Starting phenix.real_space_refine (version: dev) on Thu Apr 14 09:23:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o61_3751/04_2022/5o61_3751_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o61_3751/04_2022/5o61_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_3751/04_2022/5o61_3751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o61_3751/04_2022/5o61_3751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o61_3751/04_2022/5o61_3751_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o61_3751/04_2022/5o61_3751_neut.pdb" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'rna3p_pyr': 1190, 'rna2p_pur': 298, 'rna3p_pur': 1485, 'rna2p_pyr': 146} Link IDs: {'rna3p': 2674, 'rna2p': 444} Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2522 Classifications: {'RNA': 118} Modifications used: {'rna3p_pyr': 47, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 7} Link IDs: {'rna3p': 103, 'rna2p': 14} 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: {'PTRANS': 7, 'TRANS': 205, 'PCIS': 1} 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: {'rna3p_pyr': 577, 'rna2p_pur': 112, 'rna3p_pur': 737, 'rna2p_pyr': 85} Link IDs: {'rna3p': 1313, 'rna2p': 197} 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, 'rna3p_pur': 32, 'rna2p_pyr': 4, 'rna3p_pyr': 33} Link IDs: {'rna3p': 65, 'rna2p': 10} Chain: "BX" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'rna3p_pyr': 6, '5*END': 1} 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: {' ZN': 1, ' MG': 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: {' ZN': 1, ' MG': 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: 63.31, per 1000 atoms: 0.42 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: 53.50 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Zn2+ tetrahedral 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: 51.86 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: 452.48 Time building geometry restraints manager: 59.84 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: 83000 35.95 - 71.91: 4142 71.91 - 107.86: 318 107.86 - 143.82: 47 143.82 - 179.77: 53 Dihedral angle restraints: 87560 sinusoidal: 70288 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 87557 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 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. 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: 0.510 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: 0.160 Extract box with map and model: 13.350 Check model and map are aligned: 1.780 Convert atoms to be neutral: 0.960 Process input model: 758.120 Find NCS groups from input model: 3.480 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 781.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 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 : 17.086 179.773 76454 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 % 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 *********************** 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 : 6.609 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: symmetry clash outliers start: 539 outliers final: 172 residues processed: 2385 average time/residue: 1.5289 time to fit residues: 6173.0497 Evaluate side-chains 1597 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1425 time to evaluate : 6.980 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 2 residues processed: 172 average time/residue: 1.2558 time to fit residues: 405.1145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 275 optimal weight: 10.0000 chunk 543 optimal weight: 8.9990 chunk 430 optimal weight: 20.0000 chunk 833 optimal weight: 7.9990 chunk 322 optimal weight: 20.0000 chunk 507 optimal weight: 30.0000 chunk 620 optimal weight: 30.0000 chunk 966 optimal weight: 40.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS E 176 HIS E 208 ASN F 58 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 72 ASN ** 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 46 HIS W 94 HIS W 156 GLN X 29 GLN X 44 HIS Y 22 HIS Z 44 ASN c 48 HIS c 49 GLN e 25 GLN e 31 HIS e 63 ASN BC 122 GLN BC 138 GLN BC 143 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 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 142 HIS BI 57 ASN BI 146 GLN BJ 15 HIS BJ 70 HIS ** BK 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BK 58 HIS BL 29 GLN ** BL 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BM 52 GLN BM 92 HIS BM 101 GLN BN 11 ASN BN 31 HIS BO 28 GLN BO 37 GLN ** BO 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BP 17 GLN BP 41 HIS BP 57 GLN BQ 46 HIS BS 52 HIS BS 57 HIS BT 22 GLN BT 52 HIS ** BT 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 167 ASN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 163913 Z= 0.292 Angle : 0.683 10.033 245455 Z= 0.352 Chirality : 0.040 0.393 31408 Planarity : 0.006 0.094 13199 Dihedral : 16.278 179.979 64708 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.75 % Rotamer Outliers : 4.90 % 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: -1.31 (0.10), residues: 5979 helix: -0.50 (0.11), residues: 2044 sheet: -0.46 (0.13), residues: 1196 loop : -1.25 (0.11), residues: 2739 *********************** 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 1792 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1550 time to evaluate : 6.247 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 outliers start: 242 outliers final: 137 residues processed: 1683 average time/residue: 1.4253 time to fit residues: 4133.3332 Evaluate side-chains 1532 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1395 time to evaluate : 6.905 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 0 residues processed: 137 average time/residue: 1.1900 time to fit residues: 312.2168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 536 optimal weight: 7.9990 chunk 299 optimal weight: 20.0000 chunk 804 optimal weight: 30.0000 chunk 657 optimal weight: 3.9990 chunk 266 optimal weight: 20.0000 chunk 967 optimal weight: 10.0000 chunk 1045 optimal weight: 30.0000 chunk 862 optimal weight: 30.0000 chunk 959 optimal weight: 30.0000 chunk 329 optimal weight: 0.0980 chunk 776 optimal weight: 50.0000 overall best weight: 8.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN C 122 ASN C 135 ASN D 20 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN D 179 ASN E 176 HIS G 23 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN J 95 HIS K 117 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN N 123 HIS O 91 ASN P 56 ASN ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 ASN W 26 GLN X 29 GLN c 49 GLN BC 99 GLN BC 122 GLN BC 176 HIS ** BD 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 106 ASN BG 142 HIS BJ 47 ASN BJ 99 ASN BK 27 HIS BK 110 GLN BL 29 GLN ** BL 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BL 109 ASN BO 7 GLN ** BO 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BO 37 GLN BO 42 HIS ** BT 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.107 163913 Z= 0.277 Angle : 0.629 9.611 245455 Z= 0.323 Chirality : 0.037 0.397 31408 Planarity : 0.006 0.080 13199 Dihedral : 16.107 179.718 64708 Min Nonbonded Distance : 1.058 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.33 % Rotamer Outliers : 4.74 % 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: -0.66 (0.10), residues: 5979 helix: 0.30 (0.11), residues: 2046 sheet: -0.26 (0.14), residues: 1206 loop : -1.01 (0.11), residues: 2727 *********************** 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 1709 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1475 time to evaluate : 6.895 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 outliers start: 234 outliers final: 126 residues processed: 1606 average time/residue: 1.4198 time to fit residues: 3939.3793 Evaluate side-chains 1455 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1329 time to evaluate : 6.950 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 0 residues processed: 126 average time/residue: 1.1472 time to fit residues: 282.7921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 956 optimal weight: 7.9990 chunk 727 optimal weight: 30.0000 chunk 502 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 461 optimal weight: 8.9990 chunk 649 optimal weight: 8.9990 chunk 971 optimal weight: 10.0000 chunk 1028 optimal weight: 5.9990 chunk 507 optimal weight: 30.0000 chunk 920 optimal weight: 30.0000 chunk 277 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- 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** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 ASN K 117 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 126 GLN W 169 ASN Z 52 GLN c 49 GLN ** BC 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 122 GLN BC 138 GLN ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 115 HIS BD 134 GLN BD 185 GLN BE 163 HIS BG 86 GLN ** BG 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 142 HIS BK 110 GLN BL 29 GLN BL 77 HIS BL 109 ASN BM 52 GLN BM 101 GLN BO 37 GLN BO 42 HIS ** BQ 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 108 HIS BV 155 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.139 163913 Z= 0.272 Angle : 0.613 10.877 245455 Z= 0.314 Chirality : 0.037 0.372 31408 Planarity : 0.006 0.114 13199 Dihedral : 16.020 179.597 64708 Min Nonbonded Distance : 1.053 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.65 % Favored : 96.33 % Rotamer Outliers : 4.25 % 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: -0.39 (0.10), residues: 5979 helix: 0.61 (0.11), residues: 2042 sheet: -0.14 (0.14), residues: 1212 loop : -0.92 (0.11), residues: 2725 *********************** 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 1622 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1412 time to evaluate : 6.951 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 outliers start: 210 outliers final: 121 residues processed: 1527 average time/residue: 1.4270 time to fit residues: 3764.9753 Evaluate side-chains 1435 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1314 time to evaluate : 6.820 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 0 residues processed: 121 average time/residue: 1.1648 time to fit residues: 271.9463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 856 optimal weight: 30.0000 chunk 583 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 765 optimal weight: 20.0000 chunk 424 optimal weight: 9.9990 chunk 877 optimal weight: 5.9990 chunk 710 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 525 optimal weight: 8.9990 chunk 923 optimal weight: 9.9990 chunk 259 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN D 20 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN I 100 ASN J 121 ASN ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 GLN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 HIS ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 126 GLN W 169 ASN X 46 HIS Z 40 GLN c 49 GLN ** BC 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 122 GLN ** BD 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 78 GLN BG 86 GLN ** BG 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 148 ASN BL 29 GLN BL 109 ASN BM 52 GLN ** BQ 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 108 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.106 163913 Z= 0.265 Angle : 0.604 11.186 245455 Z= 0.308 Chirality : 0.036 0.301 31408 Planarity : 0.005 0.098 13199 Dihedral : 15.967 179.633 64708 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.18 % Rotamer Outliers : 3.08 % 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: -0.27 (0.11), residues: 5979 helix: 0.76 (0.11), residues: 2055 sheet: -0.14 (0.14), residues: 1225 loop : -0.87 (0.12), residues: 2699 *********************** 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 1538 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1386 time to evaluate : 6.845 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 outliers start: 152 outliers final: 98 residues processed: 1467 average time/residue: 1.4820 time to fit residues: 3838.7830 Evaluate side-chains 1406 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1308 time to evaluate : 6.949 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 0 residues processed: 98 average time/residue: 1.2302 time to fit residues: 240.5746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 346 optimal weight: 3.9990 chunk 926 optimal weight: 40.0000 chunk 203 optimal weight: 20.0000 chunk 603 optimal weight: 40.0000 chunk 253 optimal weight: 20.0000 chunk 1029 optimal weight: 20.0000 chunk 854 optimal weight: 8.9990 chunk 476 optimal weight: 6.9990 chunk 85 optimal weight: 30.0000 chunk 340 optimal weight: 20.0000 chunk 540 optimal weight: 10.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- 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** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** K 96 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN ** W 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN W 126 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 25 GLN ** BC 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 78 GLN BG 110 GLN BL 29 GLN BM 52 GLN BM 75 GLN ** BT 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 108 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.115 163913 Z= 0.313 Angle : 0.629 10.591 245455 Z= 0.320 Chirality : 0.037 0.373 31408 Planarity : 0.005 0.125 13199 Dihedral : 15.987 179.965 64708 Min Nonbonded Distance : 1.032 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.15 % Favored : 95.82 % Rotamer Outliers : 2.63 % 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: -0.31 (0.11), residues: 5979 helix: 0.79 (0.11), residues: 2047 sheet: -0.25 (0.14), residues: 1218 loop : -0.89 (0.12), residues: 2714 *********************** 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 1483 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1353 time to evaluate : 6.938 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 outliers start: 130 outliers final: 86 residues processed: 1415 average time/residue: 1.4046 time to fit residues: 3436.5512 Evaluate side-chains 1378 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1292 time to evaluate : 6.687 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 0 residues processed: 86 average time/residue: 1.0983 time to fit residues: 186.7151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 751 optimal weight: 20.0000 chunk 582 optimal weight: 10.0000 chunk 866 optimal weight: 20.0000 chunk 574 optimal weight: 7.9990 chunk 1025 optimal weight: 10.0000 chunk 641 optimal weight: 8.9990 chunk 625 optimal weight: 7.9990 chunk 473 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 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 ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 HIS W 169 ASN X 29 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 78 GLN BL 29 GLN BL 109 ASN BM 75 GLN BM 101 GLN BN 11 ASN ** BT 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 108 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 163913 Z= 0.247 Angle : 0.597 12.088 245455 Z= 0.304 Chirality : 0.035 0.325 31408 Planarity : 0.005 0.109 13199 Dihedral : 15.916 179.875 64708 Min Nonbonded Distance : 1.068 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.00 % Favored : 95.98 % Rotamer Outliers : 2.07 % 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: -0.23 (0.11), residues: 5979 helix: 0.90 (0.12), residues: 2048 sheet: -0.28 (0.14), residues: 1212 loop : -0.85 (0.12), residues: 2719 *********************** 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 1457 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1355 time to evaluate : 7.164 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 outliers start: 102 outliers final: 56 residues processed: 1404 average time/residue: 1.3903 time to fit residues: 3364.0545 Evaluate side-chains 1355 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1299 time to evaluate : 6.515 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 1.1202 time to fit residues: 125.7935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 612 optimal weight: 7.9990 chunk 308 optimal weight: 20.0000 chunk 201 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 651 optimal weight: 20.0000 chunk 698 optimal weight: 30.0000 chunk 507 optimal weight: 0.0170 chunk 95 optimal weight: 10.0000 chunk 806 optimal weight: 30.0000 overall best weight: 9.6032 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 52 GLN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 146 ASN ** BF 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 29 GLN BM 101 GLN BP 107 ASN ** BT 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.056 163913 Z= 0.337 Angle : 0.659 96.522 245455 Z= 0.327 Chirality : 0.037 0.328 31408 Planarity : 0.005 0.141 13199 Dihedral : 15.926 179.854 64708 Min Nonbonded Distance : 1.030 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.44 % Favored : 95.55 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.02 % 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: -0.29 (0.11), residues: 5979 helix: 0.86 (0.12), residues: 2041 sheet: -0.33 (0.14), residues: 1214 loop : -0.88 (0.12), residues: 2724 *********************** 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 1425 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1325 time to evaluate : 6.885 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 outliers start: 100 outliers final: 64 residues processed: 1369 average time/residue: 1.5355 time to fit residues: 3660.1737 Evaluate side-chains 1353 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1289 time to evaluate : 6.891 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 1.1613 time to fit residues: 147.0856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 932 optimal weight: 20.0000 chunk 982 optimal weight: 6.9990 chunk 896 optimal weight: 40.0000 chunk 955 optimal weight: 30.0000 chunk 575 optimal weight: 5.9990 chunk 416 optimal weight: 6.9990 chunk 750 optimal weight: 20.0000 chunk 293 optimal weight: 10.0000 chunk 863 optimal weight: 20.0000 chunk 903 optimal weight: 10.0000 chunk 952 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 146 ASN ** BF 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 148 ASN ** BK 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 29 GLN BL 109 ASN ** BT 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.980 163913 Z= 0.306 Angle : 0.658 105.274 245455 Z= 0.325 Chirality : 0.036 0.326 31408 Planarity : 0.006 0.129 13199 Dihedral : 15.926 179.843 64708 Min Nonbonded Distance : 1.037 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.40 % Favored : 95.58 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.02 % 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: -0.28 (0.11), residues: 5979 helix: 0.88 (0.12), residues: 2041 sheet: -0.35 (0.14), residues: 1212 loop : -0.87 (0.12), residues: 2726 *********************** 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 1359 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1302 time to evaluate : 6.868 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 outliers start: 57 outliers final: 37 residues processed: 1325 average time/residue: 1.4134 time to fit residues: 3234.6627 Evaluate side-chains 1321 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1284 time to evaluate : 6.891 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 1.1158 time to fit residues: 86.1875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 627 optimal weight: 9.9990 chunk 1010 optimal weight: 0.8980 chunk 616 optimal weight: 20.0000 chunk 479 optimal weight: 5.9990 chunk 702 optimal weight: 30.0000 chunk 1060 optimal weight: 40.0000 chunk 975 optimal weight: 8.9990 chunk 844 optimal weight: 40.0000 chunk 87 optimal weight: 20.0000 chunk 652 optimal weight: 8.9990 chunk 517 optimal weight: 8.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 169 ASN ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 29 GLN BL 109 ASN BN 11 ASN ** BT 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.854 163913 Z= 0.274 Angle : 0.618 62.127 245455 Z= 0.312 Chirality : 0.035 0.302 31408 Planarity : 0.005 0.124 13199 Dihedral : 15.888 179.619 64708 Min Nonbonded Distance : 1.067 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.23 % Favored : 95.75 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.02 % 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: -0.27 (0.11), residues: 5979 helix: 0.85 (0.12), residues: 2040 sheet: -0.34 (0.14), residues: 1209 loop : -0.83 (0.12), residues: 2730 ********************** 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 1349 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1312 time to evaluate : 6.932 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 outliers start: 37 outliers final: 26 residues processed: 1324 average time/residue: 1.4134 time to fit residues: 3229.9999 Evaluate side-chains 1309 residues out of total 4965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1283 time to evaluate : 6.676 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 1.0990 time to fit residues: 61.7798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1064 random chunks: chunk 670 optimal weight: 50.0000 chunk 899 optimal weight: 0.8980 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: 6.9990 chunk 353 optimal weight: 6.9990 chunk 868 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 155 optimal weight: 50.0000 overall best weight: 8.5790 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 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 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 128 ASN BL 29 GLN BL 109 ASN BP 107 ASN ** BT 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 108 HIS ** 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 = 0.3568 r_free = 0.3568 target = 0.091470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.069737 restraints weight = 429963.619| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.04 r_work: 0.3040 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 1.08 restraints_weight: 0.2500 r_work: 0.3014 rms_B_bonded: 1.23 restraints_weight: 0.1250 r_work: 0.3000 rms_B_bonded: 1.43 restraints_weight: 0.0625 r_work: 0.2984 rms_B_bonded: 1.69 restraints_weight: 0.0312 r_work: 0.2965 rms_B_bonded: 2.03 restraints_weight: 0.0156 r_work: 0.2942 rms_B_bonded: 2.44 restraints_weight: 0.0078 r_work: 0.2915 rms_B_bonded: 2.97 restraints_weight: 0.0039 r_work: 0.2882 rms_B_bonded: 3.64 restraints_weight: 0.0020 r_work: 0.2840 rms_B_bonded: 4.54 restraints_weight: 0.0010 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.620 163913 Z= 0.297 Angle : 0.622 28.409 245455 Z= 0.317 Chirality : 0.036 0.284 31408 Planarity : 0.005 0.153 13199 Dihedral : 15.887 179.666 64708 Min Nonbonded Distance : 1.034 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.02 % 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: -0.29 (0.11), residues: 5979 helix: 0.86 (0.12), residues: 2047 sheet: -0.33 (0.14), residues: 1190 loop : -0.88 (0.12), residues: 2742 =============================================================================== Job complete usr+sys time: 49916.83 seconds wall clock time: 855 minutes 23.54 seconds (51323.54 seconds total)