 Processing helix chain 'BH' and resid 30 through 43 Processing helix chain 'BH' and resid 115 through 121 Processing helix chain 'BJ' and resid 14 through 32 removed outlier: 3.831A pdb=" N ILEBJ 18 " --> pdb=" O ASPBJ 14 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THRBJ 32 " --> pdb=" O THRBJ 28 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 80 through 88 Processing helix chain 'BK' and resid 62 through 67 removed outlier: 3.541A pdb=" N ARGBK 65 " --> pdb=" O LYSBK 62 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYSBK 66 " --> pdb=" O GLYBK 63 " (cutoff:3.500A) Processing helix chain 'BK' and resid 68 through 86 removed outlier: 3.770A pdb=" N HISBK 86 " --> pdb=" O LYSBK 82 " (cutoff:3.500A) Processing helix chain 'BK' and resid 101 through 111 Processing helix chain 'BL' and resid 3 through 11 Processing helix chain 'BL' and resid 21 through 25 Processing helix chain 'BM' and resid 14 through 19 Processing helix chain 'BM' and resid 20 through 22 No H-bonds generated for 'chain 'BM' and resid 20 through 22' Processing helix chain 'BM' and resid 26 through 38 removed outlier: 3.937A pdb=" N ALABM 35 " --> pdb=" O ASNBM 31 " (cutoff:3.500A) Processing helix chain 'BM' and resid 49 through 64 Processing helix chain 'BM' and resid 66 through 84 removed outlier: 3.776A pdb=" N LEUBM 70 " --> pdb=" O VALBM 66 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILEBM 84 " --> pdb=" O ARGBM 80 " (cutoff:3.500A) Processing helix chain 'BM' and resid 86 through 95 Processing helix chain 'BM' and resid 107 through 112 Processing helix chain 'BN' and resid 3 through 10 Processing helix chain 'BN' and resid 40 through 51 Processing helix chain 'BO' and resid 4 through 16 removed outlier: 3.640A pdb=" N LYSBO 8 " --> pdb=" O THRBO 4 " (cutoff:3.500A) Processing helix chain 'BO' and resid 24 through 46 removed outlier: 3.602A pdb=" N VALBO 45 " --> pdb=" O GLUBO 41 " (cutoff:3.500A) Processing helix chain 'BO' and resid 49 through 74 removed outlier: 3.756A pdb=" N ARGBO 53 " --> pdb=" O ASPBO 49 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLYBO 55 " --> pdb=" O HISBO 51 " (cutoff:3.500A) Processing helix chain 'BO' and resid 74 through 86 Processing helix chain 'BP' and resid 52 through 62 Processing helix chain 'BP' and resid 67 through 78 Processing helix chain 'BP' and resid 78 through 85 Processing helix chain 'BP' and resid 101 through 113 Processing helix chain 'BR' and resid 34 through 41 removed outlier: 3.876A pdb=" N LEUBR 38 " --> pdb=" O ASPBR 34 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYRBR 41 " --> pdb=" O LEUBR 37 " (cutoff:3.500A) Processing helix chain 'BR' and resid 50 through 55 Processing helix chain 'BR' and resid 57 through 74 Processing helix chain 'BS' and resid 4 through 8 Processing helix chain 'BS' and resid 12 through 25 removed outlier: 3.606A pdb=" N LYSBS 25 " --> pdb=" O VALBS 21 " (cutoff:3.500A) Processing helix chain 'BS' and resid 41 through 45 Processing helix chain 'BS' and resid 70 through 75 Processing helix chain 'BT' and resid 4 through 42 removed outlier: 3.562A pdb=" N ILEBT 8 " --> pdb=" O ILEBT 4 " (cutoff:3.500A) Processing helix chain 'BT' and resid 43 through 63 removed outlier: 3.571A pdb=" N ALABT 53 " --> pdb=" O GLUBT 49 " (cutoff:3.500A) Processing helix chain 'BT' and resid 68 through 86 Processing helix chain 'BV' and resid 5 through 13 Processing helix chain 'BV' and resid 24 through 28 Processing helix chain 'BV' and resid 42 through 63 Processing helix chain 'BV' and resid 73 through 88 removed outlier: 4.656A pdb=" N GLUBV 78 " --> pdb=" O LYSBV 74 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SERBV 79 " --> pdb=" O GLNBV 75 " (cutoff:3.500A) Processing helix chain 'BV' and resid 103 through 108 removed outlier: 4.264A pdb=" N VALBV 107 " --> pdb=" O ASNBV 103 " (cutoff:3.500A) Processing helix chain 'BV' and resid 108 through 123 Processing helix chain 'BV' and resid 130 through 148 removed outlier: 3.529A pdb=" N LEUBV 135 " --> pdb=" O LYSBV 131 " (cutoff:3.500A) Processing helix chain 'BV' and resid 149 through 155 removed outlier: 3.978A pdb=" N ASPBV 153 " --> pdb=" O GLYBV 149 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLNBV 155 " --> pdb=" O ILEBV 151 " (cutoff:3.500A) Processing helix chain 'BV' and resid 169 through 179 Processing helix chain 'BV' and resid 192 through 196 removed outlier: 3.583A pdb=" N VALBV 195 " --> pdb=" O ASPBV 192 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VALBV 196 " --> pdb=" O PROBV 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'BV' and resid 192 through 196' Processing helix chain 'BV' and resid 206 through 227 Processing sheet with id= A, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'C' and resid 116 through 118 removed outlier: 6.704A pdb=" N LEU C 94 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE C 82 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 92 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 130 through 132 Processing sheet with id= D, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.621A pdb=" N ARG C 176 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU C 165 " --> pdb=" O ARG C 176 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 174 through 177 removed outlier: 4.665A pdb=" N THR D 117 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU D 205 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY D 204 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL D 28 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N MET D 13 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL D 26 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLN D 15 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL D 24 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS D 184 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LYS D 195 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL D 182 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 80 through 85 removed outlier: 3.785A pdb=" N ARG D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ALA D 53 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL D 36 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 3 through 6 Processing sheet with id= H, first strand: chain 'E' and resid 124 through 127 removed outlier: 6.175A pdb=" N VAL E 194 " --> pdb=" O HIS E 125 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL E 127 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE E 196 " --> pdb=" O VAL E 127 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 135 through 139 removed outlier: 6.719A pdb=" N ARG F 75 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA F 94 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU F 73 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 16 through 20 Processing sheet with id= K, first strand: chain 'G' and resid 41 through 46 Processing sheet with id= L, first strand: chain 'G' and resid 162 through 165 Processing sheet with id= M, first strand: chain 'G' and resid 96 through 100 Processing sheet with id= N, first strand: chain 'H' and resid 18 through 20 Processing sheet with id= O, first strand: chain 'H' and resid 78 through 81 Processing sheet with id= P, first strand: chain 'I' and resid 48 through 51 removed outlier: 6.488A pdb=" N GLU I 27 " --> pdb=" O ILE I 105 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE I 105 " --> pdb=" O GLU I 27 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 11 through 15 Processing sheet with id= R, first strand: chain 'K' and resid 15 through 19 removed outlier: 6.293A pdb=" N PHE K 53 " --> pdb=" O TYR K 16 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE K 18 " --> pdb=" O PHE K 53 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE K 55 " --> pdb=" O ILE K 18 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 73 through 77 Processing sheet with id= T, first strand: chain 'L' and resid 7 through 9 removed outlier: 6.769A pdb=" N VAL L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VAL L 24 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL L 38 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP L 37 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 76 through 79 Processing sheet with id= V, first strand: chain 'M' and resid 91 through 93 removed outlier: 3.505A pdb=" N ALA M 126 " --> pdb=" O THR M 145 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'N' and resid 32 through 36 Processing sheet with id= X, first strand: chain 'N' and resid 40 through 43 Processing sheet with id= Y, first strand: chain 'N' and resid 63 through 66 Processing sheet with id= Z, first strand: chain 'N' and resid 73 through 76 removed outlier: 5.999A pdb=" N LYS N 76 " --> pdb=" O PRO N 90 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'O' and resid 33 through 37 removed outlier: 4.448A pdb=" N GLU O 101 " --> pdb=" O MET O 110 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL O 112 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LYS O 99 " --> pdb=" O VAL O 112 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU O 114 " --> pdb=" O ILE O 97 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE O 97 " --> pdb=" O GLU O 114 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'P' and resid 100 through 103 removed outlier: 7.123A pdb=" N ASP P 103 " --> pdb=" O PRO P 36 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU P 38 " --> pdb=" O ASP P 103 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 83 through 87 removed outlier: 6.769A pdb=" N THR Q 24 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N LYS Q 43 " --> pdb=" O GLU Q 63 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLU Q 63 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR Q 59 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG Q 49 " --> pdb=" O THR Q 57 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR Q 57 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'S' and resid 12 through 16 Processing sheet with id= AE, first strand: chain 'S' and resid 21 through 25 Processing sheet with id= AF, first strand: chain 'S' and resid 34 through 37 removed outlier: 6.319A pdb=" N GLU S 63 " --> pdb=" O VAL S 99 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL S 99 " --> pdb=" O GLU S 63 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'S' and resid 73 through 79 removed outlier: 3.954A pdb=" N TYR S 84 " --> pdb=" O LYS S 79 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'T' and resid 9 through 14 removed outlier: 6.431A pdb=" N GLU T 115 " --> pdb=" O VAL T 78 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL T 78 " --> pdb=" O GLU T 115 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'T' and resid 88 through 94 Processing sheet with id= AJ, first strand: chain 'U' and resid 11 through 14 removed outlier: 6.606A pdb=" N VAL U 32 " --> pdb=" O LEU U 12 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR U 30 " --> pdb=" O PRO U 14 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS U 80 " --> pdb=" O VAL U 33 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'V' and resid 20 through 22 Processing sheet with id= AL, first strand: chain 'V' and resid 40 through 45 Processing sheet with id= AM, first strand: chain 'V' and resid 83 through 88 Processing sheet with id= AN, first strand: chain 'V' and resid 23 through 27 removed outlier: 6.870A pdb=" N LEU V 34 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA V 26 " --> pdb=" O LYS V 32 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS V 32 " --> pdb=" O ALA V 26 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'W' and resid 67 through 71 removed outlier: 5.849A pdb=" N ASN W 9 " --> pdb=" O THR W 68 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASP W 70 " --> pdb=" O ASN W 9 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU W 11 " --> pdb=" O ASP W 70 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N THR W 12 " --> pdb=" O ASN W 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN W 50 " --> pdb=" O THR W 12 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL W 99 " --> pdb=" O TYR W 38 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA W 82 " --> pdb=" O ASP W 96 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU W 98 " --> pdb=" O THR W 80 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR W 80 " --> pdb=" O LEU W 98 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'W' and resid 130 through 136 Processing sheet with id= AQ, first strand: chain 'W' and resid 122 through 126 removed outlier: 7.047A pdb=" N ILE W 157 " --> pdb=" O VAL W 178 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASN W 180 " --> pdb=" O THR W 155 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR W 155 " --> pdb=" O ASN W 180 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'X' and resid 51 through 53 Processing sheet with id= AS, first strand: chain 'X' and resid 66 through 72 Processing sheet with id= AT, first strand: chain 'Y' and resid 13 through 18 Processing sheet with id= AU, first strand: chain 'Y' and resid 33 through 39 Processing sheet with id= AV, first strand: chain 'a' and resid 34 through 38 Processing sheet with id= AW, first strand: chain 'b' and resid 27 through 32 Processing sheet with id= AX, first strand: chain 'c' and resid 37 through 42 removed outlier: 6.870A pdb=" N CYS c 15 " --> pdb=" O ARG c 21 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG c 21 " --> pdb=" O CYS c 15 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'e' and resid 23 through 25 Processing sheet with id= AZ, first strand: chain 'f' and resid 2 through 4 Processing sheet with id= BA, first strand: chain 'f' and resid 15 through 19 Processing sheet with id= BB, first strand: chain 'g' and resid 21 through 26 Processing sheet with id= BC, first strand: chain 'BC' and resid 98 through 104 removed outlier: 6.930A pdb=" N VALBC 63 " --> pdb=" O GLNBC 99 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ASNBC 101 " --> pdb=" O VALBC 63 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VALBC 65 " --> pdb=" O ASNBC 101 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEUBC 103 " --> pdb=" O VALBC 65 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILEBC 67 " --> pdb=" O LEUBC 103 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'BC' and resid 164 through 170 removed outlier: 6.915A pdb=" N TYRBC 203 " --> pdb=" O LYSBC 147 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILEBC 149 " --> pdb=" O TRPBC 201 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRPBC 201 " --> pdb=" O ILEBC 149 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VALBC 151 " --> pdb=" O LYSBC 199 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYSBC 199 " --> pdb=" O VALBC 151 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYSBC 153 " --> pdb=" O GLYBC 197 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLYBC 197 " --> pdb=" O CYSBC 153 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLYBC 155 " --> pdb=" O ARGBC 195 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ARGBC 195 " --> pdb=" O GLYBC 155 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'BD' and resid 118 through 120 Processing sheet with id= BF, first strand: chain 'BE' and resid 71 through 78 removed outlier: 3.952A pdb=" N SERBE 42 " --> pdb=" O LEUBE 61 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILEBE 63 " --> pdb=" O VALBE 40 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VALBE 40 " --> pdb=" O ILEBE 63 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLYBE 65 " --> pdb=" O GLUBE 38 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLUBE 38 " --> pdb=" O GLYBE 65 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'BE' and resid 110 through 114 removed outlier: 3.788A pdb=" N VALBE 118 " --> pdb=" O GLYBE 154 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLYBE 154 " --> pdb=" O VALBE 118 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N METBE 120 " --> pdb=" O SERBE 152 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SERBE 152 " --> pdb=" O METBE 120 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ARGBE 122 " --> pdb=" O ALABE 150 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALABE 150 " --> pdb=" O ARGBE 122 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'BF' and resid 37 through 43 removed outlier: 6.478A pdb=" N ASPBF 11 " --> pdb=" O VALBF 85 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VALBF 85 " --> pdb=" O ASPBF 11 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'BG' and resid 73 through 80 Processing sheet with id= BJ, first strand: chain 'BH' and resid 24 through 28 Processing sheet with id= BK, first strand: chain 'BH' and resid 76 through 79 removed outlier: 6.574A pdb=" N ILEBH 105 " --> pdb=" O LEUBH 128 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYRBH 130 " --> pdb=" O VALBH 103 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VALBH 103 " --> pdb=" O TYRBH 130 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'BJ' and resid 70 through 77 Processing sheet with id= BN, first strand: chain 'BJ' and resid 45 through 52 Processing sheet with id= BO, first strand: chain 'BK' and resid 50 through 55 removed outlier: 7.030A pdb=" N ILEBK 43 " --> pdb=" O ILEBK 51 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TRPBK 53 " --> pdb=" O VALBK 41 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VALBK 41 " --> pdb=" O TRPBK 53 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N SERBK 55 " --> pdb=" O THRBK 39 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THRBK 39 " --> pdb=" O SERBK 55 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYSBK 90 " --> pdb=" O GLYBK 28 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALABK 30 " --> pdb=" O LYSBK 90 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASPBK 92 " --> pdb=" O ALABK 30 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILEBK 32 " --> pdb=" O ASPBK 92 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHEBK 94 " --> pdb=" O ILEBK 32 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N SERBK 34 " --> pdb=" O PHEBK 94 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYSBK 96 " --> pdb=" O SERBK 34 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'BL' and resid 29 through 33 removed outlier: 4.060A pdb=" N TYRBL 95 " --> pdb=" O THRBL 64 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYSBL 51 " --> pdb=" O ILEBL 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARGBL 36 " --> pdb=" O ARGBL 54 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LYSBL 56 " --> pdb=" O CYSBL 34 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N CYSBL 34 " --> pdb=" O LYSBL 56 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'BP' and resid 3 through 10 removed outlier: 6.762A pdb=" N VALBP 22 " --> pdb=" O VALBP 36 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VALBP 36 " --> pdb=" O VALBP 22 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'BQ' and resid 22 through 26 removed outlier: 9.066A pdb=" N ARGBQ 87 " --> pdb=" O LYSBQ 58 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LYSBQ 60 " --> pdb=" O ARGBQ 87 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARGBQ 89 " --> pdb=" O LYSBQ 60 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N HISBQ 62 " --> pdb=" O ARGBQ 89 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SERBQ 29 " --> pdb=" O VALBQ 37 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLUBQ 39 " --> pdb=" O VALBQ 27 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VALBQ 27 " --> pdb=" O GLUBQ 39 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLUBQ 41 " --> pdb=" O GLYBQ 25 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLYBQ 25 " --> pdb=" O GLUBQ 41 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'BQ' and resid 73 through 75 removed outlier: 6.512A pdb=" N SERBQ 75 " --> pdb=" O ILEBQ 93 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILEBQ 93 " --> pdb=" O SERBQ 75 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'BS' and resid 30 through 33 removed outlier: 7.118A pdb=" N THRBS 48 " --> pdb=" O ILEBS 31 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THRBS 33 " --> pdb=" O THRBS 48 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ALABS 50 " --> pdb=" O THRBS 33 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'BV' and resid 67 through 70 removed outlier: 7.406A pdb=" N ALABV 160 " --> pdb=" O LEUBV 68 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VALBV 70 " --> pdb=" O ALABV 160 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TRPBV 162 " --> pdb=" O VALBV 70 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VALBV 163 " --> pdb=" O PROBV 182 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILEBV 184 " --> pdb=" O VALBV 163 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYRBV 198 " --> pdb=" O ALABV 185 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEUBV 187 " --> pdb=" O TYRBV 198 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILEBV 200 " --> pdb=" O LEUBV 187 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'BV' and resid 31 through 34 removed outlier: 6.606A pdb=" N ILEBV 40 " --> pdb=" O PHEBV 32 " (cutoff:3.500A) 1975 hydrogen bonds defined for protein. 5601 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4039 hydrogen bonds 6486 hydrogen bond angles 0 basepair planarities 1582 basepair parallelities 2642 stacking parallelities Total time for adding SS restraints: 358.63 Time building geometry restraints manager: 72.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 15534 1.32 - 1.45: 73346 1.45 - 1.58: 65250 1.58 - 1.71: 9608 1.71 - 1.84: 175 Bond restraints: 163913 Sorted by residual: bond pdb=" ND1 HISBD 115 " pdb=" CE1 HISBD 115 " ideal model delta sigma weight residual 1.321 1.185 0.136 1.00e-02 1.00e+04 1.84e+02 bond pdb=" CG HIS T 109 " pdb=" ND1 HIS T 109 " ideal model delta sigma weight residual 1.378 1.470 -0.092 1.10e-02 8.26e+03 7.07e+01 bond pdb=" CE1 HIS T 109 " pdb=" NE2 HIS T 109 " ideal model delta sigma weight residual 1.321 1.399 -0.078 1.00e-02 1.00e+04 6.07e+01 bond pdb=" ND1 HIS T 109 " pdb=" CE1 HIS T 109 " ideal model delta sigma weight residual 1.321 1.243 0.078 1.00e-02 1.00e+04 6.04e+01 bond pdb=" CG HISBD 115 " pdb=" CD2 HISBD 115 " ideal model delta sigma weight residual 1.354 1.433 -0.079 1.10e-02 8.26e+03 5.21e+01 ... (remaining 163908 not shown) Histogram of bond angle deviations from ideal: 98.20 - 107.21: 33766 107.21 - 116.22: 110474 116.22 - 125.22: 82778 125.22 - 134.23: 18431 134.23 - 143.24: 6 Bond angle restraints: 245455 Sorted by residual: angle pdb=" C LEU E 20 " pdb=" N PRO E 21 " pdb=" CA PRO E 21 " ideal model delta sigma weight residual 119.90 129.79 -9.89 1.02e+00 9.61e-01 9.40e+01 angle pdb=" CG TRP R 61 " pdb=" CD2 TRP R 61 " pdb=" CE3 TRP R 61 " ideal model delta sigma weight residual 133.90 143.24 -9.34 1.00e+00 1.00e+00 8.72e+01 angle pdb=" C CYS c 42 " pdb=" N PRO c 43 " pdb=" CA PRO c 43 " ideal model delta sigma weight residual 118.97 128.61 -9.64 1.04e+00 9.25e-01 8.59e+01 angle pdb=" C HIS K 130 " pdb=" N PRO K 131 " pdb=" CA PRO K 131 " ideal model delta sigma weight residual 119.82 128.42 -8.60 9.80e-01 1.04e+00 7.70e+01 angle pdb=" C LEU N 125 " pdb=" N PRO N 126 " pdb=" CA PRO N 126 " ideal model delta sigma weight residual 119.82 128.28 -8.46 9.80e-01 1.04e+00 7.46e+01 ... (remaining 245450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 91541 35.95 - 71.91: 12532 71.91 - 107.86: 1447 107.86 - 143.82: 47 143.82 - 179.77: 53 Dihedral angle restraints: 105620 sinusoidal: 88348 harmonic: 17272 Sorted by residual: dihedral pdb=" O4' UBA 328 " pdb=" C1' UBA 328 " pdb=" N1 UBA 328 " pdb=" C2 UBA 328 " ideal model delta sinusoidal sigma weight residual -160.00 19.48 -179.48 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' CBA 179 " pdb=" C1' CBA 179 " pdb=" N1 CBA 179 " pdb=" C2 CBA 179 " ideal model delta sinusoidal sigma weight residual -160.00 17.88 -177.88 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' CBA 415 " pdb=" C1' CBA 415 " pdb=" N1 CBA 415 " pdb=" C2 CBA 415 " ideal model delta sinusoidal sigma weight residual 200.00 24.07 175.93 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 105617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 29962 0.091 - 0.182: 1359 0.182 - 0.273: 81 0.273 - 0.364: 4 0.364 - 0.455: 2 Chirality restraints: 31408 Sorted by residual: chirality pdb=" C3' UBA1482 " pdb=" C4' UBA1482 " pdb=" O3' UBA1482 " pdb=" C2' UBA1482 " both_signs ideal model delta sigma weight residual False -2.74 -2.29 -0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" C3' C A2085 " pdb=" C4' C A2085 " pdb=" O3' C A2085 " pdb=" C2' C A2085 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" C3' ABA 895 " pdb=" C4' ABA 895 " pdb=" O3' ABA 895 " pdb=" C2' ABA 895 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 31405 not shown) Planarity restraints: 13199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG T 117 " -0.031 2.00e-02 2.50e+03 6.23e-02 3.89e+01 pdb=" C ARG T 117 " 0.108 2.00e-02 2.50e+03 pdb=" O ARG T 117 " -0.041 2.00e-02 2.50e+03 pdb=" N PRO T 118 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS g 41 " -0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C CYS g 41 " 0.076 2.00e-02 2.50e+03 pdb=" O CYS g 41 " -0.029 2.00e-02 2.50e+03 pdb=" N HIS g 42 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU M 146 " -0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" C GLU M 146 " 0.069 2.00e-02 2.50e+03 pdb=" O GLU M 146 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU M 147 " -0.022 2.00e-02 2.50e+03 ... (remaining 13196 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 308 2.24 - 2.91: 54171 2.91 - 3.57: 219322 3.57 - 4.24: 471468 4.24 - 4.90: 622945 Nonbonded interactions: 1368214 Sorted by model distance: nonbonded pdb=" O3' ABW 76 " pdb=" C PHEBW 101 " model vdw 1.579 3.270 nonbonded pdb=" OP2 U A2906 " pdb="MG MG A4189 " model vdw 1.776 2.170 nonbonded pdb=" OP1 A A1832 " pdb="MG MG A4006 " model vdw 1.825 2.170 nonbonded pdb=" OP1 GBA1074 " pdb="MG MGBA1647 " model vdw 1.830 2.170 nonbonded pdb=" OP1 U A 782 " pdb="MG MG A4188 " model vdw 1.840 2.170 ... (remaining 1368209 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 9.450 Check model and map are aligned: 1.610 Set scattering table: 1.090 Process input model: 675.020 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.360 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:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 693.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 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 : 0.007 0.136 163913 Z= 0.450 Angle : 0.994 13.753 245455 Z= 0.588 Chirality : 0.043 0.455 31408 Planarity : 0.005 0.097 13199 Dihedral : 24.460 179.773 94514 Min Nonbonded Distance : 1.579 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.69 % Favored : 95.15 % Rotamer: Outliers : 10.91 % Allowed : 10.75 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: -3.02 (0.09), residues: 5979 helix: -2.79 (0.08), residues: 2001 sheet: -0.95 (0.13), residues: 1169 loop : -1.74 (0.10), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 250 HIS 0.023 0.002 HISBD 115 PHE 0.023 0.002 PHE N 69 TYR 0.023 0.002 TYRBI 58 ARG 0.011 0.001 ARGBF 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2601 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 539 poor density : 2062 time to evaluate : 6.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 3 11 ARG cc_start: 0.8806 (ptt90) cc_final: 0.8520 (ptt180) REVERT: C 28 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8131 (p) REVERT: C 63 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.8917 (mpt90) REVERT: C 124 ASP cc_start: 0.7637 (t0) cc_final: 0.7214 (t70) REVERT: C 172 TYR cc_start: 0.8186 (m-80) cc_final: 0.7961 (m-10) REVERT: D 13 MET cc_start: 0.9112 (mtp) cc_final: 0.8827 (ttm) REVERT: D 58 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8283 (t) REVERT: D 86 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8598 (mt) REVERT: D 88 ASP cc_start: 0.8147 (p0) cc_final: 0.7652 (p0) REVERT: D 101 LEU cc_start: 0.8412 (mt) cc_final: 0.7671 (mp) REVERT: D 129 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.9024 (ttt180) REVERT: D 198 ILE cc_start: 0.9492 (pt) cc_final: 0.9069 (pt) REVERT: E 112 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8541 (mtt180) REVERT: F 13 GLN cc_start: 0.8836 (tt0) cc_final: 0.8497 (tm-30) REVERT: F 44 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8767 (t0) REVERT: F 45 MET cc_start: 0.7890 (mtp) cc_final: 0.7491 (mtt) REVERT: F 52 ARG cc_start: 0.7245 (mtt180) cc_final: 0.6948 (mmt90) REVERT: F 58 ASN cc_start: 0.7829 (m-40) cc_final: 0.7416 (m-40) REVERT: F 63 ASP cc_start: 0.8186 (m-30) cc_final: 0.7887 (m-30) REVERT: F 102 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8547 (mtp85) REVERT: F 139 LEU cc_start: 0.8362 (mt) cc_final: 0.8058 (mp) REVERT: F 142 GLN cc_start: 0.8844 (pm20) cc_final: 0.8000 (pm20) REVERT: F 185 LYS cc_start: 0.8219 (mttt) cc_final: 0.7773 (mttp) REVERT: G 6 LYS cc_start: 0.8300 (pttt) cc_final: 0.8032 (pttm) REVERT: G 48 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.6371 (p0) REVERT: G 75 ASN cc_start: 0.8055 (m-40) cc_final: 0.7732 (m-40) REVERT: G 84 TYR cc_start: 0.8096 (m-80) cc_final: 0.7474 (m-80) REVERT: G 89 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.8005 (tp30) REVERT: G 110 TYR cc_start: 0.8118 (m-80) cc_final: 0.7891 (m-10) REVERT: G 149 ILE cc_start: 0.9341 (mt) cc_final: 0.9130 (mp) REVERT: G 171 ARG cc_start: 0.8549 (ptp-110) cc_final: 0.8337 (ttm110) REVERT: H 6 THR cc_start: 0.8136 (m) cc_final: 0.7395 (p) REVERT: H 137 HIS cc_start: 0.6338 (OUTLIER) cc_final: 0.5927 (t-90) REVERT: H 143 LYS cc_start: 0.8547 (mttt) cc_final: 0.8317 (tptm) REVERT: I 24 VAL cc_start: 0.7628 (t) cc_final: 0.7130 (p) REVERT: I 82 VAL cc_start: 0.3172 (OUTLIER) cc_final: 0.2527 (p) REVERT: J 37 ILE cc_start: 0.2349 (OUTLIER) cc_final: 0.2081 (tt) REVERT: K 85 ARG cc_start: 0.8556 (ptm-80) cc_final: 0.8199 (ptt90) REVERT: K 96 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.7708 (p-80) REVERT: K 106 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9012 (mp) REVERT: K 145 VAL cc_start: 0.9312 (OUTLIER) cc_final: 0.9082 (p) REVERT: L 1 MET cc_start: 0.8795 (tpt) cc_final: 0.8219 (tpp) REVERT: L 28 SER cc_start: 0.8932 (p) cc_final: 0.8550 (t) REVERT: L 65 THR cc_start: 0.9277 (p) cc_final: 0.9051 (m) REVERT: M 105 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7877 (mmm-85) REVERT: M 138 THR cc_start: 0.8660 (m) cc_final: 0.8405 (p) REVERT: N 82 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8859 (mtt-85) REVERT: O 95 THR cc_start: 0.9125 (p) cc_final: 0.8907 (m) REVERT: O 110 MET cc_start: 0.8314 (mtp) cc_final: 0.7995 (mtt) REVERT: P 16 ASN cc_start: 0.8916 (p0) cc_final: 0.8558 (p0) REVERT: P 24 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8873 (ptp90) REVERT: P 64 SER cc_start: 0.8296 (p) cc_final: 0.7855 (t) REVERT: P 74 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6931 (p0) REVERT: P 99 THR cc_start: 0.8703 (m) cc_final: 0.8487 (p) REVERT: P 126 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7901 (mmmt) REVERT: Q 57 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.9051 (p) REVERT: Q 64 SER cc_start: 0.8884 (m) cc_final: 0.8657 (p) REVERT: Q 93 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8875 (mmt180) REVERT: Q 101 GLU cc_start: 0.8431 (mp0) cc_final: 0.8200 (mp0) REVERT: R 42 SER cc_start: 0.9088 (t) cc_final: 0.8642 (m) REVERT: R 73 ASP cc_start: 0.8593 (t0) cc_final: 0.8371 (t0) REVERT: S 51 LYS cc_start: 0.8877 (mttt) cc_final: 0.8667 (ttmm) REVERT: S 72 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.9026 (tptp) REVERT: T 35 SER cc_start: 0.9264 (p) cc_final: 0.9014 (t) REVERT: T 56 LYS cc_start: 0.9118 (mttt) cc_final: 0.8624 (mttm) REVERT: T 104 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.9144 (mpt180) REVERT: U 20 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8545 (p) REVERT: U 21 TYR cc_start: 0.8793 (m-80) cc_final: 0.8454 (m-10) REVERT: U 50 PHE cc_start: 0.8647 (m-80) cc_final: 0.8170 (m-10) REVERT: U 66 ARG cc_start: 0.8640 (mtp180) cc_final: 0.8244 (mtm180) REVERT: V 24 LEU cc_start: 0.8594 (mt) cc_final: 0.8261 (mt) REVERT: W 6 ASN cc_start: 0.6984 (m-40) cc_final: 0.6020 (t0) REVERT: W 64 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7724 (m-40) REVERT: W 70 ASP cc_start: 0.8608 (t0) cc_final: 0.8117 (p0) REVERT: W 91 ASN cc_start: 0.8998 (m-40) cc_final: 0.8764 (m110) REVERT: W 114 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.6797 (t) REVERT: W 119 THR cc_start: 0.5282 (OUTLIER) cc_final: 0.5026 (p) REVERT: W 148 VAL cc_start: 0.7116 (OUTLIER) cc_final: 0.6753 (m) REVERT: W 171 ILE cc_start: 0.8375 (mt) cc_final: 0.7619 (mt) REVERT: W 172 SER cc_start: 0.7592 (OUTLIER) cc_final: 0.6691 (m) REVERT: X 80 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8635 (mt) REVERT: Y 10 LYS cc_start: 0.8845 (tttt) cc_final: 0.8621 (tttt) REVERT: Y 24 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8905 (mtp180) REVERT: Y 46 LYS cc_start: 0.8769 (mttt) cc_final: 0.8543 (mttt) REVERT: Y 50 ASN cc_start: 0.8528 (m-40) cc_final: 0.8314 (m-40) REVERT: Z 15 ASP cc_start: 0.8487 (t0) cc_final: 0.8258 (t0) REVERT: Z 24 GLU cc_start: 0.8998 (tp30) cc_final: 0.8626 (mt-10) REVERT: Z 25 SER cc_start: 0.9252 (m) cc_final: 0.9049 (p) REVERT: Z 49 THR cc_start: 0.9090 (p) cc_final: 0.8889 (p) REVERT: a 7 THR cc_start: 0.9217 (m) cc_final: 0.8973 (p) REVERT: a 33 GLN cc_start: 0.8453 (mt0) cc_final: 0.8230 (mt0) REVERT: a 37 ARG cc_start: 0.8435 (mmt180) cc_final: 0.8055 (mtt-85) REVERT: a 48 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8482 (t0) REVERT: b 14 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8619 (mmt-90) REVERT: b 31 SER cc_start: 0.9260 (p) cc_final: 0.9037 (p) REVERT: c 6 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7326 (p0) REVERT: c 23 TYR cc_start: 0.8906 (m-80) cc_final: 0.8575 (m-80) REVERT: c 25 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8447 (p) REVERT: c 36 LEU cc_start: 0.8842 (tp) cc_final: 0.8591 (tp) REVERT: c 49 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8387 (mm-40) REVERT: d 15 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8755 (ttm-80) REVERT: e 11 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8615 (m) REVERT: e 47 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8443 (mtm110) REVERT: e 59 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8869 (t0) REVERT: f 16 VAL cc_start: 0.9490 (t) cc_final: 0.9215 (p) REVERT: g 1 MET cc_start: 0.8406 (tpp) cc_final: 0.7661 (tpp) REVERT: g 9 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.6249 (t80) REVERT: g 12 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7493 (p) REVERT: g 20 HIS cc_start: 0.7605 (t70) cc_final: 0.7173 (t-170) REVERT: g 25 ARG cc_start: 0.7890 (mmt180) cc_final: 0.7544 (mmt180) REVERT: g 28 LYS cc_start: 0.7777 (mmtp) cc_final: 0.7531 (ttmt) REVERT: g 32 THR cc_start: 0.7130 (OUTLIER) cc_final: 0.6767 (p) REVERT: BB 6 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7946 (ptpt) REVERT: BB 14 LYS cc_start: 0.9389 (tttt) cc_final: 0.9084 (tttm) REVERT: BB 27 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7299 (mt0) REVERT: BC 22 TRP cc_start: 0.8537 (p90) cc_final: 0.8189 (p90) REVERT: BC 31 TYR cc_start: 0.8689 (m-10) cc_final: 0.8141 (m-10) REVERT: BC 35 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8248 (m-30) REVERT: BC 59 THR cc_start: 0.5982 (p) cc_final: 0.5738 (p) REVERT: BC 65 VAL cc_start: 0.9001 (t) cc_final: 0.8786 (p) REVERT: BC 66 ASP cc_start: 0.7927 (m-30) cc_final: 0.7619 (m-30) REVERT: BC 68 HIS cc_start: 0.7819 (m90) cc_final: 0.7255 (m170) REVERT: BC 105 VAL cc_start: 0.6849 (m) cc_final: 0.6392 (p) REVERT: BC 106 LYS cc_start: 0.7710 (mttt) cc_final: 0.7345 (mmtt) REVERT: BC 109 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7590 (mp0) REVERT: BC 113 GLN cc_start: 0.8087 (tp40) cc_final: 0.7868 (tp40) REVERT: BC 133 MET cc_start: 0.8501 (mmm) cc_final: 0.8151 (mtt) REVERT: BC 166 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7248 (tm-30) REVERT: BC 167 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.7797 (p90) REVERT: BC 168 TYR cc_start: 0.8103 (m-80) cc_final: 0.7706 (m-10) REVERT: BC 169 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7886 (ptm-80) REVERT: BC 183 ASP cc_start: 0.8785 (t0) cc_final: 0.8274 (t0) REVERT: BC 184 TYR cc_start: 0.8929 (t80) cc_final: 0.8601 (t80) REVERT: BC 187 TYR cc_start: 0.8529 (t80) cc_final: 0.8230 (t80) REVERT: BD 19 LEU cc_start: 0.5026 (mt) cc_final: 0.4323 (mp) REVERT: BD 58 PHE cc_start: 0.7969 (m-10) cc_final: 0.7669 (m-10) REVERT: BD 63 MET cc_start: 0.8363 (mmp) cc_final: 0.8030 (mmp) REVERT: BD 64 GLU cc_start: 0.8097 (tp30) cc_final: 0.7577 (tp30) REVERT: BD 145 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.7034 (tp) REVERT: BE 41 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8657 (t) REVERT: BE 141 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7903 (mt-10) REVERT: BE 177 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7941 (pt0) REVERT: BF 2 ARG cc_start: 0.8570 (mtt180) cc_final: 0.8280 (mtt180) REVERT: BF 7 MET cc_start: 0.8527 (tpp) cc_final: 0.8190 (tpp) REVERT: BF 18 THR cc_start: 0.8569 (m) cc_final: 0.8090 (p) REVERT: BF 27 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8437 (mt) REVERT: BF 43 TRP cc_start: 0.7380 (OUTLIER) cc_final: 0.5863 (p-90) REVERT: BF 72 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8240 (p) REVERT: BF 77 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7794 (ttt-90) REVERT: BG 21 GLN cc_start: 0.8512 (pt0) cc_final: 0.8232 (pt0) REVERT: BG 77 SER cc_start: 0.8079 (p) cc_final: 0.7822 (m) REVERT: BG 85 TYR cc_start: 0.7299 (m-10) cc_final: 0.7078 (m-80) REVERT: BG 86 GLN cc_start: 0.8538 (mm-40) cc_final: 0.7861 (mm-40) REVERT: BG 99 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8995 (mt) REVERT: BG 106 ASN cc_start: 0.8946 (m110) cc_final: 0.8694 (m-40) REVERT: BG 108 SER cc_start: 0.8825 (m) cc_final: 0.8505 (t) REVERT: BG 122 ASN cc_start: 0.8113 (m-40) cc_final: 0.7841 (m-40) REVERT: BG 135 VAL cc_start: 0.8409 (OUTLIER) cc_final: 0.7364 (p) REVERT: BG 136 LYS cc_start: 0.8987 (tttt) cc_final: 0.8588 (tptp) REVERT: BG 143 LYS cc_start: 0.8746 (tttt) cc_final: 0.8415 (ttpp) REVERT: BG 151 PHE cc_start: 0.8553 (m-80) cc_final: 0.8263 (m-80) REVERT: BI 39 VAL cc_start: 0.9246 (t) cc_final: 0.9021 (t) REVERT: BI 48 PHE cc_start: 0.7491 (m-80) cc_final: 0.7111 (m-10) REVERT: BI 61 ASN cc_start: 0.8645 (m-40) cc_final: 0.8139 (t0) REVERT: BI 67 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8432 (mt) REVERT: BI 84 TYR cc_start: 0.7562 (m-80) cc_final: 0.7075 (m-80) REVERT: BI 105 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7724 (mtt180) REVERT: BI 110 VAL cc_start: 0.7644 (t) cc_final: 0.7407 (p) REVERT: BI 125 THR cc_start: 0.9023 (m) cc_final: 0.8730 (p) REVERT: BI 149 LYS cc_start: 0.7007 (pttt) cc_final: 0.6577 (pttt) REVERT: BJ 18 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8131 (tt) REVERT: BJ 24 LYS cc_start: 0.8025 (mttt) cc_final: 0.7814 (tptp) REVERT: BJ 32 THR cc_start: 0.7071 (OUTLIER) cc_final: 0.6860 (p) REVERT: BJ 62 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7833 (mtt-85) REVERT: BK 25 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8544 (m) REVERT: BK 116 VAL cc_start: 0.9146 (t) cc_final: 0.8868 (m) REVERT: BL 15 LYS cc_start: 0.7449 (mttt) cc_final: 0.7210 (mmmm) REVERT: BL 24 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8231 (mt) REVERT: BL 70 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5777 (mp0) REVERT: BL 89 ASP cc_start: 0.8165 (m-30) cc_final: 0.7933 (m-30) REVERT: BL 105 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7600 (mp10) REVERT: BM 13 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8443 (mmtp) REVERT: BM 21 TYR cc_start: 0.8111 (m-80) cc_final: 0.7623 (m-80) REVERT: BM 23 TYR cc_start: 0.8432 (t80) cc_final: 0.8230 (t80) REVERT: BM 59 TYR cc_start: 0.8809 (t80) cc_final: 0.8143 (t80) REVERT: BM 77 ASP cc_start: 0.8363 (m-30) cc_final: 0.7914 (m-30) REVERT: BM 78 ILE cc_start: 0.8735 (mt) cc_final: 0.8438 (mm) REVERT: BN 25 ASN cc_start: 0.9298 (m110) cc_final: 0.8804 (m110) REVERT: BN 26 LYS cc_start: 0.8578 (tttt) cc_final: 0.8221 (mtpt) REVERT: BO 8 LYS cc_start: 0.8513 (mttt) cc_final: 0.8253 (mttt) REVERT: BO 11 ILE cc_start: 0.9519 (mm) cc_final: 0.9045 (mm) REVERT: BO 22 THR cc_start: 0.8946 (p) cc_final: 0.8728 (p) REVERT: BO 33 THR cc_start: 0.9327 (m) cc_final: 0.9025 (p) REVERT: BO 36 ILE cc_start: 0.9131 (mt) cc_final: 0.8712 (mp) REVERT: BO 46 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.8678 (m90) REVERT: BP 9 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7327 (tmt170) REVERT: BP 14 ARG cc_start: 0.7677 (mmt180) cc_final: 0.7289 (tpp80) REVERT: BP 24 ASP cc_start: 0.8901 (t70) cc_final: 0.8598 (t70) REVERT: BP 55 ARG cc_start: 0.8702 (mmt180) cc_final: 0.8387 (mmt180) REVERT: BP 90 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: BP 94 LYS cc_start: 0.6778 (mttt) cc_final: 0.6516 (tttt) REVERT: BQ 32 MET cc_start: 0.7259 (mtm) cc_final: 0.6913 (mpp) REVERT: BQ 49 TYR cc_start: 0.8660 (m-80) cc_final: 0.8373 (m-80) REVERT: BQ 73 ARG cc_start: 0.8206 (ttt180) cc_final: 0.7812 (ttp80) REVERT: BQ 93 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.6738 (tt) REVERT: BQ 95 GLU cc_start: 0.7296 (tt0) cc_final: 0.6950 (tm-30) REVERT: BR 34 ASP cc_start: 0.8053 (m-30) cc_final: 0.7782 (t0) REVERT: BS 3 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7913 (ttt180) REVERT: BS 16 LEU cc_start: 0.8756 (tp) cc_final: 0.8078 (tp) REVERT: BS 22 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7594 (tp-100) REVERT: BS 44 PHE cc_start: 0.8419 (m-80) cc_final: 0.8185 (m-10) REVERT: BS 48 THR cc_start: 0.7650 (m) cc_final: 0.7204 (p) REVERT: BS 63 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7955 (p) REVERT: BS 78 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7633 (ptt-90) REVERT: BT 36 ARG cc_start: 0.8437 (mmt90) cc_final: 0.8163 (mmm-85) REVERT: BV 21 ARG cc_start: 0.7347 (mtt180) cc_final: 0.6939 (mmt180) REVERT: BV 27 MET cc_start: 0.7871 (mtp) cc_final: 0.7173 (mmm) REVERT: BV 34 ASP cc_start: 0.6184 (t0) cc_final: 0.5142 (p0) REVERT: BV 89 MET cc_start: 0.7211 (mmp) cc_final: 0.6761 (mmp) REVERT: BV 106 THR cc_start: 0.8626 (m) cc_final: 0.8274 (p) REVERT: BV 113 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7724 (tpt-90) REVERT: BV 116 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6750 (tm-30) REVERT: BV 143 LYS cc_start: 0.5226 (mttt) cc_final: 0.4931 (mttm) REVERT: BV 165 ASP cc_start: 0.5429 (t0) cc_final: 0.5171 (t0) REVERT: BV 167 ASN cc_start: 0.6902 (OUTLIER) cc_final: 0.6529 (t160) REVERT: BV 169 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6846 (tp30) REVERT: BV 204 ASP cc_start: 0.4754 (p0) cc_final: 0.4525 (p0) REVERT: BV 217 ILE cc_start: 0.7673 (tt) cc_final: 0.7418 (pt) outliers start: 539 outliers final: 173 residues processed: 2385 average time/residue: 1.4245 time to fit residues: 5668.7460 Evaluate side-chains 1744 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1498 time to evaluate : 6.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 127 PRO Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 137 HIS Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 43 ARG Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 105 ARG Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 51 ARG Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 82 ARG Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 24 ARG Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 79 ASN Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 72 LYS Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 104 ARG Chi-restraints excluded: chain U residue 20 SER Chi-restraints excluded: chain V residue 38 VAL Chi-restraints excluded: chain V residue 91 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain W residue 172 SER Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain Y residue 24 ARG Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 45 ASN Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain a residue 48 ASN Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 14 ARG Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 12 THR Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain e residue 11 SER Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 59 ASN Chi-restraints excluded: chain g residue 9 TYR Chi-restraints excluded: chain g residue 12 THR Chi-restraints excluded: chain g residue 32 THR Chi-restraints excluded: chain BB residue 4 VAL Chi-restraints excluded: chain BB residue 6 LYS Chi-restraints excluded: chain BB residue 27 GLN Chi-restraints excluded: chain BC residue 35 ASP Chi-restraints excluded: chain BC residue 103 LEU Chi-restraints excluded: chain BC residue 153 CYS Chi-restraints excluded: chain BC residue 167 PHE Chi-restraints excluded: chain BC residue 169 ARG Chi-restraints excluded: chain BC residue 182 ILE Chi-restraints excluded: chain BD residue 20 VAL Chi-restraints excluded: chain BD residue 86 LEU Chi-restraints excluded: chain BD residue 123 VAL Chi-restraints excluded: chain BD residue 145 LEU Chi-restraints excluded: chain BD residue 177 VAL Chi-restraints excluded: chain BE residue 37 ILE Chi-restraints excluded: chain BE residue 41 VAL Chi-restraints excluded: chain BE residue 91 GLU Chi-restraints excluded: chain BE residue 97 PHE Chi-restraints excluded: chain BE residue 110 VAL Chi-restraints excluded: chain BF residue 27 LEU Chi-restraints excluded: chain BF residue 43 TRP Chi-restraints excluded: chain BF residue 57 GLU Chi-restraints excluded: chain BF residue 72 VAL Chi-restraints excluded: chain BF residue 77 ARG Chi-restraints excluded: chain BF residue 91 LEU Chi-restraints excluded: chain BG residue 27 VAL Chi-restraints excluded: chain BG residue 99 LEU Chi-restraints excluded: chain BG residue 102 ARG Chi-restraints excluded: chain BG residue 135 VAL Chi-restraints excluded: chain BH residue 36 ILE Chi-restraints excluded: chain BH residue 92 THR Chi-restraints excluded: chain BI residue 37 VAL Chi-restraints excluded: chain BI residue 42 VAL Chi-restraints excluded: chain BI residue 67 LEU Chi-restraints excluded: chain BI residue 87 LEU Chi-restraints excluded: chain BI residue 105 ARG Chi-restraints excluded: chain BI residue 147 TYR Chi-restraints excluded: chain BJ residue 15 HIS Chi-restraints excluded: chain BJ residue 18 ILE Chi-restraints excluded: chain BJ residue 32 THR Chi-restraints excluded: chain BJ residue 50 CYS Chi-restraints excluded: chain BJ residue 97 ASP Chi-restraints excluded: chain BK residue 25 VAL Chi-restraints excluded: chain BK residue 40 ILE Chi-restraints excluded: chain BK residue 91 VAL Chi-restraints excluded: chain BL residue 3 THR Chi-restraints excluded: chain BL residue 19 VAL Chi-restraints excluded: chain BL residue 21 THR Chi-restraints excluded: chain BL residue 24 LEU Chi-restraints excluded: chain BL residue 27 SER Chi-restraints excluded: chain BL residue 38 TYR Chi-restraints excluded: chain BL residue 39 THR Chi-restraints excluded: chain BL residue 49 LEU Chi-restraints excluded: chain BL residue 70 GLU Chi-restraints excluded: chain BL residue 104 THR Chi-restraints excluded: chain BM residue 5 VAL Chi-restraints excluded: chain BM residue 51 ASP Chi-restraints excluded: chain BM residue 56 LEU Chi-restraints excluded: chain BM residue 60 ILE Chi-restraints excluded: chain BM residue 109 THR Chi-restraints excluded: chain BN residue 24 CYS Chi-restraints excluded: chain BO residue 46 HIS Chi-restraints excluded: chain BO residue 75 VAL Chi-restraints excluded: chain BO residue 82 ILE Chi-restraints excluded: chain BO residue 89 ARG Chi-restraints excluded: chain BP residue 3 VAL Chi-restraints excluded: chain BP residue 9 ARG Chi-restraints excluded: chain BP residue 70 VAL Chi-restraints excluded: chain BP residue 86 LEU Chi-restraints excluded: chain BP residue 90 GLU Chi-restraints excluded: chain BQ residue 28 VAL Chi-restraints excluded: chain BQ residue 74 VAL Chi-restraints excluded: chain BQ residue 93 ILE Chi-restraints excluded: chain BR residue 21 VAL Chi-restraints excluded: chain BS residue 3 ARG Chi-restraints excluded: chain BS residue 12 ASP Chi-restraints excluded: chain BS residue 63 THR Chi-restraints excluded: chain BS residue 67 VAL Chi-restraints excluded: chain BS residue 78 ARG Chi-restraints excluded: chain BT residue 50 LEU Chi-restraints excluded: chain BT residue 51 LEU Chi-restraints excluded: chain BV residue 4 VAL Chi-restraints excluded: chain BV residue 38 ILE Chi-restraints excluded: chain BV residue 66 THR Chi-restraints excluded: chain BV residue 79 SER Chi-restraints excluded: chain BV residue 113 ARG Chi-restraints excluded: chain BV residue 157 VAL Chi-restraints excluded: chain BV residue 167 ASN Chi-restraints excluded: chain BV residue 169 GLU Chi-restraints excluded: chain BV residue 186 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 898 optimal weight: 6.9990 chunk 806 optimal weight: 30.0000 chunk 447 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 543 optimal weight: 8.9990 chunk 430 optimal weight: 20.0000 chunk 833 optimal weight: 8.9990 chunk 322 optimal weight: 20.0000 chunk 507 optimal weight: 20.0000 chunk 620 optimal weight: 8.9990 chunk 966 optimal weight: 30.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 17 ASN 3 18 HIS C 38 HIS C 76 ASN C 87 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS C 205 ASN D 20 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 HIS D 145 HIS D 179 ASN E 125 HIS E 176 HIS E 208 ASN F 187 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN H 28 ASN H 147 ASN J 33 HIS K 77 HIS K 103 ASN K 132 HIS M 58 HIS M 127 ASN N 17 GLN N 46 GLN O 17 GLN Q 79 ASN R 11 GLN R 41 HIS ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 122 ASN S 67 HIS S 76 HIS S 85 HIS ** T 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 61 ASN V 67 HIS W 6 ASN W 46 HIS W 91 ASN W 94 HIS W 156 GLN X 29 GLN X 44 HIS Y 22 HIS Y 45 ASN Z 44 ASN c 48 HIS e 25 GLN e 31 HIS e 59 ASN e 63 ASN BC 122 GLN BC 138 GLN BD 51 GLN ** BD 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BD 193 GLN BE 95 ASN BE 160 ASN BG 28 ASN BG 142 HIS ** BI 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 57 ASN BI 64 HIS BI 146 GLN BJ 70 HIS BK 27 HIS BK 58 HIS BK 110 GLN BL 29 GLN ** BL 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BM 52 GLN BM 101 GLN BN 11 ASN BN 31 HIS BO 28 GLN BO 37 GLN BP 17 GLN BP 41 HIS BP 57 GLN BQ 46 HIS BS 52 HIS BS 57 HIS BT 22 GLN BT 68 HIS BT 70 ASN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 163913 Z= 0.285 Angle : 0.683 10.371 245455 Z= 0.350 Chirality : 0.040 0.395 31408 Planarity : 0.006 0.083 13199 Dihedral : 24.618 179.936 83231 Min Nonbonded Distance : 1.245 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.89 % Rotamer: Outliers : 8.18 % Allowed : 19.42 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.10), residues: 5979 helix: -0.36 (0.11), residues: 2051 sheet: -0.44 (0.13), residues: 1228 loop : -1.22 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPBF 43 HIS 0.014 0.001 HIS W 86 PHE 0.025 0.002 PHEBV 32 TYR 0.018 0.002 TYR D 95 ARG 0.015 0.001 ARG g 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2038 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 404 poor density : 1634 time to evaluate : 6.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 8 LYS cc_start: 0.8725 (mttt) cc_final: 0.8453 (mttt) REVERT: C 28 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8225 (p) REVERT: C 62 TYR cc_start: 0.9108 (t80) cc_final: 0.8835 (t80) REVERT: C 63 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8858 (mtt90) REVERT: C 99 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7764 (p0) REVERT: C 122 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8242 (t0) REVERT: C 135 ASN cc_start: 0.9259 (OUTLIER) cc_final: 0.9036 (m-40) REVERT: D 56 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8398 (tp30) REVERT: D 58 SER cc_start: 0.8921 (m) cc_final: 0.8539 (p) REVERT: D 86 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8448 (mt) REVERT: D 88 ASP cc_start: 0.8048 (p0) cc_final: 0.7801 (p0) REVERT: D 100 GLU cc_start: 0.8659 (tp30) cc_final: 0.8409 (tp30) REVERT: E 26 ASP cc_start: 0.8290 (t0) cc_final: 0.7994 (t0) REVERT: E 28 GLU cc_start: 0.8195 (tp30) cc_final: 0.7857 (tp30) REVERT: E 67 ARG cc_start: 0.8632 (mmt90) cc_final: 0.8416 (mmt90) REVERT: E 106 MET cc_start: 0.8771 (mtp) cc_final: 0.8561 (mtm) REVERT: E 163 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7948 (mp0) REVERT: E 192 ASP cc_start: 0.7922 (m-30) cc_final: 0.7559 (m-30) REVERT: F 44 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8681 (t0) REVERT: F 45 MET cc_start: 0.7676 (mtp) cc_final: 0.7346 (mtt) REVERT: F 52 ARG cc_start: 0.7097 (mtt180) cc_final: 0.6771 (mmt-90) REVERT: F 63 ASP cc_start: 0.8116 (m-30) cc_final: 0.7905 (m-30) REVERT: F 105 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8213 (mt-10) REVERT: F 142 GLN cc_start: 0.8759 (pm20) cc_final: 0.8444 (pp30) REVERT: F 159 MET cc_start: 0.8891 (pmm) cc_final: 0.8628 (pmm) REVERT: G 23 ASN cc_start: 0.8104 (t0) cc_final: 0.7840 (t0) REVERT: G 88 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7656 (mmt) REVERT: G 90 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8647 (mm) REVERT: G 115 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7858 (mm) REVERT: G 171 ARG cc_start: 0.8390 (ptp-110) cc_final: 0.8174 (ptt-90) REVERT: H 6 THR cc_start: 0.8080 (m) cc_final: 0.7305 (p) REVERT: H 143 LYS cc_start: 0.8443 (mttt) cc_final: 0.8240 (tppt) REVERT: I 49 TYR cc_start: 0.5210 (t80) cc_final: 0.4873 (t80) REVERT: J 45 ASN cc_start: 0.4883 (m-40) cc_final: 0.4607 (t0) REVERT: J 79 LYS cc_start: 0.5652 (mmtt) cc_final: 0.4956 (mmtm) REVERT: K 37 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8357 (ttt180) REVERT: K 85 ARG cc_start: 0.8741 (ptm-80) cc_final: 0.8537 (ptt90) REVERT: L 1 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8112 (tpp) REVERT: L 28 SER cc_start: 0.8841 (p) cc_final: 0.8631 (t) REVERT: M 31 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8643 (pttp) REVERT: M 105 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7781 (mmm-85) REVERT: M 138 THR cc_start: 0.8680 (m) cc_final: 0.8461 (p) REVERT: O 110 MET cc_start: 0.8152 (mtp) cc_final: 0.7747 (mtt) REVERT: O 115 LEU cc_start: 0.9054 (mp) cc_final: 0.8837 (mp) REVERT: P 69 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7810 (p0) REVERT: P 118 ASP cc_start: 0.8818 (m-30) cc_final: 0.8321 (p0) REVERT: P 122 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7804 (mm-30) REVERT: Q 93 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8853 (mmp80) REVERT: R 42 SER cc_start: 0.9064 (t) cc_final: 0.8572 (m) REVERT: R 63 SER cc_start: 0.9308 (m) cc_final: 0.8944 (m) REVERT: R 102 ASP cc_start: 0.8153 (t0) cc_final: 0.7805 (t0) REVERT: S 87 ARG cc_start: 0.8716 (mtt90) cc_final: 0.8417 (mtt90) REVERT: T 35 SER cc_start: 0.9226 (p) cc_final: 0.8940 (t) REVERT: T 56 LYS cc_start: 0.9097 (mttt) cc_final: 0.8635 (mttm) REVERT: T 93 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8593 (ttm170) REVERT: T 115 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7910 (mt-10) REVERT: U 50 PHE cc_start: 0.8671 (m-80) cc_final: 0.8397 (m-10) REVERT: W 6 ASN cc_start: 0.7327 (m110) cc_final: 0.5957 (t0) REVERT: W 59 ARG cc_start: 0.8804 (mtm-85) cc_final: 0.8340 (ttm-80) REVERT: W 70 ASP cc_start: 0.8639 (t0) cc_final: 0.7946 (p0) REVERT: W 89 ARG cc_start: 0.8559 (mtm-85) cc_final: 0.8321 (mtm-85) REVERT: X 37 LEU cc_start: 0.8976 (mt) cc_final: 0.8734 (mt) REVERT: Y 10 LYS cc_start: 0.8538 (tttt) cc_final: 0.8266 (tttt) REVERT: Y 24 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8780 (mtm180) REVERT: Z 9 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7622 (mt-10) REVERT: Z 11 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7746 (mtt180) REVERT: Z 19 LYS cc_start: 0.9026 (mttt) cc_final: 0.8748 (mttt) REVERT: Z 23 ARG cc_start: 0.8642 (mtm180) cc_final: 0.8313 (mtt90) REVERT: Z 24 GLU cc_start: 0.8901 (tp30) cc_final: 0.8360 (tp30) REVERT: a 5 LYS cc_start: 0.8904 (ttmm) cc_final: 0.8445 (ttmm) REVERT: a 16 ARG cc_start: 0.8696 (mtt-85) cc_final: 0.8449 (mtm180) REVERT: a 37 ARG cc_start: 0.8539 (mmt180) cc_final: 0.8297 (mtp85) REVERT: a 48 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8358 (t0) REVERT: b 31 SER cc_start: 0.9291 (p) cc_final: 0.9029 (p) REVERT: c 25 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8576 (p) REVERT: c 49 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8438 (mm-40) REVERT: d 15 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8337 (ttt-90) REVERT: e 15 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8367 (ttt180) REVERT: e 47 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8467 (mtm110) REVERT: g 1 MET cc_start: 0.8171 (tpp) cc_final: 0.7750 (tpp) REVERT: g 9 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.6650 (t80) REVERT: g 25 ARG cc_start: 0.7999 (mmt180) cc_final: 0.7461 (mmt180) REVERT: g 32 THR cc_start: 0.6952 (OUTLIER) cc_final: 0.6632 (p) REVERT: g 60 ARG cc_start: 0.7271 (tpm170) cc_final: 0.6399 (tpm170) REVERT: BB 6 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8057 (ptpt) REVERT: BB 27 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7424 (mt0) REVERT: BC 23 TYR cc_start: 0.7371 (t80) cc_final: 0.6722 (t80) REVERT: BC 31 TYR cc_start: 0.8794 (m-10) cc_final: 0.8115 (m-10) REVERT: BC 35 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: BC 57 GLU cc_start: 0.7760 (mp0) cc_final: 0.7297 (mp0) REVERT: BC 96 LYS cc_start: 0.7612 (mttp) cc_final: 0.7178 (mmtt) REVERT: BC 97 GLN cc_start: 0.6782 (tm-30) cc_final: 0.6247 (tm-30) REVERT: BC 99 GLN cc_start: 0.8185 (tt0) cc_final: 0.7828 (tt0) REVERT: BC 105 VAL cc_start: 0.7060 (m) cc_final: 0.6733 (p) REVERT: BC 106 LYS cc_start: 0.7642 (mttt) cc_final: 0.7402 (mmtt) REVERT: BC 117 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8390 (mm-40) REVERT: BC 124 SER cc_start: 0.8406 (t) cc_final: 0.8128 (m) REVERT: BC 168 TYR cc_start: 0.8141 (m-80) cc_final: 0.7776 (m-10) REVERT: BC 183 ASP cc_start: 0.8483 (t0) cc_final: 0.8089 (t0) REVERT: BC 184 TYR cc_start: 0.8947 (t80) cc_final: 0.8669 (t80) REVERT: BC 187 TYR cc_start: 0.8451 (t80) cc_final: 0.8025 (t80) REVERT: BD 59 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8270 (p) REVERT: BD 63 MET cc_start: 0.8224 (mmp) cc_final: 0.7922 (mmp) REVERT: BD 64 GLU cc_start: 0.8111 (tp30) cc_final: 0.7376 (tp30) REVERT: BD 72 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7553 (tm-30) REVERT: BD 73 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6596 (mm-30) REVERT: BD 98 TYR cc_start: 0.7091 (t80) cc_final: 0.6867 (t80) REVERT: BD 139 ASP cc_start: 0.7306 (m-30) cc_final: 0.7069 (m-30) REVERT: BD 199 TYR cc_start: 0.7130 (m-80) cc_final: 0.5973 (m-80) REVERT: BE 97 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8254 (p90) REVERT: BE 176 GLU cc_start: 0.8615 (pm20) cc_final: 0.8415 (pm20) REVERT: BE 196 LYS cc_start: 0.8274 (mttp) cc_final: 0.8060 (mmtm) REVERT: BF 2 ARG cc_start: 0.8341 (mtt180) cc_final: 0.7994 (mtt180) REVERT: BF 27 LEU cc_start: 0.8842 (tp) cc_final: 0.8608 (tp) REVERT: BF 72 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8565 (p) REVERT: BF 74 GLU cc_start: 0.8163 (tp30) cc_final: 0.7455 (tp30) REVERT: BF 78 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8078 (mm-40) REVERT: BG 48 GLU cc_start: 0.7658 (mm-30) cc_final: 0.6542 (mm-30) REVERT: BG 52 GLU cc_start: 0.7521 (mp0) cc_final: 0.7035 (mp0) REVERT: BG 85 TYR cc_start: 0.7132 (m-10) cc_final: 0.6665 (m-80) REVERT: BG 86 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7699 (mm-40) REVERT: BG 102 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.6451 (ttp-110) REVERT: BG 118 GLU cc_start: 0.8711 (tp30) cc_final: 0.7136 (tp30) REVERT: BG 122 ASN cc_start: 0.7896 (m-40) cc_final: 0.7011 (m-40) REVERT: BG 141 THR cc_start: 0.8454 (m) cc_final: 0.8172 (p) REVERT: BG 143 LYS cc_start: 0.8796 (tttt) cc_final: 0.8521 (ttpp) REVERT: BH 41 LYS cc_start: 0.9189 (tttp) cc_final: 0.8928 (tttp) REVERT: BI 75 VAL cc_start: 0.8409 (p) cc_final: 0.8182 (m) REVERT: BI 105 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7996 (mtt180) REVERT: BI 125 THR cc_start: 0.8897 (m) cc_final: 0.8634 (p) REVERT: BI 132 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8015 (mt-10) REVERT: BI 136 TYR cc_start: 0.8960 (p90) cc_final: 0.8709 (p90) REVERT: BJ 23 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7424 (mmt180) REVERT: BK 65 ARG cc_start: 0.9109 (ttm110) cc_final: 0.8890 (ttm110) REVERT: BL 58 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8358 (t) REVERT: BL 59 SER cc_start: 0.8936 (m) cc_final: 0.8611 (t) REVERT: BL 70 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5855 (mp0) REVERT: BL 105 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7704 (mp10) REVERT: BM 13 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8508 (mmtp) REVERT: BM 32 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7598 (tm-30) REVERT: BM 59 TYR cc_start: 0.8562 (t80) cc_final: 0.8256 (t80) REVERT: BM 73 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8512 (tm-30) REVERT: BM 77 ASP cc_start: 0.8160 (m-30) cc_final: 0.7739 (m-30) REVERT: BN 25 ASN cc_start: 0.9074 (m110) cc_final: 0.8679 (m110) REVERT: BO 8 LYS cc_start: 0.8616 (mttt) cc_final: 0.8296 (mttt) REVERT: BO 10 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8001 (tm-30) REVERT: BO 14 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8115 (tm-30) REVERT: BO 26 GLU cc_start: 0.8437 (mp0) cc_final: 0.8078 (mp0) REVERT: BP 32 ARG cc_start: 0.8510 (ttm-80) cc_final: 0.8296 (ttm-80) REVERT: BP 39 ARG cc_start: 0.8703 (ptp90) cc_final: 0.8445 (ptp90) REVERT: BP 50 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8030 (mt0) REVERT: BP 51 ILE cc_start: 0.8959 (mm) cc_final: 0.8755 (mm) REVERT: BP 55 ARG cc_start: 0.8569 (mmt180) cc_final: 0.8239 (mmt180) REVERT: BQ 32 MET cc_start: 0.7415 (mtm) cc_final: 0.7174 (mpp) REVERT: BQ 49 TYR cc_start: 0.8530 (m-80) cc_final: 0.8301 (m-80) REVERT: BQ 77 MET cc_start: 0.7930 (tmm) cc_final: 0.7708 (tpp) REVERT: BR 34 ASP cc_start: 0.8367 (m-30) cc_final: 0.8038 (t0) REVERT: BS 16 LEU cc_start: 0.8711 (tp) cc_final: 0.8454 (tp) REVERT: BS 48 THR cc_start: 0.7627 (m) cc_final: 0.7226 (p) REVERT: BS 61 PHE cc_start: 0.8017 (t80) cc_final: 0.7769 (t80) REVERT: BS 63 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8002 (p) REVERT: BS 78 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.6891 (ptt-90) REVERT: BV 57 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7581 (m) REVERT: BV 59 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6408 (tm-30) REVERT: BV 89 MET cc_start: 0.7305 (mmp) cc_final: 0.6881 (mmp) REVERT: BV 134 ILE cc_start: 0.2812 (OUTLIER) cc_final: 0.2019 (tp) REVERT: BV 168 LYS cc_start: 0.7814 (tptt) cc_final: 0.7525 (ttmm) REVERT: BV 169 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7166 (tp30) REVERT: BV 175 GLU cc_start: 0.6196 (mt-10) cc_final: 0.5354 (mt-10) outliers start: 404 outliers final: 241 residues processed: 1880 average time/residue: 1.4511 time to fit residues: 4645.3801 Evaluate side-chains 1713 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1431 time to evaluate : 5.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 44 ASN Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 105 ARG Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 91 ASN Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 24 ARG Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 93 ARG Chi-restraints excluded: chain T residue 109 HIS Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 38 VAL Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 91 ASN Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 24 ARG Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 48 ASN Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain e residue 15 ARG Chi-restraints excluded: chain e residue 25 GLN Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 56 SER Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 9 TYR Chi-restraints excluded: chain g residue 32 THR Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain BB residue 4 VAL Chi-restraints excluded: chain BB residue 6 LYS Chi-restraints excluded: chain BB residue 13 SER Chi-restraints excluded: chain BB residue 27 GLN Chi-restraints excluded: chain BC residue 35 ASP Chi-restraints excluded: chain BC residue 67 ILE Chi-restraints excluded: chain BC residue 74 ILE Chi-restraints excluded: chain BC residue 119 VAL Chi-restraints excluded: chain BC residue 182 ILE Chi-restraints excluded: chain BD residue 20 VAL Chi-restraints excluded: chain BD residue 59 SER Chi-restraints excluded: chain BD residue 123 VAL Chi-restraints excluded: chain BD residue 145 LEU Chi-restraints excluded: chain BD residue 177 VAL Chi-restraints excluded: chain BE residue 71 VAL Chi-restraints excluded: chain BE residue 73 VAL Chi-restraints excluded: chain BE residue 81 VAL Chi-restraints excluded: chain BE residue 97 PHE Chi-restraints excluded: chain BF residue 37 VAL Chi-restraints excluded: chain BF residue 43 TRP Chi-restraints excluded: chain BF residue 57 GLU Chi-restraints excluded: chain BF residue 72 VAL Chi-restraints excluded: chain BF residue 73 SER Chi-restraints excluded: chain BG residue 27 VAL Chi-restraints excluded: chain BG residue 102 ARG Chi-restraints excluded: chain BG residue 111 ARG Chi-restraints excluded: chain BG residue 135 VAL Chi-restraints excluded: chain BH residue 4 THR Chi-restraints excluded: chain BH residue 36 ILE Chi-restraints excluded: chain BH residue 92 THR Chi-restraints excluded: chain BI residue 28 THR Chi-restraints excluded: chain BI residue 42 VAL Chi-restraints excluded: chain BI residue 103 ILE Chi-restraints excluded: chain BI residue 105 ARG Chi-restraints excluded: chain BI residue 146 GLN Chi-restraints excluded: chain BI residue 147 TYR Chi-restraints excluded: chain BJ residue 15 HIS Chi-restraints excluded: chain BJ residue 40 VAL Chi-restraints excluded: chain BJ residue 42 LEU Chi-restraints excluded: chain BJ residue 48 VAL Chi-restraints excluded: chain BJ residue 69 THR Chi-restraints excluded: chain BJ residue 80 THR Chi-restraints excluded: chain BJ residue 83 THR Chi-restraints excluded: chain BK residue 40 ILE Chi-restraints excluded: chain BK residue 44 THR Chi-restraints excluded: chain BK residue 67 SER Chi-restraints excluded: chain BK residue 68 THR Chi-restraints excluded: chain BK residue 74 LEU Chi-restraints excluded: chain BK residue 91 VAL Chi-restraints excluded: chain BK residue 108 SER Chi-restraints excluded: chain BK residue 120 SER Chi-restraints excluded: chain BL residue 3 THR Chi-restraints excluded: chain BL residue 21 THR Chi-restraints excluded: chain BL residue 34 CYS Chi-restraints excluded: chain BL residue 38 TYR Chi-restraints excluded: chain BL residue 41 THR Chi-restraints excluded: chain BL residue 49 LEU Chi-restraints excluded: chain BL residue 58 THR Chi-restraints excluded: chain BL residue 61 VAL Chi-restraints excluded: chain BL residue 70 GLU Chi-restraints excluded: chain BL residue 87 VAL Chi-restraints excluded: chain BL residue 104 THR Chi-restraints excluded: chain BM residue 51 ASP Chi-restraints excluded: chain BM residue 56 LEU Chi-restraints excluded: chain BM residue 60 ILE Chi-restraints excluded: chain BM residue 109 THR Chi-restraints excluded: chain BN residue 24 CYS Chi-restraints excluded: chain BN residue 37 PHE Chi-restraints excluded: chain BO residue 75 VAL Chi-restraints excluded: chain BO residue 80 SER Chi-restraints excluded: chain BO residue 82 ILE Chi-restraints excluded: chain BP residue 3 VAL Chi-restraints excluded: chain BP residue 15 ASN Chi-restraints excluded: chain BP residue 27 THR Chi-restraints excluded: chain BP residue 86 LEU Chi-restraints excluded: chain BP residue 110 LEU Chi-restraints excluded: chain BQ residue 28 VAL Chi-restraints excluded: chain BQ residue 55 THR Chi-restraints excluded: chain BQ residue 56 THR Chi-restraints excluded: chain BQ residue 65 ASN Chi-restraints excluded: chain BQ residue 72 ASP Chi-restraints excluded: chain BQ residue 74 VAL Chi-restraints excluded: chain BR residue 53 VAL Chi-restraints excluded: chain BS residue 12 ASP Chi-restraints excluded: chain BS residue 33 THR Chi-restraints excluded: chain BS residue 38 SER Chi-restraints excluded: chain BS residue 63 THR Chi-restraints excluded: chain BS residue 67 VAL Chi-restraints excluded: chain BS residue 78 ARG Chi-restraints excluded: chain BT residue 50 LEU Chi-restraints excluded: chain BT residue 51 LEU Chi-restraints excluded: chain BT residue 55 SER Chi-restraints excluded: chain BV residue 4 VAL Chi-restraints excluded: chain BV residue 38 ILE Chi-restraints excluded: chain BV residue 57 VAL Chi-restraints excluded: chain BV residue 66 THR Chi-restraints excluded: chain BV residue 68 LEU Chi-restraints excluded: chain BV residue 85 THR Chi-restraints excluded: chain BV residue 92 VAL Chi-restraints excluded: chain BV residue 117 LEU Chi-restraints excluded: chain BV residue 134 ILE Chi-restraints excluded: chain BV residue 157 VAL Chi-restraints excluded: chain BV residue 169 GLU Chi-restraints excluded: chain BV residue 186 ILE Chi-restraints excluded: chain BV residue 205 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 536 optimal weight: 20.0000 chunk 299 optimal weight: 20.0000 chunk 804 optimal weight: 30.0000 chunk 657 optimal weight: 8.9990 chunk 266 optimal weight: 20.0000 chunk 967 optimal weight: 10.0000 chunk 1045 optimal weight: 30.0000 chunk 862 optimal weight: 10.0000 chunk 959 optimal weight: 8.9990 chunk 329 optimal weight: 20.0000 chunk 776 optimal weight: 40.0000 overall best weight: 11.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN D 20 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN F 58 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 HIS K 117 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 HIS P 22 HIS R 72 ASN ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 ASN W 26 GLN W 86 HIS X 29 GLN Z 52 GLN ** e 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 122 GLN BC 138 GLN BC 176 HIS ** BD 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 106 ASN BG 142 HIS BI 61 ASN BI 146 GLN BJ 47 ASN BJ 99 ASN BK 110 GLN BL 29 GLN ** BL 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BM 101 GLN BO 37 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 163913 Z= 0.366 Angle : 0.690 9.450 245455 Z= 0.352 Chirality : 0.040 0.402 31408 Planarity : 0.006 0.079 13199 Dihedral : 24.540 179.771 83013 Min Nonbonded Distance : 0.950 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.87 % Favored : 96.12 % Rotamer: Outliers : 8.81 % Allowed : 21.08 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: -0.77 (0.10), residues: 5979 helix: 0.24 (0.11), residues: 2046 sheet: -0.40 (0.14), residues: 1221 loop : -1.06 (0.11), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPBF 43 HIS 0.008 0.002 HISBL 77 PHE 0.020 0.002 PHE G 91 TYR 0.023 0.002 TYR H 25 ARG 0.015 0.001 ARGBD 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1890 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 435 poor density : 1455 time to evaluate : 6.499 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: C 28 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8514 (p) REVERT: C 109 GLN cc_start: 0.9196 (tp40) cc_final: 0.8963 (tp40) REVERT: C 198 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8626 (m110) REVERT: C 237 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8034 (mm-30) REVERT: C 265 ASP cc_start: 0.8252 (m-30) cc_final: 0.7940 (m-30) REVERT: D 56 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8337 (tp30) REVERT: D 87 ASP cc_start: 0.8100 (m-30) cc_final: 0.7755 (m-30) REVERT: D 88 ASP cc_start: 0.7998 (p0) cc_final: 0.7724 (p0) REVERT: E 26 ASP cc_start: 0.8377 (t0) cc_final: 0.7987 (t0) REVERT: E 28 GLU cc_start: 0.8261 (tp30) cc_final: 0.7962 (tp30) REVERT: E 30 ASN cc_start: 0.8655 (t0) cc_final: 0.8268 (t0) REVERT: E 67 ARG cc_start: 0.8636 (mmt90) cc_final: 0.8368 (mmt90) REVERT: E 106 MET cc_start: 0.8830 (mtp) cc_final: 0.8595 (mtm) REVERT: E 192 ASP cc_start: 0.7974 (m-30) cc_final: 0.7640 (m-30) REVERT: F 13 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8230 (pp30) REVERT: F 45 MET cc_start: 0.8031 (mtp) cc_final: 0.7827 (mtt) REVERT: F 142 GLN cc_start: 0.8733 (pm20) cc_final: 0.8479 (pp30) REVERT: F 159 MET cc_start: 0.8888 (pmm) cc_final: 0.8641 (pmm) REVERT: G 88 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7255 (mmt) REVERT: G 89 GLU cc_start: 0.8313 (tp30) cc_final: 0.8080 (tp30) REVERT: G 90 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8649 (mm) REVERT: H 6 THR cc_start: 0.8115 (m) cc_final: 0.7289 (p) REVERT: H 25 TYR cc_start: 0.9048 (t80) cc_final: 0.8791 (t80) REVERT: H 137 HIS cc_start: 0.6667 (OUTLIER) cc_final: 0.6406 (t-170) REVERT: H 143 LYS cc_start: 0.8625 (mttt) cc_final: 0.8264 (tptm) REVERT: J 79 LYS cc_start: 0.5890 (mmtt) cc_final: 0.5410 (mmtm) REVERT: K 37 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8489 (ttt90) REVERT: K 102 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8219 (mt-10) REVERT: K 106 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8875 (mp) REVERT: L 1 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8140 (tpp) REVERT: M 24 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.7937 (tpp80) REVERT: M 105 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7918 (mmm-85) REVERT: M 138 THR cc_start: 0.8708 (m) cc_final: 0.8471 (p) REVERT: N 104 PHE cc_start: 0.8993 (m-80) cc_final: 0.8770 (m-80) REVERT: O 110 MET cc_start: 0.8295 (mtp) cc_final: 0.8078 (mtt) REVERT: O 115 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9017 (mp) REVERT: P 69 ASP cc_start: 0.8116 (p0) cc_final: 0.7817 (p0) REVERT: P 118 ASP cc_start: 0.8771 (m-30) cc_final: 0.8419 (m-30) REVERT: P 126 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7858 (mmtt) REVERT: R 18 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9053 (mm) REVERT: R 42 SER cc_start: 0.9161 (OUTLIER) cc_final: 0.8587 (m) REVERT: R 63 SER cc_start: 0.9310 (m) cc_final: 0.8966 (m) REVERT: R 102 ASP cc_start: 0.7903 (t0) cc_final: 0.7578 (t0) REVERT: S 51 LYS cc_start: 0.8369 (mmmt) cc_final: 0.8169 (ttmm) REVERT: T 42 ILE cc_start: 0.9489 (mt) cc_final: 0.9177 (tt) REVERT: T 56 LYS cc_start: 0.9094 (mttt) cc_final: 0.8791 (mttp) REVERT: T 93 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8635 (ttm170) REVERT: W 70 ASP cc_start: 0.8574 (t0) cc_final: 0.8150 (p0) REVERT: W 123 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8423 (mp) REVERT: Y 10 LYS cc_start: 0.8645 (tttt) cc_final: 0.8387 (mttt) REVERT: Z 23 ARG cc_start: 0.8466 (mtm180) cc_final: 0.7916 (mtt90) REVERT: a 5 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8538 (ttmm) REVERT: a 48 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8319 (t0) REVERT: b 6 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7617 (mtt90) REVERT: b 31 SER cc_start: 0.9363 (p) cc_final: 0.9096 (p) REVERT: c 25 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8617 (p) REVERT: c 54 SER cc_start: 0.8617 (t) cc_final: 0.8415 (p) REVERT: d 15 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8307 (ttm110) REVERT: e 47 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8644 (mtm110) REVERT: g 9 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.6606 (t80) REVERT: g 25 ARG cc_start: 0.8167 (mmt180) cc_final: 0.7289 (mmt180) REVERT: g 32 THR cc_start: 0.7118 (OUTLIER) cc_final: 0.6907 (p) REVERT: BB 6 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8272 (ptpt) REVERT: BB 22 ARG cc_start: 0.8131 (mmt180) cc_final: 0.7558 (mtt180) REVERT: BB 27 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7524 (mt0) REVERT: BC 31 TYR cc_start: 0.8739 (m-10) cc_final: 0.8195 (m-10) REVERT: BC 35 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: BC 51 ILE cc_start: 0.8843 (mt) cc_final: 0.8627 (mm) REVERT: BC 96 LYS cc_start: 0.7592 (mttp) cc_final: 0.7054 (mmtt) REVERT: BC 97 GLN cc_start: 0.6723 (tm-30) cc_final: 0.6264 (tm-30) REVERT: BC 117 GLN cc_start: 0.8854 (mm-40) cc_final: 0.7978 (mm-40) REVERT: BC 143 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8124 (mp10) REVERT: BC 166 GLU cc_start: 0.7574 (tp30) cc_final: 0.7042 (tm-30) REVERT: BC 183 ASP cc_start: 0.8536 (t0) cc_final: 0.8100 (t0) REVERT: BC 184 TYR cc_start: 0.8984 (t80) cc_final: 0.8659 (t80) REVERT: BC 187 TYR cc_start: 0.8587 (t80) cc_final: 0.7879 (t80) REVERT: BD 20 VAL cc_start: 0.7197 (t) cc_final: 0.6606 (p) REVERT: BD 64 GLU cc_start: 0.8297 (tp30) cc_final: 0.7994 (tp30) REVERT: BD 165 TRP cc_start: 0.7232 (p90) cc_final: 0.6779 (p90) REVERT: BD 182 GLU cc_start: 0.7782 (mp0) cc_final: 0.7358 (pm20) REVERT: BE 55 ARG cc_start: 0.8877 (mmm160) cc_final: 0.8565 (ttm-80) REVERT: BE 97 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8576 (p90) REVERT: BE 196 LYS cc_start: 0.8224 (mttp) cc_final: 0.7989 (mttp) REVERT: BF 27 LEU cc_start: 0.8953 (tp) cc_final: 0.8600 (tp) REVERT: BF 74 GLU cc_start: 0.8435 (tp30) cc_final: 0.7532 (tp30) REVERT: BF 78 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7468 (mm-40) REVERT: BF 80 ASN cc_start: 0.8750 (m-40) cc_final: 0.8515 (m-40) REVERT: BF 84 SER cc_start: 0.7979 (p) cc_final: 0.7617 (p) REVERT: BG 85 TYR cc_start: 0.7270 (m-10) cc_final: 0.6973 (m-80) REVERT: BG 86 GLN cc_start: 0.8533 (mm-40) cc_final: 0.7843 (mm-40) REVERT: BG 102 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.6128 (ttp-110) REVERT: BG 106 ASN cc_start: 0.8745 (m110) cc_final: 0.8526 (m110) REVERT: BG 122 ASN cc_start: 0.7723 (m-40) cc_final: 0.7500 (m-40) REVERT: BG 139 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8424 (tp30) REVERT: BG 141 THR cc_start: 0.8583 (m) cc_final: 0.8372 (p) REVERT: BG 143 LYS cc_start: 0.8738 (tttt) cc_final: 0.8445 (ttpp) REVERT: BG 151 PHE cc_start: 0.8110 (m-80) cc_final: 0.7793 (m-80) REVERT: BH 21 TYR cc_start: 0.8837 (m-10) cc_final: 0.8561 (m-80) REVERT: BH 41 LYS cc_start: 0.9277 (tttp) cc_final: 0.9070 (tttp) REVERT: BI 105 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7814 (mtt180) REVERT: BI 115 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7109 (tpt-90) REVERT: BK 77 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8547 (mm-30) REVERT: BK 90 LYS cc_start: 0.8473 (tptm) cc_final: 0.8263 (tptm) REVERT: BK 96 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8159 (ttpt) REVERT: BL 18 LYS cc_start: 0.7628 (tttt) cc_final: 0.7280 (tptm) REVERT: BL 58 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8339 (p) REVERT: BL 59 SER cc_start: 0.9038 (m) cc_final: 0.8681 (t) REVERT: BL 95 TYR cc_start: 0.9108 (m-80) cc_final: 0.8804 (m-80) REVERT: BM 23 TYR cc_start: 0.8292 (t80) cc_final: 0.8023 (t80) REVERT: BM 59 TYR cc_start: 0.8768 (t80) cc_final: 0.8434 (t80) REVERT: BM 73 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8412 (tm-30) REVERT: BM 77 ASP cc_start: 0.8186 (m-30) cc_final: 0.7624 (m-30) REVERT: BM 117 ILE cc_start: 0.6258 (OUTLIER) cc_final: 0.5732 (mm) REVERT: BN 25 ASN cc_start: 0.9194 (m110) cc_final: 0.8804 (m110) REVERT: BO 8 LYS cc_start: 0.8506 (mttt) cc_final: 0.8174 (mttm) REVERT: BO 10 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8177 (tm-30) REVERT: BO 26 GLU cc_start: 0.8379 (mp0) cc_final: 0.8122 (mp0) REVERT: BQ 27 VAL cc_start: 0.9108 (t) cc_final: 0.8720 (p) REVERT: BQ 32 MET cc_start: 0.7633 (mtm) cc_final: 0.7350 (mpp) REVERT: BR 19 LYS cc_start: 0.8473 (mtmt) cc_final: 0.8262 (mmtm) REVERT: BR 26 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7312 (mptt) REVERT: BS 16 LEU cc_start: 0.8703 (tp) cc_final: 0.8039 (tp) REVERT: BS 18 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8472 (mtmm) REVERT: BS 48 THR cc_start: 0.8016 (m) cc_final: 0.7756 (p) REVERT: BS 63 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8044 (m) REVERT: BS 78 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.6867 (ptt-90) REVERT: BT 22 GLN cc_start: 0.9077 (tt0) cc_final: 0.8831 (tt0) REVERT: BT 75 LYS cc_start: 0.9040 (mmtp) cc_final: 0.8703 (mmmt) REVERT: BT 85 LYS cc_start: 0.8043 (ttpp) cc_final: 0.7821 (ttpp) REVERT: BV 23 TRP cc_start: 0.7901 (OUTLIER) cc_final: 0.7352 (p-90) REVERT: BV 57 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7608 (m) REVERT: BV 82 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6385 (pt0) REVERT: BV 109 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8453 (mmmt) REVERT: BV 168 LYS cc_start: 0.7820 (tptt) cc_final: 0.7482 (ttmm) outliers start: 435 outliers final: 291 residues processed: 1725 average time/residue: 1.3900 time to fit residues: 4092.3365 Evaluate side-chains 1707 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1374 time to evaluate : 6.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 137 HIS Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 105 ARG Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 93 ARG Chi-restraints excluded: chain T residue 99 ARG Chi-restraints excluded: chain T residue 109 HIS Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 38 VAL Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 123 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 48 ASN Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 15 SER Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 56 SER Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 5 ILE Chi-restraints excluded: chain g residue 9 TYR Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 32 THR Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain BB residue 4 VAL Chi-restraints excluded: chain BB residue 6 LYS Chi-restraints excluded: chain BB residue 27 GLN Chi-restraints excluded: chain BC residue 14 ILE Chi-restraints excluded: chain BC residue 16 THR Chi-restraints excluded: chain BC residue 35 ASP Chi-restraints excluded: chain BC residue 59 THR Chi-restraints excluded: chain BC residue 67 ILE Chi-restraints excluded: chain BC residue 141 MET Chi-restraints excluded: chain BC residue 143 GLN Chi-restraints excluded: chain BC residue 202 ILE Chi-restraints excluded: chain BD residue 93 LEU Chi-restraints excluded: chain BD residue 123 VAL Chi-restraints excluded: chain BD residue 145 LEU Chi-restraints excluded: chain BD residue 177 VAL Chi-restraints excluded: chain BE residue 71 VAL Chi-restraints excluded: chain BE residue 73 VAL Chi-restraints excluded: chain BE residue 81 VAL Chi-restraints excluded: chain BE residue 97 PHE Chi-restraints excluded: chain BE residue 110 VAL Chi-restraints excluded: chain BF residue 23 LEU Chi-restraints excluded: chain BF residue 42 ILE Chi-restraints excluded: chain BF residue 43 TRP Chi-restraints excluded: chain BF residue 57 GLU Chi-restraints excluded: chain BF residue 73 SER Chi-restraints excluded: chain BG residue 27 VAL Chi-restraints excluded: chain BG residue 53 LYS Chi-restraints excluded: chain BG residue 102 ARG Chi-restraints excluded: chain BG residue 108 SER Chi-restraints excluded: chain BG residue 124 ILE Chi-restraints excluded: chain BG residue 135 VAL Chi-restraints excluded: chain BG residue 139 GLU Chi-restraints excluded: chain BH residue 4 THR Chi-restraints excluded: chain BH residue 36 ILE Chi-restraints excluded: chain BH residue 51 THR Chi-restraints excluded: chain BH residue 87 VAL Chi-restraints excluded: chain BH residue 92 THR Chi-restraints excluded: chain BH residue 108 THR Chi-restraints excluded: chain BI residue 28 THR Chi-restraints excluded: chain BI residue 36 VAL Chi-restraints excluded: chain BI residue 103 ILE Chi-restraints excluded: chain BI residue 105 ARG Chi-restraints excluded: chain BI residue 115 ARG Chi-restraints excluded: chain BI residue 120 LYS Chi-restraints excluded: chain BI residue 147 TYR Chi-restraints excluded: chain BJ residue 37 VAL Chi-restraints excluded: chain BJ residue 42 LEU Chi-restraints excluded: chain BJ residue 50 CYS Chi-restraints excluded: chain BJ residue 69 THR Chi-restraints excluded: chain BJ residue 76 ILE Chi-restraints excluded: chain BJ residue 78 ASP Chi-restraints excluded: chain BJ residue 80 THR Chi-restraints excluded: chain BK residue 40 ILE Chi-restraints excluded: chain BK residue 45 ASP Chi-restraints excluded: chain BK residue 67 SER Chi-restraints excluded: chain BK residue 91 VAL Chi-restraints excluded: chain BK residue 95 VAL Chi-restraints excluded: chain BK residue 96 LYS Chi-restraints excluded: chain BK residue 114 LEU Chi-restraints excluded: chain BK residue 120 SER Chi-restraints excluded: chain BL residue 3 THR Chi-restraints excluded: chain BL residue 21 THR Chi-restraints excluded: chain BL residue 34 CYS Chi-restraints excluded: chain BL residue 38 TYR Chi-restraints excluded: chain BL residue 39 THR Chi-restraints excluded: chain BL residue 41 THR Chi-restraints excluded: chain BL residue 58 THR Chi-restraints excluded: chain BL residue 61 VAL Chi-restraints excluded: chain BL residue 87 VAL Chi-restraints excluded: chain BL residue 104 THR Chi-restraints excluded: chain BL residue 107 VAL Chi-restraints excluded: chain BM residue 51 ASP Chi-restraints excluded: chain BM residue 56 LEU Chi-restraints excluded: chain BM residue 117 ILE Chi-restraints excluded: chain BN residue 6 LEU Chi-restraints excluded: chain BN residue 24 CYS Chi-restraints excluded: chain BN residue 47 MET Chi-restraints excluded: chain BO residue 20 THR Chi-restraints excluded: chain BO residue 80 SER Chi-restraints excluded: chain BO residue 82 ILE Chi-restraints excluded: chain BP residue 3 VAL Chi-restraints excluded: chain BP residue 15 ASN Chi-restraints excluded: chain BP residue 27 THR Chi-restraints excluded: chain BP residue 45 GLU Chi-restraints excluded: chain BP residue 70 VAL Chi-restraints excluded: chain BP residue 86 LEU Chi-restraints excluded: chain BP residue 92 THR Chi-restraints excluded: chain BQ residue 28 VAL Chi-restraints excluded: chain BQ residue 55 THR Chi-restraints excluded: chain BQ residue 56 THR Chi-restraints excluded: chain BQ residue 72 ASP Chi-restraints excluded: chain BQ residue 74 VAL Chi-restraints excluded: chain BQ residue 77 MET Chi-restraints excluded: chain BQ residue 93 ILE Chi-restraints excluded: chain BQ residue 95 GLU Chi-restraints excluded: chain BR residue 21 VAL Chi-restraints excluded: chain BR residue 26 LYS Chi-restraints excluded: chain BR residue 51 ARG Chi-restraints excluded: chain BR residue 53 VAL Chi-restraints excluded: chain BS residue 12 ASP Chi-restraints excluded: chain BS residue 18 LYS Chi-restraints excluded: chain BS residue 33 THR Chi-restraints excluded: chain BS residue 38 SER Chi-restraints excluded: chain BS residue 63 THR Chi-restraints excluded: chain BS residue 67 VAL Chi-restraints excluded: chain BS residue 78 ARG Chi-restraints excluded: chain BT residue 13 THR Chi-restraints excluded: chain BT residue 26 SER Chi-restraints excluded: chain BT residue 45 ASP Chi-restraints excluded: chain BT residue 50 LEU Chi-restraints excluded: chain BT residue 55 SER Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BV residue 4 VAL Chi-restraints excluded: chain BV residue 6 MET Chi-restraints excluded: chain BV residue 23 TRP Chi-restraints excluded: chain BV residue 31 ILE Chi-restraints excluded: chain BV residue 38 ILE Chi-restraints excluded: chain BV residue 57 VAL Chi-restraints excluded: chain BV residue 66 THR Chi-restraints excluded: chain BV residue 68 LEU Chi-restraints excluded: chain BV residue 82 GLU Chi-restraints excluded: chain BV residue 92 VAL Chi-restraints excluded: chain BV residue 117 LEU Chi-restraints excluded: chain BV residue 155 GLN Chi-restraints excluded: chain BV residue 157 VAL Chi-restraints excluded: chain BV residue 186 ILE Chi-restraints excluded: chain BV residue 205 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 956 optimal weight: 5.9990 chunk 727 optimal weight: 20.0000 chunk 502 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 461 optimal weight: 30.0000 chunk 649 optimal weight: 8.9990 chunk 971 optimal weight: 9.9990 chunk 1028 optimal weight: 20.0000 chunk 507 optimal weight: 20.0000 chunk 920 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 overall best weight: 10.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 135 ASN D 20 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN G 23 ASN K 96 HIS K 117 GLN L 89 ASN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 169 ASN X 46 HIS Z 52 GLN ** b 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 122 GLN ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BD 134 GLN BI 146 GLN BK 110 GLN ** BL 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BL 109 ASN BM 92 HIS BO 7 GLN BQ 65 ASN BV 108 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 163913 Z= 0.337 Angle : 0.654 10.108 245455 Z= 0.334 Chirality : 0.039 0.382 31408 Planarity : 0.005 0.079 13199 Dihedral : 24.492 179.840 82951 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.87 % Favored : 96.12 % Rotamer: Outliers : 8.52 % Allowed : 22.31 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: -0.55 (0.10), residues: 5979 helix: 0.54 (0.11), residues: 2045 sheet: -0.34 (0.14), residues: 1175 loop : -1.00 (0.11), residues: 2759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPBF 43 HIS 0.007 0.001 HISBL 77 PHE 0.024 0.002 PHEBP 106 TYR 0.017 0.002 TYRBV 49 ARG 0.013 0.001 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1838 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 421 poor density : 1417 time to evaluate : 6.893 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: 3 8 LYS cc_start: 0.8777 (mttt) cc_final: 0.8538 (mttt) REVERT: C 28 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8508 (p) REVERT: C 66 ASP cc_start: 0.8439 (t0) cc_final: 0.8171 (t0) REVERT: C 237 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8055 (mm-30) REVERT: C 265 ASP cc_start: 0.8230 (m-30) cc_final: 0.7977 (m-30) REVERT: D 56 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8368 (tp30) REVERT: D 87 ASP cc_start: 0.7987 (m-30) cc_final: 0.7672 (m-30) REVERT: E 26 ASP cc_start: 0.8311 (t0) cc_final: 0.7915 (t0) REVERT: E 28 GLU cc_start: 0.8180 (tp30) cc_final: 0.7775 (tp30) REVERT: E 30 ASN cc_start: 0.8644 (t0) cc_final: 0.8240 (t0) REVERT: E 106 MET cc_start: 0.8873 (mtp) cc_final: 0.8663 (mtm) REVERT: E 192 ASP cc_start: 0.8028 (m-30) cc_final: 0.7656 (m-30) REVERT: F 13 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8205 (pp30) REVERT: F 142 GLN cc_start: 0.8892 (pm20) cc_final: 0.8227 (pm20) REVERT: F 159 MET cc_start: 0.8849 (pmm) cc_final: 0.8582 (pmm) REVERT: G 59 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8715 (tm-30) REVERT: G 88 MET cc_start: 0.7996 (mtp) cc_final: 0.7451 (mmt) REVERT: G 90 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.9011 (mm) REVERT: H 6 THR cc_start: 0.8150 (m) cc_final: 0.7276 (p) REVERT: H 25 TYR cc_start: 0.9070 (t80) cc_final: 0.8859 (t80) REVERT: H 137 HIS cc_start: 0.6522 (OUTLIER) cc_final: 0.5888 (t70) REVERT: H 143 LYS cc_start: 0.8513 (mttt) cc_final: 0.8226 (tptm) REVERT: I 110 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.5268 (ttm) REVERT: K 23 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8783 (m) REVERT: K 37 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8514 (ttt180) REVERT: K 102 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8208 (mt-10) REVERT: K 106 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8852 (mp) REVERT: L 1 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8179 (tpp) REVERT: M 24 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7944 (tpp80) REVERT: O 110 MET cc_start: 0.8314 (mtp) cc_final: 0.8039 (mtt) REVERT: P 69 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8101 (p0) REVERT: P 122 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7739 (mm-30) REVERT: P 126 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7918 (mmtt) REVERT: R 18 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9032 (mm) REVERT: R 42 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8559 (m) REVERT: R 63 SER cc_start: 0.9321 (m) cc_final: 0.8968 (m) REVERT: R 102 ASP cc_start: 0.7983 (t0) cc_final: 0.7470 (t0) REVERT: S 44 ASP cc_start: 0.7581 (p0) cc_final: 0.7087 (p0) REVERT: T 42 ILE cc_start: 0.9494 (mt) cc_final: 0.9187 (tt) REVERT: T 93 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8537 (ttm170) REVERT: W 50 ASN cc_start: 0.8745 (t0) cc_final: 0.8198 (t0) REVERT: W 53 ASP cc_start: 0.8596 (m-30) cc_final: 0.8325 (p0) REVERT: W 70 ASP cc_start: 0.8530 (t0) cc_final: 0.8039 (p0) REVERT: W 89 ARG cc_start: 0.8555 (mtm-85) cc_final: 0.8292 (mtm-85) REVERT: W 123 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8518 (mp) REVERT: Y 10 LYS cc_start: 0.8604 (tttt) cc_final: 0.8279 (mttt) REVERT: Z 23 ARG cc_start: 0.8296 (mtm180) cc_final: 0.7982 (mtt90) REVERT: Z 24 GLU cc_start: 0.8692 (tp30) cc_final: 0.7943 (tp30) REVERT: a 5 LYS cc_start: 0.8955 (ttmm) cc_final: 0.8508 (ttmm) REVERT: a 48 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8323 (t0) REVERT: b 6 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7997 (mtt90) REVERT: b 31 SER cc_start: 0.9251 (p) cc_final: 0.9011 (p) REVERT: b 35 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7250 (pp30) REVERT: c 25 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8631 (p) REVERT: c 34 ASP cc_start: 0.8984 (p0) cc_final: 0.8770 (p0) REVERT: c 49 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8261 (mm-40) REVERT: d 15 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8239 (ttm110) REVERT: e 47 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8671 (mtm110) REVERT: g 9 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.6478 (t80) REVERT: g 25 ARG cc_start: 0.8170 (mmt180) cc_final: 0.7141 (mmt180) REVERT: BB 6 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8311 (ptpt) REVERT: BC 31 TYR cc_start: 0.8813 (m-10) cc_final: 0.8237 (m-10) REVERT: BC 35 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: BC 51 ILE cc_start: 0.8881 (mt) cc_final: 0.8631 (mm) REVERT: BC 96 LYS cc_start: 0.7495 (mttp) cc_final: 0.7021 (mmtt) REVERT: BC 97 GLN cc_start: 0.6746 (tm-30) cc_final: 0.6242 (tm-30) REVERT: BC 117 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8117 (mm-40) REVERT: BC 133 MET cc_start: 0.8296 (mtp) cc_final: 0.7849 (mtp) REVERT: BC 166 GLU cc_start: 0.7646 (tp30) cc_final: 0.7355 (tm-30) REVERT: BC 183 ASP cc_start: 0.8604 (t0) cc_final: 0.8401 (t0) REVERT: BC 184 TYR cc_start: 0.8954 (t80) cc_final: 0.8633 (t80) REVERT: BC 187 TYR cc_start: 0.8674 (t80) cc_final: 0.8083 (t80) REVERT: BD 12 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7405 (p) REVERT: BD 20 VAL cc_start: 0.7562 (t) cc_final: 0.7133 (p) REVERT: BD 165 TRP cc_start: 0.7613 (p90) cc_final: 0.6810 (p90) REVERT: BD 182 GLU cc_start: 0.7937 (mp0) cc_final: 0.7550 (mp0) REVERT: BE 87 LYS cc_start: 0.8665 (mtmt) cc_final: 0.8461 (mtmt) REVERT: BF 11 ASP cc_start: 0.8204 (m-30) cc_final: 0.7940 (m-30) REVERT: BF 27 LEU cc_start: 0.8911 (tp) cc_final: 0.8525 (tp) REVERT: BF 43 TRP cc_start: 0.7453 (OUTLIER) cc_final: 0.6429 (m-90) REVERT: BF 74 GLU cc_start: 0.8403 (tp30) cc_final: 0.7279 (tp30) REVERT: BF 78 GLN cc_start: 0.8406 (mm-40) cc_final: 0.7270 (mm-40) REVERT: BF 84 SER cc_start: 0.7738 (p) cc_final: 0.7195 (p) REVERT: BG 85 TYR cc_start: 0.7207 (m-10) cc_final: 0.7000 (m-80) REVERT: BG 86 GLN cc_start: 0.8535 (mm-40) cc_final: 0.7736 (mm-40) REVERT: BG 106 ASN cc_start: 0.8770 (m110) cc_final: 0.8500 (m-40) REVERT: BG 118 GLU cc_start: 0.8492 (tp30) cc_final: 0.8209 (tp30) REVERT: BG 141 THR cc_start: 0.8628 (m) cc_final: 0.8371 (p) REVERT: BG 143 LYS cc_start: 0.8721 (tttt) cc_final: 0.8404 (ttpp) REVERT: BI 105 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7849 (mtt180) REVERT: BI 115 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7224 (tpt-90) REVERT: BK 65 ARG cc_start: 0.9075 (ttm110) cc_final: 0.8872 (ttm110) REVERT: BK 73 GLN cc_start: 0.8325 (tt0) cc_final: 0.8108 (tt0) REVERT: BK 96 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8346 (ttpt) REVERT: BL 18 LYS cc_start: 0.7610 (tttt) cc_final: 0.7388 (tptm) REVERT: BL 58 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8362 (p) REVERT: BL 59 SER cc_start: 0.9043 (m) cc_final: 0.8756 (t) REVERT: BM 23 TYR cc_start: 0.8373 (t80) cc_final: 0.8125 (t80) REVERT: BM 59 TYR cc_start: 0.8800 (t80) cc_final: 0.8409 (t80) REVERT: BM 73 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8203 (tm-30) REVERT: BM 77 ASP cc_start: 0.8155 (m-30) cc_final: 0.7551 (m-30) REVERT: BN 25 ASN cc_start: 0.9175 (m110) cc_final: 0.8816 (m110) REVERT: BO 8 LYS cc_start: 0.8475 (mttt) cc_final: 0.8191 (mttm) REVERT: BO 10 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8155 (tm-30) REVERT: BO 79 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7574 (ttm-80) REVERT: BQ 32 MET cc_start: 0.7446 (mtm) cc_final: 0.7178 (mpp) REVERT: BQ 92 GLU cc_start: 0.8104 (pp20) cc_final: 0.7353 (pp20) REVERT: BR 26 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7073 (mptt) REVERT: BR 39 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7912 (mmm-85) REVERT: BR 44 GLU cc_start: 0.8017 (pm20) cc_final: 0.7094 (pm20) REVERT: BS 16 LEU cc_start: 0.8789 (tp) cc_final: 0.8339 (tp) REVERT: BS 18 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8365 (mtmm) REVERT: BS 48 THR cc_start: 0.8405 (m) cc_final: 0.8153 (p) REVERT: BS 73 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8271 (mt-10) REVERT: BS 78 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.6923 (ptt-90) REVERT: BT 20 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8173 (mtm110) REVERT: BT 22 GLN cc_start: 0.8994 (tt0) cc_final: 0.8794 (tt0) REVERT: BV 1 MET cc_start: 0.1544 (mpp) cc_final: 0.1178 (tpp) REVERT: BV 23 TRP cc_start: 0.7795 (OUTLIER) cc_final: 0.7263 (p-90) REVERT: BV 82 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6510 (pt0) REVERT: BV 89 MET cc_start: 0.6791 (mmt) cc_final: 0.5714 (mmp) outliers start: 421 outliers final: 310 residues processed: 1671 average time/residue: 1.3771 time to fit residues: 3941.2106 Evaluate side-chains 1709 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 1365 time to evaluate : 6.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 137 HIS Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 110 MET Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 83 ILE Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 93 ARG Chi-restraints excluded: chain T residue 99 ARG Chi-restraints excluded: chain T residue 109 HIS Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 38 VAL Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 123 LEU Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 169 ASN Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 48 ASN Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 15 SER Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 35 GLN Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 56 SER Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 9 TYR Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain BB residue 6 LYS Chi-restraints excluded: chain BB residue 22 ARG Chi-restraints excluded: chain BC residue 16 THR Chi-restraints excluded: chain BC residue 35 ASP Chi-restraints excluded: chain BC residue 67 ILE Chi-restraints excluded: chain BC residue 202 ILE Chi-restraints excluded: chain BD residue 12 SER Chi-restraints excluded: chain BD residue 23 ASP Chi-restraints excluded: chain BD residue 93 LEU Chi-restraints excluded: chain BD residue 145 LEU Chi-restraints excluded: chain BD residue 177 VAL Chi-restraints excluded: chain BD residue 188 VAL Chi-restraints excluded: chain BD residue 200 SER Chi-restraints excluded: chain BE residue 71 VAL Chi-restraints excluded: chain BE residue 73 VAL Chi-restraints excluded: chain BE residue 81 VAL Chi-restraints excluded: chain BE residue 110 VAL Chi-restraints excluded: chain BE residue 152 SER Chi-restraints excluded: chain BE residue 177 GLU Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BF residue 13 THR Chi-restraints excluded: chain BF residue 23 LEU Chi-restraints excluded: chain BF residue 29 VAL Chi-restraints excluded: chain BF residue 42 ILE Chi-restraints excluded: chain BF residue 43 TRP Chi-restraints excluded: chain BF residue 57 GLU Chi-restraints excluded: chain BF residue 76 ASP Chi-restraints excluded: chain BG residue 27 VAL Chi-restraints excluded: chain BG residue 53 LYS Chi-restraints excluded: chain BG residue 61 THR Chi-restraints excluded: chain BG residue 74 GLU Chi-restraints excluded: chain BG residue 84 THR Chi-restraints excluded: chain BG residue 108 SER Chi-restraints excluded: chain BG residue 124 ILE Chi-restraints excluded: chain BG residue 129 ASN Chi-restraints excluded: chain BG residue 135 VAL Chi-restraints excluded: chain BG residue 139 GLU Chi-restraints excluded: chain BH residue 4 THR Chi-restraints excluded: chain BH residue 92 THR Chi-restraints excluded: chain BH residue 108 THR Chi-restraints excluded: chain BH residue 115 ASP Chi-restraints excluded: chain BI residue 36 VAL Chi-restraints excluded: chain BI residue 59 PHE Chi-restraints excluded: chain BI residue 74 THR Chi-restraints excluded: chain BI residue 80 GLN Chi-restraints excluded: chain BI residue 103 ILE Chi-restraints excluded: chain BI residue 105 ARG Chi-restraints excluded: chain BI residue 115 ARG Chi-restraints excluded: chain BI residue 120 LYS Chi-restraints excluded: chain BJ residue 10 LEU Chi-restraints excluded: chain BJ residue 42 LEU Chi-restraints excluded: chain BJ residue 69 THR Chi-restraints excluded: chain BJ residue 71 LYS Chi-restraints excluded: chain BJ residue 73 LEU Chi-restraints excluded: chain BJ residue 76 ILE Chi-restraints excluded: chain BJ residue 78 ASP Chi-restraints excluded: chain BJ residue 80 THR Chi-restraints excluded: chain BJ residue 99 ASN Chi-restraints excluded: chain BK residue 40 ILE Chi-restraints excluded: chain BK residue 67 SER Chi-restraints excluded: chain BK residue 68 THR Chi-restraints excluded: chain BK residue 91 VAL Chi-restraints excluded: chain BK residue 95 VAL Chi-restraints excluded: chain BK residue 96 LYS Chi-restraints excluded: chain BK residue 108 SER Chi-restraints excluded: chain BK residue 114 LEU Chi-restraints excluded: chain BK residue 120 SER Chi-restraints excluded: chain BK residue 123 THR Chi-restraints excluded: chain BL residue 34 CYS Chi-restraints excluded: chain BL residue 38 TYR Chi-restraints excluded: chain BL residue 41 THR Chi-restraints excluded: chain BL residue 49 LEU Chi-restraints excluded: chain BL residue 58 THR Chi-restraints excluded: chain BL residue 61 VAL Chi-restraints excluded: chain BL residue 63 VAL Chi-restraints excluded: chain BL residue 87 VAL Chi-restraints excluded: chain BL residue 104 THR Chi-restraints excluded: chain BM residue 51 ASP Chi-restraints excluded: chain BM residue 56 LEU Chi-restraints excluded: chain BN residue 6 LEU Chi-restraints excluded: chain BN residue 24 CYS Chi-restraints excluded: chain BN residue 47 MET Chi-restraints excluded: chain BN residue 53 LEU Chi-restraints excluded: chain BO residue 7 GLN Chi-restraints excluded: chain BO residue 20 THR Chi-restraints excluded: chain BO residue 80 SER Chi-restraints excluded: chain BO residue 82 ILE Chi-restraints excluded: chain BP residue 3 VAL Chi-restraints excluded: chain BP residue 15 ASN Chi-restraints excluded: chain BP residue 27 THR Chi-restraints excluded: chain BP residue 30 ASP Chi-restraints excluded: chain BP residue 44 GLU Chi-restraints excluded: chain BP residue 45 GLU Chi-restraints excluded: chain BP residue 81 GLN Chi-restraints excluded: chain BP residue 86 LEU Chi-restraints excluded: chain BP residue 92 THR Chi-restraints excluded: chain BQ residue 35 THR Chi-restraints excluded: chain BQ residue 36 ILE Chi-restraints excluded: chain BQ residue 55 THR Chi-restraints excluded: chain BQ residue 56 THR Chi-restraints excluded: chain BQ residue 65 ASN Chi-restraints excluded: chain BQ residue 72 ASP Chi-restraints excluded: chain BQ residue 74 VAL Chi-restraints excluded: chain BQ residue 93 ILE Chi-restraints excluded: chain BQ residue 95 GLU Chi-restraints excluded: chain BR residue 21 VAL Chi-restraints excluded: chain BR residue 26 LYS Chi-restraints excluded: chain BR residue 53 VAL Chi-restraints excluded: chain BS residue 12 ASP Chi-restraints excluded: chain BS residue 33 THR Chi-restraints excluded: chain BS residue 38 SER Chi-restraints excluded: chain BS residue 56 LYS Chi-restraints excluded: chain BS residue 67 VAL Chi-restraints excluded: chain BS residue 78 ARG Chi-restraints excluded: chain BT residue 13 THR Chi-restraints excluded: chain BT residue 45 ASP Chi-restraints excluded: chain BT residue 50 LEU Chi-restraints excluded: chain BT residue 55 SER Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BV residue 4 VAL Chi-restraints excluded: chain BV residue 6 MET Chi-restraints excluded: chain BV residue 23 TRP Chi-restraints excluded: chain BV residue 38 ILE Chi-restraints excluded: chain BV residue 66 THR Chi-restraints excluded: chain BV residue 68 LEU Chi-restraints excluded: chain BV residue 82 GLU Chi-restraints excluded: chain BV residue 85 THR Chi-restraints excluded: chain BV residue 92 VAL Chi-restraints excluded: chain BV residue 117 LEU Chi-restraints excluded: chain BV residue 155 GLN Chi-restraints excluded: chain BV residue 157 VAL Chi-restraints excluded: chain BV residue 164 VAL Chi-restraints excluded: chain BV residue 186 ILE Chi-restraints excluded: chain BV residue 205 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 856 optimal weight: 9.9990 chunk 583 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 765 optimal weight: 20.0000 chunk 424 optimal weight: 20.0000 chunk 877 optimal weight: 6.9990 chunk 710 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 525 optimal weight: 9.9990 chunk 923 optimal weight: 30.0000 chunk 259 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN D 20 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 ASN K 117 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 HIS ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 52 GLN ** b 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 122 GLN ** BD 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 163 HIS BI 146 GLN BK 110 GLN BL 77 HIS BL 109 ASN BO 7 GLN BV 108 HIS BV 167 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 163913 Z= 0.250 Angle : 0.602 10.066 245455 Z= 0.308 Chirality : 0.036 0.315 31408 Planarity : 0.005 0.075 13199 Dihedral : 24.434 179.733 82918 Min Nonbonded Distance : 1.054 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 8.12 % Allowed : 23.34 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: 5979 helix: 0.81 (0.11), residues: 2052 sheet: -0.25 (0.14), residues: 1172 loop : -0.89 (0.11), residues: 2755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPBF 43 HIS 0.006 0.001 HISBL 72 PHE 0.026 0.002 PHEBP 106 TYR 0.025 0.002 TYR Q 98 ARG 0.009 0.001 ARGBM 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1799 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 401 poor density : 1398 time to evaluate : 6.643 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: 3 8 LYS cc_start: 0.8657 (mttt) cc_final: 0.8433 (mttt) REVERT: C 13 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7802 (mtm180) REVERT: C 28 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8670 (p) REVERT: C 66 ASP cc_start: 0.8500 (t0) cc_final: 0.8249 (t0) REVERT: C 198 ASN cc_start: 0.8975 (OUTLIER) cc_final: 0.8498 (m110) REVERT: C 265 ASP cc_start: 0.8233 (m-30) cc_final: 0.7988 (m-30) REVERT: C 270 ARG cc_start: 0.7547 (ptt-90) cc_final: 0.7296 (ptt-90) REVERT: D 56 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8452 (tp30) REVERT: D 87 ASP cc_start: 0.7998 (m-30) cc_final: 0.7710 (m-30) REVERT: E 28 GLU cc_start: 0.8227 (tp30) cc_final: 0.7971 (tp30) REVERT: E 30 ASN cc_start: 0.8597 (t0) cc_final: 0.8346 (t0) REVERT: E 106 MET cc_start: 0.8836 (mtp) cc_final: 0.8596 (mtm) REVERT: E 208 ASN cc_start: 0.8885 (m-40) cc_final: 0.8551 (m110) REVERT: F 13 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8390 (pp30) REVERT: F 142 GLN cc_start: 0.8933 (pm20) cc_final: 0.8213 (pm20) REVERT: F 159 MET cc_start: 0.8846 (pmm) cc_final: 0.8617 (pmm) REVERT: G 88 MET cc_start: 0.8114 (mtp) cc_final: 0.7674 (mmt) REVERT: G 90 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9035 (mm) REVERT: G 153 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8324 (tpp-160) REVERT: H 2 LYS cc_start: 0.8414 (mtpp) cc_final: 0.8151 (ptmm) REVERT: H 6 THR cc_start: 0.8198 (m) cc_final: 0.7323 (p) REVERT: H 25 TYR cc_start: 0.9059 (t80) cc_final: 0.8854 (t80) REVERT: H 137 HIS cc_start: 0.6436 (OUTLIER) cc_final: 0.6228 (t70) REVERT: H 143 LYS cc_start: 0.8705 (mttt) cc_final: 0.8372 (tptm) REVERT: K 23 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8776 (m) REVERT: K 37 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8427 (ttt180) REVERT: K 108 MET cc_start: 0.9132 (mtm) cc_final: 0.8901 (mtm) REVERT: L 1 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8226 (tpp) REVERT: L 80 ASP cc_start: 0.7813 (m-30) cc_final: 0.7600 (m-30) REVERT: L 90 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7593 (p0) REVERT: M 24 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.7895 (tpp80) REVERT: M 138 THR cc_start: 0.8790 (m) cc_final: 0.8427 (p) REVERT: P 24 ARG cc_start: 0.9446 (OUTLIER) cc_final: 0.9226 (ttp-110) REVERT: P 28 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8634 (mtpp) REVERT: P 69 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7911 (p0) REVERT: P 122 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7622 (mm-30) REVERT: P 126 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7737 (mmtt) REVERT: R 18 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8967 (mm) REVERT: R 42 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8520 (m) REVERT: R 63 SER cc_start: 0.9325 (m) cc_final: 0.8979 (m) REVERT: R 102 ASP cc_start: 0.7908 (t0) cc_final: 0.7383 (t0) REVERT: S 44 ASP cc_start: 0.7655 (p0) cc_final: 0.7084 (p0) REVERT: S 87 ARG cc_start: 0.8706 (mtt90) cc_final: 0.8416 (mtt90) REVERT: T 93 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8464 (ttm170) REVERT: W 50 ASN cc_start: 0.8781 (t0) cc_final: 0.8229 (t0) REVERT: W 53 ASP cc_start: 0.8614 (m-30) cc_final: 0.8318 (p0) REVERT: W 70 ASP cc_start: 0.8529 (t0) cc_final: 0.8164 (p0) REVERT: W 89 ARG cc_start: 0.8677 (mtm-85) cc_final: 0.8366 (mtm-85) REVERT: Y 10 LYS cc_start: 0.8579 (tttt) cc_final: 0.8254 (mttt) REVERT: Y 28 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7223 (ptp-170) REVERT: Z 19 LYS cc_start: 0.9311 (mmtt) cc_final: 0.9090 (mmtt) REVERT: Z 24 GLU cc_start: 0.8617 (tp30) cc_final: 0.7549 (tp30) REVERT: Z 28 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7620 (mm-30) REVERT: a 5 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8625 (ttmm) REVERT: a 48 ASN cc_start: 0.8743 (t0) cc_final: 0.8345 (t0) REVERT: b 6 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7990 (mtt90) REVERT: b 31 SER cc_start: 0.9230 (p) cc_final: 0.9005 (p) REVERT: b 35 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7150 (pp30) REVERT: c 25 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8642 (p) REVERT: c 34 ASP cc_start: 0.8957 (p0) cc_final: 0.8720 (p0) REVERT: c 49 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8232 (mm-40) REVERT: d 15 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8183 (ttm110) REVERT: g 1 MET cc_start: 0.8093 (tpp) cc_final: 0.7467 (tpp) REVERT: g 9 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.6411 (t80) REVERT: g 25 ARG cc_start: 0.8187 (mmt180) cc_final: 0.7214 (mmt180) REVERT: BB 6 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8151 (ptpt) REVERT: BC 31 TYR cc_start: 0.8786 (m-10) cc_final: 0.8192 (m-10) REVERT: BC 35 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: BC 51 ILE cc_start: 0.8798 (mt) cc_final: 0.8533 (mm) REVERT: BC 96 LYS cc_start: 0.7489 (mttp) cc_final: 0.7051 (mmtt) REVERT: BC 133 MET cc_start: 0.8224 (mtp) cc_final: 0.7692 (mtp) REVERT: BC 166 GLU cc_start: 0.7527 (tp30) cc_final: 0.7243 (tm-30) REVERT: BC 183 ASP cc_start: 0.8618 (t0) cc_final: 0.8401 (t0) REVERT: BC 184 TYR cc_start: 0.8922 (t80) cc_final: 0.8653 (t80) REVERT: BC 187 TYR cc_start: 0.8918 (t80) cc_final: 0.8396 (t80) REVERT: BD 12 SER cc_start: 0.8007 (OUTLIER) cc_final: 0.7623 (p) REVERT: BD 19 LEU cc_start: 0.6116 (OUTLIER) cc_final: 0.5870 (mm) REVERT: BD 20 VAL cc_start: 0.7633 (t) cc_final: 0.7189 (p) REVERT: BD 64 GLU cc_start: 0.7941 (tp30) cc_final: 0.7603 (tp30) REVERT: BD 136 ASP cc_start: 0.8710 (m-30) cc_final: 0.8231 (m-30) REVERT: BD 165 TRP cc_start: 0.7648 (p90) cc_final: 0.6774 (p90) REVERT: BD 182 GLU cc_start: 0.8157 (mp0) cc_final: 0.7713 (mp0) REVERT: BE 91 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7690 (mt-10) REVERT: BE 177 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7863 (pm20) REVERT: BF 27 LEU cc_start: 0.8962 (tp) cc_final: 0.8413 (tt) REVERT: BF 43 TRP cc_start: 0.7290 (OUTLIER) cc_final: 0.6424 (m-90) REVERT: BF 74 GLU cc_start: 0.8516 (tp30) cc_final: 0.7591 (tp30) REVERT: BF 78 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7309 (mm-40) REVERT: BF 84 SER cc_start: 0.7780 (p) cc_final: 0.7268 (p) REVERT: BG 91 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7862 (p) REVERT: BG 118 GLU cc_start: 0.8439 (tp30) cc_final: 0.7869 (tp30) REVERT: BG 139 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8247 (tp30) REVERT: BG 143 LYS cc_start: 0.8659 (tttt) cc_final: 0.8336 (ttpp) REVERT: BG 151 PHE cc_start: 0.8056 (m-80) cc_final: 0.7708 (m-10) REVERT: BI 105 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7757 (mtt180) REVERT: BJ 24 LYS cc_start: 0.8621 (mmmm) cc_final: 0.8015 (tmtt) REVERT: BK 65 ARG cc_start: 0.9071 (ttm110) cc_final: 0.8808 (ttm110) REVERT: BK 73 GLN cc_start: 0.8472 (tt0) cc_final: 0.7999 (tt0) REVERT: BK 96 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8295 (ttpt) REVERT: BK 119 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8643 (pt) REVERT: BL 18 LYS cc_start: 0.7573 (tttt) cc_final: 0.7344 (tptm) REVERT: BL 58 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8257 (p) REVERT: BL 59 SER cc_start: 0.9092 (m) cc_final: 0.8806 (t) REVERT: BM 13 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8693 (mmtp) REVERT: BM 23 TYR cc_start: 0.8336 (t80) cc_final: 0.8096 (t80) REVERT: BM 49 THR cc_start: 0.8269 (p) cc_final: 0.8041 (t) REVERT: BM 59 TYR cc_start: 0.8720 (t80) cc_final: 0.8498 (t80) REVERT: BM 73 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8114 (tm-30) REVERT: BM 77 ASP cc_start: 0.8127 (m-30) cc_final: 0.7470 (m-30) REVERT: BM 117 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6509 (mm) REVERT: BN 25 ASN cc_start: 0.9115 (m110) cc_final: 0.8829 (m110) REVERT: BO 8 LYS cc_start: 0.8335 (mttt) cc_final: 0.8053 (mttm) REVERT: BO 10 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8180 (tm-30) REVERT: BO 26 GLU cc_start: 0.8185 (mp0) cc_final: 0.7723 (mp0) REVERT: BO 79 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7474 (ttm-80) REVERT: BP 55 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7671 (mmt180) REVERT: BQ 32 MET cc_start: 0.7400 (mtm) cc_final: 0.7098 (mpp) REVERT: BQ 73 ARG cc_start: 0.8181 (ttt-90) cc_final: 0.7821 (ttp80) REVERT: BQ 92 GLU cc_start: 0.8117 (pp20) cc_final: 0.7679 (pp20) REVERT: BR 35 THR cc_start: 0.8179 (m) cc_final: 0.7917 (t) REVERT: BR 45 ARG cc_start: 0.8083 (mmp80) cc_final: 0.7793 (mmp-170) REVERT: BS 16 LEU cc_start: 0.8737 (tp) cc_final: 0.8456 (tp) REVERT: BS 18 LYS cc_start: 0.8584 (mtpp) cc_final: 0.8330 (mtmm) REVERT: BS 48 THR cc_start: 0.8227 (m) cc_final: 0.7967 (p) REVERT: BS 73 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8458 (mt-10) REVERT: BT 46 LYS cc_start: 0.8273 (tppt) cc_final: 0.8037 (tptp) REVERT: BV 1 MET cc_start: 0.1443 (mpp) cc_final: 0.0761 (tpp) REVERT: BV 23 TRP cc_start: 0.7851 (OUTLIER) cc_final: 0.7358 (p-90) REVERT: BV 82 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6607 (pt0) REVERT: BV 89 MET cc_start: 0.7101 (mmt) cc_final: 0.6325 (mmt) outliers start: 401 outliers final: 302 residues processed: 1638 average time/residue: 1.3501 time to fit residues: 3788.3518 Evaluate side-chains 1690 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1349 time to evaluate : 6.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 137 HIS Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 24 ARG Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 93 ARG Chi-restraints excluded: chain T residue 99 ARG Chi-restraints excluded: chain T residue 109 HIS Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 38 VAL Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 35 GLN Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain e residue 56 SER Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 9 TYR Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain BB residue 6 LYS Chi-restraints excluded: chain BB residue 13 SER Chi-restraints excluded: chain BC residue 14 ILE Chi-restraints excluded: chain BC residue 16 THR Chi-restraints excluded: chain BC residue 35 ASP Chi-restraints excluded: chain BC residue 67 ILE Chi-restraints excluded: chain BC residue 105 VAL Chi-restraints excluded: chain BC residue 119 VAL Chi-restraints excluded: chain BD residue 12 SER Chi-restraints excluded: chain BD residue 19 LEU Chi-restraints excluded: chain BD residue 23 ASP Chi-restraints excluded: chain BD residue 85 LEU Chi-restraints excluded: chain BD residue 93 LEU Chi-restraints excluded: chain BD residue 145 LEU Chi-restraints excluded: chain BD residue 177 VAL Chi-restraints excluded: chain BD residue 188 VAL Chi-restraints excluded: chain BE residue 73 VAL Chi-restraints excluded: chain BE residue 110 VAL Chi-restraints excluded: chain BE residue 130 VAL Chi-restraints excluded: chain BE residue 177 GLU Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BF residue 13 THR Chi-restraints excluded: chain BF residue 23 LEU Chi-restraints excluded: chain BF residue 42 ILE Chi-restraints excluded: chain BF residue 43 TRP Chi-restraints excluded: chain BF residue 57 GLU Chi-restraints excluded: chain BF residue 73 SER Chi-restraints excluded: chain BF residue 76 ASP Chi-restraints excluded: chain BF residue 85 VAL Chi-restraints excluded: chain BF residue 91 LEU Chi-restraints excluded: chain BG residue 27 VAL Chi-restraints excluded: chain BG residue 48 GLU Chi-restraints excluded: chain BG residue 61 THR Chi-restraints excluded: chain BG residue 74 GLU Chi-restraints excluded: chain BG residue 84 THR Chi-restraints excluded: chain BG residue 91 VAL Chi-restraints excluded: chain BG residue 108 SER Chi-restraints excluded: chain BG residue 124 ILE Chi-restraints excluded: chain BG residue 135 VAL Chi-restraints excluded: chain BG residue 139 GLU Chi-restraints excluded: chain BH residue 4 THR Chi-restraints excluded: chain BH residue 87 VAL Chi-restraints excluded: chain BH residue 92 THR Chi-restraints excluded: chain BH residue 108 THR Chi-restraints excluded: chain BH residue 115 ASP Chi-restraints excluded: chain BI residue 36 VAL Chi-restraints excluded: chain BI residue 42 VAL Chi-restraints excluded: chain BI residue 80 GLN Chi-restraints excluded: chain BI residue 103 ILE Chi-restraints excluded: chain BI residue 105 ARG Chi-restraints excluded: chain BI residue 120 LYS Chi-restraints excluded: chain BJ residue 37 VAL Chi-restraints excluded: chain BJ residue 42 LEU Chi-restraints excluded: chain BJ residue 48 VAL Chi-restraints excluded: chain BJ residue 50 CYS Chi-restraints excluded: chain BJ residue 71 LYS Chi-restraints excluded: chain BJ residue 76 ILE Chi-restraints excluded: chain BJ residue 78 ASP Chi-restraints excluded: chain BJ residue 80 THR Chi-restraints excluded: chain BK residue 40 ILE Chi-restraints excluded: chain BK residue 45 ASP Chi-restraints excluded: chain BK residue 67 SER Chi-restraints excluded: chain BK residue 68 THR Chi-restraints excluded: chain BK residue 91 VAL Chi-restraints excluded: chain BK residue 95 VAL Chi-restraints excluded: chain BK residue 96 LYS Chi-restraints excluded: chain BK residue 104 THR Chi-restraints excluded: chain BK residue 108 SER Chi-restraints excluded: chain BK residue 114 LEU Chi-restraints excluded: chain BK residue 119 ILE Chi-restraints excluded: chain BK residue 120 SER Chi-restraints excluded: chain BK residue 123 THR Chi-restraints excluded: chain BL residue 3 THR Chi-restraints excluded: chain BL residue 34 CYS Chi-restraints excluded: chain BL residue 38 TYR Chi-restraints excluded: chain BL residue 41 THR Chi-restraints excluded: chain BL residue 58 THR Chi-restraints excluded: chain BL residue 61 VAL Chi-restraints excluded: chain BL residue 63 VAL Chi-restraints excluded: chain BL residue 87 VAL Chi-restraints excluded: chain BL residue 104 THR Chi-restraints excluded: chain BL residue 109 ASN Chi-restraints excluded: chain BM residue 32 GLU Chi-restraints excluded: chain BM residue 51 ASP Chi-restraints excluded: chain BM residue 117 ILE Chi-restraints excluded: chain BN residue 11 ASN Chi-restraints excluded: chain BN residue 24 CYS Chi-restraints excluded: chain BN residue 47 MET Chi-restraints excluded: chain BN residue 53 LEU Chi-restraints excluded: chain BO residue 20 THR Chi-restraints excluded: chain BO residue 24 SER Chi-restraints excluded: chain BO residue 75 VAL Chi-restraints excluded: chain BO residue 80 SER Chi-restraints excluded: chain BP residue 3 VAL Chi-restraints excluded: chain BP residue 15 ASN Chi-restraints excluded: chain BP residue 27 THR Chi-restraints excluded: chain BP residue 30 ASP Chi-restraints excluded: chain BP residue 44 GLU Chi-restraints excluded: chain BP residue 45 GLU Chi-restraints excluded: chain BP residue 55 ARG Chi-restraints excluded: chain BP residue 81 GLN Chi-restraints excluded: chain BP residue 86 LEU Chi-restraints excluded: chain BP residue 92 THR Chi-restraints excluded: chain BQ residue 35 THR Chi-restraints excluded: chain BQ residue 42 ASP Chi-restraints excluded: chain BQ residue 55 THR Chi-restraints excluded: chain BQ residue 56 THR Chi-restraints excluded: chain BQ residue 72 ASP Chi-restraints excluded: chain BQ residue 93 ILE Chi-restraints excluded: chain BQ residue 95 GLU Chi-restraints excluded: chain BR residue 21 VAL Chi-restraints excluded: chain BR residue 51 ARG Chi-restraints excluded: chain BR residue 53 VAL Chi-restraints excluded: chain BS residue 12 ASP Chi-restraints excluded: chain BS residue 33 THR Chi-restraints excluded: chain BS residue 38 SER Chi-restraints excluded: chain BS residue 39 THR Chi-restraints excluded: chain BS residue 56 LYS Chi-restraints excluded: chain BS residue 67 VAL Chi-restraints excluded: chain BT residue 13 THR Chi-restraints excluded: chain BT residue 45 ASP Chi-restraints excluded: chain BT residue 50 LEU Chi-restraints excluded: chain BT residue 55 SER Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BV residue 4 VAL Chi-restraints excluded: chain BV residue 6 MET Chi-restraints excluded: chain BV residue 23 TRP Chi-restraints excluded: chain BV residue 31 ILE Chi-restraints excluded: chain BV residue 38 ILE Chi-restraints excluded: chain BV residue 66 THR Chi-restraints excluded: chain BV residue 68 LEU Chi-restraints excluded: chain BV residue 82 GLU Chi-restraints excluded: chain BV residue 92 VAL Chi-restraints excluded: chain BV residue 117 LEU Chi-restraints excluded: chain BV residue 137 LEU Chi-restraints excluded: chain BV residue 155 GLN Chi-restraints excluded: chain BV residue 157 VAL Chi-restraints excluded: chain BV residue 186 ILE Chi-restraints excluded: chain BV residue 205 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 346 optimal weight: 2.9990 chunk 926 optimal weight: 50.0000 chunk 203 optimal weight: 20.0000 chunk 603 optimal weight: 30.0000 chunk 253 optimal weight: 20.0000 chunk 1029 optimal weight: 20.0000 chunk 854 optimal weight: 8.9990 chunk 476 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 340 optimal weight: 6.9990 chunk 540 optimal weight: 30.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN K 117 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 169 ASN Z 40 GLN Z 52 GLN ** b 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 29 GLN BM 101 GLN BV 108 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 163913 Z= 0.305 Angle : 0.628 10.869 245455 Z= 0.319 Chirality : 0.037 0.344 31408 Planarity : 0.005 0.074 13199 Dihedral : 24.419 179.782 82898 Min Nonbonded Distance : 1.033 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.13 % Favored : 95.85 % Rotamer: Outliers : 9.01 % Allowed : 23.91 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: -0.32 (0.11), residues: 5979 helix: 0.81 (0.11), residues: 2059 sheet: -0.30 (0.14), residues: 1184 loop : -0.90 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPBF 43 HIS 0.006 0.001 HIS O 54 PHE 0.025 0.002 PHEBP 106 TYR 0.029 0.002 TYRBC 23 ARG 0.012 0.001 ARG f 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1830 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 445 poor density : 1385 time to evaluate : 6.644 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: 3 8 LYS cc_start: 0.8759 (mttt) cc_final: 0.8532 (mttt) REVERT: C 13 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.7761 (mtm180) REVERT: C 66 ASP cc_start: 0.8539 (t0) cc_final: 0.8214 (t0) REVERT: C 198 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8488 (m110) REVERT: C 265 ASP cc_start: 0.8250 (m-30) cc_final: 0.8008 (m-30) REVERT: D 56 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8428 (tp30) REVERT: D 87 ASP cc_start: 0.7934 (m-30) cc_final: 0.7643 (m-30) REVERT: D 147 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8314 (ptt180) REVERT: E 30 ASN cc_start: 0.8439 (t0) cc_final: 0.8185 (t0) REVERT: E 106 MET cc_start: 0.8836 (mtp) cc_final: 0.8601 (mtm) REVERT: E 192 ASP cc_start: 0.8046 (m-30) cc_final: 0.7709 (m-30) REVERT: F 13 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8380 (pp30) REVERT: F 142 GLN cc_start: 0.8984 (pm20) cc_final: 0.8554 (pp30) REVERT: F 159 MET cc_start: 0.8833 (pmm) cc_final: 0.8627 (pmm) REVERT: G 23 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.6546 (p0) REVERT: G 90 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9082 (mm) REVERT: H 6 THR cc_start: 0.8249 (m) cc_final: 0.7383 (p) REVERT: H 29 TYR cc_start: 0.8480 (t80) cc_final: 0.8275 (t80) REVERT: H 143 LYS cc_start: 0.8781 (mttt) cc_final: 0.8485 (tptm) REVERT: K 23 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8790 (m) REVERT: K 37 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8490 (ttt180) REVERT: K 48 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8589 (p) REVERT: K 106 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8845 (mp) REVERT: L 1 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8222 (tpp) REVERT: L 80 ASP cc_start: 0.7820 (m-30) cc_final: 0.7524 (m-30) REVERT: L 105 GLU cc_start: 0.7999 (mp0) cc_final: 0.7793 (mp0) REVERT: M 24 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7890 (tpp80) REVERT: M 138 THR cc_start: 0.8808 (m) cc_final: 0.8444 (p) REVERT: P 24 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.9088 (ttp-110) REVERT: P 28 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8681 (mtpp) REVERT: P 69 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7952 (p0) REVERT: P 126 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7831 (mmtt) REVERT: R 18 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9031 (mm) REVERT: R 42 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8537 (m) REVERT: R 63 SER cc_start: 0.9331 (m) cc_final: 0.8973 (m) REVERT: R 102 ASP cc_start: 0.7994 (t0) cc_final: 0.7448 (t0) REVERT: S 44 ASP cc_start: 0.7701 (p0) cc_final: 0.7059 (p0) REVERT: S 87 ARG cc_start: 0.8719 (mtt90) cc_final: 0.8436 (mtt90) REVERT: T 93 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8501 (ttm170) REVERT: W 50 ASN cc_start: 0.8830 (t0) cc_final: 0.8326 (t0) REVERT: W 53 ASP cc_start: 0.8618 (m-30) cc_final: 0.8365 (p0) REVERT: W 70 ASP cc_start: 0.8698 (t0) cc_final: 0.8212 (p0) REVERT: W 89 ARG cc_start: 0.8719 (mtm-85) cc_final: 0.8387 (mtm-85) REVERT: Y 10 LYS cc_start: 0.8597 (tttt) cc_final: 0.8269 (mttt) REVERT: Z 24 GLU cc_start: 0.8652 (tp30) cc_final: 0.8096 (tp30) REVERT: Z 28 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7967 (mm-30) REVERT: a 5 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8614 (ttmm) REVERT: a 48 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8352 (t0) REVERT: b 6 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8041 (mtt90) REVERT: b 31 SER cc_start: 0.9307 (p) cc_final: 0.9027 (p) REVERT: b 35 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7291 (pp30) REVERT: c 25 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8684 (p) REVERT: c 34 ASP cc_start: 0.8953 (p0) cc_final: 0.8743 (p0) REVERT: c 49 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8260 (mm-40) REVERT: d 15 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8220 (ttm110) REVERT: e 47 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8504 (mtm110) REVERT: g 1 MET cc_start: 0.8100 (tpp) cc_final: 0.7569 (tpp) REVERT: g 9 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.6514 (t80) REVERT: g 25 ARG cc_start: 0.8168 (mmt180) cc_final: 0.7094 (mmt180) REVERT: BB 6 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8245 (ptpt) REVERT: BC 31 TYR cc_start: 0.8819 (m-10) cc_final: 0.8219 (m-10) REVERT: BC 35 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: BC 51 ILE cc_start: 0.8802 (mt) cc_final: 0.8531 (mm) REVERT: BC 96 LYS cc_start: 0.7462 (mttp) cc_final: 0.7049 (mmtt) REVERT: BC 124 SER cc_start: 0.8432 (t) cc_final: 0.8128 (m) REVERT: BC 133 MET cc_start: 0.8212 (mtp) cc_final: 0.7953 (mtp) REVERT: BC 134 ARG cc_start: 0.8325 (tpm170) cc_final: 0.7803 (mmm160) REVERT: BC 166 GLU cc_start: 0.7510 (tp30) cc_final: 0.7145 (tm-30) REVERT: BC 184 TYR cc_start: 0.8925 (t80) cc_final: 0.8708 (t80) REVERT: BC 187 TYR cc_start: 0.8999 (t80) cc_final: 0.8576 (t80) REVERT: BD 12 SER cc_start: 0.7984 (OUTLIER) cc_final: 0.7480 (p) REVERT: BD 20 VAL cc_start: 0.7918 (t) cc_final: 0.7528 (p) REVERT: BD 136 ASP cc_start: 0.8516 (m-30) cc_final: 0.7995 (m-30) REVERT: BD 148 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.6941 (mp) REVERT: BD 165 TRP cc_start: 0.7741 (p90) cc_final: 0.6915 (p90) REVERT: BD 182 GLU cc_start: 0.8158 (mp0) cc_final: 0.7768 (mp0) REVERT: BE 91 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7746 (mt-10) REVERT: BE 177 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: BF 26 PHE cc_start: 0.7722 (m-80) cc_final: 0.7166 (m-80) REVERT: BF 27 LEU cc_start: 0.8977 (tp) cc_final: 0.8430 (tt) REVERT: BF 43 TRP cc_start: 0.6899 (OUTLIER) cc_final: 0.6570 (m-90) REVERT: BF 74 GLU cc_start: 0.8189 (tp30) cc_final: 0.7477 (tp30) REVERT: BF 78 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7365 (mm-40) REVERT: BG 118 GLU cc_start: 0.8503 (tp30) cc_final: 0.7991 (tp30) REVERT: BG 143 LYS cc_start: 0.8678 (tttt) cc_final: 0.8324 (ttpp) REVERT: BG 151 PHE cc_start: 0.8202 (m-80) cc_final: 0.7822 (m-10) REVERT: BI 105 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.7848 (mtt180) REVERT: BI 115 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7193 (tpt-90) REVERT: BI 127 ASP cc_start: 0.7823 (t0) cc_final: 0.7381 (t0) REVERT: BK 73 GLN cc_start: 0.8332 (tt0) cc_final: 0.7845 (tt0) REVERT: BK 96 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8231 (ttpt) REVERT: BL 18 LYS cc_start: 0.7587 (tttt) cc_final: 0.7345 (tptm) REVERT: BL 29 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.9067 (mp10) REVERT: BL 58 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8245 (p) REVERT: BL 59 SER cc_start: 0.9113 (m) cc_final: 0.8855 (t) REVERT: BM 49 THR cc_start: 0.8279 (p) cc_final: 0.8069 (t) REVERT: BM 59 TYR cc_start: 0.8639 (t80) cc_final: 0.8358 (t80) REVERT: BM 73 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8104 (tp30) REVERT: BN 25 ASN cc_start: 0.9078 (m110) cc_final: 0.8813 (m110) REVERT: BO 7 GLN cc_start: 0.7841 (pt0) cc_final: 0.7241 (pm20) REVERT: BO 8 LYS cc_start: 0.8339 (mttt) cc_final: 0.8068 (mttm) REVERT: BO 10 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8193 (tm-30) REVERT: BO 26 GLU cc_start: 0.8206 (mp0) cc_final: 0.7828 (mp0) REVERT: BO 79 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7630 (ttm-80) REVERT: BQ 32 MET cc_start: 0.7560 (mtm) cc_final: 0.7276 (mpp) REVERT: BQ 92 GLU cc_start: 0.8148 (pp20) cc_final: 0.7711 (pp20) REVERT: BR 35 THR cc_start: 0.8119 (m) cc_final: 0.7900 (t) REVERT: BS 18 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8379 (mtmm) REVERT: BT 20 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8167 (mtm110) REVERT: BT 85 LYS cc_start: 0.8633 (mtmm) cc_final: 0.8418 (mmtt) REVERT: BV 23 TRP cc_start: 0.7859 (OUTLIER) cc_final: 0.7312 (p-90) REVERT: BV 82 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6633 (pt0) REVERT: BV 89 MET cc_start: 0.7118 (mmt) cc_final: 0.5786 (mmt) REVERT: BV 109 LYS cc_start: 0.8403 (mmmt) cc_final: 0.8107 (mmmt) REVERT: BV 179 LEU cc_start: 0.7320 (mt) cc_final: 0.7090 (mt) outliers start: 445 outliers final: 345 residues processed: 1648 average time/residue: 1.3556 time to fit residues: 3833.4092 Evaluate side-chains 1724 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 1341 time to evaluate : 6.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 24 ARG Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 41 HIS Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 71 LEU Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 93 ARG Chi-restraints excluded: chain T residue 99 ARG Chi-restraints excluded: chain T residue 109 HIS Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 38 VAL Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 169 ASN Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 45 ASN Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 48 ASN Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 35 GLN Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain e residue 56 SER Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 3 THR Chi-restraints excluded: chain g residue 5 ILE Chi-restraints excluded: chain g residue 8 GLU Chi-restraints excluded: chain g residue 9 TYR Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain BB residue 6 LYS Chi-restraints excluded: chain BB residue 13 SER Chi-restraints excluded: chain BB residue 22 ARG Chi-restraints excluded: chain BB residue 31 LEU Chi-restraints excluded: chain BC residue 14 ILE Chi-restraints excluded: chain BC residue 16 THR Chi-restraints excluded: chain BC residue 35 ASP Chi-restraints excluded: chain BC residue 41 LEU Chi-restraints excluded: chain BC residue 67 ILE Chi-restraints excluded: chain BC residue 105 VAL Chi-restraints excluded: chain BC residue 107 ASN Chi-restraints excluded: chain BC residue 143 GLN Chi-restraints excluded: chain BC residue 149 ILE Chi-restraints excluded: chain BC residue 163 SER Chi-restraints excluded: chain BD residue 12 SER Chi-restraints excluded: chain BD residue 85 LEU Chi-restraints excluded: chain BD residue 93 LEU Chi-restraints excluded: chain BD residue 123 VAL Chi-restraints excluded: chain BD residue 145 LEU Chi-restraints excluded: chain BD residue 148 LEU Chi-restraints excluded: chain BD residue 177 VAL Chi-restraints excluded: chain BD residue 188 VAL Chi-restraints excluded: chain BE residue 73 VAL Chi-restraints excluded: chain BE residue 110 VAL Chi-restraints excluded: chain BE residue 130 VAL Chi-restraints excluded: chain BE residue 177 GLU Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BF residue 13 THR Chi-restraints excluded: chain BF residue 23 LEU Chi-restraints excluded: chain BF residue 29 VAL Chi-restraints excluded: chain BF residue 42 ILE Chi-restraints excluded: chain BF residue 43 TRP Chi-restraints excluded: chain BF residue 57 GLU Chi-restraints excluded: chain BF residue 73 SER Chi-restraints excluded: chain BF residue 76 ASP Chi-restraints excluded: chain BF residue 91 LEU Chi-restraints excluded: chain BG residue 27 VAL Chi-restraints excluded: chain BG residue 48 GLU Chi-restraints excluded: chain BG residue 59 VAL Chi-restraints excluded: chain BG residue 61 THR Chi-restraints excluded: chain BG residue 74 GLU Chi-restraints excluded: chain BG residue 84 THR Chi-restraints excluded: chain BG residue 92 ARG Chi-restraints excluded: chain BG residue 108 SER Chi-restraints excluded: chain BG residue 124 ILE Chi-restraints excluded: chain BG residue 129 ASN Chi-restraints excluded: chain BG residue 135 VAL Chi-restraints excluded: chain BH residue 4 THR Chi-restraints excluded: chain BH residue 51 THR Chi-restraints excluded: chain BH residue 87 VAL Chi-restraints excluded: chain BH residue 92 THR Chi-restraints excluded: chain BH residue 108 THR Chi-restraints excluded: chain BH residue 115 ASP Chi-restraints excluded: chain BI residue 36 VAL Chi-restraints excluded: chain BI residue 42 VAL Chi-restraints excluded: chain BI residue 58 TYR Chi-restraints excluded: chain BI residue 59 PHE Chi-restraints excluded: chain BI residue 80 GLN Chi-restraints excluded: chain BI residue 103 ILE Chi-restraints excluded: chain BI residue 105 ARG Chi-restraints excluded: chain BI residue 110 VAL Chi-restraints excluded: chain BI residue 115 ARG Chi-restraints excluded: chain BI residue 120 LYS Chi-restraints excluded: chain BJ residue 10 LEU Chi-restraints excluded: chain BJ residue 37 VAL Chi-restraints excluded: chain BJ residue 40 VAL Chi-restraints excluded: chain BJ residue 42 LEU Chi-restraints excluded: chain BJ residue 48 VAL Chi-restraints excluded: chain BJ residue 50 CYS Chi-restraints excluded: chain BJ residue 71 LYS Chi-restraints excluded: chain BJ residue 76 ILE Chi-restraints excluded: chain BJ residue 78 ASP Chi-restraints excluded: chain BJ residue 80 THR Chi-restraints excluded: chain BK residue 40 ILE Chi-restraints excluded: chain BK residue 41 VAL Chi-restraints excluded: chain BK residue 67 SER Chi-restraints excluded: chain BK residue 68 THR Chi-restraints excluded: chain BK residue 91 VAL Chi-restraints excluded: chain BK residue 95 VAL Chi-restraints excluded: chain BK residue 96 LYS Chi-restraints excluded: chain BK residue 100 SER Chi-restraints excluded: chain BK residue 114 LEU Chi-restraints excluded: chain BK residue 120 SER Chi-restraints excluded: chain BK residue 123 THR Chi-restraints excluded: chain BL residue 3 THR Chi-restraints excluded: chain BL residue 29 GLN Chi-restraints excluded: chain BL residue 34 CYS Chi-restraints excluded: chain BL residue 38 TYR Chi-restraints excluded: chain BL residue 39 THR Chi-restraints excluded: chain BL residue 40 THR Chi-restraints excluded: chain BL residue 41 THR Chi-restraints excluded: chain BL residue 58 THR Chi-restraints excluded: chain BL residue 61 VAL Chi-restraints excluded: chain BL residue 63 VAL Chi-restraints excluded: chain BL residue 87 VAL Chi-restraints excluded: chain BL residue 89 ASP Chi-restraints excluded: chain BL residue 98 ILE Chi-restraints excluded: chain BL residue 104 THR Chi-restraints excluded: chain BM residue 32 GLU Chi-restraints excluded: chain BM residue 45 THR Chi-restraints excluded: chain BM residue 51 ASP Chi-restraints excluded: chain BM residue 56 LEU Chi-restraints excluded: chain BN residue 11 ASN Chi-restraints excluded: chain BN residue 24 CYS Chi-restraints excluded: chain BN residue 47 MET Chi-restraints excluded: chain BN residue 53 LEU Chi-restraints excluded: chain BO residue 20 THR Chi-restraints excluded: chain BO residue 24 SER Chi-restraints excluded: chain BO residue 75 VAL Chi-restraints excluded: chain BO residue 80 SER Chi-restraints excluded: chain BP residue 3 VAL Chi-restraints excluded: chain BP residue 15 ASN Chi-restraints excluded: chain BP residue 27 THR Chi-restraints excluded: chain BP residue 30 ASP Chi-restraints excluded: chain BP residue 44 GLU Chi-restraints excluded: chain BP residue 45 GLU Chi-restraints excluded: chain BP residue 81 GLN Chi-restraints excluded: chain BP residue 86 LEU Chi-restraints excluded: chain BP residue 92 THR Chi-restraints excluded: chain BQ residue 35 THR Chi-restraints excluded: chain BQ residue 42 ASP Chi-restraints excluded: chain BQ residue 55 THR Chi-restraints excluded: chain BQ residue 72 ASP Chi-restraints excluded: chain BQ residue 93 ILE Chi-restraints excluded: chain BQ residue 95 GLU Chi-restraints excluded: chain BR residue 21 VAL Chi-restraints excluded: chain BR residue 51 ARG Chi-restraints excluded: chain BR residue 53 VAL Chi-restraints excluded: chain BS residue 12 ASP Chi-restraints excluded: chain BS residue 14 HIS Chi-restraints excluded: chain BS residue 18 LYS Chi-restraints excluded: chain BS residue 33 THR Chi-restraints excluded: chain BS residue 38 SER Chi-restraints excluded: chain BS residue 39 THR Chi-restraints excluded: chain BS residue 56 LYS Chi-restraints excluded: chain BS residue 67 VAL Chi-restraints excluded: chain BT residue 13 THR Chi-restraints excluded: chain BT residue 45 ASP Chi-restraints excluded: chain BT residue 50 LEU Chi-restraints excluded: chain BT residue 55 SER Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BV residue 4 VAL Chi-restraints excluded: chain BV residue 6 MET Chi-restraints excluded: chain BV residue 23 TRP Chi-restraints excluded: chain BV residue 31 ILE Chi-restraints excluded: chain BV residue 38 ILE Chi-restraints excluded: chain BV residue 66 THR Chi-restraints excluded: chain BV residue 68 LEU Chi-restraints excluded: chain BV residue 82 GLU Chi-restraints excluded: chain BV residue 92 VAL Chi-restraints excluded: chain BV residue 117 LEU Chi-restraints excluded: chain BV residue 155 GLN Chi-restraints excluded: chain BV residue 157 VAL Chi-restraints excluded: chain BV residue 186 ILE Chi-restraints excluded: chain BV residue 204 ASP Chi-restraints excluded: chain BV residue 205 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 992 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 586 optimal weight: 20.0000 chunk 751 optimal weight: 20.0000 chunk 582 optimal weight: 6.9990 chunk 866 optimal weight: 50.0000 chunk 574 optimal weight: 7.9990 chunk 1025 optimal weight: 30.0000 chunk 641 optimal weight: 20.0000 chunk 625 optimal weight: 10.0000 chunk 473 optimal weight: 10.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN D 20 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 208 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN H 137 HIS K 117 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 52 GLN ** b 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 110 GLN BL 73 ASN BL 105 GLN BL 109 ASN BM 31 ASN BV 108 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 163913 Z= 0.265 Angle : 0.605 12.019 245455 Z= 0.307 Chirality : 0.036 0.287 31408 Planarity : 0.005 0.072 13199 Dihedral : 24.393 179.943 82894 Min Nonbonded Distance : 1.063 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 8.24 % Allowed : 25.45 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: -0.26 (0.11), residues: 5979 helix: 0.90 (0.12), residues: 2046 sheet: -0.31 (0.14), residues: 1206 loop : -0.89 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPBF 43 HIS 0.006 0.001 HIS e 7 PHE 0.024 0.002 PHEBP 106 TYR 0.028 0.002 TYRBC 23 ARG 0.013 0.001 ARG U 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1788 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 407 poor density : 1381 time to evaluate : 6.571 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: 3 8 LYS cc_start: 0.8734 (mttt) cc_final: 0.8525 (mttt) REVERT: 3 15 LYS cc_start: 0.9000 (tppt) cc_final: 0.8699 (tttp) REVERT: C 13 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.7836 (mtm180) REVERT: C 66 ASP cc_start: 0.8537 (t0) cc_final: 0.8179 (t0) REVERT: C 71 ASP cc_start: 0.8960 (p0) cc_final: 0.8741 (p0) REVERT: C 198 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8541 (m110) REVERT: C 265 ASP cc_start: 0.8227 (m-30) cc_final: 0.8025 (m-30) REVERT: C 270 ARG cc_start: 0.7631 (ptt-90) cc_final: 0.7413 (ptt-90) REVERT: D 56 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8406 (tp30) REVERT: D 87 ASP cc_start: 0.7983 (m-30) cc_final: 0.7718 (m-30) REVERT: E 30 ASN cc_start: 0.8426 (t0) cc_final: 0.8152 (t0) REVERT: E 106 MET cc_start: 0.8818 (mtp) cc_final: 0.8598 (mtm) REVERT: E 192 ASP cc_start: 0.8060 (m-30) cc_final: 0.7705 (m-30) REVERT: F 13 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8333 (pp30) REVERT: F 142 GLN cc_start: 0.9000 (pm20) cc_final: 0.8584 (pp30) REVERT: G 59 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8371 (tm-30) REVERT: G 90 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9096 (mm) REVERT: G 165 TYR cc_start: 0.7942 (m-80) cc_final: 0.7615 (m-80) REVERT: H 6 THR cc_start: 0.8255 (m) cc_final: 0.7396 (p) REVERT: H 143 LYS cc_start: 0.8749 (mttt) cc_final: 0.8442 (tptm) REVERT: K 23 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8769 (m) REVERT: K 37 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8415 (ttt180) REVERT: K 106 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8870 (mp) REVERT: K 108 MET cc_start: 0.9142 (mtm) cc_final: 0.8885 (mtm) REVERT: L 1 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8317 (tpp) REVERT: L 80 ASP cc_start: 0.7801 (m-30) cc_final: 0.7491 (m-30) REVERT: L 90 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7620 (p0) REVERT: M 24 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.7881 (tpp80) REVERT: M 138 THR cc_start: 0.8795 (m) cc_final: 0.8419 (p) REVERT: P 24 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.9092 (ttp-110) REVERT: P 28 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8653 (mtpp) REVERT: P 126 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7722 (mmtt) REVERT: R 18 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8988 (mm) REVERT: R 42 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8515 (m) REVERT: R 63 SER cc_start: 0.9339 (m) cc_final: 0.8990 (m) REVERT: R 102 ASP cc_start: 0.7981 (t0) cc_final: 0.7431 (t0) REVERT: S 44 ASP cc_start: 0.7686 (p0) cc_final: 0.7100 (p0) REVERT: S 87 ARG cc_start: 0.8700 (mtt90) cc_final: 0.8427 (mtt90) REVERT: T 93 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8455 (ttm170) REVERT: W 50 ASN cc_start: 0.8800 (t0) cc_final: 0.8266 (t0) REVERT: W 53 ASP cc_start: 0.8617 (m-30) cc_final: 0.8363 (p0) REVERT: W 70 ASP cc_start: 0.8748 (t0) cc_final: 0.8231 (p0) REVERT: W 89 ARG cc_start: 0.8868 (mtm-85) cc_final: 0.8613 (mtm-85) REVERT: Y 10 LYS cc_start: 0.8592 (tttt) cc_final: 0.8258 (mttt) REVERT: Y 28 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7214 (ptp-170) REVERT: Z 35 GLN cc_start: 0.8433 (mp10) cc_final: 0.7936 (mp10) REVERT: Z 42 SER cc_start: 0.8085 (p) cc_final: 0.7884 (m) REVERT: a 48 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8326 (t0) REVERT: b 6 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7997 (mtt90) REVERT: b 31 SER cc_start: 0.9304 (p) cc_final: 0.9029 (p) REVERT: b 35 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7123 (pp30) REVERT: c 25 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8645 (p) REVERT: c 49 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8251 (mm-40) REVERT: d 15 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8192 (ttm110) REVERT: e 47 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8490 (mtm110) REVERT: g 1 MET cc_start: 0.8086 (tpp) cc_final: 0.7440 (tpp) REVERT: g 9 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7073 (t80) REVERT: BB 6 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8163 (ptpt) REVERT: BC 31 TYR cc_start: 0.8800 (m-10) cc_final: 0.8224 (m-10) REVERT: BC 35 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7869 (m-30) REVERT: BC 51 ILE cc_start: 0.8806 (mt) cc_final: 0.8523 (mm) REVERT: BC 96 LYS cc_start: 0.7453 (mttp) cc_final: 0.7088 (mmtt) REVERT: BC 134 ARG cc_start: 0.8275 (tpm170) cc_final: 0.7936 (tpp-160) REVERT: BC 187 TYR cc_start: 0.8983 (t80) cc_final: 0.8596 (t80) REVERT: BD 12 SER cc_start: 0.7931 (OUTLIER) cc_final: 0.7420 (p) REVERT: BD 20 VAL cc_start: 0.7985 (t) cc_final: 0.7549 (p) REVERT: BD 136 ASP cc_start: 0.8742 (m-30) cc_final: 0.8321 (m-30) REVERT: BD 165 TRP cc_start: 0.7477 (p90) cc_final: 0.6749 (p90) REVERT: BD 182 GLU cc_start: 0.8145 (mp0) cc_final: 0.7773 (mp0) REVERT: BE 80 GLU cc_start: 0.7883 (tp30) cc_final: 0.7210 (tp30) REVERT: BE 177 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: BF 1 MET cc_start: 0.7672 (tmm) cc_final: 0.7140 (tmm) REVERT: BF 27 LEU cc_start: 0.9000 (tp) cc_final: 0.8522 (tt) REVERT: BF 43 TRP cc_start: 0.7027 (OUTLIER) cc_final: 0.6760 (m-90) REVERT: BF 74 GLU cc_start: 0.8455 (tp30) cc_final: 0.7748 (tp30) REVERT: BF 78 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7313 (mm-40) REVERT: BG 118 GLU cc_start: 0.8449 (tp30) cc_final: 0.7989 (tp30) REVERT: BG 143 LYS cc_start: 0.8675 (tttt) cc_final: 0.8415 (ttpp) REVERT: BG 151 PHE cc_start: 0.8211 (m-10) cc_final: 0.7757 (m-10) REVERT: BI 105 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7855 (mtt180) REVERT: BI 115 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7194 (tpt-90) REVERT: BI 127 ASP cc_start: 0.7790 (t0) cc_final: 0.7336 (t0) REVERT: BJ 23 ARG cc_start: 0.8000 (mmm160) cc_final: 0.7129 (mmt-90) REVERT: BJ 24 LYS cc_start: 0.8562 (mmmm) cc_final: 0.7956 (tmtt) REVERT: BK 65 ARG cc_start: 0.9090 (ttm110) cc_final: 0.8855 (ttm110) REVERT: BK 73 GLN cc_start: 0.8375 (tt0) cc_final: 0.7916 (tt0) REVERT: BK 96 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8226 (ttpt) REVERT: BL 18 LYS cc_start: 0.7571 (tttt) cc_final: 0.7322 (tptm) REVERT: BL 58 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8254 (p) REVERT: BL 59 SER cc_start: 0.9116 (m) cc_final: 0.8834 (t) REVERT: BM 59 TYR cc_start: 0.8605 (t80) cc_final: 0.8315 (t80) REVERT: BM 117 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6637 (mm) REVERT: BN 25 ASN cc_start: 0.9055 (m110) cc_final: 0.8810 (m110) REVERT: BO 10 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8115 (tm-30) REVERT: BO 26 GLU cc_start: 0.8132 (mp0) cc_final: 0.7814 (mp0) REVERT: BO 79 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7697 (ttm-80) REVERT: BQ 32 MET cc_start: 0.7563 (mtm) cc_final: 0.7275 (mpp) REVERT: BQ 73 ARG cc_start: 0.8167 (ttt-90) cc_final: 0.7818 (ttp80) REVERT: BR 35 THR cc_start: 0.8158 (m) cc_final: 0.7935 (t) REVERT: BS 18 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8366 (mtmm) REVERT: BT 20 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8165 (mtm110) REVERT: BT 85 LYS cc_start: 0.8592 (mtmm) cc_final: 0.8355 (mmtt) REVERT: BV 23 TRP cc_start: 0.7776 (OUTLIER) cc_final: 0.7230 (p-90) REVERT: BV 82 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6783 (pt0) REVERT: BV 89 MET cc_start: 0.7235 (mmt) cc_final: 0.5829 (mmt) REVERT: BV 121 GLU cc_start: 0.6168 (tm-30) cc_final: 0.5814 (mm-30) REVERT: BV 178 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6272 (tttt) REVERT: BV 179 LEU cc_start: 0.7334 (mt) cc_final: 0.7059 (mt) outliers start: 407 outliers final: 329 residues processed: 1633 average time/residue: 1.4063 time to fit residues: 3965.0228 Evaluate side-chains 1712 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 1348 time to evaluate : 6.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 15 GLU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 24 ARG Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 41 HIS Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 93 ARG Chi-restraints excluded: chain T residue 99 ARG Chi-restraints excluded: chain T residue 109 HIS Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 38 VAL Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 169 ASN Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 45 ASN Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 13 LEU Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 48 ASN Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 35 GLN Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain e residue 56 SER Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 5 ILE Chi-restraints excluded: chain g residue 8 GLU Chi-restraints excluded: chain g residue 9 TYR Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain BB residue 6 LYS Chi-restraints excluded: chain BB residue 13 SER Chi-restraints excluded: chain BB residue 22 ARG Chi-restraints excluded: chain BB residue 31 LEU Chi-restraints excluded: chain BC residue 16 THR Chi-restraints excluded: chain BC residue 35 ASP Chi-restraints excluded: chain BC residue 67 ILE Chi-restraints excluded: chain BC residue 110 SER Chi-restraints excluded: chain BC residue 143 GLN Chi-restraints excluded: chain BC residue 149 ILE Chi-restraints excluded: chain BC residue 163 SER Chi-restraints excluded: chain BD residue 12 SER Chi-restraints excluded: chain BD residue 85 LEU Chi-restraints excluded: chain BD residue 93 LEU Chi-restraints excluded: chain BD residue 145 LEU Chi-restraints excluded: chain BD residue 177 VAL Chi-restraints excluded: chain BD residue 188 VAL Chi-restraints excluded: chain BE residue 71 VAL Chi-restraints excluded: chain BE residue 73 VAL Chi-restraints excluded: chain BE residue 110 VAL Chi-restraints excluded: chain BE residue 130 VAL Chi-restraints excluded: chain BE residue 177 GLU Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BF residue 13 THR Chi-restraints excluded: chain BF residue 23 LEU Chi-restraints excluded: chain BF residue 29 VAL Chi-restraints excluded: chain BF residue 42 ILE Chi-restraints excluded: chain BF residue 43 TRP Chi-restraints excluded: chain BF residue 57 GLU Chi-restraints excluded: chain BF residue 76 ASP Chi-restraints excluded: chain BF residue 84 SER Chi-restraints excluded: chain BF residue 91 LEU Chi-restraints excluded: chain BG residue 27 VAL Chi-restraints excluded: chain BG residue 48 GLU Chi-restraints excluded: chain BG residue 61 THR Chi-restraints excluded: chain BG residue 84 THR Chi-restraints excluded: chain BG residue 92 ARG Chi-restraints excluded: chain BG residue 108 SER Chi-restraints excluded: chain BG residue 124 ILE Chi-restraints excluded: chain BG residue 129 ASN Chi-restraints excluded: chain BG residue 135 VAL Chi-restraints excluded: chain BH residue 4 THR Chi-restraints excluded: chain BH residue 51 THR Chi-restraints excluded: chain BH residue 87 VAL Chi-restraints excluded: chain BH residue 108 THR Chi-restraints excluded: chain BH residue 115 ASP Chi-restraints excluded: chain BH residue 123 VAL Chi-restraints excluded: chain BI residue 36 VAL Chi-restraints excluded: chain BI residue 42 VAL Chi-restraints excluded: chain BI residue 48 PHE Chi-restraints excluded: chain BI residue 58 TYR Chi-restraints excluded: chain BI residue 59 PHE Chi-restraints excluded: chain BI residue 80 GLN Chi-restraints excluded: chain BI residue 103 ILE Chi-restraints excluded: chain BI residue 105 ARG Chi-restraints excluded: chain BI residue 115 ARG Chi-restraints excluded: chain BI residue 120 LYS Chi-restraints excluded: chain BJ residue 37 VAL Chi-restraints excluded: chain BJ residue 48 VAL Chi-restraints excluded: chain BJ residue 50 CYS Chi-restraints excluded: chain BJ residue 71 LYS Chi-restraints excluded: chain BJ residue 76 ILE Chi-restraints excluded: chain BJ residue 78 ASP Chi-restraints excluded: chain BJ residue 80 THR Chi-restraints excluded: chain BK residue 37 ASN Chi-restraints excluded: chain BK residue 40 ILE Chi-restraints excluded: chain BK residue 41 VAL Chi-restraints excluded: chain BK residue 67 SER Chi-restraints excluded: chain BK residue 68 THR Chi-restraints excluded: chain BK residue 91 VAL Chi-restraints excluded: chain BK residue 95 VAL Chi-restraints excluded: chain BK residue 96 LYS Chi-restraints excluded: chain BK residue 104 THR Chi-restraints excluded: chain BK residue 108 SER Chi-restraints excluded: chain BK residue 114 LEU Chi-restraints excluded: chain BK residue 120 SER Chi-restraints excluded: chain BK residue 123 THR Chi-restraints excluded: chain BL residue 3 THR Chi-restraints excluded: chain BL residue 34 CYS Chi-restraints excluded: chain BL residue 38 TYR Chi-restraints excluded: chain BL residue 39 THR Chi-restraints excluded: chain BL residue 40 THR Chi-restraints excluded: chain BL residue 41 THR Chi-restraints excluded: chain BL residue 58 THR Chi-restraints excluded: chain BL residue 61 VAL Chi-restraints excluded: chain BL residue 63 VAL Chi-restraints excluded: chain BL residue 87 VAL Chi-restraints excluded: chain BL residue 89 ASP Chi-restraints excluded: chain BL residue 104 THR Chi-restraints excluded: chain BL residue 109 ASN Chi-restraints excluded: chain BM residue 45 THR Chi-restraints excluded: chain BM residue 51 ASP Chi-restraints excluded: chain BM residue 56 LEU Chi-restraints excluded: chain BM residue 117 ILE Chi-restraints excluded: chain BN residue 24 CYS Chi-restraints excluded: chain BN residue 47 MET Chi-restraints excluded: chain BN residue 53 LEU Chi-restraints excluded: chain BO residue 20 THR Chi-restraints excluded: chain BO residue 24 SER Chi-restraints excluded: chain BO residue 75 VAL Chi-restraints excluded: chain BO residue 80 SER Chi-restraints excluded: chain BP residue 15 ASN Chi-restraints excluded: chain BP residue 27 THR Chi-restraints excluded: chain BP residue 30 ASP Chi-restraints excluded: chain BP residue 44 GLU Chi-restraints excluded: chain BP residue 45 GLU Chi-restraints excluded: chain BP residue 81 GLN Chi-restraints excluded: chain BP residue 86 LEU Chi-restraints excluded: chain BP residue 92 THR Chi-restraints excluded: chain BQ residue 35 THR Chi-restraints excluded: chain BQ residue 42 ASP Chi-restraints excluded: chain BQ residue 55 THR Chi-restraints excluded: chain BQ residue 72 ASP Chi-restraints excluded: chain BQ residue 93 ILE Chi-restraints excluded: chain BQ residue 95 GLU Chi-restraints excluded: chain BR residue 21 VAL Chi-restraints excluded: chain BR residue 47 LYS Chi-restraints excluded: chain BR residue 51 ARG Chi-restraints excluded: chain BR residue 53 VAL Chi-restraints excluded: chain BS residue 12 ASP Chi-restraints excluded: chain BS residue 33 THR Chi-restraints excluded: chain BS residue 38 SER Chi-restraints excluded: chain BS residue 39 THR Chi-restraints excluded: chain BS residue 56 LYS Chi-restraints excluded: chain BS residue 67 VAL Chi-restraints excluded: chain BT residue 13 THR Chi-restraints excluded: chain BT residue 45 ASP Chi-restraints excluded: chain BT residue 55 SER Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BV residue 4 VAL Chi-restraints excluded: chain BV residue 6 MET Chi-restraints excluded: chain BV residue 23 TRP Chi-restraints excluded: chain BV residue 31 ILE Chi-restraints excluded: chain BV residue 38 ILE Chi-restraints excluded: chain BV residue 66 THR Chi-restraints excluded: chain BV residue 68 LEU Chi-restraints excluded: chain BV residue 82 GLU Chi-restraints excluded: chain BV residue 92 VAL Chi-restraints excluded: chain BV residue 117 LEU Chi-restraints excluded: chain BV residue 137 LEU Chi-restraints excluded: chain BV residue 155 GLN Chi-restraints excluded: chain BV residue 157 VAL Chi-restraints excluded: chain BV residue 178 LYS Chi-restraints excluded: chain BV residue 186 ILE Chi-restraints excluded: chain BV residue 188 ASP Chi-restraints excluded: chain BV residue 204 ASP Chi-restraints excluded: chain BV residue 205 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 634 optimal weight: 10.0000 chunk 409 optimal weight: 9.9990 chunk 612 optimal weight: 20.0000 chunk 308 optimal weight: 20.0000 chunk 201 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 651 optimal weight: 2.9990 chunk 698 optimal weight: 30.0000 chunk 507 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 806 optimal weight: 30.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN D 20 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 GLN K 119 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 GLN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 GLN ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 52 GLN ** b 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BD 146 ASN BG 106 ASN ** BK 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 110 GLN BM 101 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 163913 Z= 0.268 Angle : 0.607 12.661 245455 Z= 0.308 Chirality : 0.036 0.284 31408 Planarity : 0.005 0.072 13199 Dihedral : 24.368 179.877 82887 Min Nonbonded Distance : 1.053 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.49 % Favored : 95.50 % Rotamer: Outliers : 8.14 % Allowed : 25.81 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: -0.22 (0.11), residues: 5979 helix: 0.93 (0.12), residues: 2046 sheet: -0.26 (0.14), residues: 1200 loop : -0.86 (0.12), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPBQ 88 HIS 0.006 0.001 HIS E 176 PHE 0.027 0.002 PHEBP 106 TYR 0.028 0.002 TYRBC 23 ARG 0.012 0.001 ARG U 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1791 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 402 poor density : 1389 time to evaluate : 6.680 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: 3 8 LYS cc_start: 0.8737 (mttt) cc_final: 0.8512 (mttt) REVERT: 3 15 LYS cc_start: 0.9010 (tppt) cc_final: 0.8690 (tttp) REVERT: C 10 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.8893 (p) REVERT: C 13 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7780 (mtm180) REVERT: C 66 ASP cc_start: 0.8564 (t0) cc_final: 0.8199 (t0) REVERT: C 71 ASP cc_start: 0.8971 (p0) cc_final: 0.8739 (p0) REVERT: C 198 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8538 (m110) REVERT: D 56 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8429 (tp30) REVERT: D 87 ASP cc_start: 0.8006 (m-30) cc_final: 0.7753 (m-30) REVERT: E 30 ASN cc_start: 0.8612 (t0) cc_final: 0.8307 (t0) REVERT: E 106 MET cc_start: 0.8822 (mtp) cc_final: 0.8604 (mtm) REVERT: E 192 ASP cc_start: 0.8087 (m-30) cc_final: 0.7729 (m-30) REVERT: F 13 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8322 (pp30) REVERT: F 142 GLN cc_start: 0.9005 (pm20) cc_final: 0.8599 (pp30) REVERT: G 23 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.6953 (p0) REVERT: G 90 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9075 (mm) REVERT: G 172 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6727 (ptm160) REVERT: H 6 THR cc_start: 0.8268 (m) cc_final: 0.7427 (p) REVERT: H 143 LYS cc_start: 0.8815 (mttt) cc_final: 0.8465 (tptm) REVERT: K 23 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8748 (m) REVERT: K 37 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8414 (ttt180) REVERT: K 106 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8869 (mp) REVERT: K 108 MET cc_start: 0.9140 (mtm) cc_final: 0.8888 (mtm) REVERT: L 1 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8292 (tpp) REVERT: L 80 ASP cc_start: 0.7827 (m-30) cc_final: 0.7471 (m-30) REVERT: M 24 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.7883 (tpp80) REVERT: M 138 THR cc_start: 0.8789 (m) cc_final: 0.8414 (p) REVERT: O 9 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8730 (mmt90) REVERT: O 30 GLU cc_start: 0.8334 (tt0) cc_final: 0.7983 (tt0) REVERT: P 24 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.9084 (ttp-110) REVERT: P 28 LYS cc_start: 0.8982 (mmmm) cc_final: 0.8661 (mtpp) REVERT: P 126 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7671 (mmtt) REVERT: R 18 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8976 (mm) REVERT: R 42 SER cc_start: 0.9128 (OUTLIER) cc_final: 0.8516 (m) REVERT: R 63 SER cc_start: 0.9341 (m) cc_final: 0.8988 (m) REVERT: R 102 ASP cc_start: 0.7990 (t0) cc_final: 0.7425 (t0) REVERT: S 44 ASP cc_start: 0.7845 (p0) cc_final: 0.7235 (p0) REVERT: S 87 ARG cc_start: 0.8706 (mtt90) cc_final: 0.8435 (mtt90) REVERT: T 37 GLU cc_start: 0.7934 (pm20) cc_final: 0.7575 (pm20) REVERT: T 93 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8443 (ttm170) REVERT: U 66 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8045 (mtp85) REVERT: W 70 ASP cc_start: 0.8775 (t0) cc_final: 0.8286 (p0) REVERT: W 89 ARG cc_start: 0.8862 (mtm-85) cc_final: 0.8571 (mtm-85) REVERT: Y 10 LYS cc_start: 0.8598 (tttt) cc_final: 0.8258 (mttt) REVERT: Y 28 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7290 (ptp-170) REVERT: Z 24 GLU cc_start: 0.8630 (tp30) cc_final: 0.7921 (tp30) REVERT: Z 35 GLN cc_start: 0.8458 (mp10) cc_final: 0.7859 (mp10) REVERT: a 48 ASN cc_start: 0.8520 (t0) cc_final: 0.8125 (t0) REVERT: b 6 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7973 (mtt90) REVERT: b 31 SER cc_start: 0.9303 (p) cc_final: 0.9031 (p) REVERT: b 35 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7405 (pp30) REVERT: b 55 ASP cc_start: 0.6928 (m-30) cc_final: 0.6651 (m-30) REVERT: c 25 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8678 (p) REVERT: c 49 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8311 (mm-40) REVERT: d 15 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8193 (ttm110) REVERT: e 47 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8685 (mtm110) REVERT: g 1 MET cc_start: 0.8108 (tpp) cc_final: 0.7476 (tpp) REVERT: g 9 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7022 (t80) REVERT: BB 6 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8169 (ptpt) REVERT: BC 31 TYR cc_start: 0.8787 (m-10) cc_final: 0.8239 (m-10) REVERT: BC 35 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: BC 96 LYS cc_start: 0.7372 (mttp) cc_final: 0.7135 (mmtt) REVERT: BC 124 SER cc_start: 0.8552 (t) cc_final: 0.8203 (m) REVERT: BC 134 ARG cc_start: 0.8440 (tpm170) cc_final: 0.8122 (tpp-160) REVERT: BC 166 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7288 (tm-30) REVERT: BC 187 TYR cc_start: 0.8993 (t80) cc_final: 0.8617 (t80) REVERT: BD 20 VAL cc_start: 0.7940 (t) cc_final: 0.7494 (p) REVERT: BD 40 ARG cc_start: 0.4976 (tpm170) cc_final: 0.4501 (ttm-80) REVERT: BD 136 ASP cc_start: 0.8607 (m-30) cc_final: 0.8115 (m-30) REVERT: BD 182 GLU cc_start: 0.8158 (mp0) cc_final: 0.7830 (mp0) REVERT: BE 80 GLU cc_start: 0.7887 (tp30) cc_final: 0.7211 (tp30) REVERT: BE 177 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: BF 1 MET cc_start: 0.7633 (tmm) cc_final: 0.7223 (tmm) REVERT: BF 27 LEU cc_start: 0.9073 (tp) cc_final: 0.8680 (tt) REVERT: BF 28 ASN cc_start: 0.8141 (m110) cc_final: 0.7710 (p0) REVERT: BF 43 TRP cc_start: 0.6997 (OUTLIER) cc_final: 0.6087 (m-90) REVERT: BF 74 GLU cc_start: 0.8484 (tp30) cc_final: 0.7709 (tp30) REVERT: BF 78 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7436 (mm-40) REVERT: BG 118 GLU cc_start: 0.8454 (tp30) cc_final: 0.8014 (tp30) REVERT: BG 136 LYS cc_start: 0.8582 (tptp) cc_final: 0.7913 (tptt) REVERT: BG 143 LYS cc_start: 0.8747 (tttt) cc_final: 0.8387 (ttpp) REVERT: BG 151 PHE cc_start: 0.8227 (m-10) cc_final: 0.7727 (m-10) REVERT: BI 105 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7833 (mtt180) REVERT: BI 115 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7221 (tpt-90) REVERT: BI 127 ASP cc_start: 0.7683 (t0) cc_final: 0.7197 (t0) REVERT: BJ 24 LYS cc_start: 0.8612 (mmmm) cc_final: 0.7993 (tmtt) REVERT: BK 65 ARG cc_start: 0.9117 (ttm110) cc_final: 0.8839 (ttm110) REVERT: BK 73 GLN cc_start: 0.8324 (tt0) cc_final: 0.7878 (tt0) REVERT: BK 96 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8233 (ttpt) REVERT: BL 18 LYS cc_start: 0.7560 (tttt) cc_final: 0.7311 (tptm) REVERT: BL 59 SER cc_start: 0.9118 (m) cc_final: 0.8842 (t) REVERT: BM 21 TYR cc_start: 0.8131 (m-80) cc_final: 0.7913 (m-80) REVERT: BM 59 TYR cc_start: 0.8593 (t80) cc_final: 0.8314 (t80) REVERT: BM 73 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8058 (tp30) REVERT: BM 101 GLN cc_start: 0.8585 (mt0) cc_final: 0.8276 (mt0) REVERT: BN 25 ASN cc_start: 0.9050 (m110) cc_final: 0.8850 (m110) REVERT: BO 10 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8158 (tm-30) REVERT: BO 26 GLU cc_start: 0.8148 (mp0) cc_final: 0.7844 (mp0) REVERT: BO 36 ILE cc_start: 0.9179 (mt) cc_final: 0.8946 (mt) REVERT: BO 79 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7759 (ttm-80) REVERT: BP 86 LEU cc_start: 0.6062 (OUTLIER) cc_final: 0.5201 (tp) REVERT: BP 96 LYS cc_start: 0.7319 (tptp) cc_final: 0.7108 (tppt) REVERT: BQ 32 MET cc_start: 0.7581 (mtm) cc_final: 0.7284 (mpp) REVERT: BQ 73 ARG cc_start: 0.8180 (ttt-90) cc_final: 0.7856 (ttp80) REVERT: BR 35 THR cc_start: 0.8348 (m) cc_final: 0.8003 (t) REVERT: BT 20 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8172 (mtm110) REVERT: BT 33 ARG cc_start: 0.8672 (ttt180) cc_final: 0.8433 (ttp80) REVERT: BV 23 TRP cc_start: 0.7717 (OUTLIER) cc_final: 0.7136 (p-90) REVERT: BV 82 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6784 (pt0) REVERT: BV 89 MET cc_start: 0.7116 (mmt) cc_final: 0.5684 (mmt) REVERT: BV 121 GLU cc_start: 0.5865 (tm-30) cc_final: 0.5500 (mm-30) REVERT: BV 178 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6280 (tttt) REVERT: BV 179 LEU cc_start: 0.7331 (mt) cc_final: 0.7055 (mt) outliers start: 402 outliers final: 329 residues processed: 1627 average time/residue: 1.4012 time to fit residues: 3922.2102 Evaluate side-chains 1719 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 1354 time to evaluate : 6.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 172 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 76 GLN Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 9 ARG Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 24 ARG Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 41 HIS Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 93 ARG Chi-restraints excluded: chain T residue 99 ARG Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 66 ARG Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 38 VAL Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 45 ASN Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 13 LEU Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 35 GLN Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain e residue 56 SER Chi-restraints excluded: chain e residue 60 LYS Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 5 ILE Chi-restraints excluded: chain g residue 8 GLU Chi-restraints excluded: chain g residue 9 TYR Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain BB residue 6 LYS Chi-restraints excluded: chain BB residue 13 SER Chi-restraints excluded: chain BB residue 22 ARG Chi-restraints excluded: chain BB residue 31 LEU Chi-restraints excluded: chain BC residue 16 THR Chi-restraints excluded: chain BC residue 35 ASP Chi-restraints excluded: chain BC residue 67 ILE Chi-restraints excluded: chain BC residue 107 ASN Chi-restraints excluded: chain BC residue 137 ILE Chi-restraints excluded: chain BC residue 149 ILE Chi-restraints excluded: chain BC residue 163 SER Chi-restraints excluded: chain BD residue 85 LEU Chi-restraints excluded: chain BD residue 93 LEU Chi-restraints excluded: chain BD residue 145 LEU Chi-restraints excluded: chain BD residue 146 ASN Chi-restraints excluded: chain BD residue 177 VAL Chi-restraints excluded: chain BD residue 188 VAL Chi-restraints excluded: chain BD residue 200 SER Chi-restraints excluded: chain BE residue 71 VAL Chi-restraints excluded: chain BE residue 73 VAL Chi-restraints excluded: chain BE residue 110 VAL Chi-restraints excluded: chain BE residue 130 VAL Chi-restraints excluded: chain BE residue 140 LEU Chi-restraints excluded: chain BE residue 177 GLU Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BF residue 13 THR Chi-restraints excluded: chain BF residue 23 LEU Chi-restraints excluded: chain BF residue 29 VAL Chi-restraints excluded: chain BF residue 42 ILE Chi-restraints excluded: chain BF residue 43 TRP Chi-restraints excluded: chain BF residue 57 GLU Chi-restraints excluded: chain BF residue 76 ASP Chi-restraints excluded: chain BF residue 91 LEU Chi-restraints excluded: chain BG residue 27 VAL Chi-restraints excluded: chain BG residue 48 GLU Chi-restraints excluded: chain BG residue 53 LYS Chi-restraints excluded: chain BG residue 59 VAL Chi-restraints excluded: chain BG residue 61 THR Chi-restraints excluded: chain BG residue 84 THR Chi-restraints excluded: chain BG residue 92 ARG Chi-restraints excluded: chain BG residue 108 SER Chi-restraints excluded: chain BG residue 124 ILE Chi-restraints excluded: chain BG residue 129 ASN Chi-restraints excluded: chain BG residue 135 VAL Chi-restraints excluded: chain BH residue 4 THR Chi-restraints excluded: chain BH residue 51 THR Chi-restraints excluded: chain BH residue 87 VAL Chi-restraints excluded: chain BH residue 108 THR Chi-restraints excluded: chain BH residue 115 ASP Chi-restraints excluded: chain BH residue 123 VAL Chi-restraints excluded: chain BI residue 36 VAL Chi-restraints excluded: chain BI residue 42 VAL Chi-restraints excluded: chain BI residue 58 TYR Chi-restraints excluded: chain BI residue 59 PHE Chi-restraints excluded: chain BI residue 80 GLN Chi-restraints excluded: chain BI residue 103 ILE Chi-restraints excluded: chain BI residue 105 ARG Chi-restraints excluded: chain BI residue 110 VAL Chi-restraints excluded: chain BI residue 115 ARG Chi-restraints excluded: chain BI residue 120 LYS Chi-restraints excluded: chain BJ residue 37 VAL Chi-restraints excluded: chain BJ residue 40 VAL Chi-restraints excluded: chain BJ residue 48 VAL Chi-restraints excluded: chain BJ residue 71 LYS Chi-restraints excluded: chain BJ residue 76 ILE Chi-restraints excluded: chain BJ residue 78 ASP Chi-restraints excluded: chain BJ residue 80 THR Chi-restraints excluded: chain BK residue 37 ASN Chi-restraints excluded: chain BK residue 40 ILE Chi-restraints excluded: chain BK residue 41 VAL Chi-restraints excluded: chain BK residue 67 SER Chi-restraints excluded: chain BK residue 68 THR Chi-restraints excluded: chain BK residue 91 VAL Chi-restraints excluded: chain BK residue 95 VAL Chi-restraints excluded: chain BK residue 96 LYS Chi-restraints excluded: chain BK residue 100 SER Chi-restraints excluded: chain BK residue 104 THR Chi-restraints excluded: chain BK residue 108 SER Chi-restraints excluded: chain BK residue 114 LEU Chi-restraints excluded: chain BK residue 120 SER Chi-restraints excluded: chain BK residue 123 THR Chi-restraints excluded: chain BL residue 3 THR Chi-restraints excluded: chain BL residue 34 CYS Chi-restraints excluded: chain BL residue 38 TYR Chi-restraints excluded: chain BL residue 39 THR Chi-restraints excluded: chain BL residue 41 THR Chi-restraints excluded: chain BL residue 61 VAL Chi-restraints excluded: chain BL residue 63 VAL Chi-restraints excluded: chain BL residue 87 VAL Chi-restraints excluded: chain BL residue 89 ASP Chi-restraints excluded: chain BL residue 104 THR Chi-restraints excluded: chain BM residue 45 THR Chi-restraints excluded: chain BM residue 51 ASP Chi-restraints excluded: chain BM residue 56 LEU Chi-restraints excluded: chain BN residue 24 CYS Chi-restraints excluded: chain BN residue 47 MET Chi-restraints excluded: chain BN residue 53 LEU Chi-restraints excluded: chain BO residue 20 THR Chi-restraints excluded: chain BO residue 24 SER Chi-restraints excluded: chain BO residue 75 VAL Chi-restraints excluded: chain BP residue 15 ASN Chi-restraints excluded: chain BP residue 27 THR Chi-restraints excluded: chain BP residue 30 ASP Chi-restraints excluded: chain BP residue 44 GLU Chi-restraints excluded: chain BP residue 81 GLN Chi-restraints excluded: chain BP residue 86 LEU Chi-restraints excluded: chain BP residue 92 THR Chi-restraints excluded: chain BQ residue 35 THR Chi-restraints excluded: chain BQ residue 42 ASP Chi-restraints excluded: chain BQ residue 55 THR Chi-restraints excluded: chain BQ residue 72 ASP Chi-restraints excluded: chain BQ residue 95 GLU Chi-restraints excluded: chain BR residue 21 VAL Chi-restraints excluded: chain BR residue 47 LYS Chi-restraints excluded: chain BR residue 51 ARG Chi-restraints excluded: chain BR residue 53 VAL Chi-restraints excluded: chain BS residue 33 THR Chi-restraints excluded: chain BS residue 38 SER Chi-restraints excluded: chain BS residue 39 THR Chi-restraints excluded: chain BS residue 56 LYS Chi-restraints excluded: chain BS residue 67 VAL Chi-restraints excluded: chain BT residue 13 THR Chi-restraints excluded: chain BT residue 45 ASP Chi-restraints excluded: chain BT residue 55 SER Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BV residue 4 VAL Chi-restraints excluded: chain BV residue 23 TRP Chi-restraints excluded: chain BV residue 31 ILE Chi-restraints excluded: chain BV residue 38 ILE Chi-restraints excluded: chain BV residue 66 THR Chi-restraints excluded: chain BV residue 68 LEU Chi-restraints excluded: chain BV residue 82 GLU Chi-restraints excluded: chain BV residue 92 VAL Chi-restraints excluded: chain BV residue 117 LEU Chi-restraints excluded: chain BV residue 137 LEU Chi-restraints excluded: chain BV residue 155 GLN Chi-restraints excluded: chain BV residue 178 LYS Chi-restraints excluded: chain BV residue 186 ILE Chi-restraints excluded: chain BV residue 204 ASP Chi-restraints excluded: chain BV residue 205 ASP Chi-restraints excluded: chain BV residue 207 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 932 optimal weight: 0.2980 chunk 982 optimal weight: 0.0980 chunk 896 optimal weight: 20.0000 chunk 955 optimal weight: 20.0000 chunk 575 optimal weight: 9.9990 chunk 416 optimal weight: 30.0000 chunk 750 optimal weight: 20.0000 chunk 293 optimal weight: 10.0000 chunk 863 optimal weight: 8.9990 chunk 903 optimal weight: 30.0000 chunk 952 optimal weight: 8.9990 overall best weight: 5.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN D 20 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 HIS K 117 GLN K 119 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 GLN ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 169 ASN Z 52 GLN ** b 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BK 110 GLN BK 128 ASN BL 109 ASN BM 52 GLN BP 107 ASN ** BV 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 163913 Z= 0.201 Angle : 0.579 15.818 245455 Z= 0.295 Chirality : 0.034 0.270 31408 Planarity : 0.005 0.071 13199 Dihedral : 24.341 179.514 82881 Min Nonbonded Distance : 1.094 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.12 % Favored : 95.87 % Rotamer: Outliers : 6.88 % Allowed : 27.35 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: -0.10 (0.11), residues: 5979 helix: 1.01 (0.12), residues: 2046 sheet: -0.20 (0.15), residues: 1196 loop : -0.78 (0.12), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPBQ 88 HIS 0.006 0.001 HISBJ 56 PHE 0.026 0.001 PHEBP 106 TYR 0.030 0.002 TYRBC 168 ARG 0.010 0.001 ARG U 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1706 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 1366 time to evaluate : 6.791 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: 3 8 LYS cc_start: 0.8636 (mttt) cc_final: 0.8417 (mttt) REVERT: 3 15 LYS cc_start: 0.8981 (tppt) cc_final: 0.8661 (tttp) REVERT: C 10 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8795 (p) REVERT: C 13 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7666 (mtm180) REVERT: C 66 ASP cc_start: 0.8538 (t0) cc_final: 0.8170 (t0) REVERT: C 71 ASP cc_start: 0.8903 (p0) cc_final: 0.8674 (p0) REVERT: C 198 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8496 (m110) REVERT: D 56 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8440 (tp30) REVERT: D 87 ASP cc_start: 0.7986 (m-30) cc_final: 0.7728 (m-30) REVERT: E 28 GLU cc_start: 0.8191 (tp30) cc_final: 0.7965 (tp30) REVERT: E 106 MET cc_start: 0.8794 (mtp) cc_final: 0.8562 (mtm) REVERT: F 13 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8273 (pp30) REVERT: F 142 GLN cc_start: 0.8973 (pm20) cc_final: 0.8594 (pp30) REVERT: G 172 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7294 (mtp180) REVERT: H 6 THR cc_start: 0.8252 (m) cc_final: 0.7345 (p) REVERT: H 8 GLU cc_start: 0.7259 (tp30) cc_final: 0.6831 (tp30) REVERT: H 137 HIS cc_start: 0.6276 (OUTLIER) cc_final: 0.6070 (t70) REVERT: H 143 LYS cc_start: 0.8708 (mttt) cc_final: 0.8410 (tptm) REVERT: K 37 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8353 (ttt90) REVERT: K 106 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8854 (mp) REVERT: K 108 MET cc_start: 0.9109 (mtm) cc_final: 0.8864 (mtm) REVERT: L 1 MET cc_start: 0.8584 (tpt) cc_final: 0.8335 (tpp) REVERT: L 80 ASP cc_start: 0.7896 (m-30) cc_final: 0.7566 (m-30) REVERT: L 90 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7417 (p0) REVERT: M 24 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.7861 (tpp80) REVERT: M 96 ASP cc_start: 0.8545 (p0) cc_final: 0.8277 (p0) REVERT: M 138 THR cc_start: 0.8836 (m) cc_final: 0.8471 (p) REVERT: O 30 GLU cc_start: 0.8314 (tt0) cc_final: 0.7989 (tt0) REVERT: P 28 LYS cc_start: 0.8997 (mmmm) cc_final: 0.8673 (mtpp) REVERT: P 126 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7600 (mmtt) REVERT: R 18 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8917 (mm) REVERT: R 42 SER cc_start: 0.9096 (OUTLIER) cc_final: 0.8479 (m) REVERT: R 63 SER cc_start: 0.9340 (m) cc_final: 0.8990 (m) REVERT: R 102 ASP cc_start: 0.7952 (t0) cc_final: 0.7403 (t0) REVERT: S 44 ASP cc_start: 0.7830 (p0) cc_final: 0.7191 (p0) REVERT: S 87 ARG cc_start: 0.8678 (mtt90) cc_final: 0.8417 (mtt90) REVERT: T 93 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8403 (ttm170) REVERT: W 70 ASP cc_start: 0.8764 (t0) cc_final: 0.8283 (p0) REVERT: W 89 ARG cc_start: 0.8862 (mtm-85) cc_final: 0.8589 (mtm-85) REVERT: Y 10 LYS cc_start: 0.8575 (tttt) cc_final: 0.8244 (mttt) REVERT: Y 28 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8000 (ptp-170) REVERT: Z 35 GLN cc_start: 0.8420 (mp10) cc_final: 0.7808 (mp10) REVERT: Z 51 ARG cc_start: 0.8950 (mtm-85) cc_final: 0.8738 (mtm-85) REVERT: a 48 ASN cc_start: 0.8518 (t0) cc_final: 0.8127 (t0) REVERT: b 31 SER cc_start: 0.9314 (p) cc_final: 0.9043 (p) REVERT: b 35 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7319 (pp30) REVERT: c 10 LYS cc_start: 0.8521 (mmmm) cc_final: 0.8279 (mmmm) REVERT: c 25 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8646 (p) REVERT: c 49 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8220 (mm-40) REVERT: d 15 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8126 (ttm110) REVERT: e 47 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8466 (mtm110) REVERT: g 1 MET cc_start: 0.8090 (tpp) cc_final: 0.7462 (tpp) REVERT: g 9 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7028 (t80) REVERT: BB 6 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8129 (ptpt) REVERT: BC 31 TYR cc_start: 0.8775 (m-10) cc_final: 0.8240 (m-10) REVERT: BC 35 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: BC 96 LYS cc_start: 0.7354 (mttp) cc_final: 0.7133 (mmtt) REVERT: BC 134 ARG cc_start: 0.8324 (tpm170) cc_final: 0.8058 (tpp-160) REVERT: BC 187 TYR cc_start: 0.8978 (t80) cc_final: 0.8600 (t80) REVERT: BD 20 VAL cc_start: 0.7943 (t) cc_final: 0.7480 (p) REVERT: BD 40 ARG cc_start: 0.5203 (tpm170) cc_final: 0.4681 (ttm-80) REVERT: BD 136 ASP cc_start: 0.8517 (m-30) cc_final: 0.8082 (m-30) REVERT: BD 182 GLU cc_start: 0.8152 (mp0) cc_final: 0.7823 (mp0) REVERT: BE 80 GLU cc_start: 0.7829 (tp30) cc_final: 0.7160 (tp30) REVERT: BE 177 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: BF 1 MET cc_start: 0.7441 (tmm) cc_final: 0.7003 (tmm) REVERT: BF 27 LEU cc_start: 0.9019 (tp) cc_final: 0.8635 (tt) REVERT: BF 28 ASN cc_start: 0.8132 (m110) cc_final: 0.7668 (p0) REVERT: BF 43 TRP cc_start: 0.7016 (OUTLIER) cc_final: 0.6162 (m-90) REVERT: BF 74 GLU cc_start: 0.8586 (tp30) cc_final: 0.7790 (tp30) REVERT: BF 78 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7080 (mm-40) REVERT: BG 73 LEU cc_start: 0.8030 (tp) cc_final: 0.7768 (tp) REVERT: BG 118 GLU cc_start: 0.8378 (tp30) cc_final: 0.7965 (tp30) REVERT: BG 143 LYS cc_start: 0.8666 (tttt) cc_final: 0.8399 (ttpp) REVERT: BG 151 PHE cc_start: 0.8208 (m-10) cc_final: 0.7702 (m-10) REVERT: BI 105 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7864 (mtt180) REVERT: BI 115 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7497 (tpt-90) REVERT: BI 127 ASP cc_start: 0.7651 (t0) cc_final: 0.7199 (t0) REVERT: BJ 23 ARG cc_start: 0.8026 (mmp-170) cc_final: 0.7723 (mmt-90) REVERT: BJ 24 LYS cc_start: 0.8594 (mmmm) cc_final: 0.7995 (tmtt) REVERT: BK 65 ARG cc_start: 0.9096 (ttm110) cc_final: 0.8817 (ttm110) REVERT: BK 73 GLN cc_start: 0.8300 (tt0) cc_final: 0.7875 (tt0) REVERT: BK 96 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8111 (ttpt) REVERT: BL 18 LYS cc_start: 0.7453 (tttt) cc_final: 0.7226 (tptm) REVERT: BL 59 SER cc_start: 0.9079 (m) cc_final: 0.8831 (t) REVERT: BM 21 TYR cc_start: 0.8091 (m-80) cc_final: 0.7863 (m-80) REVERT: BM 59 TYR cc_start: 0.8480 (t80) cc_final: 0.8235 (t80) REVERT: BM 77 ASP cc_start: 0.8116 (m-30) cc_final: 0.7587 (m-30) REVERT: BO 10 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8211 (tm-30) REVERT: BO 26 GLU cc_start: 0.8114 (mp0) cc_final: 0.7763 (mp0) REVERT: BO 36 ILE cc_start: 0.9173 (mt) cc_final: 0.8924 (mt) REVERT: BO 79 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7741 (ttm-80) REVERT: BP 86 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5258 (tp) REVERT: BQ 32 MET cc_start: 0.7181 (mtm) cc_final: 0.6843 (mpp) REVERT: BQ 73 ARG cc_start: 0.8193 (ttt-90) cc_final: 0.7848 (ttp80) REVERT: BR 35 THR cc_start: 0.8297 (m) cc_final: 0.7972 (t) REVERT: BT 20 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8217 (mtm110) REVERT: BT 46 LYS cc_start: 0.8363 (ttpp) cc_final: 0.7907 (ttpp) REVERT: BT 75 LYS cc_start: 0.8915 (mmtp) cc_final: 0.8607 (mmmt) REVERT: BV 23 TRP cc_start: 0.7686 (OUTLIER) cc_final: 0.7183 (p-90) REVERT: BV 82 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6964 (pt0) REVERT: BV 89 MET cc_start: 0.7089 (mmt) cc_final: 0.5664 (mmt) REVERT: BV 121 GLU cc_start: 0.5833 (tm-30) cc_final: 0.5512 (mm-30) REVERT: BV 178 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6259 (tttt) outliers start: 340 outliers final: 281 residues processed: 1574 average time/residue: 1.3407 time to fit residues: 3615.5855 Evaluate side-chains 1647 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1336 time to evaluate : 6.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 172 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 137 HIS Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 41 HIS Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 71 LEU Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 93 ARG Chi-restraints excluded: chain T residue 99 ARG Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 38 VAL Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 45 ASN Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 13 LEU Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 35 GLN Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain e residue 56 SER Chi-restraints excluded: chain e residue 60 LYS Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 24 MET Chi-restraints excluded: chain g residue 9 TYR Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain BB residue 6 LYS Chi-restraints excluded: chain BB residue 13 SER Chi-restraints excluded: chain BB residue 22 ARG Chi-restraints excluded: chain BB residue 31 LEU Chi-restraints excluded: chain BC residue 16 THR Chi-restraints excluded: chain BC residue 35 ASP Chi-restraints excluded: chain BC residue 67 ILE Chi-restraints excluded: chain BC residue 107 ASN Chi-restraints excluded: chain BC residue 137 ILE Chi-restraints excluded: chain BC residue 143 GLN Chi-restraints excluded: chain BC residue 149 ILE Chi-restraints excluded: chain BC residue 163 SER Chi-restraints excluded: chain BD residue 85 LEU Chi-restraints excluded: chain BD residue 93 LEU Chi-restraints excluded: chain BD residue 145 LEU Chi-restraints excluded: chain BD residue 177 VAL Chi-restraints excluded: chain BD residue 188 VAL Chi-restraints excluded: chain BD residue 200 SER Chi-restraints excluded: chain BE residue 71 VAL Chi-restraints excluded: chain BE residue 73 VAL Chi-restraints excluded: chain BE residue 130 VAL Chi-restraints excluded: chain BE residue 140 LEU Chi-restraints excluded: chain BE residue 177 GLU Chi-restraints excluded: chain BF residue 23 LEU Chi-restraints excluded: chain BF residue 29 VAL Chi-restraints excluded: chain BF residue 42 ILE Chi-restraints excluded: chain BF residue 43 TRP Chi-restraints excluded: chain BF residue 57 GLU Chi-restraints excluded: chain BF residue 76 ASP Chi-restraints excluded: chain BF residue 91 LEU Chi-restraints excluded: chain BG residue 27 VAL Chi-restraints excluded: chain BG residue 48 GLU Chi-restraints excluded: chain BG residue 84 THR Chi-restraints excluded: chain BG residue 92 ARG Chi-restraints excluded: chain BG residue 108 SER Chi-restraints excluded: chain BG residue 124 ILE Chi-restraints excluded: chain BG residue 135 VAL Chi-restraints excluded: chain BH residue 4 THR Chi-restraints excluded: chain BH residue 51 THR Chi-restraints excluded: chain BH residue 108 THR Chi-restraints excluded: chain BH residue 115 ASP Chi-restraints excluded: chain BI residue 36 VAL Chi-restraints excluded: chain BI residue 42 VAL Chi-restraints excluded: chain BI residue 58 TYR Chi-restraints excluded: chain BI residue 59 PHE Chi-restraints excluded: chain BI residue 80 GLN Chi-restraints excluded: chain BI residue 103 ILE Chi-restraints excluded: chain BI residue 105 ARG Chi-restraints excluded: chain BI residue 110 VAL Chi-restraints excluded: chain BI residue 115 ARG Chi-restraints excluded: chain BI residue 120 LYS Chi-restraints excluded: chain BJ residue 37 VAL Chi-restraints excluded: chain BJ residue 71 LYS Chi-restraints excluded: chain BJ residue 76 ILE Chi-restraints excluded: chain BJ residue 78 ASP Chi-restraints excluded: chain BJ residue 80 THR Chi-restraints excluded: chain BK residue 37 ASN Chi-restraints excluded: chain BK residue 40 ILE Chi-restraints excluded: chain BK residue 41 VAL Chi-restraints excluded: chain BK residue 67 SER Chi-restraints excluded: chain BK residue 68 THR Chi-restraints excluded: chain BK residue 91 VAL Chi-restraints excluded: chain BK residue 95 VAL Chi-restraints excluded: chain BK residue 96 LYS Chi-restraints excluded: chain BK residue 100 SER Chi-restraints excluded: chain BK residue 104 THR Chi-restraints excluded: chain BK residue 108 SER Chi-restraints excluded: chain BK residue 114 LEU Chi-restraints excluded: chain BK residue 123 THR Chi-restraints excluded: chain BK residue 128 ASN Chi-restraints excluded: chain BL residue 3 THR Chi-restraints excluded: chain BL residue 34 CYS Chi-restraints excluded: chain BL residue 38 TYR Chi-restraints excluded: chain BL residue 39 THR Chi-restraints excluded: chain BL residue 41 THR Chi-restraints excluded: chain BL residue 61 VAL Chi-restraints excluded: chain BL residue 63 VAL Chi-restraints excluded: chain BL residue 87 VAL Chi-restraints excluded: chain BL residue 89 ASP Chi-restraints excluded: chain BL residue 104 THR Chi-restraints excluded: chain BM residue 45 THR Chi-restraints excluded: chain BM residue 47 ASP Chi-restraints excluded: chain BM residue 51 ASP Chi-restraints excluded: chain BM residue 56 LEU Chi-restraints excluded: chain BN residue 24 CYS Chi-restraints excluded: chain BN residue 47 MET Chi-restraints excluded: chain BO residue 75 VAL Chi-restraints excluded: chain BP residue 15 ASN Chi-restraints excluded: chain BP residue 27 THR Chi-restraints excluded: chain BP residue 30 ASP Chi-restraints excluded: chain BP residue 81 GLN Chi-restraints excluded: chain BP residue 86 LEU Chi-restraints excluded: chain BP residue 92 THR Chi-restraints excluded: chain BQ residue 35 THR Chi-restraints excluded: chain BQ residue 42 ASP Chi-restraints excluded: chain BQ residue 55 THR Chi-restraints excluded: chain BQ residue 72 ASP Chi-restraints excluded: chain BQ residue 95 GLU Chi-restraints excluded: chain BR residue 21 VAL Chi-restraints excluded: chain BR residue 47 LYS Chi-restraints excluded: chain BR residue 51 ARG Chi-restraints excluded: chain BR residue 53 VAL Chi-restraints excluded: chain BS residue 33 THR Chi-restraints excluded: chain BS residue 38 SER Chi-restraints excluded: chain BS residue 48 THR Chi-restraints excluded: chain BS residue 67 VAL Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BV residue 4 VAL Chi-restraints excluded: chain BV residue 23 TRP Chi-restraints excluded: chain BV residue 31 ILE Chi-restraints excluded: chain BV residue 38 ILE Chi-restraints excluded: chain BV residue 66 THR Chi-restraints excluded: chain BV residue 68 LEU Chi-restraints excluded: chain BV residue 82 GLU Chi-restraints excluded: chain BV residue 92 VAL Chi-restraints excluded: chain BV residue 155 GLN Chi-restraints excluded: chain BV residue 178 LYS Chi-restraints excluded: chain BV residue 186 ILE Chi-restraints excluded: chain BV residue 204 ASP Chi-restraints excluded: chain BV residue 205 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 627 optimal weight: 6.9990 chunk 1010 optimal weight: 0.6980 chunk 616 optimal weight: 30.0000 chunk 479 optimal weight: 10.0000 chunk 702 optimal weight: 30.0000 chunk 1060 optimal weight: 40.0000 chunk 975 optimal weight: 10.0000 chunk 844 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 652 optimal weight: 5.9990 chunk 517 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS E 208 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 ASN K 117 GLN K 119 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN ** W 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 GLN ** b 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 115 HIS ** BF 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BK 110 GLN BK 128 ASN BM 52 GLN ** BP 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 163913 Z= 0.193 Angle : 0.572 13.253 245455 Z= 0.291 Chirality : 0.033 0.266 31408 Planarity : 0.005 0.073 13199 Dihedral : 24.292 179.894 82875 Min Nonbonded Distance : 1.096 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.12 % Favored : 95.87 % Rotamer: Outliers : 6.56 % Allowed : 27.78 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: -0.03 (0.11), residues: 5979 helix: 1.03 (0.12), residues: 2053 sheet: -0.12 (0.15), residues: 1183 loop : -0.72 (0.12), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPBQ 88 HIS 0.013 0.001 HISBK 127 PHE 0.042 0.001 PHE U 50 TYR 0.030 0.001 TYRBC 168 ARG 0.016 0.000 ARGBF 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1704 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1380 time to evaluate : 6.639 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: 3 8 LYS cc_start: 0.8616 (mttt) cc_final: 0.8395 (mttt) REVERT: 3 15 LYS cc_start: 0.8974 (tppt) cc_final: 0.8661 (tttp) REVERT: C 10 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8763 (p) REVERT: C 13 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7606 (mtm180) REVERT: C 66 ASP cc_start: 0.8532 (t0) cc_final: 0.8156 (t0) REVERT: C 71 ASP cc_start: 0.8868 (p0) cc_final: 0.8651 (p0) REVERT: C 198 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8466 (m110) REVERT: D 56 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8440 (tp30) REVERT: D 87 ASP cc_start: 0.7960 (m-30) cc_final: 0.7710 (m-30) REVERT: E 106 MET cc_start: 0.8776 (mtp) cc_final: 0.8543 (mtm) REVERT: E 192 ASP cc_start: 0.8129 (m-30) cc_final: 0.7781 (m-30) REVERT: F 13 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8266 (pp30) REVERT: F 142 GLN cc_start: 0.8982 (pm20) cc_final: 0.8582 (pp30) REVERT: G 172 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7324 (mtp180) REVERT: H 6 THR cc_start: 0.8155 (m) cc_final: 0.7195 (p) REVERT: H 8 GLU cc_start: 0.7340 (tp30) cc_final: 0.7009 (tp30) REVERT: H 137 HIS cc_start: 0.6263 (OUTLIER) cc_final: 0.6058 (t70) REVERT: H 143 LYS cc_start: 0.8696 (mttt) cc_final: 0.8403 (tptm) REVERT: K 23 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8681 (m) REVERT: K 37 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8336 (ttt90) REVERT: K 106 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8855 (mp) REVERT: K 108 MET cc_start: 0.9108 (mtm) cc_final: 0.8867 (mtm) REVERT: L 1 MET cc_start: 0.8565 (tpt) cc_final: 0.8299 (tpp) REVERT: L 80 ASP cc_start: 0.7905 (m-30) cc_final: 0.7562 (m-30) REVERT: L 90 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7389 (p0) REVERT: M 24 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.7877 (tpp80) REVERT: M 96 ASP cc_start: 0.8521 (p0) cc_final: 0.7947 (p0) REVERT: M 138 THR cc_start: 0.8802 (m) cc_final: 0.8429 (p) REVERT: O 30 GLU cc_start: 0.8287 (tt0) cc_final: 0.7969 (tt0) REVERT: P 28 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8672 (mtpp) REVERT: P 126 LYS cc_start: 0.7835 (mmtt) cc_final: 0.7620 (mmtt) REVERT: R 18 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8853 (mm) REVERT: R 42 SER cc_start: 0.9089 (OUTLIER) cc_final: 0.8470 (m) REVERT: R 63 SER cc_start: 0.9340 (m) cc_final: 0.8984 (m) REVERT: R 102 ASP cc_start: 0.7940 (t0) cc_final: 0.7391 (t0) REVERT: S 87 ARG cc_start: 0.8682 (mtt90) cc_final: 0.8427 (mtt90) REVERT: T 93 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8360 (ttm170) REVERT: V 1 MET cc_start: 0.7409 (mtt) cc_final: 0.7155 (mtt) REVERT: W 59 ARG cc_start: 0.8725 (ptp90) cc_final: 0.8429 (mtm110) REVERT: W 70 ASP cc_start: 0.8757 (t0) cc_final: 0.8287 (p0) REVERT: W 89 ARG cc_start: 0.8859 (mtm-85) cc_final: 0.8590 (mtm-85) REVERT: Y 10 LYS cc_start: 0.8580 (tttt) cc_final: 0.8257 (mttt) REVERT: Y 28 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7891 (ptp-170) REVERT: Z 35 GLN cc_start: 0.8299 (mp10) cc_final: 0.8013 (mp10) REVERT: Z 51 ARG cc_start: 0.8965 (mtm-85) cc_final: 0.8757 (mtm-85) REVERT: a 48 ASN cc_start: 0.8504 (t0) cc_final: 0.8119 (t0) REVERT: b 31 SER cc_start: 0.9310 (p) cc_final: 0.9041 (p) REVERT: b 35 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7138 (pp30) REVERT: c 10 LYS cc_start: 0.8527 (mmmm) cc_final: 0.8244 (mmmm) REVERT: c 25 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8645 (p) REVERT: c 49 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8527 (mm-40) REVERT: c 53 GLU cc_start: 0.7601 (tp30) cc_final: 0.7052 (tp30) REVERT: d 15 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8151 (ttm110) REVERT: e 47 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8421 (mtm110) REVERT: g 1 MET cc_start: 0.8143 (tpp) cc_final: 0.7498 (tpp) REVERT: g 9 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.6921 (t80) REVERT: BB 6 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8107 (ptpt) REVERT: BC 31 TYR cc_start: 0.8768 (m-10) cc_final: 0.8244 (m-10) REVERT: BC 35 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: BC 96 LYS cc_start: 0.7332 (mttp) cc_final: 0.7122 (mmtt) REVERT: BC 187 TYR cc_start: 0.8992 (t80) cc_final: 0.8589 (t80) REVERT: BD 20 VAL cc_start: 0.7965 (t) cc_final: 0.7642 (p) REVERT: BD 40 ARG cc_start: 0.5243 (tpm170) cc_final: 0.4689 (ttm-80) REVERT: BD 136 ASP cc_start: 0.8479 (m-30) cc_final: 0.8144 (m-30) REVERT: BD 145 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7300 (tp) REVERT: BD 148 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.6904 (mp) REVERT: BD 182 GLU cc_start: 0.8153 (mp0) cc_final: 0.7814 (mp0) REVERT: BD 192 GLU cc_start: 0.7086 (pm20) cc_final: 0.6692 (pt0) REVERT: BE 80 GLU cc_start: 0.7804 (tp30) cc_final: 0.7148 (tp30) REVERT: BF 27 LEU cc_start: 0.9093 (tp) cc_final: 0.8743 (tt) REVERT: BF 28 ASN cc_start: 0.8132 (m110) cc_final: 0.7675 (p0) REVERT: BF 74 GLU cc_start: 0.8508 (tp30) cc_final: 0.7565 (tp30) REVERT: BF 78 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7320 (mm-40) REVERT: BG 73 LEU cc_start: 0.8022 (tp) cc_final: 0.7754 (tp) REVERT: BG 118 GLU cc_start: 0.8375 (tp30) cc_final: 0.7916 (tp30) REVERT: BG 143 LYS cc_start: 0.8563 (tttt) cc_final: 0.8172 (ttpp) REVERT: BG 151 PHE cc_start: 0.8200 (m-10) cc_final: 0.7722 (m-10) REVERT: BH 9 ASP cc_start: 0.8213 (t0) cc_final: 0.7742 (m-30) REVERT: BI 105 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7807 (mtt180) REVERT: BI 115 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7464 (tpt-90) REVERT: BI 127 ASP cc_start: 0.7640 (t0) cc_final: 0.7200 (t0) REVERT: BJ 24 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8184 (tmtt) REVERT: BK 65 ARG cc_start: 0.9025 (ttm110) cc_final: 0.8748 (ttm110) REVERT: BK 73 GLN cc_start: 0.8274 (tt0) cc_final: 0.7876 (tt0) REVERT: BK 96 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8174 (ttpt) REVERT: BL 18 LYS cc_start: 0.7520 (tttt) cc_final: 0.7269 (tptm) REVERT: BL 59 SER cc_start: 0.9064 (m) cc_final: 0.8834 (t) REVERT: BM 21 TYR cc_start: 0.8095 (m-80) cc_final: 0.7889 (m-80) REVERT: BM 59 TYR cc_start: 0.8476 (t80) cc_final: 0.8263 (t80) REVERT: BN 47 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8567 (ttt) REVERT: BO 10 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8202 (tm-30) REVERT: BO 26 GLU cc_start: 0.8106 (mp0) cc_final: 0.7756 (mp0) REVERT: BO 79 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7744 (ttm-80) REVERT: BP 62 VAL cc_start: 0.8306 (m) cc_final: 0.8015 (t) REVERT: BP 86 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5479 (tp) REVERT: BQ 32 MET cc_start: 0.7178 (mtm) cc_final: 0.6842 (mpp) REVERT: BQ 54 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7102 (tmm-80) REVERT: BQ 73 ARG cc_start: 0.8192 (ttt-90) cc_final: 0.7844 (ttp80) REVERT: BR 35 THR cc_start: 0.8255 (m) cc_final: 0.8049 (t) REVERT: BR 39 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7790 (mmm-85) REVERT: BT 17 ARG cc_start: 0.8694 (mtt180) cc_final: 0.8483 (mtt180) REVERT: BT 20 ARG cc_start: 0.8426 (ttp80) cc_final: 0.8175 (mtm110) REVERT: BV 23 TRP cc_start: 0.7725 (OUTLIER) cc_final: 0.7228 (p-90) REVERT: BV 82 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6993 (pt0) REVERT: BV 89 MET cc_start: 0.7074 (mmt) cc_final: 0.5758 (mmt) REVERT: BV 92 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.8004 (m) REVERT: BV 121 GLU cc_start: 0.5806 (tm-30) cc_final: 0.5530 (mm-30) REVERT: BV 178 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6243 (tttt) outliers start: 324 outliers final: 272 residues processed: 1577 average time/residue: 1.3617 time to fit residues: 3682.9844 Evaluate side-chains 1642 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1337 time to evaluate : 6.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 172 ARG Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 137 HIS Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 84 ASN Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 74 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 41 HIS Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 71 LEU Chi-restraints excluded: chain T residue 93 ARG Chi-restraints excluded: chain T residue 111 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 38 VAL Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Y residue 28 ARG Chi-restraints excluded: chain Y residue 45 ASN Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 13 LEU Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain a residue 7 THR Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 35 GLN Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain e residue 56 SER Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain g residue 9 TYR Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain BB residue 6 LYS Chi-restraints excluded: chain BB residue 22 ARG Chi-restraints excluded: chain BB residue 31 LEU Chi-restraints excluded: chain BC residue 16 THR Chi-restraints excluded: chain BC residue 35 ASP Chi-restraints excluded: chain BC residue 67 ILE Chi-restraints excluded: chain BC residue 107 ASN Chi-restraints excluded: chain BC residue 119 VAL Chi-restraints excluded: chain BC residue 137 ILE Chi-restraints excluded: chain BC residue 143 GLN Chi-restraints excluded: chain BC residue 149 ILE Chi-restraints excluded: chain BC residue 163 SER Chi-restraints excluded: chain BD residue 85 LEU Chi-restraints excluded: chain BD residue 93 LEU Chi-restraints excluded: chain BD residue 145 LEU Chi-restraints excluded: chain BD residue 148 LEU Chi-restraints excluded: chain BD residue 177 VAL Chi-restraints excluded: chain BD residue 188 VAL Chi-restraints excluded: chain BD residue 200 SER Chi-restraints excluded: chain BE residue 71 VAL Chi-restraints excluded: chain BE residue 73 VAL Chi-restraints excluded: chain BE residue 130 VAL Chi-restraints excluded: chain BE residue 140 LEU Chi-restraints excluded: chain BE residue 186 ILE Chi-restraints excluded: chain BF residue 23 LEU Chi-restraints excluded: chain BF residue 29 VAL Chi-restraints excluded: chain BF residue 42 ILE Chi-restraints excluded: chain BF residue 57 GLU Chi-restraints excluded: chain BF residue 76 ASP Chi-restraints excluded: chain BF residue 91 LEU Chi-restraints excluded: chain BG residue 27 VAL Chi-restraints excluded: chain BG residue 48 GLU Chi-restraints excluded: chain BG residue 63 LYS Chi-restraints excluded: chain BG residue 84 THR Chi-restraints excluded: chain BG residue 92 ARG Chi-restraints excluded: chain BG residue 108 SER Chi-restraints excluded: chain BG residue 124 ILE Chi-restraints excluded: chain BG residue 135 VAL Chi-restraints excluded: chain BH residue 4 THR Chi-restraints excluded: chain BH residue 51 THR Chi-restraints excluded: chain BH residue 108 THR Chi-restraints excluded: chain BH residue 115 ASP Chi-restraints excluded: chain BI residue 36 VAL Chi-restraints excluded: chain BI residue 42 VAL Chi-restraints excluded: chain BI residue 58 TYR Chi-restraints excluded: chain BI residue 59 PHE Chi-restraints excluded: chain BI residue 80 GLN Chi-restraints excluded: chain BI residue 99 LEU Chi-restraints excluded: chain BI residue 103 ILE Chi-restraints excluded: chain BI residue 105 ARG Chi-restraints excluded: chain BI residue 110 VAL Chi-restraints excluded: chain BI residue 115 ARG Chi-restraints excluded: chain BI residue 120 LYS Chi-restraints excluded: chain BJ residue 37 VAL Chi-restraints excluded: chain BJ residue 71 LYS Chi-restraints excluded: chain BJ residue 76 ILE Chi-restraints excluded: chain BJ residue 78 ASP Chi-restraints excluded: chain BJ residue 80 THR Chi-restraints excluded: chain BK residue 37 ASN Chi-restraints excluded: chain BK residue 40 ILE Chi-restraints excluded: chain BK residue 41 VAL Chi-restraints excluded: chain BK residue 67 SER Chi-restraints excluded: chain BK residue 68 THR Chi-restraints excluded: chain BK residue 91 VAL Chi-restraints excluded: chain BK residue 96 LYS Chi-restraints excluded: chain BK residue 100 SER Chi-restraints excluded: chain BK residue 104 THR Chi-restraints excluded: chain BK residue 108 SER Chi-restraints excluded: chain BK residue 114 LEU Chi-restraints excluded: chain BK residue 123 THR Chi-restraints excluded: chain BK residue 128 ASN Chi-restraints excluded: chain BL residue 3 THR Chi-restraints excluded: chain BL residue 34 CYS Chi-restraints excluded: chain BL residue 38 TYR Chi-restraints excluded: chain BL residue 39 THR Chi-restraints excluded: chain BL residue 41 THR Chi-restraints excluded: chain BL residue 61 VAL Chi-restraints excluded: chain BL residue 87 VAL Chi-restraints excluded: chain BL residue 89 ASP Chi-restraints excluded: chain BL residue 104 THR Chi-restraints excluded: chain BM residue 45 THR Chi-restraints excluded: chain BM residue 47 ASP Chi-restraints excluded: chain BM residue 51 ASP Chi-restraints excluded: chain BM residue 56 LEU Chi-restraints excluded: chain BN residue 24 CYS Chi-restraints excluded: chain BN residue 47 MET Chi-restraints excluded: chain BO residue 75 VAL Chi-restraints excluded: chain BP residue 15 ASN Chi-restraints excluded: chain BP residue 27 THR Chi-restraints excluded: chain BP residue 30 ASP Chi-restraints excluded: chain BP residue 81 GLN Chi-restraints excluded: chain BP residue 86 LEU Chi-restraints excluded: chain BP residue 92 THR Chi-restraints excluded: chain BQ residue 35 THR Chi-restraints excluded: chain BQ residue 55 THR Chi-restraints excluded: chain BQ residue 72 ASP Chi-restraints excluded: chain BQ residue 83 SER Chi-restraints excluded: chain BQ residue 95 GLU Chi-restraints excluded: chain BR residue 21 VAL Chi-restraints excluded: chain BR residue 51 ARG Chi-restraints excluded: chain BR residue 53 VAL Chi-restraints excluded: chain BS residue 33 THR Chi-restraints excluded: chain BS residue 38 SER Chi-restraints excluded: chain BS residue 48 THR Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BV residue 4 VAL Chi-restraints excluded: chain BV residue 23 TRP Chi-restraints excluded: chain BV residue 31 ILE Chi-restraints excluded: chain BV residue 38 ILE Chi-restraints excluded: chain BV residue 68 LEU Chi-restraints excluded: chain BV residue 82 GLU Chi-restraints excluded: chain BV residue 92 VAL Chi-restraints excluded: chain BV residue 137 LEU Chi-restraints excluded: chain BV residue 155 GLN Chi-restraints excluded: chain BV residue 178 LYS Chi-restraints excluded: chain BV residue 186 ILE Chi-restraints excluded: chain BV residue 204 ASP Chi-restraints excluded: chain BV residue 205 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 670 optimal weight: 0.0470 chunk 899 optimal weight: 9.9990 chunk 258 optimal weight: 20.0000 chunk 778 optimal weight: 30.0000 chunk 124 optimal weight: 50.0000 chunk 234 optimal weight: 50.0000 chunk 845 optimal weight: 30.0000 chunk 353 optimal weight: 10.0000 chunk 868 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 155 optimal weight: 50.0000 overall best weight: 9.4090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN D 20 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 GLN K 119 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 GLN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 GLN ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 128 ASN BM 101 GLN ** BP 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.091352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.069601 restraints weight = 429871.118| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.04 r_work: 0.2924 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 163913 Z= 0.292 Angle : 0.619 14.458 245455 Z= 0.313 Chirality : 0.036 0.283 31408 Planarity : 0.005 0.074 13199 Dihedral : 24.296 179.982 82867 Min Nonbonded Distance : 1.052 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 6.92 % Allowed : 27.68 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % 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: -0.14 (0.11), residues: 5979 helix: 0.96 (0.12), residues: 2054 sheet: -0.24 (0.15), residues: 1199 loop : -0.78 (0.12), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPBF 43 HIS 0.019 0.001 HISBK 127 PHE 0.027 0.002 PHE U 50 TYR 0.028 0.002 TYRBC 23 ARG 0.024 0.001 ARGBK 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 53565.83 seconds wall clock time: 929 minutes 39.37 seconds (55779.37 seconds total)