Starting phenix.real_space_refine on Sun Mar 3 16:45:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v08_26941/03_2024/7v08_26941_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v08_26941/03_2024/7v08_26941.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v08_26941/03_2024/7v08_26941_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v08_26941/03_2024/7v08_26941_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v08_26941/03_2024/7v08_26941_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v08_26941/03_2024/7v08_26941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v08_26941/03_2024/7v08_26941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v08_26941/03_2024/7v08_26941_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v08_26941/03_2024/7v08_26941_updated.pdb" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 5 6.06 5 P 3327 5.49 5 Mg 81 5.21 5 S 229 5.16 5 C 86337 2.51 5 N 28759 2.21 5 O 39100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 157839 Number of models: 1 Model: "" Number of chains: 86 Chain: "A" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1634 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 201} Chain: "1" Number of atoms: 63938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2986, 63938 Classifications: {'RNA': 2986} Modifications used: {'rna2p': 6, 'rna2p_pur': 308, 'rna2p_pyr': 205, 'rna3p': 40, 'rna3p_pur': 1343, 'rna3p_pyr': 1077} Link IDs: {'rna2p': 519, 'rna3p': 2466} Chain breaks: 15 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 17 Chain: "2" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 16, 'rna3p': 1, 'rna3p_pur': 60, 'rna3p_pyr': 63} Link IDs: {'rna2p': 33, 'rna3p': 124} Chain: "3" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p': 1, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 107} Chain: "5" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 645 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "6" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1227 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 13, 'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna2p': 21, 'rna3p': 36} Chain breaks: 3 Chain: "8" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1196 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain: "9" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain breaks: 3 Chain: "B" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3081 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 371} Chain: "C" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2749 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain: "D" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2180 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Chain: "E" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 146} Chain breaks: 1 Chain: "F" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1761 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "G" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 211} Chain breaks: 1 Chain: "H" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain: "I" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "J" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1368 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "K" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2155 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 11, 'TRANS': 256} Chain breaks: 2 Chain: "L" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1438 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 171} Chain: "M" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1059 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "N" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1620 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1388 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Chain breaks: 1 Chain: "Q" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1136 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 7, 'TRANS': 139} Chain: "R" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1258 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "S" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "T" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 905 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain breaks: 1 Chain: "U" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 844 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "V" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "W" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1888 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain: "X" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1088 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "Y" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "a" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 731 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "b" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5185 Classifications: {'peptide': 642} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 616} Chain breaks: 1 Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "d" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 873 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 771 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "j" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 665 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 81} Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "l" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "m" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3754 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 1 Chain: "n" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3014 Classifications: {'peptide': 369} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 347} Chain breaks: 2 Chain: "o" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "p" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "q" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1298 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain breaks: 1 Chain: "r" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1860 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "s" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 602 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain breaks: 1 Chain: "t" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2306 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 1 Chain: "u" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1265 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "v" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2366 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 279} Chain: "w" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "x" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3927 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 25, 'TRANS': 478} Chain breaks: 1 Chain: "y" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1849 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain: "z" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 714 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain breaks: 1 Chain: "4" Number of atoms: 4166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4166 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Chain breaks: 1 Chain: "1" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 112 Unusual residues: {' MG': 74, 'B3P': 2} Classifications: {'undetermined': 76} Link IDs: {None: 75} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' K': 1, ' MG': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'B3P': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 339 Classifications: {'water': 339} Link IDs: {None: 338} Chain: "2" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "m" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 90205 SG CYS I 51 185.579 153.057 140.023 1.00 22.32 S ATOM 90229 SG CYS I 54 184.197 149.494 138.908 1.00 24.45 S ATOM A0HLV SG CYS g 44 147.711 130.054 208.839 1.00 9.18 S ATOM A0HMD SG CYS g 47 149.605 132.837 207.047 1.00 10.85 S ATOM A0HTF SG CYS g 81 151.225 130.876 209.991 1.00 9.18 S ATOM A0HTY SG CYS g 84 148.749 133.386 210.674 1.00 9.18 S ATOM A0JGQ SG CYS j 19 109.624 104.724 172.773 1.00 9.18 S ATOM A0JHF SG CYS j 22 108.000 103.528 169.365 1.00 9.18 S ATOM A0JK7 SG CYS j 34 108.442 107.104 170.199 1.00 9.18 S ATOM A0JKP SG CYS j 37 105.879 105.135 172.100 1.00 9.18 S ATOM A0QZW SG CYS p 39 149.039 149.682 204.134 1.00 11.53 S ATOM A0R0J SG CYS p 42 152.458 148.704 205.201 1.00 10.98 S ATOM A0R3K SG CYS p 57 150.935 147.386 201.974 1.00 12.86 S ATOM A0R42 SG CYS p 60 149.657 146.072 205.447 1.00 19.39 S ATOM A0W0K SG CYS u 6 184.990 135.855 115.862 1.00 9.18 S ATOM A0W1B SG CYS u 9 186.631 132.337 116.559 1.00 9.18 S ATOM A0W6G SG CYS u 32 183.687 132.779 114.244 1.00 9.18 S ATOM A0W7C SG CYS u 36 183.436 133.013 118.091 1.00 9.18 S Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N VAL O 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 residue: pdb=" N HIS O 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS O 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 59.56, per 1000 atoms: 0.38 Number of scatterers: 157839 At special positions: 0 Unit cell: (228.96, 271.08, 312.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 5 29.99 K 1 19.00 S 229 16.00 P 3327 15.00 Mg 81 11.99 O 39100 8.00 N 28759 7.00 C 86337 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: 57.98 Conformation dependent library (CDL) restraints added in 12.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 67 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 73 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 51 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 54 " pdb=" ZN g 601 " pdb="ZN ZN g 601 " - pdb=" SG CYS g 81 " pdb="ZN ZN g 601 " - pdb=" SG CYS g 47 " pdb="ZN ZN g 601 " - pdb=" SG CYS g 84 " pdb="ZN ZN g 601 " - pdb=" SG CYS g 44 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb=" ZN p 501 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 39 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 57 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 60 " pdb=" ZN u 201 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 36 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 9 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 32 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 6 " Number of angles added : 25 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20316 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 382 helices and 103 sheets defined 45.3% alpha, 14.6% beta 1021 base pairs and 1642 stacking pairs defined. Time for finding SS restraints: 85.12 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 4.753A pdb=" N GLY A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLY A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.904A pdb=" N VAL A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.899A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.671A pdb=" N MET A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain '5' and resid 42 through 99 removed outlier: 3.838A pdb=" N LYS 5 98 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) Processing helix chain '5' and resid 100 through 114 removed outlier: 3.574A pdb=" N ARG 5 113 " --> pdb=" O ARG 5 109 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN 5 114 " --> pdb=" O ARG 5 110 " (cutoff:3.500A) Processing helix chain '8' and resid 28 through 36 Proline residue: 8 34 - end of helix Processing helix chain '8' and resid 38 through 51 Processing helix chain '8' and resid 76 through 86 removed outlier: 3.758A pdb=" N LYS 8 86 " --> pdb=" O ILE 8 82 " (cutoff:3.500A) Processing helix chain '8' and resid 105 through 118 removed outlier: 4.571A pdb=" N ASP 8 118 " --> pdb=" O ARG 8 114 " (cutoff:3.500A) Processing helix chain '8' and resid 124 through 140 Processing helix chain '8' and resid 147 through 158 Processing helix chain '9' and resid 10 through 34 removed outlier: 4.685A pdb=" N SER 9 14 " --> pdb=" O PRO 9 10 " (cutoff:3.500A) Processing helix chain '9' and resid 52 through 64 Processing helix chain '9' and resid 90 through 111 Processing helix chain '9' and resid 138 through 152 Processing helix chain 'B' and resid 111 through 120 removed outlier: 4.404A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.661A pdb=" N ALA B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 removed outlier: 6.028A pdb=" N ARG B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 4.294A pdb=" N THR B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix No H-bonds generated for 'chain 'B' and resid 165 through 170' Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.701A pdb=" N VAL B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 347 through 353 removed outlier: 3.911A pdb=" N LEU B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLU B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 23 through 29 removed outlier: 4.436A pdb=" N SER C 27 " --> pdb=" O PRO C 23 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Proline residue: C 29 - end of helix No H-bonds generated for 'chain 'C' and resid 23 through 29' Processing helix chain 'C' and resid 31 through 46 removed outlier: 3.944A pdb=" N ASN C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 4.073A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 153 through 159 removed outlier: 4.801A pdb=" N GLU C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 159' Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 185 removed outlier: 4.026A pdb=" N LYS C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 4.021A pdb=" N ARG C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 196' Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.888A pdb=" N ASN C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 251 through 262 removed outlier: 4.551A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 316 through 321 removed outlier: 4.823A pdb=" N LYS C 321 " --> pdb=" O PRO C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 328 Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.417A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 20 through 26 removed outlier: 3.831A pdb=" N GLY D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.968A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.622A pdb=" N LEU D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.938A pdb=" N ALA D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 170 Processing helix chain 'D' and resid 191 through 201 Processing helix chain 'D' and resid 202 through 215 Processing helix chain 'D' and resid 216 through 223 removed outlier: 4.892A pdb=" N PHE D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 235 through 251 Proline residue: D 251 - end of helix Processing helix chain 'D' and resid 261 through 274 removed outlier: 3.685A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 287 Processing helix chain 'E' and resid 80 through 85 removed outlier: 3.983A pdb=" N VAL E 84 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 85' Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 131 through 150 removed outlier: 6.203A pdb=" N VAL E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 5.286A pdb=" N SER E 162 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 73 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'F' and resid 120 through 131 removed outlier: 3.754A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 165 through 173 removed outlier: 4.107A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 191 removed outlier: 4.286A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 removed outlier: 5.232A pdb=" N TRP F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 244 removed outlier: 4.536A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 69 Processing helix chain 'G' and resid 72 through 80 removed outlier: 5.037A pdb=" N PHE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLN G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 98 removed outlier: 3.849A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.669A pdb=" N LYS G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU G 107 " --> pdb=" O ALA G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 146 Processing helix chain 'G' and resid 160 through 174 removed outlier: 4.625A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU G 166 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Proline residue: G 167 - end of helix Processing helix chain 'G' and resid 182 through 191 Processing helix chain 'G' and resid 204 through 227 removed outlier: 4.962A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA G 223 " --> pdb=" O ASP G 219 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS G 225 " --> pdb=" O ASN G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 233 removed outlier: 3.983A pdb=" N HIS G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N TRP G 233 " --> pdb=" O VAL G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 228 through 233' Processing helix chain 'G' and resid 239 through 255 Processing helix chain 'H' and resid 61 through 84 Processing helix chain 'H' and resid 150 through 166 removed outlier: 4.010A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 5.008A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 9 Processing helix chain 'I' and resid 17 through 27 removed outlier: 3.961A pdb=" N THR I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 4.052A pdb=" N GLN I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 71 removed outlier: 4.098A pdb=" N GLY I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS I 71 " --> pdb=" O HIS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 82 removed outlier: 3.598A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLY I 82 " --> pdb=" O LYS I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 95 removed outlier: 4.059A pdb=" N SER I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 131 removed outlier: 3.853A pdb=" N VAL I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLY I 113 " --> pdb=" O THR I 109 " (cutoff:3.500A) Proline residue: I 114 - end of helix Processing helix chain 'J' and resid 27 through 42 Processing helix chain 'J' and resid 73 through 88 Processing helix chain 'J' and resid 136 through 141 removed outlier: 4.723A pdb=" N ARG J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 167 Processing helix chain 'J' and resid 92 through 97 removed outlier: 3.822A pdb=" N ASN J 95 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE J 96 " --> pdb=" O ASP J 93 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N SER J 97 " --> pdb=" O ARG J 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 92 through 97' Processing helix chain 'J' and resid 108 through 113 removed outlier: 4.022A pdb=" N ASP J 111 " --> pdb=" O GLU J 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 50 removed outlier: 4.054A pdb=" N SER K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS K 50 " --> pdb=" O LYS K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 118 Proline residue: K 109 - end of helix removed outlier: 3.986A pdb=" N ALA K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL K 118 " --> pdb=" O SER K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 136 removed outlier: 4.475A pdb=" N LYS K 133 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LYS K 134 " --> pdb=" O SER K 130 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL K 135 " --> pdb=" O ASP K 131 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER K 136 " --> pdb=" O ILE K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 145 removed outlier: 3.880A pdb=" N GLN K 143 " --> pdb=" O ASP K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 163 Processing helix chain 'K' and resid 166 through 178 removed outlier: 3.905A pdb=" N GLN K 176 " --> pdb=" O ALA K 172 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N SER K 178 " --> pdb=" O ILE K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 194 removed outlier: 4.614A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N SER K 189 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU K 190 " --> pdb=" O ILE K 186 " (cutoff:3.500A) Proline residue: K 191 - end of helix Processing helix chain 'K' and resid 195 through 201 removed outlier: 4.220A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN K 200 " --> pdb=" O GLY K 196 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS K 201 " --> pdb=" O LYS K 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 195 through 201' Processing helix chain 'K' and resid 218 through 232 Processing helix chain 'K' and resid 250 through 255 removed outlier: 3.721A pdb=" N LEU K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG K 255 " --> pdb=" O LEU K 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 250 through 255' Processing helix chain 'K' and resid 256 through 274 removed outlier: 3.850A pdb=" N LYS K 272 " --> pdb=" O GLU K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 302 removed outlier: 3.841A pdb=" N ASP K 299 " --> pdb=" O GLN K 295 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU K 300 " --> pdb=" O ASP K 296 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU K 301 " --> pdb=" O VAL K 297 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU K 302 " --> pdb=" O LEU K 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 295 through 302' Processing helix chain 'K' and resid 327 through 337 Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.488A pdb=" N ARG L 21 " --> pdb=" O HIS L 17 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL L 22 " --> pdb=" O TRP L 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 17 through 22' Processing helix chain 'L' and resid 27 through 47 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 94 Processing helix chain 'L' and resid 105 through 123 Processing helix chain 'L' and resid 140 through 146 Proline residue: L 146 - end of helix Processing helix chain 'L' and resid 165 through 194 removed outlier: 5.187A pdb=" N GLY L 181 " --> pdb=" O LYS L 177 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE L 182 " --> pdb=" O LYS L 178 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLU L 194 " --> pdb=" O LYS L 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 64 removed outlier: 4.076A pdb=" N VAL M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL M 64 " --> pdb=" O LEU M 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 59 through 64' Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 90 through 98 removed outlier: 3.810A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER M 98 " --> pdb=" O TRP M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 112 Processing helix chain 'M' and resid 113 through 138 removed outlier: 3.619A pdb=" N LYS M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 14 removed outlier: 4.763A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 4.973A pdb=" N ASN N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 111 Processing helix chain 'N' and resid 139 through 145 Processing helix chain 'N' and resid 148 through 153 removed outlier: 4.372A pdb=" N CYS N 152 " --> pdb=" O TYR N 148 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP N 153 " --> pdb=" O ASN N 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 148 through 153' Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 186 through 196 removed outlier: 3.656A pdb=" N THR N 196 " --> pdb=" O LYS N 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 Processing helix chain 'O' and resid 46 through 61 removed outlier: 5.459A pdb=" N ALA O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 4.049A pdb=" N GLY O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix No H-bonds generated for 'chain 'O' and resid 65 through 70' Processing helix chain 'O' and resid 75 through 89 removed outlier: 3.691A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N SER O 89 " --> pdb=" O ARG O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 103 removed outlier: 3.686A pdb=" N ARG O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 116 removed outlier: 8.203A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LYS O 116 " --> pdb=" O TYR O 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 110 through 116' Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 151 through 183 Processing helix chain 'O' and resid 188 through 198 Processing helix chain 'P' and resid 10 through 15 removed outlier: 4.323A pdb=" N SER P 14 " --> pdb=" O ASN P 10 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ALA P 15 " --> pdb=" O PRO P 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 10 through 15' Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 54 Processing helix chain 'P' and resid 70 through 75 removed outlier: 4.833A pdb=" N LYS P 74 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLU P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 70 through 75' Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'P' and resid 169 through 184 removed outlier: 4.724A pdb=" N ALA P 184 " --> pdb=" O LYS P 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 42 through 54 removed outlier: 3.866A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 60 Proline residue: Q 60 - end of helix Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.914A pdb=" N GLN Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 118 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 36 removed outlier: 3.705A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 77 through 82 removed outlier: 5.621A pdb=" N LYS R 82 " --> pdb=" O TYR R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 6.490A pdb=" N VAL R 93 " --> pdb=" O LEU R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 Processing helix chain 'R' and resid 134 through 157 Processing helix chain 'S' and resid 33 through 49 Processing helix chain 'S' and resid 98 through 114 Processing helix chain 'S' and resid 117 through 122 removed outlier: 5.514A pdb=" N HIS S 122 " --> pdb=" O PHE S 118 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 145 removed outlier: 5.129A pdb=" N PHE S 143 " --> pdb=" O TYR S 139 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU S 144 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR S 145 " --> pdb=" O LYS S 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 97 removed outlier: 4.135A pdb=" N ILE T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LYS T 97 " --> pdb=" O VAL T 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 92 through 97' Processing helix chain 'T' and resid 102 through 123 removed outlier: 3.759A pdb=" N GLY T 123 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 26 Processing helix chain 'U' and resid 29 through 41 Processing helix chain 'U' and resid 72 through 88 Processing helix chain 'V' and resid 66 through 71 removed outlier: 4.987A pdb=" N LYS V 71 " --> pdb=" O PRO V 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 127 Proline residue: V 127 - end of helix Processing helix chain 'V' and resid 128 through 133 Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.917A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 61 removed outlier: 3.579A pdb=" N ALA W 61 " --> pdb=" O ARG W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 88 through 96 removed outlier: 4.794A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS W 96 " --> pdb=" O LEU W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 Processing helix chain 'W' and resid 150 through 155 removed outlier: 4.816A pdb=" N VAL W 155 " --> pdb=" O ALA W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 168 removed outlier: 4.366A pdb=" N GLU W 162 " --> pdb=" O ILE W 158 " (cutoff:3.500A) Proline residue: W 163 - end of helix Processing helix chain 'W' and resid 196 through 207 Processing helix chain 'X' and resid 4 through 16 Processing helix chain 'X' and resid 58 through 64 removed outlier: 4.732A pdb=" N GLU X 64 " --> pdb=" O TYR X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 79 removed outlier: 3.854A pdb=" N LYS X 75 " --> pdb=" O THR X 71 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 103 Processing helix chain 'X' and resid 131 through 140 removed outlier: 3.581A pdb=" N ILE X 135 " --> pdb=" O ASP X 131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 22 Processing helix chain 'Y' and resid 23 through 32 removed outlier: 3.741A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER Y 32 " --> pdb=" O ARG Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 100 through 105 removed outlier: 3.721A pdb=" N LEU Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Z' and resid 58 through 67 removed outlier: 4.017A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.759A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU Z 81 " --> pdb=" O TYR Z 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 76 through 81' Processing helix chain 'Z' and resid 92 through 97 removed outlier: 3.876A pdb=" N VAL Z 96 " --> pdb=" O PHE Z 92 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N SER Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 92 through 97' Processing helix chain 'Z' and resid 98 through 104 removed outlier: 3.720A pdb=" N GLU Z 102 " --> pdb=" O THR Z 98 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN Z 103 " --> pdb=" O GLU Z 99 " (cutoff:3.500A) Proline residue: Z 104 - end of helix No H-bonds generated for 'chain 'Z' and resid 98 through 104' Processing helix chain 'Z' and resid 105 through 125 removed outlier: 4.263A pdb=" N GLU Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 132 Processing helix chain 'a' and resid 74 through 82 removed outlier: 4.339A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 94 removed outlier: 3.937A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN a 89 " --> pdb=" O ASP a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 108 Processing helix chain 'a' and resid 131 through 142 Processing helix chain 'b' and resid 13 through 29 Processing helix chain 'b' and resid 38 through 66 Processing helix chain 'b' and resid 75 through 86 Processing helix chain 'b' and resid 87 through 119 removed outlier: 4.348A pdb=" N PHE b 118 " --> pdb=" O ARG b 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY b 119 " --> pdb=" O LEU b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 144 removed outlier: 3.840A pdb=" N LEU b 143 " --> pdb=" O ILE b 139 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG b 144 " --> pdb=" O VAL b 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 160 removed outlier: 3.896A pdb=" N ARG b 159 " --> pdb=" O GLN b 155 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU b 160 " --> pdb=" O HIS b 156 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.948A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 279 Proline residue: b 276 - end of helix removed outlier: 4.579A pdb=" N ALA b 279 " --> pdb=" O LYS b 275 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 312 removed outlier: 3.986A pdb=" N VAL b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 351 removed outlier: 3.732A pdb=" N LYS b 349 " --> pdb=" O GLU b 345 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLN b 351 " --> pdb=" O LYS b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 352 through 362 removed outlier: 5.703A pdb=" N ASN b 356 " --> pdb=" O SER b 352 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL b 357 " --> pdb=" O ARG b 353 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 Processing helix chain 'b' and resid 398 through 407 Processing helix chain 'b' and resid 415 through 420 removed outlier: 5.016A pdb=" N LYS b 419 " --> pdb=" O ASN b 415 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR b 420 " --> pdb=" O LEU b 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 415 through 420' Processing helix chain 'b' and resid 424 through 429 removed outlier: 4.359A pdb=" N LYS b 428 " --> pdb=" O ASP b 424 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASN b 429 " --> pdb=" O ASP b 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 424 through 429' Processing helix chain 'b' and resid 440 through 445 removed outlier: 3.804A pdb=" N PHE b 444 " --> pdb=" O ASN b 440 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 467 Processing helix chain 'b' and resid 482 through 511 Processing helix chain 'b' and resid 520 through 525 removed outlier: 4.809A pdb=" N THR b 525 " --> pdb=" O ARG b 521 " (cutoff:3.500A) Processing helix chain 'b' and resid 527 through 539 Processing helix chain 'b' and resid 542 through 557 removed outlier: 4.662A pdb=" N ARG b 557 " --> pdb=" O ALA b 553 " (cutoff:3.500A) Processing helix chain 'b' and resid 561 through 567 Processing helix chain 'b' and resid 595 through 617 removed outlier: 4.050A pdb=" N ARG b 611 " --> pdb=" O LYS b 607 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU b 612 " --> pdb=" O MET b 608 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ARG b 613 " --> pdb=" O GLU b 609 " (cutoff:3.500A) Processing helix chain 'b' and resid 631 through 636 Processing helix chain 'c' and resid 9 through 20 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 82 Processing helix chain 'd' and resid 15 through 21 removed outlier: 3.938A pdb=" N ARG d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 45 removed outlier: 5.199A pdb=" N ALA d 29 " --> pdb=" O PHE d 25 " (cutoff:3.500A) Proline residue: d 30 - end of helix Processing helix chain 'd' and resid 52 through 61 Processing helix chain 'e' and resid 21 through 26 removed outlier: 5.182A pdb=" N HIS e 26 " --> pdb=" O SER e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 45 Processing helix chain 'e' and resid 78 through 87 removed outlier: 3.621A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU e 85 " --> pdb=" O ASP e 81 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR e 86 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N MET e 87 " --> pdb=" O GLU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.759A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 45 removed outlier: 4.314A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU f 45 " --> pdb=" O ALA f 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 66 removed outlier: 3.742A pdb=" N TYR g 62 " --> pdb=" O ARG g 58 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA g 63 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL g 65 " --> pdb=" O GLN g 61 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N SER g 66 " --> pdb=" O TYR g 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 58 through 66' Processing helix chain 'g' and resid 81 through 113 Processing helix chain 'h' and resid 5 through 13 removed outlier: 4.141A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS h 12 " --> pdb=" O GLU h 8 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 38 removed outlier: 3.828A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 71 removed outlier: 4.196A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 82 removed outlier: 5.278A pdb=" N ALA h 82 " --> pdb=" O LYS h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 91 Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 25 through 31 removed outlier: 4.276A pdb=" N LYS i 29 " --> pdb=" O LYS i 25 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS i 30 " --> pdb=" O ILE i 26 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLY i 31 " --> pdb=" O SER i 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 31' Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 64 Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 98 Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.524A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS j 10 " --> pdb=" O PRO j 6 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 65 through 77 removed outlier: 5.598A pdb=" N HIS j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 Processing helix chain 'k' and resid 58 through 69 Processing helix chain 'l' and resid 6 through 21 removed outlier: 5.542A pdb=" N ARG l 21 " --> pdb=" O LYS l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.223A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG l 30 " --> pdb=" O TRP l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 24 through 30' Processing helix chain 'm' and resid 2 through 7 removed outlier: 3.843A pdb=" N LYS m 6 " --> pdb=" O GLY m 2 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLU m 7 " --> pdb=" O THR m 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 2 through 7' Processing helix chain 'm' and resid 8 through 14 Processing helix chain 'm' and resid 32 through 44 removed outlier: 4.445A pdb=" N TYR m 42 " --> pdb=" O PHE m 38 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N THR m 43 " --> pdb=" O LEU m 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 74 through 80 removed outlier: 4.691A pdb=" N PHE m 78 " --> pdb=" O ASP m 74 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY m 79 " --> pdb=" O ARG m 75 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASN m 80 " --> pdb=" O ARG m 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 74 through 80' Processing helix chain 'm' and resid 85 through 99 removed outlier: 5.280A pdb=" N GLY m 97 " --> pdb=" O ARG m 93 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU m 98 " --> pdb=" O SER m 94 " (cutoff:3.500A) Processing helix chain 'm' and resid 114 through 120 removed outlier: 5.035A pdb=" N GLU m 120 " --> pdb=" O SER m 116 " (cutoff:3.500A) Processing helix chain 'm' and resid 130 through 135 removed outlier: 4.508A pdb=" N THR m 134 " --> pdb=" O ARG m 130 " (cutoff:3.500A) Processing helix chain 'm' and resid 136 through 141 Processing helix chain 'm' and resid 156 through 185 removed outlier: 4.059A pdb=" N LEU m 181 " --> pdb=" O LEU m 177 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU m 183 " --> pdb=" O ALA m 179 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N MET m 184 " --> pdb=" O THR m 180 " (cutoff:3.500A) Processing helix chain 'm' and resid 186 through 193 removed outlier: 3.840A pdb=" N LYS m 190 " --> pdb=" O ASN m 186 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU m 191 " --> pdb=" O GLN m 187 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN m 192 " --> pdb=" O GLU m 188 " (cutoff:3.500A) Processing helix chain 'm' and resid 200 through 205 removed outlier: 4.359A pdb=" N SER m 204 " --> pdb=" O GLU m 200 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS m 205 " --> pdb=" O ALA m 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 200 through 205' Processing helix chain 'm' and resid 208 through 222 Processing helix chain 'm' and resid 233 through 238 Processing helix chain 'm' and resid 239 through 249 Processing helix chain 'm' and resid 261 through 266 removed outlier: 4.376A pdb=" N VAL m 265 " --> pdb=" O LYS m 261 " (cutoff:3.500A) Proline residue: m 266 - end of helix No H-bonds generated for 'chain 'm' and resid 261 through 266' Processing helix chain 'm' and resid 267 through 281 removed outlier: 3.612A pdb=" N LYS m 279 " --> pdb=" O LYS m 275 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU m 280 " --> pdb=" O HIS m 276 " (cutoff:3.500A) Processing helix chain 'm' and resid 295 through 311 Processing helix chain 'm' and resid 327 through 337 Processing helix chain 'm' and resid 378 through 386 removed outlier: 3.768A pdb=" N GLY m 386 " --> pdb=" O ILE m 382 " (cutoff:3.500A) Processing helix chain 'm' and resid 389 through 394 removed outlier: 3.868A pdb=" N VAL m 393 " --> pdb=" O ARG m 389 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR m 394 " --> pdb=" O VAL m 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 389 through 394' Processing helix chain 'm' and resid 395 through 407 removed outlier: 4.456A pdb=" N TYR m 399 " --> pdb=" O HIS m 395 " (cutoff:3.500A) Proline residue: m 401 - end of helix Processing helix chain 'm' and resid 408 through 417 Processing helix chain 'm' and resid 423 through 436 Processing helix chain 'm' and resid 445 through 460 Processing helix chain 'n' and resid 10 through 15 Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 48 through 54 Processing helix chain 'n' and resid 64 through 74 removed outlier: 4.263A pdb=" N HIS n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU n 74 " --> pdb=" O TYR n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 97 Processing helix chain 'n' and resid 98 through 109 removed outlier: 4.122A pdb=" N ARG n 109 " --> pdb=" O LEU n 105 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 123 Proline residue: n 123 - end of helix Processing helix chain 'n' and resid 124 through 146 removed outlier: 4.914A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA n 135 " --> pdb=" O ASP n 131 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN n 144 " --> pdb=" O PHE n 140 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) Proline residue: n 146 - end of helix Processing helix chain 'n' and resid 152 through 174 Processing helix chain 'n' and resid 214 through 241 Processing helix chain 'n' and resid 249 through 256 Processing helix chain 'n' and resid 354 through 359 removed outlier: 6.739A pdb=" N SER n 358 " --> pdb=" O SER n 354 " (cutoff:3.500A) Processing helix chain 'n' and resid 372 through 384 Processing helix chain 'n' and resid 389 through 394 removed outlier: 3.808A pdb=" N MET n 393 " --> pdb=" O SER n 389 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP n 394 " --> pdb=" O GLU n 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 389 through 394' Processing helix chain 'n' and resid 428 through 439 removed outlier: 4.300A pdb=" N ILE n 432 " --> pdb=" O GLN n 428 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE n 433 " --> pdb=" O PRO n 429 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 115 removed outlier: 4.325A pdb=" N GLN o 113 " --> pdb=" O LYS o 109 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE o 114 " --> pdb=" O TYR o 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 141 through 153 Processing helix chain 'o' and resid 192 through 215 removed outlier: 3.657A pdb=" N GLY o 215 " --> pdb=" O LEU o 211 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.811A pdb=" N LEU p 29 " --> pdb=" O GLN p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 Processing helix chain 'q' and resid 204 through 210 removed outlier: 4.382A pdb=" N ASP q 208 " --> pdb=" O PRO q 204 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE q 209 " --> pdb=" O SER q 205 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLU q 210 " --> pdb=" O THR q 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 204 through 210' Processing helix chain 'q' and resid 232 through 269 Processing helix chain 'q' and resid 398 through 403 removed outlier: 5.795A pdb=" N SER q 403 " --> pdb=" O SER q 399 " (cutoff:3.500A) Processing helix chain 'q' and resid 414 through 427 Processing helix chain 'q' and resid 448 through 454 Processing helix chain 'r' and resid 5 through 14 Processing helix chain 'r' and resid 19 through 42 removed outlier: 4.598A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 74 Processing helix chain 'r' and resid 88 through 93 removed outlier: 5.708A pdb=" N ASP r 93 " --> pdb=" O THR r 89 " (cutoff:3.500A) Processing helix chain 'r' and resid 129 through 134 Processing helix chain 'r' and resid 174 through 179 removed outlier: 3.556A pdb=" N ARG r 178 " --> pdb=" O PRO r 174 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN r 179 " --> pdb=" O SER r 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 174 through 179' Processing helix chain 'r' and resid 206 through 213 Processing helix chain 'r' and resid 248 through 253 Processing helix chain 's' and resid 12 through 37 Processing helix chain 's' and resid 56 through 77 removed outlier: 3.737A pdb=" N GLU s 73 " --> pdb=" O MET s 69 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG s 75 " --> pdb=" O ASP s 71 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU s 76 " --> pdb=" O LEU s 72 " (cutoff:3.500A) Processing helix chain 't' and resid 15 through 52 removed outlier: 4.234A pdb=" N LEU t 19 " --> pdb=" O ASN t 15 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS t 52 " --> pdb=" O LYS t 48 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 88 Processing helix chain 't' and resid 156 through 167 Processing helix chain 't' and resid 180 through 191 Proline residue: t 185 - end of helix Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 231 through 239 removed outlier: 3.561A pdb=" N VAL t 235 " --> pdb=" O ASP t 231 " (cutoff:3.500A) Processing helix chain 't' and resid 246 through 257 Processing helix chain 't' and resid 260 through 269 removed outlier: 4.830A pdb=" N GLN t 269 " --> pdb=" O ASN t 265 " (cutoff:3.500A) Processing helix chain 't' and resid 281 through 299 Processing helix chain 't' and resid 313 through 322 Processing helix chain 'u' and resid 33 through 43 Processing helix chain 'u' and resid 45 through 50 removed outlier: 5.381A pdb=" N LYS u 50 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 60 Processing helix chain 'u' and resid 66 through 71 removed outlier: 3.996A pdb=" N THR u 70 " --> pdb=" O ASP u 66 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE u 71 " --> pdb=" O SER u 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 66 through 71' Processing helix chain 'u' and resid 82 through 131 removed outlier: 3.612A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLY u 114 " --> pdb=" O ASN u 110 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN u 115 " --> pdb=" O ARG u 111 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LYS u 116 " --> pdb=" O MET u 112 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLU u 117 " --> pdb=" O ARG u 113 " (cutoff:3.500A) Proline residue: u 131 - end of helix Processing helix chain 'u' and resid 132 through 150 Processing helix chain 'v' and resid 9 through 21 removed outlier: 5.448A pdb=" N ALA v 21 " --> pdb=" O VAL v 17 " (cutoff:3.500A) Processing helix chain 'v' and resid 39 through 54 Processing helix chain 'v' and resid 72 through 83 Processing helix chain 'v' and resid 124 through 129 removed outlier: 4.397A pdb=" N PHE v 128 " --> pdb=" O LEU v 124 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS v 129 " --> pdb=" O LEU v 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 124 through 129' Processing helix chain 'v' and resid 145 through 151 removed outlier: 4.312A pdb=" N ASP v 149 " --> pdb=" O GLY v 145 " (cutoff:3.500A) Processing helix chain 'v' and resid 152 through 166 Processing helix chain 'v' and resid 241 through 250 Processing helix chain 'v' and resid 281 through 286 removed outlier: 4.658A pdb=" N LEU v 285 " --> pdb=" O ASP v 281 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLN v 286 " --> pdb=" O LEU v 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 281 through 286' Processing helix chain 'w' and resid 35 through 40 removed outlier: 3.606A pdb=" N LEU w 39 " --> pdb=" O ASP w 35 " (cutoff:3.500A) Processing helix chain 'w' and resid 45 through 69 Proline residue: w 69 - end of helix Processing helix chain 'w' and resid 112 through 122 Processing helix chain 'w' and resid 149 through 157 removed outlier: 4.289A pdb=" N LYS w 153 " --> pdb=" O GLY w 149 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU w 154 " --> pdb=" O ALA w 150 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP w 155 " --> pdb=" O ASN w 151 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP w 156 " --> pdb=" O LYS w 152 " (cutoff:3.500A) Processing helix chain 'w' and resid 163 through 168 removed outlier: 4.111A pdb=" N LYS w 167 " --> pdb=" O ASP w 163 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLY w 168 " --> pdb=" O ASP w 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 163 through 168' Processing helix chain 'w' and resid 175 through 201 Processing helix chain 'w' and resid 169 through 174 removed outlier: 3.947A pdb=" N GLU w 172 " --> pdb=" O THR w 169 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU w 173 " --> pdb=" O ASP w 170 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE w 174 " --> pdb=" O ASN w 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 169 through 174' Processing helix chain 'x' and resid 9 through 19 Proline residue: x 19 - end of helix Processing helix chain 'x' and resid 56 through 69 Processing helix chain 'x' and resid 100 through 105 Processing helix chain 'x' and resid 239 through 244 removed outlier: 4.975A pdb=" N LYS x 244 " --> pdb=" O ILE x 240 " (cutoff:3.500A) Processing helix chain 'x' and resid 330 through 337 Processing helix chain 'x' and resid 348 through 365 removed outlier: 3.958A pdb=" N ILE x 363 " --> pdb=" O ASN x 359 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 17 removed outlier: 3.594A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 43 removed outlier: 3.854A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 89 Proline residue: y 89 - end of helix Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 133 Processing helix chain 'y' and resid 147 through 152 Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 197 Processing helix chain 'y' and resid 211 through 223 Processing helix chain 'y' and resid 232 through 244 removed outlier: 5.093A pdb=" N ASP y 238 " --> pdb=" O GLY y 234 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR y 239 " --> pdb=" O ASN y 235 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 56 removed outlier: 4.103A pdb=" N GLY z 20 " --> pdb=" O VAL z 16 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL z 21 " --> pdb=" O LYS z 17 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE z 22 " --> pdb=" O ARG z 18 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLN z 23 " --> pdb=" O ARG z 19 " (cutoff:3.500A) Processing helix chain 'z' and resid 82 through 100 Processing helix chain '4' and resid 21 through 50 Processing helix chain '4' and resid 60 through 80 removed outlier: 4.090A pdb=" N GLN 4 78 " --> pdb=" O THR 4 74 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR 4 79 " --> pdb=" O ARG 4 75 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR 4 80 " --> pdb=" O LEU 4 76 " (cutoff:3.500A) Processing helix chain '4' and resid 110 through 119 Processing helix chain '4' and resid 125 through 131 Processing helix chain '4' and resid 178 through 204 removed outlier: 3.530A pdb=" N ALA 4 201 " --> pdb=" O LEU 4 197 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU 4 202 " --> pdb=" O LEU 4 198 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR 4 203 " --> pdb=" O ALA 4 199 " (cutoff:3.500A) Proline residue: 4 204 - end of helix Processing helix chain '4' and resid 219 through 235 Processing helix chain '4' and resid 270 through 280 Processing helix chain '4' and resid 372 through 386 removed outlier: 3.675A pdb=" N GLY 4 386 " --> pdb=" O ILE 4 382 " (cutoff:3.500A) Processing helix chain '4' and resid 391 through 396 removed outlier: 3.727A pdb=" N LEU 4 395 " --> pdb=" O LYS 4 391 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER 4 396 " --> pdb=" O LEU 4 392 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 391 through 396' Processing helix chain '4' and resid 405 through 427 removed outlier: 3.867A pdb=" N SER 4 418 " --> pdb=" O LYS 4 414 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU 4 425 " --> pdb=" O LEU 4 421 " (cutoff:3.500A) Processing helix chain '4' and resid 444 through 451 removed outlier: 3.673A pdb=" N ILE 4 448 " --> pdb=" O PRO 4 444 " (cutoff:3.500A) Processing helix chain '4' and resid 466 through 471 Processing helix chain '4' and resid 481 through 493 removed outlier: 5.746A pdb=" N LYS 4 493 " --> pdb=" O MET 4 489 " (cutoff:3.500A) Processing helix chain '4' and resid 547 through 563 removed outlier: 5.054A pdb=" N LYS 4 563 " --> pdb=" O LEU 4 559 " (cutoff:3.500A) Processing helix chain '4' and resid 528 through 533 removed outlier: 3.901A pdb=" N GLN 4 533 " --> pdb=" O GLY 4 528 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 528 through 533' Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.724A pdb=" N GLN A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 111 through 114 removed outlier: 4.453A pdb=" N THR A 111 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 58 through 64 Processing sheet with id= 4, first strand: chain 'A' and resid 145 through 150 removed outlier: 4.289A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '8' and resid 11 through 16 removed outlier: 4.368A pdb=" N THR 8 59 " --> pdb=" O VAL 8 74 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.699A pdb=" N GLN B 182 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N HIS B 177 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL B 158 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N GLY B 185 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 12.551A pdb=" N SER B 156 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 272 through 278 removed outlier: 4.387A pdb=" N HIS B 273 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 284 through 288 removed outlier: 3.828A pdb=" N GLY B 288 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASN B 319 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 357 through 360 removed outlier: 3.538A pdb=" N TRP B 358 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR B 55 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 53 through 58 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'B' and resid 87 through 91 removed outlier: 7.976A pdb=" N VAL B 87 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 84 through 87 removed outlier: 4.016A pdb=" N LYS B 201 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 215 through 219 Processing sheet with id= 14, first strand: chain 'C' and resid 4 through 8 removed outlier: 5.202A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 224 through 229 removed outlier: 5.388A pdb=" N PHE C 247 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 60 through 66 Processing sheet with id= 17, first strand: chain 'E' and resid 37 through 43 removed outlier: 4.021A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS E 50 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU E 64 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 133 through 138 removed outlier: 7.703A pdb=" N TYR F 133 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LYS F 82 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN F 112 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'F' and resid 152 through 155 removed outlier: 6.887A pdb=" N GLY F 152 " --> pdb=" O LEU F 163 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 176 through 181 Processing sheet with id= 21, first strand: chain 'H' and resid 5 through 12 removed outlier: 4.641A pdb=" N GLN H 51 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 17 through 20 removed outlier: 6.293A pdb=" N ARG H 23 " --> pdb=" O LEU H 38 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 100 through 104 removed outlier: 6.358A pdb=" N LYS H 110 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 132 through 137 removed outlier: 5.855A pdb=" N GLU H 143 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP H 142 " --> pdb=" O TYR H 92 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 49 through 52 removed outlier: 4.996A pdb=" N HIS I 49 " --> pdb=" O MET I 58 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 45 through 48 removed outlier: 4.398A pdb=" N ALA J 66 " --> pdb=" O SER J 48 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE J 65 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER J 22 " --> pdb=" O GLY J 124 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N GLY J 124 " --> pdb=" O SER J 22 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 97 through 101 Processing sheet with id= 28, first strand: chain 'K' and resid 123 through 126 Processing sheet with id= 29, first strand: chain 'K' and resid 242 through 248 removed outlier: 5.688A pdb=" N THR K 242 " --> pdb=" O ASN K 84 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU K 78 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'L' and resid 56 through 59 Processing sheet with id= 31, first strand: chain 'M' and resid 19 through 24 removed outlier: 4.366A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS M 31 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.579A pdb=" N VAL N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'N' and resid 117 through 121 removed outlier: 3.698A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 35, first strand: chain 'P' and resid 16 through 20 removed outlier: 6.389A pdb=" N VAL P 149 " --> pdb=" O SER P 115 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'P' and resid 57 through 60 removed outlier: 5.428A pdb=" N LYS P 80 " --> pdb=" O PHE P 60 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'P' and resid 116 through 122 Processing sheet with id= 38, first strand: chain 'P' and resid 124 through 131 Processing sheet with id= 39, first strand: chain 'Q' and resid 79 through 83 Processing sheet with id= 40, first strand: chain 'R' and resid 21 through 25 removed outlier: 6.489A pdb=" N LYS R 21 " --> pdb=" O LYS R 53 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR R 49 " --> pdb=" O ASP R 25 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'S' and resid 24 through 31 removed outlier: 6.655A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'S' and resid 87 through 96 removed outlier: 3.587A pdb=" N HIS S 88 " --> pdb=" O TYR S 81 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'S' and resid 6 through 10 removed outlier: 4.582A pdb=" N GLU S 6 " --> pdb=" O ILE S 64 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'T' and resid 38 through 43 removed outlier: 4.117A pdb=" N ASP T 38 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS T 60 " --> pdb=" O ILE T 42 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'U' and resid 54 through 58 removed outlier: 5.945A pdb=" N ASN U 101 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N TRP U 92 " --> pdb=" O TYR U 108 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'V' and resid 21 through 24 removed outlier: 4.459A pdb=" N ALA V 21 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP V 56 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP V 97 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA V 82 " --> pdb=" O ASP V 97 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 84 through 87 removed outlier: 3.601A pdb=" N VAL V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'W' and resid 63 through 67 removed outlier: 5.809A pdb=" N VAL W 99 " --> pdb=" O LEU W 45 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL W 42 " --> pdb=" O SER W 218 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'W' and resid 128 through 131 removed outlier: 6.379A pdb=" N THR W 129 " --> pdb=" O LYS W 194 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS W 194 " --> pdb=" O THR W 129 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ALA W 131 " --> pdb=" O GLY W 192 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'W' and resid 135 through 139 removed outlier: 6.832A pdb=" N PHE W 135 " --> pdb=" O VAL W 188 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU W 139 " --> pdb=" O SER W 184 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER W 184 " --> pdb=" O GLU W 139 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'W' and resid 173 through 176 Processing sheet with id= 52, first strand: chain 'W' and resid 226 through 230 removed outlier: 3.995A pdb=" N THR W 227 " --> pdb=" O ASP W 222 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'W' and resid 38 through 42 removed outlier: 8.258A pdb=" N ARG W 38 " --> pdb=" O ASN W 223 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'X' and resid 81 through 86 removed outlier: 3.883A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'Y' and resid 72 through 75 Processing sheet with id= 56, first strand: chain 'Y' and resid 86 through 89 removed outlier: 4.001A pdb=" N ALA Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Z' and resid 9 through 14 removed outlier: 4.094A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'Z' and resid 42 through 45 Processing sheet with id= 59, first strand: chain 'a' and resid 99 through 102 Processing sheet with id= 60, first strand: chain 'b' and resid 204 through 210 removed outlier: 4.923A pdb=" N ARG b 168 " --> pdb=" O ARG b 215 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR b 221 " --> pdb=" O ILE b 172 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY b 174 " --> pdb=" O THR b 221 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU b 316 " --> pdb=" O VAL b 283 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.386A pdb=" N LYS c 22 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS c 66 " --> pdb=" O LYS c 40 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA c 46 " --> pdb=" O PHE c 70 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'd' and resid 48 through 51 removed outlier: 5.015A pdb=" N ASP d 48 " --> pdb=" O LEU d 89 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR d 9 " --> pdb=" O VAL d 109 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'e' and resid 71 through 77 Processing sheet with id= 64, first strand: chain 'f' and resid 10 through 15 removed outlier: 5.960A pdb=" N LYS f 10 " --> pdb=" O GLU f 33 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG f 82 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS f 47 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'f' and resid 8 through 14 removed outlier: 4.090A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.553A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'k' and resid 2 through 5 removed outlier: 4.505A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE k 27 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'm' and resid 282 through 286 removed outlier: 3.826A pdb=" N CYS m 367 " --> pdb=" O PHE m 320 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLY m 322 " --> pdb=" O CYS m 367 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE m 362 " --> pdb=" O LEU m 358 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'n' and resid 177 through 182 Processing sheet with id= 70, first strand: chain 'n' and resid 385 through 388 Processing sheet with id= 71, first strand: chain 'o' and resid 118 through 123 removed outlier: 3.743A pdb=" N GLU o 119 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'p' and resid 47 through 50 removed outlier: 6.911A pdb=" N ILE p 54 " --> pdb=" O GLY p 50 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'r' and resid 148 through 151 Processing sheet with id= 74, first strand: chain 'r' and resid 190 through 196 removed outlier: 3.819A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL r 255 " --> pdb=" O LYS r 181 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN r 256 " --> pdb=" O THR r 246 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR r 242 " --> pdb=" O LEU r 260 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR r 219 " --> pdb=" O VAL r 245 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE r 220 " --> pdb=" O LYS r 201 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 't' and resid 128 through 134 Processing sheet with id= 76, first strand: chain 't' and resid 193 through 198 removed outlier: 5.605A pdb=" N TYR t 193 " --> pdb=" O VAL t 147 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASN t 172 " --> pdb=" O LEU t 273 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 't' and resid 213 through 217 removed outlier: 3.623A pdb=" N HIS t 225 " --> pdb=" O TYR t 216 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'u' and resid 3 through 6 removed outlier: 4.558A pdb=" N SER u 11 " --> pdb=" O CYS u 6 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'u' and resid 18 through 23 removed outlier: 3.925A pdb=" N LYS u 27 " --> pdb=" O ARG u 23 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'v' and resid 56 through 60 removed outlier: 7.059A pdb=" N SER v 92 " --> pdb=" O GLY v 35 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N SER v 85 " --> pdb=" O THR v 105 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASN v 98 " --> pdb=" O VAL v 118 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU v 115 " --> pdb=" O GLY v 235 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP v 231 " --> pdb=" O ALA v 119 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASN v 198 " --> pdb=" O GLN v 187 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN v 179 " --> pdb=" O LEU v 206 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'v' and resid 262 through 266 removed outlier: 5.772A pdb=" N ASN v 262 " --> pdb=" O ARG v 274 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP v 270 " --> pdb=" O ASP v 266 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'v' and resid 111 through 115 removed outlier: 9.091A pdb=" N TYR v 111 " --> pdb=" O PRO v 240 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'v' and resid 204 through 208 No H-bonds generated for sheet with id= 83 Processing sheet with id= 84, first strand: chain 'w' and resid 19 through 23 Processing sheet with id= 85, first strand: chain 'x' and resid 48 through 51 removed outlier: 6.785A pdb=" N THR x 118 " --> pdb=" O THR x 82 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR x 82 " --> pdb=" O THR x 118 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'x' and resid 136 through 140 removed outlier: 4.958A pdb=" N MET x 509 " --> pdb=" O GLY x 505 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY x 505 " --> pdb=" O MET x 509 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG x 500 " --> pdb=" O SER x 495 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'x' and resid 148 through 152 removed outlier: 6.447A pdb=" N ARG x 158 " --> pdb=" O ALA x 152 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER x 157 " --> pdb=" O CYS x 173 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE x 170 " --> pdb=" O MET x 179 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'x' and resid 191 through 195 removed outlier: 5.649A pdb=" N VAL x 200 " --> pdb=" O SER x 195 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR x 209 " --> pdb=" O SER x 205 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU x 212 " --> pdb=" O LEU x 221 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'x' and resid 233 through 238 removed outlier: 3.669A pdb=" N SER x 234 " --> pdb=" O SER x 254 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ARG x 250 " --> pdb=" O GLU x 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER x 255 " --> pdb=" O THR x 259 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR x 259 " --> pdb=" O SER x 255 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR x 272 " --> pdb=" O ILE x 262 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'x' and resid 283 through 287 removed outlier: 4.410A pdb=" N LEU x 291 " --> pdb=" O GLY x 287 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL x 303 " --> pdb=" O ILE x 313 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG x 311 " --> pdb=" O ASP x 305 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'x' and resid 325 through 329 removed outlier: 7.062A pdb=" N MET x 373 " --> pdb=" O SER x 329 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR x 382 " --> pdb=" O SER x 378 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'x' and resid 406 through 411 removed outlier: 5.619A pdb=" N TYR x 416 " --> pdb=" O SER x 411 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER x 425 " --> pdb=" O SER x 421 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'x' and resid 449 through 453 removed outlier: 3.881A pdb=" N GLN x 449 " --> pdb=" O CYS x 462 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU x 458 " --> pdb=" O SER x 453 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ARG x 457 " --> pdb=" O VAL x 473 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR x 467 " --> pdb=" O SER x 463 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'x' and resid 167 through 170 Processing sheet with id= 95, first strand: chain 'x' and resid 300 through 303 Processing sheet with id= 96, first strand: chain 'y' and resid 1 through 5 Processing sheet with id= 97, first strand: chain 'y' and resid 23 through 27 Processing sheet with id= 98, first strand: chain 'y' and resid 69 through 73 Processing sheet with id= 99, first strand: chain 'y' and resid 158 through 161 Processing sheet with id=100, first strand: chain '4' and resid 93 through 97 removed outlier: 3.882A pdb=" N ASP 4 137 " --> pdb=" O ILE 4 160 " (cutoff:3.500A) removed outlier: 13.199A pdb=" N THR 4 151 " --> pdb=" O VAL 4 508 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N VAL 4 508 " --> pdb=" O THR 4 151 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU 4 153 " --> pdb=" O THR 4 506 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR 4 506 " --> pdb=" O GLU 4 153 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG 4 502 " --> pdb=" O THR 4 157 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N VAL 4 159 " --> pdb=" O VAL 4 500 " (cutoff:3.500A) removed outlier: 13.886A pdb=" N VAL 4 500 " --> pdb=" O VAL 4 159 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU 4 315 " --> pdb=" O LEU 4 509 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain '4' and resid 335 through 340 removed outlier: 4.932A pdb=" N ILE 4 437 " --> pdb=" O VAL 4 340 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain '4' and resid 568 through 572 Processing sheet with id=103, first strand: chain '4' and resid 506 through 511 removed outlier: 6.640A pdb=" N THR 4 506 " --> pdb=" O LEU 4 525 " (cutoff:3.500A) 3889 hydrogen bonds defined for protein. 11556 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2517 hydrogen bonds 4048 hydrogen bond angles 0 basepair planarities 1021 basepair parallelities 1642 stacking parallelities Total time for adding SS restraints: 214.88 Time building geometry restraints manager: 63.30 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: 19236 1.32 - 1.44: 63323 1.44 - 1.57: 77773 1.57 - 1.70: 6628 1.70 - 1.83: 381 Bond restraints: 167341 Sorted by residual: bond pdb=" C2' A2M 1 807 " pdb=" C1' A2M 1 807 " ideal model delta sigma weight residual 1.305 1.582 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C2' A2M 12220 " pdb=" C1' A2M 12220 " ideal model delta sigma weight residual 1.305 1.573 -0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" C2' A2M 1 876 " pdb=" C1' A2M 1 876 " ideal model delta sigma weight residual 1.305 1.553 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C2' A2M 11449 " pdb=" C1' A2M 11449 " ideal model delta sigma weight residual 1.305 1.553 -0.248 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C2' A2M 1 649 " pdb=" C1' A2M 1 649 " ideal model delta sigma weight residual 1.305 1.552 -0.247 2.00e-02 2.50e+03 1.52e+02 ... (remaining 167336 not shown) Histogram of bond angle deviations from ideal: 97.32 - 105.14: 16196 105.14 - 112.95: 97466 112.95 - 120.76: 74345 120.76 - 128.57: 49453 128.57 - 136.39: 4484 Bond angle restraints: 241944 Sorted by residual: angle pdb=" C1' A2M 1 817 " pdb=" N9 A2M 1 817 " pdb=" C8 A2M 1 817 " ideal model delta sigma weight residual 88.50 129.64 -41.14 3.00e+00 1.11e-01 1.88e+02 angle pdb=" C1' A2M 1 876 " pdb=" N9 A2M 1 876 " pdb=" C8 A2M 1 876 " ideal model delta sigma weight residual 88.50 128.91 -40.41 3.00e+00 1.11e-01 1.81e+02 angle pdb=" C1' A2M 1 807 " pdb=" N9 A2M 1 807 " pdb=" C8 A2M 1 807 " ideal model delta sigma weight residual 88.50 128.45 -39.95 3.00e+00 1.11e-01 1.77e+02 angle pdb=" C1' A2M 12220 " pdb=" N9 A2M 12220 " pdb=" C8 A2M 12220 " ideal model delta sigma weight residual 88.50 128.36 -39.86 3.00e+00 1.11e-01 1.77e+02 angle pdb=" C1' A2M 11133 " pdb=" N9 A2M 11133 " pdb=" C8 A2M 11133 " ideal model delta sigma weight residual 88.50 128.09 -39.59 3.00e+00 1.11e-01 1.74e+02 ... (remaining 241939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 97044 35.88 - 71.76: 7718 71.76 - 107.64: 837 107.64 - 143.52: 14 143.52 - 179.40: 41 Dihedral angle restraints: 105654 sinusoidal: 74275 harmonic: 31379 Sorted by residual: dihedral pdb=" O4' U 12822 " pdb=" C1' U 12822 " pdb=" N1 U 12822 " pdb=" C2 U 12822 " ideal model delta sinusoidal sigma weight residual 200.00 23.19 176.81 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 12550 " pdb=" C1' U 12550 " pdb=" N1 U 12550 " pdb=" C2 U 12550 " ideal model delta sinusoidal sigma weight residual 200.00 29.95 170.05 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' C 12899 " pdb=" C1' C 12899 " pdb=" N1 C 12899 " pdb=" C2 C 12899 " ideal model delta sinusoidal sigma weight residual 200.00 34.86 165.14 1 1.50e+01 4.44e-03 8.39e+01 ... (remaining 105651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 26175 0.066 - 0.131: 3144 0.131 - 0.197: 255 0.197 - 0.263: 32 0.263 - 0.329: 11 Chirality restraints: 29617 Sorted by residual: chirality pdb=" C2' A2M 1 876 " pdb=" C3' A2M 1 876 " pdb=" O2' A2M 1 876 " pdb=" C1' A2M 1 876 " both_signs ideal model delta sigma weight residual False -2.39 -2.72 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C2' A2M 1 817 " pdb=" C3' A2M 1 817 " pdb=" O2' A2M 1 817 " pdb=" C1' A2M 1 817 " both_signs ideal model delta sigma weight residual False -2.39 -2.71 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ARG f 60 " pdb=" N ARG f 60 " pdb=" C ARG f 60 " pdb=" CB ARG f 60 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 29614 not shown) Planarity restraints: 18328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12793 " 0.077 2.00e-02 2.50e+03 6.45e-01 9.35e+03 pdb=" C4' OMG 12793 " 0.490 2.00e-02 2.50e+03 pdb=" O4' OMG 12793 " 0.781 2.00e-02 2.50e+03 pdb=" C3' OMG 12793 " -0.576 2.00e-02 2.50e+03 pdb=" O3' OMG 12793 " -0.676 2.00e-02 2.50e+03 pdb=" C2' OMG 12793 " -0.195 2.00e-02 2.50e+03 pdb=" O2' OMG 12793 " 0.972 2.00e-02 2.50e+03 pdb=" C1' OMG 12793 " 0.168 2.00e-02 2.50e+03 pdb=" N9 OMG 12793 " -1.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 1MA 12142 " -0.970 2.00e-02 2.50e+03 6.23e-01 8.73e+03 pdb=" C4' 1MA 12142 " 0.162 2.00e-02 2.50e+03 pdb=" O4' 1MA 12142 " 0.885 2.00e-02 2.50e+03 pdb=" C3' 1MA 12142 " -0.264 2.00e-02 2.50e+03 pdb=" O3' 1MA 12142 " 0.850 2.00e-02 2.50e+03 pdb=" C2' 1MA 12142 " -0.596 2.00e-02 2.50e+03 pdb=" O2' 1MA 12142 " -0.592 2.00e-02 2.50e+03 pdb=" C1' 1MA 12142 " 0.493 2.00e-02 2.50e+03 pdb=" N9 1MA 12142 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12791 " -0.059 2.00e-02 2.50e+03 5.98e-01 8.05e+03 pdb=" C4' OMG 12791 " -0.440 2.00e-02 2.50e+03 pdb=" O4' OMG 12791 " -0.633 2.00e-02 2.50e+03 pdb=" C3' OMG 12791 " 0.595 2.00e-02 2.50e+03 pdb=" O3' OMG 12791 " 0.635 2.00e-02 2.50e+03 pdb=" C2' OMG 12791 " 0.180 2.00e-02 2.50e+03 pdb=" O2' OMG 12791 " -0.975 2.00e-02 2.50e+03 pdb=" C1' OMG 12791 " -0.217 2.00e-02 2.50e+03 pdb=" N9 OMG 12791 " 0.914 2.00e-02 2.50e+03 ... (remaining 18325 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.55: 1180 2.55 - 3.19: 127182 3.19 - 3.84: 356263 3.84 - 4.49: 485260 4.49 - 5.14: 680969 Nonbonded interactions: 1650854 Sorted by model distance: nonbonded pdb=" OP2 C 1 861 " pdb="MG MG 13461 " model vdw 1.897 2.170 nonbonded pdb=" OP1 C 1 893 " pdb="MG MG 13461 " model vdw 1.898 2.170 nonbonded pdb="MG MG 13438 " pdb=" O HOH 13507 " model vdw 1.920 2.170 nonbonded pdb="MG MG 13468 " pdb=" O HOH 13721 " model vdw 1.956 2.170 nonbonded pdb="MG MG 13458 " pdb=" O HOH 13577 " model vdw 1.956 2.170 ... (remaining 1650849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.920 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: 0.110 Extract box with map and model: 14.430 Check model and map are aligned: 1.750 Set scattering table: 1.090 Process input model: 557.900 Find NCS groups from input model: 4.000 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 592.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.006 0.277 167341 Z= 0.387 Angle : 0.818 41.136 241944 Z= 0.399 Chirality : 0.044 0.329 29617 Planarity : 0.018 0.645 18328 Dihedral : 20.706 179.401 85338 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.55 % Allowed : 4.91 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.08), residues: 10648 helix: 1.48 (0.08), residues: 4192 sheet: 0.25 (0.13), residues: 1557 loop : -0.18 (0.08), residues: 4899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP e 32 HIS 0.009 0.001 HIS O 55 PHE 0.037 0.002 PHE F 229 TYR 0.029 0.002 TYR C 194 ARG 0.008 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2107 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 2056 time to evaluate : 10.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8256 (pttm) cc_final: 0.7510 (mttm) REVERT: A 74 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8143 (mm-30) REVERT: A 93 LYS cc_start: 0.8092 (mmtp) cc_final: 0.7731 (mttt) REVERT: A 144 ASN cc_start: 0.7982 (t0) cc_final: 0.7738 (t0) REVERT: A 191 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8333 (mm) REVERT: 8 98 VAL cc_start: 0.6455 (m) cc_final: 0.6224 (t) REVERT: 8 146 LYS cc_start: 0.5657 (mmmm) cc_final: 0.5313 (mtmm) REVERT: B 59 ASP cc_start: 0.7399 (t0) cc_final: 0.7195 (t0) REVERT: B 300 ARG cc_start: 0.7871 (mmt90) cc_final: 0.7524 (mmt90) REVERT: C 5 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7142 (mm-40) REVERT: C 287 THR cc_start: 0.6945 (p) cc_final: 0.6703 (t) REVERT: E 70 LYS cc_start: 0.7744 (tptp) cc_final: 0.7533 (tptp) REVERT: E 154 LEU cc_start: 0.7929 (mt) cc_final: 0.7698 (mp) REVERT: G 92 LYS cc_start: 0.8102 (ttmt) cc_final: 0.7847 (mtmt) REVERT: G 100 GLU cc_start: 0.6543 (tt0) cc_final: 0.5888 (tt0) REVERT: H 8 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8097 (mm-40) REVERT: H 150 SER cc_start: 0.8227 (t) cc_final: 0.7862 (t) REVERT: I 10 LYS cc_start: 0.6029 (mttm) cc_final: 0.5783 (ttmt) REVERT: I 62 ILE cc_start: 0.7145 (tp) cc_final: 0.6738 (tp) REVERT: J 125 MET cc_start: 0.2638 (ptp) cc_final: 0.2137 (mtp) REVERT: J 130 VAL cc_start: 0.5630 (t) cc_final: 0.4362 (p) REVERT: J 131 MET cc_start: 0.5573 (mmt) cc_final: 0.4864 (mpp) REVERT: K 98 LYS cc_start: 0.4259 (tttp) cc_final: 0.4038 (tmtt) REVERT: K 136 SER cc_start: 0.3742 (p) cc_final: 0.3528 (m) REVERT: K 170 ARG cc_start: 0.7353 (ttp-170) cc_final: 0.7106 (ttp-110) REVERT: K 173 PHE cc_start: 0.7447 (t80) cc_final: 0.7242 (t80) REVERT: K 330 ASN cc_start: 0.3927 (m110) cc_final: 0.3619 (m-40) REVERT: M 6 ILE cc_start: 0.8169 (tt) cc_final: 0.7823 (tt) REVERT: M 8 LYS cc_start: 0.6577 (mmmt) cc_final: 0.6253 (mtpt) REVERT: M 105 GLN cc_start: 0.8337 (tt0) cc_final: 0.8136 (tt0) REVERT: N 71 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8159 (ttp80) REVERT: N 179 LYS cc_start: 0.8583 (mttt) cc_final: 0.8309 (mmtp) REVERT: Q 12 ARG cc_start: 0.6312 (mtt90) cc_final: 0.6091 (mtt90) REVERT: S 13 ARG cc_start: 0.7075 (mtt-85) cc_final: 0.6859 (tpp80) REVERT: S 45 LEU cc_start: 0.7611 (tp) cc_final: 0.7403 (mm) REVERT: T 38 ASP cc_start: 0.6407 (m-30) cc_final: 0.5974 (t70) REVERT: T 140 ILE cc_start: 0.8301 (mt) cc_final: 0.7996 (mp) REVERT: T 142 SER cc_start: 0.7908 (t) cc_final: 0.7594 (m) REVERT: U 82 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7923 (tttp) REVERT: V 23 MET cc_start: 0.8753 (ptt) cc_final: 0.8082 (ptt) REVERT: V 40 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8352 (mmmt) REVERT: V 70 ARG cc_start: 0.6982 (mtt180) cc_final: 0.6603 (mtt90) REVERT: V 108 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7124 (mt-10) REVERT: V 133 SER cc_start: 0.8611 (m) cc_final: 0.8386 (m) REVERT: W 20 ARG cc_start: 0.6456 (ttt90) cc_final: 0.6246 (ttm170) REVERT: W 41 TRP cc_start: 0.7074 (m100) cc_final: 0.6787 (m100) REVERT: W 67 MET cc_start: 0.7368 (mmm) cc_final: 0.7157 (mmm) REVERT: a 120 ASN cc_start: 0.6784 (m-40) cc_final: 0.6566 (t0) REVERT: a 146 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7809 (mt-10) REVERT: b 212 LYS cc_start: 0.7498 (mttm) cc_final: 0.7254 (mtpp) REVERT: b 231 GLU cc_start: 0.6487 (pt0) cc_final: 0.6177 (tp30) REVERT: b 419 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7530 (ttmm) REVERT: b 643 LYS cc_start: 0.6270 (tptm) cc_final: 0.5367 (mtpp) REVERT: c 55 GLU cc_start: 0.7859 (tt0) cc_final: 0.7196 (tt0) REVERT: e 111 ARG cc_start: 0.8258 (tpt170) cc_final: 0.8046 (tpt170) REVERT: g 102 LYS cc_start: 0.7252 (mtmt) cc_final: 0.6727 (tttm) REVERT: i 76 ARG cc_start: 0.7180 (mmm-85) cc_final: 0.6933 (mmt180) REVERT: k 8 ILE cc_start: 0.6994 (mp) cc_final: 0.6770 (mt) REVERT: l 8 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.8301 (ttm-80) REVERT: m 246 MET cc_start: 0.8239 (mtp) cc_final: 0.7941 (mtp) REVERT: m 361 ARG cc_start: 0.7571 (mtp85) cc_final: 0.7343 (mmm-85) REVERT: m 382 ILE cc_start: 0.8084 (mm) cc_final: 0.7882 (mp) REVERT: n 1 MET cc_start: 0.7477 (ttm) cc_final: 0.7044 (ttp) REVERT: n 66 LYS cc_start: 0.7400 (mtmt) cc_final: 0.7173 (mmmt) REVERT: n 104 ARG cc_start: 0.7347 (ttp80) cc_final: 0.6988 (ttp-110) REVERT: n 157 ASN cc_start: 0.6961 (m110) cc_final: 0.6713 (m-40) REVERT: n 160 GLN cc_start: 0.6944 (tp40) cc_final: 0.6734 (tp-100) REVERT: n 173 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6296 (mm-30) REVERT: n 448 LEU cc_start: 0.6299 (mt) cc_final: 0.5715 (tt) REVERT: o 96 SER cc_start: 0.7657 (p) cc_final: 0.7313 (t) REVERT: o 102 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7569 (t80) REVERT: o 124 ARG cc_start: 0.6872 (mtp85) cc_final: 0.6334 (mmt180) REVERT: o 152 MET cc_start: 0.7232 (mmm) cc_final: 0.6991 (mmm) REVERT: q 236 GLU cc_start: 0.5401 (mt-10) cc_final: 0.5142 (mt-10) REVERT: q 257 LYS cc_start: 0.6291 (ttpt) cc_final: 0.6037 (tmmt) REVERT: q 381 HIS cc_start: 0.6880 (m90) cc_final: 0.6641 (m-70) REVERT: q 412 GLU cc_start: 0.6129 (mm-30) cc_final: 0.5817 (mm-30) REVERT: q 436 ARG cc_start: 0.5765 (ttt90) cc_final: 0.5302 (mtm180) REVERT: r 250 ASP cc_start: 0.8036 (p0) cc_final: 0.7816 (p0) REVERT: s 20 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8107 (tttm) REVERT: t 24 ARG cc_start: 0.5378 (mtm180) cc_final: 0.5022 (mtm-85) REVERT: t 33 ARG cc_start: 0.5572 (mtm110) cc_final: 0.5238 (ttm-80) REVERT: t 45 ILE cc_start: 0.6243 (mt) cc_final: 0.5957 (mt) REVERT: t 102 LYS cc_start: 0.5758 (mttt) cc_final: 0.5551 (tptp) REVERT: t 129 ILE cc_start: 0.5505 (pt) cc_final: 0.5002 (mm) REVERT: t 245 ILE cc_start: 0.5302 (mm) cc_final: 0.5040 (pt) REVERT: t 248 GLU cc_start: 0.6153 (mm-30) cc_final: 0.5592 (pm20) REVERT: u 4 TYR cc_start: 0.8618 (m-80) cc_final: 0.8237 (m-80) REVERT: u 69 LEU cc_start: 0.7889 (mt) cc_final: 0.7605 (mt) REVERT: u 93 MET cc_start: 0.8443 (mtp) cc_final: 0.8107 (mtp) REVERT: u 118 LYS cc_start: 0.7697 (mmtp) cc_final: 0.7267 (mtpt) REVERT: v 48 ASP cc_start: 0.5015 (m-30) cc_final: 0.4807 (m-30) REVERT: v 50 SER cc_start: 0.6770 (p) cc_final: 0.6487 (m) REVERT: v 76 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6617 (mp0) REVERT: v 81 LYS cc_start: 0.6870 (mmtt) cc_final: 0.6625 (mmtp) REVERT: v 140 MET cc_start: 0.7735 (mtm) cc_final: 0.7379 (mpp) REVERT: w 8 ASN cc_start: 0.3415 (p0) cc_final: 0.3209 (p0) REVERT: w 173 LEU cc_start: 0.5726 (mt) cc_final: 0.5415 (mt) REVERT: x 104 SER cc_start: 0.5905 (m) cc_final: 0.5581 (p) REVERT: x 119 LEU cc_start: 0.5015 (mt) cc_final: 0.4517 (tt) REVERT: x 122 THR cc_start: 0.5723 (m) cc_final: 0.5200 (p) REVERT: x 174 ASP cc_start: 0.6379 (m-30) cc_final: 0.6174 (m-30) REVERT: x 216 LYS cc_start: 0.6308 (mttm) cc_final: 0.6099 (mppt) REVERT: x 509 MET cc_start: 0.8142 (mmt) cc_final: 0.7929 (mmt) REVERT: y 1 MET cc_start: 0.4626 (mtt) cc_final: 0.4359 (mtt) REVERT: y 62 MET cc_start: 0.8194 (mmm) cc_final: 0.7862 (mmm) REVERT: y 171 GLU cc_start: 0.6731 (mm-30) cc_final: 0.6385 (mt-10) REVERT: y 188 ARG cc_start: 0.7934 (ttt180) cc_final: 0.7505 (ttm-80) REVERT: z 41 LEU cc_start: 0.8525 (tp) cc_final: 0.8313 (tp) REVERT: 4 29 ARG cc_start: 0.6828 (ttm110) cc_final: 0.6218 (ttp-110) REVERT: 4 47 ASN cc_start: 0.6885 (m-40) cc_final: 0.6677 (m-40) REVERT: 4 77 GLU cc_start: 0.5782 (tp30) cc_final: 0.5283 (mt-10) REVERT: 4 205 GLU cc_start: 0.3590 (pm20) cc_final: 0.3124 (mp0) REVERT: 4 371 LYS cc_start: 0.7186 (mmtt) cc_final: 0.6665 (mmtp) REVERT: 4 384 LYS cc_start: 0.6493 (mmtp) cc_final: 0.6229 (mptp) REVERT: 4 401 PHE cc_start: 0.5821 (OUTLIER) cc_final: 0.4624 (p90) outliers start: 51 outliers final: 22 residues processed: 2097 average time/residue: 2.4742 time to fit residues: 7302.6012 Evaluate side-chains 1491 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1465 time to evaluate : 9.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain m residue 393 VAL Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain s residue 20 LYS Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 259 THR Chi-restraints excluded: chain w residue 155 ASP Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain 4 residue 255 ASN Chi-restraints excluded: chain 4 residue 401 PHE Chi-restraints excluded: chain 4 residue 543 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 1168 optimal weight: 20.0000 chunk 1049 optimal weight: 0.4980 chunk 582 optimal weight: 30.0000 chunk 358 optimal weight: 30.0000 chunk 707 optimal weight: 0.9980 chunk 560 optimal weight: 10.0000 chunk 1084 optimal weight: 3.9990 chunk 419 optimal weight: 6.9990 chunk 659 optimal weight: 7.9990 chunk 807 optimal weight: 30.0000 chunk 1256 optimal weight: 9.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 24 ASN C 316 ASN F 157 ASN G 61 GLN G 145 ASN G 192 GLN H 9 GLN H 100 ASN H 102 ASN H 125 ASN H 157 ASN H 163 GLN K 101 ASN M 11 ASN M 59 ASN M 62 GLN O 182 ASN P 45 GLN R 34 GLN S 122 HIS Y 4 GLN Y 26 GLN Z 123 GLN b 152 GLN b 208 HIS b 304 GLN b 384 ASN b 454 GLN e 52 GLN e 88 HIS ** g 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN h 104 GLN i 12 ASN k 76 ASN ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 175 GLN n 69 GLN n 144 ASN n 208 ASN p 25 GLN p 32 GLN q 228 ASN t 209 GLN u 101 GLN x 12 GLN x 176 GLN x 271 GLN z 10 HIS 4 26 ASN 4 377 GLN 4 533 GLN 4 544 ASN ** 4 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 167341 Z= 0.191 Angle : 0.674 18.392 241944 Z= 0.359 Chirality : 0.038 0.370 29617 Planarity : 0.006 0.130 18328 Dihedral : 22.185 179.683 63334 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.74 % Allowed : 12.20 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % 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: 1.02 (0.08), residues: 10648 helix: 1.83 (0.08), residues: 4198 sheet: 0.21 (0.13), residues: 1564 loop : -0.12 (0.08), residues: 4886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP m 212 HIS 0.008 0.001 HIS 4 447 PHE 0.031 0.002 PHE O 48 TYR 0.023 0.002 TYR C 194 ARG 0.007 0.001 ARG r 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1763 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1508 time to evaluate : 9.447 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: A 10 LYS cc_start: 0.8410 (pttm) cc_final: 0.7483 (mttm) REVERT: A 74 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8248 (mm-30) REVERT: A 93 LYS cc_start: 0.8076 (mmtp) cc_final: 0.7731 (mttt) REVERT: 5 53 GLU cc_start: 0.5560 (mm-30) cc_final: 0.5211 (mm-30) REVERT: 5 75 LYS cc_start: 0.5587 (OUTLIER) cc_final: 0.4868 (ttpt) REVERT: 5 84 GLU cc_start: 0.4382 (mm-30) cc_final: 0.4013 (mm-30) REVERT: 8 146 LYS cc_start: 0.5617 (mmmm) cc_final: 0.5274 (mtmm) REVERT: 9 29 GLN cc_start: 0.7704 (mt0) cc_final: 0.7368 (mt0) REVERT: B 21 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8054 (mtm-85) REVERT: B 300 ARG cc_start: 0.7862 (mmt90) cc_final: 0.7531 (mmt90) REVERT: C 5 GLN cc_start: 0.7482 (mm-40) cc_final: 0.6869 (mt0) REVERT: C 63 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7221 (pp20) REVERT: C 141 ARG cc_start: 0.8294 (mmt90) cc_final: 0.7974 (mmt90) REVERT: D 189 GLU cc_start: 0.5352 (OUTLIER) cc_final: 0.5096 (mt-10) REVERT: E 154 LEU cc_start: 0.7968 (mt) cc_final: 0.7699 (mp) REVERT: F 33 ARG cc_start: 0.6213 (ttp80) cc_final: 0.5613 (mtp-110) REVERT: F 234 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: G 92 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7829 (mtmt) REVERT: G 100 GLU cc_start: 0.6502 (tt0) cc_final: 0.5953 (tt0) REVERT: H 8 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8192 (mm-40) REVERT: I 62 ILE cc_start: 0.7122 (tp) cc_final: 0.6716 (tp) REVERT: J 125 MET cc_start: 0.2518 (ptp) cc_final: 0.2013 (mtp) REVERT: J 131 MET cc_start: 0.5623 (mmt) cc_final: 0.4985 (mpp) REVERT: K 106 PHE cc_start: 0.5245 (t80) cc_final: 0.4983 (t80) REVERT: K 153 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.5208 (tp30) REVERT: K 170 ARG cc_start: 0.7335 (ttp-170) cc_final: 0.7131 (ttp-110) REVERT: K 215 LYS cc_start: 0.5174 (OUTLIER) cc_final: 0.4260 (tptp) REVERT: M 6 ILE cc_start: 0.8070 (tt) cc_final: 0.7640 (tt) REVERT: M 8 LYS cc_start: 0.6508 (mmmt) cc_final: 0.6249 (mtpt) REVERT: M 105 GLN cc_start: 0.8329 (tt0) cc_final: 0.8100 (tt0) REVERT: N 9 GLU cc_start: 0.7632 (tp30) cc_final: 0.7402 (tp30) REVERT: N 71 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8212 (ttp80) REVERT: N 179 LYS cc_start: 0.8567 (mttt) cc_final: 0.8264 (mmtp) REVERT: O 40 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6785 (mt-10) REVERT: P 179 GLN cc_start: 0.7852 (mt0) cc_final: 0.7631 (mt0) REVERT: R 114 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7455 (mtmt) REVERT: T 38 ASP cc_start: 0.6422 (m-30) cc_final: 0.5972 (t70) REVERT: T 140 ILE cc_start: 0.8277 (mt) cc_final: 0.7977 (mp) REVERT: T 142 SER cc_start: 0.7920 (t) cc_final: 0.7607 (m) REVERT: U 35 LYS cc_start: 0.7718 (tptm) cc_final: 0.7446 (tppt) REVERT: U 91 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: V 23 MET cc_start: 0.8778 (ptt) cc_final: 0.8012 (ptt) REVERT: V 40 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8348 (mmmt) REVERT: V 70 ARG cc_start: 0.7023 (mtt180) cc_final: 0.6654 (mtt90) REVERT: V 108 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7212 (mt-10) REVERT: V 133 SER cc_start: 0.8544 (m) cc_final: 0.8297 (m) REVERT: W 20 ARG cc_start: 0.6443 (ttt90) cc_final: 0.6243 (ttm170) REVERT: W 29 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6480 (mt-10) REVERT: W 41 TRP cc_start: 0.7166 (m100) cc_final: 0.6945 (m100) REVERT: W 67 MET cc_start: 0.7311 (mmm) cc_final: 0.7097 (mmm) REVERT: W 196 ASP cc_start: 0.6671 (OUTLIER) cc_final: 0.6440 (p0) REVERT: X 104 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6631 (mm-30) REVERT: a 70 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7468 (ttpp) REVERT: a 120 ASN cc_start: 0.6887 (m-40) cc_final: 0.6644 (t0) REVERT: b 212 LYS cc_start: 0.7512 (mttm) cc_final: 0.7268 (mtpp) REVERT: b 281 LYS cc_start: 0.7044 (mttp) cc_final: 0.6804 (mtmt) REVERT: b 340 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7550 (tp) REVERT: b 343 ARG cc_start: 0.6720 (mtp180) cc_final: 0.6418 (ttt-90) REVERT: b 459 GLU cc_start: 0.6743 (tt0) cc_final: 0.6507 (tt0) REVERT: b 464 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6298 (mm-30) REVERT: b 530 LYS cc_start: 0.7790 (mmtp) cc_final: 0.7259 (tptt) REVERT: b 643 LYS cc_start: 0.6238 (tptm) cc_final: 0.5363 (mtpp) REVERT: c 55 GLU cc_start: 0.7760 (tt0) cc_final: 0.7319 (tt0) REVERT: e 111 ARG cc_start: 0.8270 (tpt170) cc_final: 0.8021 (tpt170) REVERT: e 128 LEU cc_start: 0.3716 (OUTLIER) cc_final: 0.3296 (mm) REVERT: g 102 LYS cc_start: 0.7210 (mtmt) cc_final: 0.6619 (tttm) REVERT: k 8 ILE cc_start: 0.7018 (mp) cc_final: 0.6786 (mt) REVERT: k 64 LYS cc_start: 0.6048 (mttm) cc_final: 0.5525 (mmtm) REVERT: l 8 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8209 (ttm-80) REVERT: m 23 ARG cc_start: 0.7032 (mtm-85) cc_final: 0.6773 (mtp-110) REVERT: m 162 LYS cc_start: 0.7280 (ptmm) cc_final: 0.6792 (ptmt) REVERT: m 210 ARG cc_start: 0.7268 (ttp80) cc_final: 0.6764 (ttm170) REVERT: m 246 MET cc_start: 0.8192 (mtp) cc_final: 0.7948 (mtp) REVERT: m 387 VAL cc_start: 0.8484 (t) cc_final: 0.8228 (t) REVERT: m 391 GLU cc_start: 0.7159 (mp0) cc_final: 0.6935 (mp0) REVERT: n 1 MET cc_start: 0.7556 (ttm) cc_final: 0.7085 (ttp) REVERT: n 66 LYS cc_start: 0.7385 (mtmt) cc_final: 0.7167 (mmmt) REVERT: n 107 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5788 (mm-30) REVERT: n 157 ASN cc_start: 0.6911 (m110) cc_final: 0.6670 (m-40) REVERT: n 173 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6204 (mm-30) REVERT: n 381 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5931 (tp) REVERT: n 448 LEU cc_start: 0.6358 (mt) cc_final: 0.5766 (tt) REVERT: o 102 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7552 (t80) REVERT: o 152 MET cc_start: 0.7150 (mmm) cc_final: 0.6890 (mmm) REVERT: q 242 TYR cc_start: 0.5496 (t80) cc_final: 0.5287 (t80) REVERT: q 257 LYS cc_start: 0.6188 (ttpt) cc_final: 0.5982 (tmmm) REVERT: q 381 HIS cc_start: 0.6868 (m90) cc_final: 0.6622 (m-70) REVERT: q 392 GLU cc_start: 0.5613 (OUTLIER) cc_final: 0.5397 (mt-10) REVERT: q 436 ARG cc_start: 0.5643 (ttt90) cc_final: 0.5281 (mtm180) REVERT: q 453 ASP cc_start: 0.8110 (m-30) cc_final: 0.7627 (m-30) REVERT: r 8 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7537 (mt-10) REVERT: r 141 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7249 (mttt) REVERT: r 250 ASP cc_start: 0.8000 (p0) cc_final: 0.7738 (p0) REVERT: r 252 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7954 (p0) REVERT: s 20 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8092 (tttm) REVERT: t 33 ARG cc_start: 0.5473 (mtm110) cc_final: 0.5150 (ttm-80) REVERT: t 129 ILE cc_start: 0.5459 (OUTLIER) cc_final: 0.5063 (mt) REVERT: u 4 TYR cc_start: 0.8545 (m-80) cc_final: 0.8275 (m-80) REVERT: u 118 LYS cc_start: 0.7676 (mmtp) cc_final: 0.7229 (mtpt) REVERT: v 20 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5669 (mp0) REVERT: v 22 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.5966 (mptp) REVERT: v 39 ASN cc_start: 0.5614 (OUTLIER) cc_final: 0.5408 (p0) REVERT: v 48 ASP cc_start: 0.5045 (m-30) cc_final: 0.4819 (m-30) REVERT: v 50 SER cc_start: 0.6759 (p) cc_final: 0.6467 (m) REVERT: v 73 SER cc_start: 0.5258 (OUTLIER) cc_final: 0.4701 (t) REVERT: v 140 MET cc_start: 0.7687 (mtm) cc_final: 0.7323 (mpp) REVERT: v 247 GLU cc_start: 0.6307 (mm-30) cc_final: 0.6084 (mm-30) REVERT: v 251 LYS cc_start: 0.6628 (mmtp) cc_final: 0.5715 (mptp) REVERT: w 8 ASN cc_start: 0.3436 (p0) cc_final: 0.3224 (p0) REVERT: w 70 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5827 (mtt) REVERT: w 173 LEU cc_start: 0.5629 (mt) cc_final: 0.5362 (mt) REVERT: x 104 SER cc_start: 0.5853 (m) cc_final: 0.5535 (p) REVERT: x 119 LEU cc_start: 0.5029 (mt) cc_final: 0.4519 (tt) REVERT: x 122 THR cc_start: 0.5656 (m) cc_final: 0.5324 (p) REVERT: x 335 ARG cc_start: 0.7161 (ttt-90) cc_final: 0.6906 (ttp80) REVERT: x 477 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7814 (ptpt) REVERT: x 509 MET cc_start: 0.8161 (mmt) cc_final: 0.7903 (mmt) REVERT: y 1 MET cc_start: 0.4626 (mtt) cc_final: 0.4314 (mtt) REVERT: y 62 MET cc_start: 0.8136 (mmm) cc_final: 0.7849 (mmm) REVERT: y 98 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5312 (mm-30) REVERT: y 171 GLU cc_start: 0.6563 (mm-30) cc_final: 0.6291 (mt-10) REVERT: z 38 LYS cc_start: 0.8144 (mttt) cc_final: 0.7881 (mtpt) REVERT: z 95 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7681 (ttpt) REVERT: 4 29 ARG cc_start: 0.6775 (ttm110) cc_final: 0.6272 (ttp-110) REVERT: 4 77 GLU cc_start: 0.5803 (tp30) cc_final: 0.5267 (mt-10) REVERT: 4 170 LEU cc_start: 0.4294 (OUTLIER) cc_final: 0.4010 (mp) REVERT: 4 205 GLU cc_start: 0.3855 (pm20) cc_final: 0.3458 (mp0) REVERT: 4 384 LYS cc_start: 0.6347 (mmtp) cc_final: 0.6132 (tptp) REVERT: 4 401 PHE cc_start: 0.5646 (OUTLIER) cc_final: 0.5433 (m-80) REVERT: 4 446 ASP cc_start: 0.6101 (p0) cc_final: 0.5830 (p0) REVERT: 4 577 GLN cc_start: 0.3323 (mm110) cc_final: 0.2758 (pm20) outliers start: 255 outliers final: 115 residues processed: 1653 average time/residue: 2.4645 time to fit residues: 5775.3675 Evaluate side-chains 1543 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1395 time to evaluate : 9.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain 5 residue 75 LYS Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 8 residue 46 ILE Chi-restraints excluded: chain 8 residue 58 VAL Chi-restraints excluded: chain 9 residue 41 SER Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 215 LYS Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 330 GLU Chi-restraints excluded: chain b residue 340 LEU Chi-restraints excluded: chain b residue 464 GLU Chi-restraints excluded: chain b residue 482 GLU Chi-restraints excluded: chain b residue 512 SER Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 622 SER Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 3 VAL Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 139 ASP Chi-restraints excluded: chain m residue 390 VAL Chi-restraints excluded: chain m residue 393 VAL Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 107 GLU Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 189 GLN Chi-restraints excluded: chain n residue 208 ASN Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 381 LEU Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain q residue 194 THR Chi-restraints excluded: chain q residue 392 GLU Chi-restraints excluded: chain r residue 141 LYS Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 20 LYS Chi-restraints excluded: chain s residue 50 ILE Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 79 SER Chi-restraints excluded: chain t residue 82 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 275 ARG Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain u residue 129 SER Chi-restraints excluded: chain v residue 20 GLU Chi-restraints excluded: chain v residue 22 LYS Chi-restraints excluded: chain v residue 39 ASN Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 92 SER Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 160 LEU Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 256 GLU Chi-restraints excluded: chain w residue 70 MET Chi-restraints excluded: chain w residue 75 GLU Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain x residue 225 LEU Chi-restraints excluded: chain x residue 283 CYS Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 347 SER Chi-restraints excluded: chain x residue 379 ASP Chi-restraints excluded: chain x residue 477 LYS Chi-restraints excluded: chain y residue 98 GLU Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 10 HIS Chi-restraints excluded: chain z residue 95 LYS Chi-restraints excluded: chain 4 residue 170 LEU Chi-restraints excluded: chain 4 residue 255 ASN Chi-restraints excluded: chain 4 residue 373 LYS Chi-restraints excluded: chain 4 residue 401 PHE Chi-restraints excluded: chain 4 residue 531 THR Chi-restraints excluded: chain 4 residue 558 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 698 optimal weight: 3.9990 chunk 390 optimal weight: 2.9990 chunk 1046 optimal weight: 9.9990 chunk 855 optimal weight: 4.9990 chunk 346 optimal weight: 9.9990 chunk 1259 optimal weight: 20.0000 chunk 1360 optimal weight: 9.9990 chunk 1121 optimal weight: 30.0000 chunk 1248 optimal weight: 5.9990 chunk 429 optimal weight: 0.8980 chunk 1010 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 24 ASN F 157 ASN G 61 GLN G 192 GLN H 9 GLN H 100 ASN H 102 ASN H 163 GLN M 11 ASN M 59 ASN M 62 GLN N 23 GLN R 34 GLN S 122 HIS Y 4 GLN Y 26 GLN Z 123 GLN b 152 GLN b 208 HIS b 384 ASN e 88 HIS ** g 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN k 76 ASN l 4 GLN n 69 GLN n 144 ASN p 25 GLN t 209 GLN u 101 GLN w 201 ASN ** x 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 145 ASN 4 26 ASN 4 377 GLN 4 544 ASN 4 573 GLN ** 4 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 167341 Z= 0.177 Angle : 0.643 17.850 241944 Z= 0.347 Chirality : 0.037 0.361 29617 Planarity : 0.006 0.131 18328 Dihedral : 22.112 179.714 63313 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.12 % Allowed : 13.24 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % 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: 1.13 (0.08), residues: 10648 helix: 1.98 (0.08), residues: 4184 sheet: 0.19 (0.13), residues: 1562 loop : -0.08 (0.08), residues: 4902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP m 212 HIS 0.019 0.001 HIS z 10 PHE 0.025 0.002 PHE F 229 TYR 0.020 0.002 TYR C 194 ARG 0.008 0.000 ARG b 369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1716 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1426 time to evaluate : 9.506 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: A 10 LYS cc_start: 0.8388 (pttm) cc_final: 0.7504 (mttm) REVERT: A 74 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8224 (mm-30) REVERT: A 93 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7779 (mttt) REVERT: A 191 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8319 (mm) REVERT: 5 84 GLU cc_start: 0.4215 (mm-30) cc_final: 0.3892 (mm-30) REVERT: 8 146 LYS cc_start: 0.5528 (mmmm) cc_final: 0.5191 (mtmm) REVERT: 9 29 GLN cc_start: 0.7716 (mt0) cc_final: 0.7410 (mt0) REVERT: B 21 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8054 (mtm-85) REVERT: C 5 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7207 (mm-40) REVERT: C 63 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7155 (pp20) REVERT: C 141 ARG cc_start: 0.8348 (mmt90) cc_final: 0.7990 (mmt90) REVERT: F 64 GLN cc_start: 0.8093 (tp40) cc_final: 0.7798 (tp40) REVERT: G 92 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7822 (mtmt) REVERT: G 100 GLU cc_start: 0.6528 (tt0) cc_final: 0.6007 (tt0) REVERT: G 208 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6961 (tp30) REVERT: H 8 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8166 (mm-40) REVERT: H 78 MET cc_start: 0.8334 (mtp) cc_final: 0.8017 (mtm) REVERT: I 62 ILE cc_start: 0.7129 (tp) cc_final: 0.6706 (tp) REVERT: J 131 MET cc_start: 0.5544 (mmt) cc_final: 0.4899 (mpp) REVERT: K 153 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.5267 (tp30) REVERT: K 170 ARG cc_start: 0.7338 (ttp-170) cc_final: 0.6931 (ttp-110) REVERT: K 173 PHE cc_start: 0.7465 (t80) cc_final: 0.7226 (t80) REVERT: K 215 LYS cc_start: 0.5110 (OUTLIER) cc_final: 0.4189 (tptp) REVERT: M 6 ILE cc_start: 0.8061 (tt) cc_final: 0.7651 (tt) REVERT: M 8 LYS cc_start: 0.6485 (mmmt) cc_final: 0.6184 (mtpt) REVERT: M 105 GLN cc_start: 0.8332 (tt0) cc_final: 0.8091 (tt0) REVERT: N 14 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7285 (tttp) REVERT: N 71 ARG cc_start: 0.8449 (ttp80) cc_final: 0.8215 (ttp80) REVERT: N 179 LYS cc_start: 0.8562 (mttt) cc_final: 0.8250 (mmtp) REVERT: O 40 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6783 (mt-10) REVERT: Q 12 ARG cc_start: 0.6213 (mtt90) cc_final: 0.5890 (mpt-90) REVERT: R 114 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7326 (mtmt) REVERT: S 13 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6764 (ttm110) REVERT: S 49 HIS cc_start: 0.6229 (m170) cc_final: 0.6017 (m90) REVERT: T 38 ASP cc_start: 0.6384 (m-30) cc_final: 0.5951 (t70) REVERT: T 89 LEU cc_start: 0.8060 (mp) cc_final: 0.7842 (mm) REVERT: T 140 ILE cc_start: 0.8271 (mt) cc_final: 0.7963 (mp) REVERT: T 142 SER cc_start: 0.7881 (t) cc_final: 0.7572 (m) REVERT: U 91 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: V 40 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8370 (mmmt) REVERT: V 70 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6693 (mtt90) REVERT: V 108 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7241 (mt-10) REVERT: V 133 SER cc_start: 0.8519 (m) cc_final: 0.8294 (m) REVERT: W 20 ARG cc_start: 0.6429 (ttt90) cc_final: 0.6190 (ttm170) REVERT: W 29 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6445 (mt-10) REVERT: W 179 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6978 (mtpt) REVERT: X 104 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6634 (mm-30) REVERT: X 142 ILE cc_start: 0.5334 (OUTLIER) cc_final: 0.4555 (mt) REVERT: a 70 LYS cc_start: 0.7997 (ttpt) cc_final: 0.7454 (ttpp) REVERT: a 120 ASN cc_start: 0.7033 (m-40) cc_final: 0.6623 (t0) REVERT: b 212 LYS cc_start: 0.7524 (mttm) cc_final: 0.7320 (mttt) REVERT: b 340 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7478 (tp) REVERT: b 343 ARG cc_start: 0.6720 (mtp180) cc_final: 0.6500 (ttt-90) REVERT: b 532 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6422 (tp30) REVERT: b 613 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7656 (mtp-110) REVERT: b 643 LYS cc_start: 0.6222 (tptm) cc_final: 0.5339 (mtpp) REVERT: c 55 GLU cc_start: 0.7754 (tt0) cc_final: 0.7318 (tt0) REVERT: e 128 LEU cc_start: 0.3859 (OUTLIER) cc_final: 0.3422 (mm) REVERT: g 102 LYS cc_start: 0.7169 (mtmt) cc_final: 0.6588 (tttm) REVERT: i 56 ARG cc_start: 0.6603 (ttp-170) cc_final: 0.6388 (ttp-110) REVERT: k 8 ILE cc_start: 0.7120 (mp) cc_final: 0.6832 (mt) REVERT: k 64 LYS cc_start: 0.6122 (mttm) cc_final: 0.5567 (mmtm) REVERT: l 8 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8225 (ttm-80) REVERT: m 162 LYS cc_start: 0.7277 (ptmm) cc_final: 0.6783 (ptmt) REVERT: m 210 ARG cc_start: 0.7194 (ttp80) cc_final: 0.6896 (ttm170) REVERT: m 246 MET cc_start: 0.8161 (mtp) cc_final: 0.7941 (mtp) REVERT: m 387 VAL cc_start: 0.8474 (t) cc_final: 0.8210 (t) REVERT: n 1 MET cc_start: 0.7562 (ttm) cc_final: 0.7094 (ttp) REVERT: n 66 LYS cc_start: 0.7365 (mtmt) cc_final: 0.7103 (mmmt) REVERT: n 107 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5782 (mm-30) REVERT: n 157 ASN cc_start: 0.6766 (m110) cc_final: 0.6545 (m-40) REVERT: n 173 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6324 (mm-30) REVERT: n 381 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.5939 (tp) REVERT: n 448 LEU cc_start: 0.6374 (mt) cc_final: 0.5768 (tt) REVERT: o 102 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7559 (t80) REVERT: o 152 MET cc_start: 0.7168 (mmm) cc_final: 0.6952 (mmm) REVERT: p 89 MET cc_start: 0.5027 (OUTLIER) cc_final: 0.4690 (tmm) REVERT: q 244 GLU cc_start: 0.5132 (mt-10) cc_final: 0.4806 (mm-30) REVERT: q 249 GLU cc_start: 0.5861 (mp0) cc_final: 0.5340 (mp0) REVERT: q 257 LYS cc_start: 0.6168 (ttpt) cc_final: 0.5927 (tmmm) REVERT: q 381 HIS cc_start: 0.6925 (m90) cc_final: 0.6692 (m-70) REVERT: q 436 ARG cc_start: 0.5920 (ttt90) cc_final: 0.5414 (mtm180) REVERT: q 453 ASP cc_start: 0.8075 (m-30) cc_final: 0.7593 (m-30) REVERT: r 8 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7447 (mt-10) REVERT: r 141 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6959 (mttt) REVERT: r 250 ASP cc_start: 0.7981 (p0) cc_final: 0.7730 (p0) REVERT: r 252 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7947 (p0) REVERT: t 30 ARG cc_start: 0.6299 (OUTLIER) cc_final: 0.4651 (tmm-80) REVERT: t 33 ARG cc_start: 0.5412 (mtm110) cc_final: 0.5045 (ttm-80) REVERT: t 129 ILE cc_start: 0.5444 (OUTLIER) cc_final: 0.5068 (mt) REVERT: u 4 TYR cc_start: 0.8546 (m-80) cc_final: 0.8339 (m-80) REVERT: u 25 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7154 (p0) REVERT: u 84 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6019 (pt0) REVERT: u 93 MET cc_start: 0.8366 (mtp) cc_final: 0.7985 (mtp) REVERT: u 118 LYS cc_start: 0.7662 (mmtp) cc_final: 0.7209 (mtpt) REVERT: v 20 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5793 (mp0) REVERT: v 22 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.5960 (mptp) REVERT: v 50 SER cc_start: 0.6599 (p) cc_final: 0.6167 (m) REVERT: v 65 ASP cc_start: 0.5535 (p0) cc_final: 0.5302 (m-30) REVERT: v 71 ASP cc_start: 0.5032 (t0) cc_final: 0.4726 (m-30) REVERT: v 73 SER cc_start: 0.5308 (OUTLIER) cc_final: 0.4729 (t) REVERT: v 113 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6409 (mtp) REVERT: v 140 MET cc_start: 0.7669 (mtm) cc_final: 0.7334 (mpp) REVERT: v 251 LYS cc_start: 0.6566 (mmtp) cc_final: 0.5654 (mptp) REVERT: v 279 LYS cc_start: 0.6599 (tppt) cc_final: 0.6353 (tptp) REVERT: w 70 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.5779 (mtt) REVERT: w 83 GLN cc_start: 0.7859 (tt0) cc_final: 0.7549 (tt0) REVERT: w 173 LEU cc_start: 0.5643 (mt) cc_final: 0.5397 (mt) REVERT: x 104 SER cc_start: 0.5836 (m) cc_final: 0.5518 (p) REVERT: x 119 LEU cc_start: 0.5180 (mt) cc_final: 0.4638 (tt) REVERT: x 122 THR cc_start: 0.5467 (m) cc_final: 0.5183 (p) REVERT: x 500 ARG cc_start: 0.7594 (mtt90) cc_final: 0.7228 (mpt180) REVERT: x 509 MET cc_start: 0.8185 (mmt) cc_final: 0.7927 (mmt) REVERT: y 1 MET cc_start: 0.4624 (mtt) cc_final: 0.4348 (mtt) REVERT: y 62 MET cc_start: 0.8103 (mmm) cc_final: 0.7839 (mmm) REVERT: y 98 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5251 (mm-30) REVERT: y 131 ASP cc_start: 0.6457 (OUTLIER) cc_final: 0.6242 (m-30) REVERT: y 171 GLU cc_start: 0.6528 (mm-30) cc_final: 0.6277 (mt-10) REVERT: z 95 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7635 (ttpt) REVERT: 4 29 ARG cc_start: 0.6846 (ttm110) cc_final: 0.6377 (ttp-110) REVERT: 4 72 ILE cc_start: 0.7849 (mt) cc_final: 0.7573 (mt) REVERT: 4 77 GLU cc_start: 0.5942 (tp30) cc_final: 0.5337 (mt-10) REVERT: 4 119 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7041 (pttt) REVERT: 4 170 LEU cc_start: 0.4288 (OUTLIER) cc_final: 0.3984 (mp) REVERT: 4 205 GLU cc_start: 0.3670 (pm20) cc_final: 0.3341 (mp0) REVERT: 4 371 LYS cc_start: 0.7132 (mmtt) cc_final: 0.6693 (mmtp) REVERT: 4 384 LYS cc_start: 0.6396 (mmtp) cc_final: 0.6190 (tptp) REVERT: 4 401 PHE cc_start: 0.5449 (OUTLIER) cc_final: 0.4709 (p90) REVERT: 4 446 ASP cc_start: 0.6078 (p0) cc_final: 0.5828 (p0) REVERT: 4 468 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5544 (mp) outliers start: 290 outliers final: 149 residues processed: 1589 average time/residue: 2.4542 time to fit residues: 5514.0810 Evaluate side-chains 1563 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1375 time to evaluate : 9.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 8 residue 58 VAL Chi-restraints excluded: chain 8 residue 153 GLU Chi-restraints excluded: chain 9 residue 41 SER Chi-restraints excluded: chain 9 residue 43 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 150 LYS Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 215 LYS Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 14 LYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain W residue 21 GLU Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 179 LYS Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain X residue 104 GLU Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 340 LEU Chi-restraints excluded: chain b residue 482 GLU Chi-restraints excluded: chain b residue 512 SER Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 532 GLU Chi-restraints excluded: chain b residue 613 ARG Chi-restraints excluded: chain b residue 622 SER Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain h residue 73 LYS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 3 VAL Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 125 GLU Chi-restraints excluded: chain m residue 139 ASP Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 393 VAL Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 107 GLU Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 189 GLN Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 381 LEU Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 150 GLU Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain q residue 194 THR Chi-restraints excluded: chain r residue 141 LYS Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 50 ILE Chi-restraints excluded: chain t residue 30 ARG Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 40 LYS Chi-restraints excluded: chain t residue 79 SER Chi-restraints excluded: chain t residue 82 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 275 ARG Chi-restraints excluded: chain t residue 278 SER Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain u residue 129 SER Chi-restraints excluded: chain v residue 20 GLU Chi-restraints excluded: chain v residue 22 LYS Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 113 MET Chi-restraints excluded: chain v residue 124 LEU Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 256 GLU Chi-restraints excluded: chain w residue 70 MET Chi-restraints excluded: chain w residue 75 GLU Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 155 ASP Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain x residue 136 SER Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 195 SER Chi-restraints excluded: chain x residue 225 LEU Chi-restraints excluded: chain x residue 283 CYS Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 347 SER Chi-restraints excluded: chain x residue 379 ASP Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain y residue 98 GLU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 95 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 4 residue 170 LEU Chi-restraints excluded: chain 4 residue 255 ASN Chi-restraints excluded: chain 4 residue 336 THR Chi-restraints excluded: chain 4 residue 401 PHE Chi-restraints excluded: chain 4 residue 466 LEU Chi-restraints excluded: chain 4 residue 468 LEU Chi-restraints excluded: chain 4 residue 531 THR Chi-restraints excluded: chain 4 residue 556 LEU Chi-restraints excluded: chain 4 residue 558 THR Chi-restraints excluded: chain 4 residue 572 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 1243 optimal weight: 20.0000 chunk 946 optimal weight: 10.0000 chunk 653 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 600 optimal weight: 0.0970 chunk 845 optimal weight: 9.9990 chunk 1263 optimal weight: 0.3980 chunk 1337 optimal weight: 5.9990 chunk 660 optimal weight: 20.0000 chunk 1197 optimal weight: 5.9990 chunk 360 optimal weight: 8.9990 overall best weight: 4.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 24 ASN C 175 HIS C 291 ASN F 157 ASN G 192 GLN H 9 GLN H 100 ASN H 102 ASN H 163 GLN M 11 ASN M 62 GLN N 23 GLN O 122 GLN R 34 GLN S 122 HIS W 205 GLN Y 4 GLN Y 26 GLN Z 123 GLN b 152 GLN b 384 ASN e 88 HIS ** g 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN i 12 ASN k 76 ASN ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN n 144 ASN p 25 GLN q 424 GLN u 101 GLN w 8 ASN w 25 ASN w 201 ASN x 12 GLN ** x 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 145 ASN 4 26 ASN 4 544 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 167341 Z= 0.185 Angle : 0.650 17.935 241944 Z= 0.350 Chirality : 0.038 0.340 29617 Planarity : 0.006 0.132 18328 Dihedral : 22.082 179.981 63309 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.31 % Allowed : 13.96 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % 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: 1.13 (0.08), residues: 10648 helix: 2.01 (0.08), residues: 4171 sheet: 0.17 (0.13), residues: 1569 loop : -0.09 (0.08), residues: 4908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP m 212 HIS 0.007 0.001 HIS J 68 PHE 0.025 0.002 PHE F 229 TYR 0.022 0.002 TYR C 194 ARG 0.009 0.001 ARG b 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1726 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 1418 time to evaluate : 9.577 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: A 10 LYS cc_start: 0.8384 (pttm) cc_final: 0.7501 (mttm) REVERT: A 74 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8220 (mm-30) REVERT: A 93 LYS cc_start: 0.8132 (mmtp) cc_final: 0.7805 (mttt) REVERT: A 191 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8324 (mm) REVERT: 5 53 GLU cc_start: 0.5448 (mm-30) cc_final: 0.5178 (mm-30) REVERT: 5 84 GLU cc_start: 0.4295 (mm-30) cc_final: 0.3930 (mm-30) REVERT: 8 146 LYS cc_start: 0.5528 (mmmm) cc_final: 0.5189 (mtmm) REVERT: B 21 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8067 (mtm-85) REVERT: C 5 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7149 (mm-40) REVERT: C 63 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7144 (pp20) REVERT: C 141 ARG cc_start: 0.8361 (mmt90) cc_final: 0.8155 (mmt180) REVERT: D 48 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.6715 (mtpp) REVERT: D 198 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.5025 (t80) REVERT: D 232 ASP cc_start: 0.5110 (t0) cc_final: 0.4697 (t0) REVERT: E 90 LYS cc_start: 0.6564 (OUTLIER) cc_final: 0.5898 (ttpt) REVERT: F 64 GLN cc_start: 0.8096 (tp40) cc_final: 0.7741 (tp40) REVERT: F 234 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: G 92 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7815 (mtmt) REVERT: G 100 GLU cc_start: 0.6563 (tt0) cc_final: 0.6030 (tt0) REVERT: G 208 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6830 (tp30) REVERT: H 8 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8154 (mm-40) REVERT: H 78 MET cc_start: 0.8367 (mtp) cc_final: 0.8020 (mtm) REVERT: H 150 SER cc_start: 0.8265 (t) cc_final: 0.7898 (t) REVERT: I 10 LYS cc_start: 0.5882 (OUTLIER) cc_final: 0.5667 (ttmt) REVERT: J 131 MET cc_start: 0.5547 (mmt) cc_final: 0.4949 (mpp) REVERT: K 153 GLU cc_start: 0.5884 (OUTLIER) cc_final: 0.5310 (tp30) REVERT: K 170 ARG cc_start: 0.7410 (ttp-170) cc_final: 0.6999 (ttp-110) REVERT: K 173 PHE cc_start: 0.7477 (t80) cc_final: 0.7231 (t80) REVERT: K 215 LYS cc_start: 0.5111 (OUTLIER) cc_final: 0.4155 (tptp) REVERT: M 6 ILE cc_start: 0.8092 (tt) cc_final: 0.7699 (tt) REVERT: M 8 LYS cc_start: 0.6512 (mmmt) cc_final: 0.6230 (mtpt) REVERT: M 105 GLN cc_start: 0.8403 (tt0) cc_final: 0.8168 (tt0) REVERT: N 14 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7281 (tttp) REVERT: O 40 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6803 (mt-10) REVERT: P 67 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7642 (mp) REVERT: Q 12 ARG cc_start: 0.6116 (mtt90) cc_final: 0.5829 (mpt-90) REVERT: R 114 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7339 (mtmt) REVERT: T 89 LEU cc_start: 0.8065 (mp) cc_final: 0.7852 (mm) REVERT: T 140 ILE cc_start: 0.8228 (mt) cc_final: 0.7917 (mp) REVERT: T 142 SER cc_start: 0.7914 (t) cc_final: 0.7592 (m) REVERT: U 91 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: V 70 ARG cc_start: 0.7075 (mtt180) cc_final: 0.6698 (mtt90) REVERT: V 108 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7201 (mt-10) REVERT: V 133 SER cc_start: 0.8518 (m) cc_final: 0.8298 (m) REVERT: W 29 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6441 (mt-10) REVERT: W 179 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6985 (mtpt) REVERT: X 104 GLU cc_start: 0.6857 (mp0) cc_final: 0.6631 (mm-30) REVERT: X 142 ILE cc_start: 0.5275 (OUTLIER) cc_final: 0.4968 (pt) REVERT: a 70 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7451 (ttpp) REVERT: a 120 ASN cc_start: 0.7124 (m-40) cc_final: 0.6734 (t0) REVERT: b 316 GLU cc_start: 0.5995 (tp30) cc_final: 0.5746 (mp0) REVERT: b 340 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7505 (tp) REVERT: b 343 ARG cc_start: 0.6776 (mtp180) cc_final: 0.6396 (ttt-90) REVERT: b 532 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6633 (tp30) REVERT: b 613 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7641 (mtp-110) REVERT: b 643 LYS cc_start: 0.6171 (tptm) cc_final: 0.5286 (mtpp) REVERT: c 55 GLU cc_start: 0.7755 (tt0) cc_final: 0.7314 (tt0) REVERT: e 21 HIS cc_start: 0.9016 (OUTLIER) cc_final: 0.8028 (m-70) REVERT: e 128 LEU cc_start: 0.3833 (OUTLIER) cc_final: 0.3624 (tm) REVERT: g 102 LYS cc_start: 0.7100 (mtmt) cc_final: 0.6471 (tttm) REVERT: i 3 VAL cc_start: 0.6597 (OUTLIER) cc_final: 0.6386 (p) REVERT: i 56 ARG cc_start: 0.6662 (ttp-170) cc_final: 0.6459 (ttp-110) REVERT: k 8 ILE cc_start: 0.7206 (mp) cc_final: 0.6904 (mt) REVERT: k 64 LYS cc_start: 0.6125 (mttm) cc_final: 0.5545 (mmtm) REVERT: l 8 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8260 (ttm-80) REVERT: m 8 LYS cc_start: 0.6593 (mmtt) cc_final: 0.6034 (mtpp) REVERT: m 162 LYS cc_start: 0.7280 (ptmm) cc_final: 0.6787 (ptmt) REVERT: m 210 ARG cc_start: 0.7201 (ttp80) cc_final: 0.6844 (tmm160) REVERT: m 246 MET cc_start: 0.8166 (mtp) cc_final: 0.7871 (mtp) REVERT: m 387 VAL cc_start: 0.8520 (t) cc_final: 0.8251 (t) REVERT: n 1 MET cc_start: 0.7564 (ttm) cc_final: 0.7107 (ttp) REVERT: n 66 LYS cc_start: 0.7355 (mtmt) cc_final: 0.7091 (mmmt) REVERT: n 107 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5757 (mm-30) REVERT: n 157 ASN cc_start: 0.6771 (m110) cc_final: 0.6544 (m-40) REVERT: n 173 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6321 (mm-30) REVERT: n 381 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5954 (tp) REVERT: n 448 LEU cc_start: 0.6376 (mt) cc_final: 0.5764 (tt) REVERT: o 102 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7542 (t80) REVERT: o 152 MET cc_start: 0.7282 (mmm) cc_final: 0.7045 (mmm) REVERT: o 200 MET cc_start: 0.3072 (OUTLIER) cc_final: 0.2599 (ppp) REVERT: q 244 GLU cc_start: 0.5180 (mt-10) cc_final: 0.4886 (mm-30) REVERT: q 249 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.5297 (mp0) REVERT: q 257 LYS cc_start: 0.6195 (ttpt) cc_final: 0.5962 (tmmm) REVERT: q 381 HIS cc_start: 0.6952 (m90) cc_final: 0.6715 (m-70) REVERT: q 436 ARG cc_start: 0.5960 (ttt90) cc_final: 0.5436 (mtm180) REVERT: q 453 ASP cc_start: 0.8081 (m-30) cc_final: 0.7589 (m-30) REVERT: r 141 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7285 (mttt) REVERT: r 250 ASP cc_start: 0.7982 (p0) cc_final: 0.7730 (p0) REVERT: r 252 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7973 (p0) REVERT: s 14 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7765 (ttmm) REVERT: t 101 LEU cc_start: 0.6547 (tp) cc_final: 0.6316 (tm) REVERT: t 129 ILE cc_start: 0.5400 (OUTLIER) cc_final: 0.4940 (mm) REVERT: u 4 TYR cc_start: 0.8514 (m-80) cc_final: 0.8304 (m-80) REVERT: u 93 MET cc_start: 0.8380 (mtp) cc_final: 0.7987 (mtp) REVERT: u 118 LYS cc_start: 0.7660 (mmtp) cc_final: 0.7186 (mtpt) REVERT: v 20 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5762 (mp0) REVERT: v 22 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6135 (mptp) REVERT: v 50 SER cc_start: 0.6675 (p) cc_final: 0.6255 (m) REVERT: v 54 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6669 (ttpp) REVERT: v 71 ASP cc_start: 0.5189 (t0) cc_final: 0.4807 (m-30) REVERT: v 73 SER cc_start: 0.5162 (OUTLIER) cc_final: 0.4623 (t) REVERT: v 140 MET cc_start: 0.7727 (mtm) cc_final: 0.7346 (mpp) REVERT: v 279 LYS cc_start: 0.6624 (tppt) cc_final: 0.6388 (tptp) REVERT: w 70 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.5797 (mtt) REVERT: w 83 GLN cc_start: 0.7856 (tt0) cc_final: 0.7525 (tt0) REVERT: w 173 LEU cc_start: 0.5750 (mt) cc_final: 0.5528 (mt) REVERT: x 104 SER cc_start: 0.5777 (m) cc_final: 0.5459 (p) REVERT: x 119 LEU cc_start: 0.5126 (mt) cc_final: 0.4792 (tt) REVERT: x 122 THR cc_start: 0.5484 (m) cc_final: 0.5197 (p) REVERT: x 139 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7168 (mp) REVERT: x 477 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7789 (ptpt) REVERT: x 500 ARG cc_start: 0.7562 (mtt90) cc_final: 0.7135 (mpt180) REVERT: x 509 MET cc_start: 0.8170 (mmt) cc_final: 0.7908 (mmt) REVERT: y 62 MET cc_start: 0.8097 (mmm) cc_final: 0.7851 (mmm) REVERT: y 98 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5265 (mm-30) REVERT: y 171 GLU cc_start: 0.6499 (mm-30) cc_final: 0.6257 (mt-10) REVERT: z 38 LYS cc_start: 0.8148 (mttt) cc_final: 0.7883 (mtpt) REVERT: z 95 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7624 (ttpt) REVERT: z 98 LYS cc_start: 0.6785 (tptp) cc_final: 0.6326 (tttp) REVERT: 4 29 ARG cc_start: 0.6838 (ttm110) cc_final: 0.6383 (ttp-110) REVERT: 4 72 ILE cc_start: 0.7857 (mt) cc_final: 0.7578 (mt) REVERT: 4 77 GLU cc_start: 0.5935 (tp30) cc_final: 0.5360 (mt-10) REVERT: 4 119 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6962 (pttt) REVERT: 4 170 LEU cc_start: 0.4254 (OUTLIER) cc_final: 0.3954 (mp) REVERT: 4 173 THR cc_start: 0.5710 (p) cc_final: 0.5393 (m) REVERT: 4 205 GLU cc_start: 0.3825 (pm20) cc_final: 0.3442 (mp0) REVERT: 4 371 LYS cc_start: 0.7155 (mmtt) cc_final: 0.6927 (mmtt) REVERT: 4 384 LYS cc_start: 0.6407 (mmtp) cc_final: 0.6198 (tptp) REVERT: 4 434 GLU cc_start: 0.6304 (mt-10) cc_final: 0.5917 (pt0) REVERT: 4 446 ASP cc_start: 0.6074 (p0) cc_final: 0.5849 (p0) REVERT: 4 468 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5462 (mp) REVERT: 4 496 ILE cc_start: 0.7510 (pt) cc_final: 0.7310 (pt) REVERT: 4 530 LYS cc_start: 0.5910 (mmtt) cc_final: 0.5602 (mmmt) outliers start: 308 outliers final: 166 residues processed: 1611 average time/residue: 2.4693 time to fit residues: 5675.4590 Evaluate side-chains 1566 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1356 time to evaluate : 9.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 8 residue 44 GLU Chi-restraints excluded: chain 8 residue 58 VAL Chi-restraints excluded: chain 8 residue 153 GLU Chi-restraints excluded: chain 9 residue 41 SER Chi-restraints excluded: chain 9 residue 43 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 215 LYS Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 14 LYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain W residue 21 GLU Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 179 LYS Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 340 LEU Chi-restraints excluded: chain b residue 482 GLU Chi-restraints excluded: chain b residue 512 SER Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 532 GLU Chi-restraints excluded: chain b residue 613 ARG Chi-restraints excluded: chain b residue 622 SER Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 3 VAL Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 125 GLU Chi-restraints excluded: chain m residue 139 ASP Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 390 VAL Chi-restraints excluded: chain m residue 393 VAL Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 107 GLU Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 381 LEU Chi-restraints excluded: chain n residue 408 THR Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 150 GLU Chi-restraints excluded: chain o residue 158 MET Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain q residue 194 THR Chi-restraints excluded: chain q residue 249 GLU Chi-restraints excluded: chain r residue 141 LYS Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 14 LYS Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 39 LYS Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 79 SER Chi-restraints excluded: chain t residue 82 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 275 ARG Chi-restraints excluded: chain t residue 278 SER Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain u residue 129 SER Chi-restraints excluded: chain u residue 141 ILE Chi-restraints excluded: chain v residue 20 GLU Chi-restraints excluded: chain v residue 22 LYS Chi-restraints excluded: chain v residue 39 ASN Chi-restraints excluded: chain v residue 54 LYS Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 256 GLU Chi-restraints excluded: chain v residue 259 THR Chi-restraints excluded: chain w residue 70 MET Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 155 ASP Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain x residue 136 SER Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 195 SER Chi-restraints excluded: chain x residue 225 LEU Chi-restraints excluded: chain x residue 283 CYS Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 347 SER Chi-restraints excluded: chain x residue 379 ASP Chi-restraints excluded: chain x residue 395 ILE Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain x residue 477 LYS Chi-restraints excluded: chain y residue 98 GLU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 10 HIS Chi-restraints excluded: chain z residue 95 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 4 residue 170 LEU Chi-restraints excluded: chain 4 residue 255 ASN Chi-restraints excluded: chain 4 residue 336 THR Chi-restraints excluded: chain 4 residue 367 THR Chi-restraints excluded: chain 4 residue 373 LYS Chi-restraints excluded: chain 4 residue 466 LEU Chi-restraints excluded: chain 4 residue 468 LEU Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 531 THR Chi-restraints excluded: chain 4 residue 558 THR Chi-restraints excluded: chain 4 residue 572 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 1114 optimal weight: 3.9990 chunk 759 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 996 optimal weight: 0.5980 chunk 551 optimal weight: 10.0000 chunk 1141 optimal weight: 3.9990 chunk 924 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 683 optimal weight: 20.0000 chunk 1200 optimal weight: 7.9990 chunk 337 optimal weight: 50.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 24 ASN C 175 HIS F 157 ASN G 192 GLN H 9 GLN H 100 ASN H 102 ASN H 163 GLN K 101 ASN M 11 ASN M 62 GLN N 23 GLN N 195 ASN R 34 GLN S 122 HIS U 25 ASN W 14 GLN W 205 GLN Y 4 GLN Y 26 GLN Z 123 GLN b 152 GLN e 88 HIS ** g 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN k 76 ASN ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN n 144 ASN p 25 GLN q 424 GLN v 254 GLN w 8 ASN w 25 ASN ** x 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 180 HIS x 271 GLN ** 4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 544 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 167341 Z= 0.127 Angle : 0.591 17.108 241944 Z= 0.323 Chirality : 0.035 0.351 29617 Planarity : 0.005 0.126 18328 Dihedral : 21.990 179.595 63304 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.77 % Allowed : 14.90 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.08), residues: 10648 helix: 2.24 (0.08), residues: 4174 sheet: 0.21 (0.13), residues: 1568 loop : -0.01 (0.09), residues: 4906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 212 HIS 0.006 0.001 HIS J 68 PHE 0.023 0.001 PHE D 219 TYR 0.020 0.001 TYR N 53 ARG 0.008 0.000 ARG b 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1689 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1431 time to evaluate : 9.677 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: A 10 LYS cc_start: 0.8419 (pttm) cc_final: 0.7546 (mttp) REVERT: A 72 ARG cc_start: 0.7912 (mmm160) cc_final: 0.7581 (mmm160) REVERT: A 74 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8154 (mm-30) REVERT: A 93 LYS cc_start: 0.8138 (mmtp) cc_final: 0.7790 (mttt) REVERT: A 191 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8290 (mm) REVERT: 5 84 GLU cc_start: 0.4283 (mm-30) cc_final: 0.3927 (mm-30) REVERT: 5 107 MET cc_start: 0.3135 (OUTLIER) cc_final: 0.2776 (ppp) REVERT: 8 146 LYS cc_start: 0.5512 (mmmm) cc_final: 0.5171 (mtmm) REVERT: B 248 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7765 (mtmt) REVERT: B 335 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.7925 (tp) REVERT: C 5 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7154 (mm-40) REVERT: C 63 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7075 (pp20) REVERT: D 234 ASP cc_start: 0.3256 (OUTLIER) cc_final: 0.3008 (p0) REVERT: F 46 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6821 (tp30) REVERT: F 64 GLN cc_start: 0.8110 (tp40) cc_final: 0.7761 (tp40) REVERT: F 234 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: G 92 LYS cc_start: 0.8093 (ttmt) cc_final: 0.7815 (mtmt) REVERT: G 100 GLU cc_start: 0.6413 (tt0) cc_final: 0.5930 (tt0) REVERT: G 208 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6856 (tp30) REVERT: H 1 MET cc_start: 0.5616 (OUTLIER) cc_final: 0.3832 (tpt) REVERT: H 8 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8130 (mm-40) REVERT: H 78 MET cc_start: 0.8308 (mtp) cc_final: 0.8023 (ttm) REVERT: I 62 ILE cc_start: 0.7175 (tp) cc_final: 0.6690 (tp) REVERT: J 12 LEU cc_start: 0.4681 (OUTLIER) cc_final: 0.4464 (tp) REVERT: J 131 MET cc_start: 0.5379 (mmt) cc_final: 0.4809 (mpp) REVERT: K 153 GLU cc_start: 0.5811 (OUTLIER) cc_final: 0.5273 (tp30) REVERT: K 170 ARG cc_start: 0.7402 (ttp-170) cc_final: 0.6992 (ttp-110) REVERT: K 173 PHE cc_start: 0.7465 (t80) cc_final: 0.7217 (t80) REVERT: K 215 LYS cc_start: 0.5176 (OUTLIER) cc_final: 0.4210 (tptp) REVERT: K 264 GLU cc_start: 0.3317 (tp30) cc_final: 0.3029 (tm-30) REVERT: K 276 ILE cc_start: 0.3726 (pt) cc_final: 0.3516 (mm) REVERT: M 6 ILE cc_start: 0.8055 (tt) cc_final: 0.7653 (tt) REVERT: M 105 GLN cc_start: 0.8346 (tt0) cc_final: 0.8139 (tt0) REVERT: N 14 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7248 (tttp) REVERT: O 40 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: P 67 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7572 (mm) REVERT: P 179 GLN cc_start: 0.7795 (mt0) cc_final: 0.7568 (mt0) REVERT: Q 12 ARG cc_start: 0.6113 (mtt90) cc_final: 0.5780 (mpt-90) REVERT: Q 136 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.7159 (m-40) REVERT: S 13 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6727 (ttm110) REVERT: S 158 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6536 (tppt) REVERT: T 89 LEU cc_start: 0.8049 (mp) cc_final: 0.7845 (mm) REVERT: T 140 ILE cc_start: 0.8212 (mt) cc_final: 0.7902 (mp) REVERT: T 142 SER cc_start: 0.7815 (t) cc_final: 0.7504 (m) REVERT: U 91 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: V 70 ARG cc_start: 0.7058 (mtt180) cc_final: 0.6553 (mtm-85) REVERT: V 108 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7155 (mt-10) REVERT: W 24 GLU cc_start: 0.6383 (mt-10) cc_final: 0.5811 (mt-10) REVERT: W 29 GLU cc_start: 0.6684 (mt-10) cc_final: 0.6423 (mt-10) REVERT: W 179 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6963 (mtpt) REVERT: X 70 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: X 142 ILE cc_start: 0.4951 (OUTLIER) cc_final: 0.4738 (pt) REVERT: a 70 LYS cc_start: 0.8001 (ttpt) cc_final: 0.7454 (ttpp) REVERT: a 120 ASN cc_start: 0.7020 (m-40) cc_final: 0.6759 (t0) REVERT: b 51 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7753 (mttp) REVERT: b 284 MET cc_start: 0.7200 (ttm) cc_final: 0.6980 (ttt) REVERT: b 343 ARG cc_start: 0.6740 (mtp180) cc_final: 0.6413 (ttt-90) REVERT: b 532 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6593 (tp30) REVERT: b 549 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.6988 (tp40) REVERT: b 613 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7566 (mtp-110) REVERT: b 643 LYS cc_start: 0.6169 (tptm) cc_final: 0.5304 (mtpp) REVERT: c 55 GLU cc_start: 0.7710 (tt0) cc_final: 0.7318 (tt0) REVERT: e 128 LEU cc_start: 0.3877 (OUTLIER) cc_final: 0.3510 (mm) REVERT: g 102 LYS cc_start: 0.7117 (mtmt) cc_final: 0.6498 (tttm) REVERT: k 8 ILE cc_start: 0.7045 (mp) cc_final: 0.6803 (mt) REVERT: k 64 LYS cc_start: 0.6279 (mttm) cc_final: 0.5617 (mmtm) REVERT: l 8 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.8104 (ttm-80) REVERT: m 8 LYS cc_start: 0.6673 (mmtt) cc_final: 0.6131 (mtpp) REVERT: m 162 LYS cc_start: 0.7280 (ptmm) cc_final: 0.6795 (ptmt) REVERT: m 210 ARG cc_start: 0.7181 (ttp80) cc_final: 0.6884 (tmm160) REVERT: m 246 MET cc_start: 0.8102 (mtp) cc_final: 0.7776 (mtp) REVERT: m 351 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7884 (mmtt) REVERT: m 387 VAL cc_start: 0.8452 (t) cc_final: 0.8200 (t) REVERT: n 1 MET cc_start: 0.7476 (ttm) cc_final: 0.7036 (ttp) REVERT: n 66 LYS cc_start: 0.7333 (mtmt) cc_final: 0.7089 (mmmt) REVERT: n 107 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.5726 (mm-30) REVERT: n 157 ASN cc_start: 0.6731 (m110) cc_final: 0.6526 (m-40) REVERT: n 173 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6198 (mm-30) REVERT: n 381 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5766 (tp) REVERT: n 448 LEU cc_start: 0.6338 (mt) cc_final: 0.5694 (tt) REVERT: o 102 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7619 (t80) REVERT: o 152 MET cc_start: 0.7241 (mmm) cc_final: 0.6967 (mmm) REVERT: o 200 MET cc_start: 0.3249 (OUTLIER) cc_final: 0.2886 (ppp) REVERT: q 244 GLU cc_start: 0.5187 (mt-10) cc_final: 0.4890 (mm-30) REVERT: q 249 GLU cc_start: 0.5804 (OUTLIER) cc_final: 0.5337 (mp0) REVERT: q 257 LYS cc_start: 0.6140 (ttpt) cc_final: 0.5912 (tmmm) REVERT: q 381 HIS cc_start: 0.6896 (m90) cc_final: 0.6644 (m-70) REVERT: q 436 ARG cc_start: 0.5951 (ttt90) cc_final: 0.5497 (mtm180) REVERT: q 453 ASP cc_start: 0.8077 (m-30) cc_final: 0.7575 (m-30) REVERT: r 250 ASP cc_start: 0.7930 (p0) cc_final: 0.7715 (p0) REVERT: r 252 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7907 (p0) REVERT: t 129 ILE cc_start: 0.5516 (OUTLIER) cc_final: 0.4972 (mm) REVERT: t 201 LEU cc_start: 0.6025 (tp) cc_final: 0.5705 (tp) REVERT: u 4 TYR cc_start: 0.8487 (m-80) cc_final: 0.8260 (m-80) REVERT: u 25 ASP cc_start: 0.7341 (p0) cc_final: 0.7103 (p0) REVERT: u 84 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5972 (pt0) REVERT: u 118 LYS cc_start: 0.7635 (mmtp) cc_final: 0.7193 (mtpt) REVERT: v 22 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6051 (mptp) REVERT: v 50 SER cc_start: 0.6530 (p) cc_final: 0.6286 (m) REVERT: v 54 LYS cc_start: 0.6812 (OUTLIER) cc_final: 0.6583 (ttpp) REVERT: v 71 ASP cc_start: 0.5168 (t0) cc_final: 0.4808 (m-30) REVERT: v 73 SER cc_start: 0.5036 (OUTLIER) cc_final: 0.4469 (t) REVERT: v 83 ASP cc_start: 0.6220 (t70) cc_final: 0.5941 (t70) REVERT: v 140 MET cc_start: 0.7731 (mtm) cc_final: 0.7350 (mpp) REVERT: v 279 LYS cc_start: 0.6625 (tppt) cc_final: 0.6257 (tptt) REVERT: w 70 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.5747 (mtt) REVERT: w 83 GLN cc_start: 0.7793 (tt0) cc_final: 0.7459 (tt0) REVERT: x 104 SER cc_start: 0.5726 (m) cc_final: 0.5400 (p) REVERT: x 119 LEU cc_start: 0.5208 (mt) cc_final: 0.4656 (tt) REVERT: x 122 THR cc_start: 0.5383 (m) cc_final: 0.5166 (p) REVERT: x 139 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7147 (mp) REVERT: x 474 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6244 (ttm170) REVERT: x 477 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7825 (ptpt) REVERT: x 500 ARG cc_start: 0.7548 (mtt90) cc_final: 0.7306 (mtt180) REVERT: x 509 MET cc_start: 0.8165 (mmt) cc_final: 0.7893 (mmt) REVERT: y 62 MET cc_start: 0.8061 (mmm) cc_final: 0.7833 (mmm) REVERT: y 98 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5259 (mm-30) REVERT: y 171 GLU cc_start: 0.6505 (mm-30) cc_final: 0.6260 (mt-10) REVERT: 4 29 ARG cc_start: 0.6814 (ttm110) cc_final: 0.6368 (ttp-110) REVERT: 4 72 ILE cc_start: 0.7798 (mt) cc_final: 0.7531 (mt) REVERT: 4 77 GLU cc_start: 0.5880 (tp30) cc_final: 0.5284 (mt-10) REVERT: 4 119 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6991 (pttt) REVERT: 4 158 MET cc_start: 0.7039 (ptm) cc_final: 0.6668 (ptm) REVERT: 4 170 LEU cc_start: 0.4228 (OUTLIER) cc_final: 0.3932 (mp) REVERT: 4 173 THR cc_start: 0.5698 (p) cc_final: 0.5375 (m) REVERT: 4 205 GLU cc_start: 0.3680 (pm20) cc_final: 0.3343 (mp0) REVERT: 4 371 LYS cc_start: 0.7109 (mmtt) cc_final: 0.6572 (mmtt) REVERT: 4 416 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6886 (mp) REVERT: 4 434 GLU cc_start: 0.6249 (mt-10) cc_final: 0.5901 (pt0) REVERT: 4 446 ASP cc_start: 0.6010 (p0) cc_final: 0.5776 (p0) REVERT: 4 496 ILE cc_start: 0.7489 (pt) cc_final: 0.7285 (pt) REVERT: 4 530 LYS cc_start: 0.5903 (mmtt) cc_final: 0.5593 (mmmt) outliers start: 258 outliers final: 140 residues processed: 1583 average time/residue: 2.4607 time to fit residues: 5525.1684 Evaluate side-chains 1559 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1374 time to evaluate : 9.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain 5 residue 104 VAL Chi-restraints excluded: chain 5 residue 107 MET Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 8 residue 58 VAL Chi-restraints excluded: chain 8 residue 153 GLU Chi-restraints excluded: chain 9 residue 43 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 150 LYS Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 215 LYS Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 14 LYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 158 LYS Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain W residue 20 ARG Chi-restraints excluded: chain W residue 21 GLU Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 179 LYS Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 51 LYS Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 482 GLU Chi-restraints excluded: chain b residue 512 SER Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 532 GLU Chi-restraints excluded: chain b residue 549 GLN Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain b residue 613 ARG Chi-restraints excluded: chain b residue 622 SER Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 247 LYS Chi-restraints excluded: chain m residue 390 VAL Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 107 GLU Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 381 LEU Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain q residue 194 THR Chi-restraints excluded: chain q residue 249 GLU Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain t residue 39 LYS Chi-restraints excluded: chain t residue 79 SER Chi-restraints excluded: chain t residue 82 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 234 ILE Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain t residue 275 ARG Chi-restraints excluded: chain t residue 278 SER Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain v residue 22 LYS Chi-restraints excluded: chain v residue 39 ASN Chi-restraints excluded: chain v residue 54 LYS Chi-restraints excluded: chain v residue 57 MET Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 129 LYS Chi-restraints excluded: chain v residue 210 LYS Chi-restraints excluded: chain v residue 256 GLU Chi-restraints excluded: chain w residue 70 MET Chi-restraints excluded: chain w residue 75 GLU Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain x residue 136 SER Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 195 SER Chi-restraints excluded: chain x residue 225 LEU Chi-restraints excluded: chain x residue 283 CYS Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 347 SER Chi-restraints excluded: chain x residue 379 ASP Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain x residue 474 ARG Chi-restraints excluded: chain x residue 477 LYS Chi-restraints excluded: chain y residue 98 GLU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 10 HIS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 4 residue 170 LEU Chi-restraints excluded: chain 4 residue 255 ASN Chi-restraints excluded: chain 4 residue 416 LEU Chi-restraints excluded: chain 4 residue 531 THR Chi-restraints excluded: chain 4 residue 543 LEU Chi-restraints excluded: chain 4 residue 558 THR Chi-restraints excluded: chain 4 residue 572 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 450 optimal weight: 2.9990 chunk 1204 optimal weight: 10.0000 chunk 264 optimal weight: 20.0000 chunk 785 optimal weight: 6.9990 chunk 330 optimal weight: 10.0000 chunk 1339 optimal weight: 20.0000 chunk 1111 optimal weight: 9.9990 chunk 619 optimal weight: 9.9990 chunk 111 optimal weight: 30.0000 chunk 442 optimal weight: 10.0000 chunk 702 optimal weight: 30.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 100 HIS 9 24 ASN B 198 HIS C 175 HIS F 157 ASN F 194 HIS H 9 GLN H 100 ASN H 102 ASN H 163 GLN K 101 ASN M 11 ASN N 15 GLN N 23 GLN ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 114 HIS S 122 HIS U 25 ASN U 101 ASN W 14 GLN W 205 GLN Y 4 GLN Y 26 GLN b 152 GLN e 88 HIS ** g 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN k 76 ASN l 4 GLN n 69 GLN n 144 ASN n 208 ASN p 25 GLN w 8 ASN x 12 GLN y 145 ASN y 235 ASN 4 544 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 167341 Z= 0.312 Angle : 0.777 19.128 241944 Z= 0.405 Chirality : 0.043 0.313 29617 Planarity : 0.007 0.142 18328 Dihedral : 22.169 179.906 63300 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.48 % Allowed : 14.93 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.08), residues: 10648 helix: 1.79 (0.08), residues: 4168 sheet: 0.10 (0.13), residues: 1587 loop : -0.18 (0.08), residues: 4893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP m 212 HIS 0.010 0.002 HIS O 55 PHE 0.032 0.002 PHE F 229 TYR 0.029 0.002 TYR C 194 ARG 0.009 0.001 ARG O 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1717 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1393 time to evaluate : 9.655 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: A 10 LYS cc_start: 0.8349 (pttm) cc_final: 0.7607 (mttm) REVERT: A 72 ARG cc_start: 0.7888 (mmm160) cc_final: 0.7536 (mmm160) REVERT: A 74 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8196 (mm-30) REVERT: A 93 LYS cc_start: 0.8126 (mmtp) cc_final: 0.7917 (mttp) REVERT: A 191 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8385 (mm) REVERT: 5 84 GLU cc_start: 0.4298 (mm-30) cc_final: 0.4009 (mt-10) REVERT: 5 99 MET cc_start: 0.3872 (OUTLIER) cc_final: 0.3457 (mmm) REVERT: 8 146 LYS cc_start: 0.5674 (mmmm) cc_final: 0.5323 (mtmm) REVERT: B 21 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8141 (mtm-85) REVERT: C 5 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7279 (mm110) REVERT: C 63 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7225 (pp20) REVERT: C 212 ASP cc_start: 0.7931 (t0) cc_final: 0.7574 (t0) REVERT: D 48 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.6642 (mtpp) REVERT: D 198 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.4960 (t80) REVERT: D 234 ASP cc_start: 0.3174 (OUTLIER) cc_final: 0.2945 (p0) REVERT: D 237 GLU cc_start: 0.5258 (OUTLIER) cc_final: 0.4928 (tt0) REVERT: E 90 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.5932 (ttpt) REVERT: F 234 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: G 100 GLU cc_start: 0.6633 (tt0) cc_final: 0.6133 (tt0) REVERT: G 208 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6976 (tp30) REVERT: G 230 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6260 (mtpm) REVERT: H 78 MET cc_start: 0.8520 (mtp) cc_final: 0.8034 (mtm) REVERT: H 150 SER cc_start: 0.8274 (t) cc_final: 0.7945 (t) REVERT: I 62 ILE cc_start: 0.7227 (tp) cc_final: 0.6789 (tp) REVERT: J 131 MET cc_start: 0.5528 (mmt) cc_final: 0.4913 (mpp) REVERT: J 173 ASP cc_start: 0.2693 (OUTLIER) cc_final: 0.2016 (t0) REVERT: K 153 GLU cc_start: 0.5870 (OUTLIER) cc_final: 0.5341 (tp30) REVERT: K 170 ARG cc_start: 0.7505 (ttp-170) cc_final: 0.7069 (ttp-110) REVERT: K 215 LYS cc_start: 0.5304 (OUTLIER) cc_final: 0.4351 (tptp) REVERT: K 263 VAL cc_start: 0.5139 (t) cc_final: 0.4833 (p) REVERT: L 104 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6771 (mtt90) REVERT: M 6 ILE cc_start: 0.8132 (tt) cc_final: 0.7751 (tt) REVERT: M 8 LYS cc_start: 0.6628 (mmmt) cc_final: 0.6337 (mtpt) REVERT: O 40 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6882 (mt-10) REVERT: O 134 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7972 (mttt) REVERT: P 67 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7687 (mp) REVERT: Q 136 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.7131 (m-40) REVERT: S 13 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6794 (ttm110) REVERT: T 140 ILE cc_start: 0.8262 (mt) cc_final: 0.7947 (mp) REVERT: T 142 SER cc_start: 0.7954 (t) cc_final: 0.7644 (m) REVERT: U 91 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: V 70 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6535 (mtm-85) REVERT: W 29 GLU cc_start: 0.6750 (mt-10) cc_final: 0.6491 (mt-10) REVERT: W 73 LEU cc_start: 0.6920 (mt) cc_final: 0.6712 (mt) REVERT: W 179 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6936 (mtpt) REVERT: X 70 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: X 142 ILE cc_start: 0.5358 (OUTLIER) cc_final: 0.4549 (mt) REVERT: a 70 LYS cc_start: 0.7996 (ttpt) cc_final: 0.7445 (ttpp) REVERT: a 120 ASN cc_start: 0.7163 (m-40) cc_final: 0.6797 (t0) REVERT: b 343 ARG cc_start: 0.6821 (mtp180) cc_final: 0.6378 (ttt-90) REVERT: b 613 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7772 (mtp-110) REVERT: b 643 LYS cc_start: 0.6160 (tptm) cc_final: 0.5282 (mtpp) REVERT: c 53 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7993 (ttmt) REVERT: c 55 GLU cc_start: 0.7836 (tt0) cc_final: 0.7257 (tt0) REVERT: e 21 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8036 (m-70) REVERT: e 128 LEU cc_start: 0.3865 (OUTLIER) cc_final: 0.3650 (tm) REVERT: f 49 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8512 (mt) REVERT: g 102 LYS cc_start: 0.7253 (mtmt) cc_final: 0.6549 (tttm) REVERT: i 9 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8224 (pt) REVERT: k 8 ILE cc_start: 0.7064 (mp) cc_final: 0.6797 (mt) REVERT: k 64 LYS cc_start: 0.5887 (mttm) cc_final: 0.5295 (mmtm) REVERT: l 8 ARG cc_start: 0.8454 (ttm-80) cc_final: 0.8197 (ttm-80) REVERT: m 162 LYS cc_start: 0.7321 (ptmm) cc_final: 0.6832 (ptmt) REVERT: m 184 MET cc_start: 0.1276 (pmm) cc_final: 0.0967 (pmm) REVERT: m 210 ARG cc_start: 0.7316 (ttp80) cc_final: 0.6926 (tmm160) REVERT: m 246 MET cc_start: 0.8196 (mtp) cc_final: 0.7863 (mtp) REVERT: n 1 MET cc_start: 0.7490 (ttm) cc_final: 0.7038 (ttp) REVERT: n 66 LYS cc_start: 0.7436 (mtmt) cc_final: 0.7200 (mmmt) REVERT: n 107 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5678 (mm-30) REVERT: n 157 ASN cc_start: 0.6917 (m110) cc_final: 0.6674 (m-40) REVERT: n 173 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6450 (mm-30) REVERT: n 208 ASN cc_start: 0.6210 (OUTLIER) cc_final: 0.5813 (p0) REVERT: n 381 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6157 (tp) REVERT: n 448 LEU cc_start: 0.6361 (mt) cc_final: 0.5717 (tt) REVERT: o 102 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7582 (t80) REVERT: o 152 MET cc_start: 0.7377 (mmm) cc_final: 0.7170 (mmm) REVERT: o 200 MET cc_start: 0.3294 (OUTLIER) cc_final: 0.2814 (ppp) REVERT: q 242 TYR cc_start: 0.5413 (t80) cc_final: 0.5134 (t80) REVERT: q 244 GLU cc_start: 0.5093 (mt-10) cc_final: 0.4793 (mm-30) REVERT: q 249 GLU cc_start: 0.6073 (mp0) cc_final: 0.5673 (mp0) REVERT: q 257 LYS cc_start: 0.6215 (ttpt) cc_final: 0.6001 (tmmm) REVERT: q 381 HIS cc_start: 0.6874 (m90) cc_final: 0.6658 (m-70) REVERT: q 436 ARG cc_start: 0.6121 (ttt90) cc_final: 0.5501 (mtm180) REVERT: r 141 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7351 (mttt) REVERT: r 211 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: r 250 ASP cc_start: 0.8046 (p0) cc_final: 0.7795 (p0) REVERT: r 252 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8039 (p0) REVERT: s 14 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7796 (ttmm) REVERT: t 30 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.4851 (tmm-80) REVERT: t 129 ILE cc_start: 0.5369 (OUTLIER) cc_final: 0.4923 (mm) REVERT: u 4 TYR cc_start: 0.8531 (m-80) cc_final: 0.8259 (m-80) REVERT: u 84 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6376 (pt0) REVERT: u 93 MET cc_start: 0.8416 (mtp) cc_final: 0.8061 (mtp) REVERT: u 118 LYS cc_start: 0.7659 (mmtp) cc_final: 0.7192 (mtpt) REVERT: v 22 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6062 (mptp) REVERT: v 50 SER cc_start: 0.6656 (p) cc_final: 0.6363 (m) REVERT: v 54 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6739 (ttpp) REVERT: v 65 ASP cc_start: 0.4677 (t0) cc_final: 0.4462 (m-30) REVERT: v 71 ASP cc_start: 0.5190 (t0) cc_final: 0.4905 (m-30) REVERT: v 73 SER cc_start: 0.5157 (OUTLIER) cc_final: 0.4639 (t) REVERT: v 140 MET cc_start: 0.7733 (mtm) cc_final: 0.7372 (mpp) REVERT: v 279 LYS cc_start: 0.6812 (tppt) cc_final: 0.6353 (tptt) REVERT: w 70 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.5892 (mtt) REVERT: x 104 SER cc_start: 0.5780 (m) cc_final: 0.5431 (p) REVERT: x 122 THR cc_start: 0.5519 (m) cc_final: 0.5145 (p) REVERT: x 139 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.7049 (mp) REVERT: x 474 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6421 (ttm110) REVERT: x 477 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7760 (ptpt) REVERT: x 500 ARG cc_start: 0.7592 (mtt90) cc_final: 0.7191 (mpt180) REVERT: x 509 MET cc_start: 0.8160 (mmt) cc_final: 0.7932 (mmt) REVERT: y 62 MET cc_start: 0.8128 (mmm) cc_final: 0.7886 (mmm) REVERT: y 98 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5312 (mm-30) REVERT: y 171 GLU cc_start: 0.6626 (mm-30) cc_final: 0.6404 (mt-10) REVERT: z 95 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7857 (ttpt) REVERT: z 98 LYS cc_start: 0.6785 (tptp) cc_final: 0.6321 (tttp) REVERT: 4 29 ARG cc_start: 0.6611 (ttm110) cc_final: 0.6172 (ttp-110) REVERT: 4 72 ILE cc_start: 0.7866 (mt) cc_final: 0.7566 (mt) REVERT: 4 77 GLU cc_start: 0.5983 (tp30) cc_final: 0.5389 (mt-10) REVERT: 4 99 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6675 (pm20) REVERT: 4 119 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6896 (pttt) REVERT: 4 170 LEU cc_start: 0.4278 (OUTLIER) cc_final: 0.3982 (mp) REVERT: 4 173 THR cc_start: 0.5734 (p) cc_final: 0.5372 (m) REVERT: 4 205 GLU cc_start: 0.3663 (pm20) cc_final: 0.3307 (mp0) REVERT: 4 425 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: 4 434 GLU cc_start: 0.6285 (mt-10) cc_final: 0.5888 (pt0) REVERT: 4 446 ASP cc_start: 0.5990 (p0) cc_final: 0.5709 (p0) REVERT: 4 468 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5539 (mp) REVERT: 4 496 ILE cc_start: 0.7547 (pt) cc_final: 0.7337 (pt) outliers start: 324 outliers final: 197 residues processed: 1594 average time/residue: 2.4373 time to fit residues: 5539.5328 Evaluate side-chains 1599 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1348 time to evaluate : 8.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 5 residue 104 VAL Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 8 residue 42 VAL Chi-restraints excluded: chain 8 residue 58 VAL Chi-restraints excluded: chain 8 residue 153 GLU Chi-restraints excluded: chain 9 residue 41 SER Chi-restraints excluded: chain 9 residue 43 VAL Chi-restraints excluded: chain 9 residue 141 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 150 LYS Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 215 LYS Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 104 ARG Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 14 LYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain W residue 21 GLU Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 158 ILE Chi-restraints excluded: chain W residue 179 LYS Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 190 THR Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 227 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain b residue 51 LYS Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 482 GLU Chi-restraints excluded: chain b residue 512 SER Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain b residue 613 ARG Chi-restraints excluded: chain b residue 622 SER Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 139 ASP Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 176 VAL Chi-restraints excluded: chain m residue 247 LYS Chi-restraints excluded: chain m residue 390 VAL Chi-restraints excluded: chain m residue 393 VAL Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 107 GLU Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain n residue 208 ASN Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 381 LEU Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 408 THR Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 150 GLU Chi-restraints excluded: chain o residue 158 MET Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain q residue 194 THR Chi-restraints excluded: chain r residue 141 LYS Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 211 GLN Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 14 LYS Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 50 ILE Chi-restraints excluded: chain t residue 30 ARG Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 39 LYS Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 79 SER Chi-restraints excluded: chain t residue 82 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 153 VAL Chi-restraints excluded: chain t residue 234 ILE Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain t residue 262 SER Chi-restraints excluded: chain t residue 275 ARG Chi-restraints excluded: chain t residue 278 SER Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain u residue 141 ILE Chi-restraints excluded: chain v residue 20 GLU Chi-restraints excluded: chain v residue 22 LYS Chi-restraints excluded: chain v residue 39 ASN Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 54 LYS Chi-restraints excluded: chain v residue 57 MET Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 129 LYS Chi-restraints excluded: chain v residue 160 LEU Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 210 LYS Chi-restraints excluded: chain v residue 256 GLU Chi-restraints excluded: chain v residue 259 THR Chi-restraints excluded: chain w residue 70 MET Chi-restraints excluded: chain w residue 75 GLU Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 18 LEU Chi-restraints excluded: chain x residue 136 SER Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 195 SER Chi-restraints excluded: chain x residue 225 LEU Chi-restraints excluded: chain x residue 283 CYS Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 347 SER Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain x residue 474 ARG Chi-restraints excluded: chain x residue 477 LYS Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 98 GLU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 10 HIS Chi-restraints excluded: chain z residue 95 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 99 GLN Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 4 residue 170 LEU Chi-restraints excluded: chain 4 residue 255 ASN Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 336 THR Chi-restraints excluded: chain 4 residue 373 LYS Chi-restraints excluded: chain 4 residue 416 LEU Chi-restraints excluded: chain 4 residue 425 GLU Chi-restraints excluded: chain 4 residue 468 LEU Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 531 THR Chi-restraints excluded: chain 4 residue 543 LEU Chi-restraints excluded: chain 4 residue 558 THR Chi-restraints excluded: chain 4 residue 572 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 1291 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 762 optimal weight: 5.9990 chunk 977 optimal weight: 4.9990 chunk 757 optimal weight: 7.9990 chunk 1127 optimal weight: 8.9990 chunk 747 optimal weight: 9.9990 chunk 1333 optimal weight: 7.9990 chunk 834 optimal weight: 6.9990 chunk 813 optimal weight: 8.9990 chunk 615 optimal weight: 40.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 24 ASN B 198 HIS C 175 HIS F 157 ASN G 192 GLN H 9 GLN H 100 ASN H 102 ASN H 163 GLN K 101 ASN M 11 ASN N 15 GLN N 23 GLN O 122 GLN R 34 GLN S 122 HIS W 205 GLN Y 4 GLN Y 26 GLN b 152 GLN b 429 ASN e 88 HIS ** g 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN k 76 ASN ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 398 GLN n 69 GLN n 144 ASN p 25 GLN t 209 GLN w 8 ASN w 25 ASN x 271 GLN 4 398 ASN 4 544 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 167341 Z= 0.272 Angle : 0.742 18.381 241944 Z= 0.390 Chirality : 0.042 0.331 29617 Planarity : 0.006 0.139 18328 Dihedral : 22.164 179.756 63300 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.42 % Allowed : 15.45 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % 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: 0.82 (0.08), residues: 10648 helix: 1.70 (0.08), residues: 4175 sheet: 0.04 (0.12), residues: 1592 loop : -0.24 (0.08), residues: 4881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP m 212 HIS 0.009 0.001 HIS O 55 PHE 0.029 0.002 PHE D 219 TYR 0.030 0.002 TYR N 53 ARG 0.010 0.001 ARG Q 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1697 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 1379 time to evaluate : 9.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8373 (pttm) cc_final: 0.7603 (mttm) REVERT: A 72 ARG cc_start: 0.7890 (mmm160) cc_final: 0.7544 (mmm160) REVERT: A 74 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8160 (mm-30) REVERT: A 191 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8328 (mm) REVERT: 5 84 GLU cc_start: 0.4500 (mm-30) cc_final: 0.4137 (mt-10) REVERT: 5 99 MET cc_start: 0.3712 (OUTLIER) cc_final: 0.3324 (mmm) REVERT: 5 104 VAL cc_start: 0.4715 (OUTLIER) cc_final: 0.4339 (m) REVERT: 8 146 LYS cc_start: 0.5695 (mmmm) cc_final: 0.5337 (mtmm) REVERT: B 21 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8106 (mtm-85) REVERT: B 248 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7546 (mtmt) REVERT: C 5 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7247 (mm-40) REVERT: C 63 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7193 (pp20) REVERT: C 212 ASP cc_start: 0.7934 (t0) cc_final: 0.7578 (t0) REVERT: D 48 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.6650 (mtpp) REVERT: D 198 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.4995 (t80) REVERT: D 232 ASP cc_start: 0.4563 (t0) cc_final: 0.4310 (m-30) REVERT: D 237 GLU cc_start: 0.5260 (OUTLIER) cc_final: 0.4929 (tt0) REVERT: E 90 LYS cc_start: 0.6609 (OUTLIER) cc_final: 0.5931 (ttpt) REVERT: F 46 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7029 (tp30) REVERT: F 182 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: G 100 GLU cc_start: 0.6684 (tt0) cc_final: 0.6107 (tt0) REVERT: G 203 VAL cc_start: 0.7443 (OUTLIER) cc_final: 0.6697 (m) REVERT: G 208 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6984 (tp30) REVERT: G 230 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6158 (mtpm) REVERT: H 1 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.4256 (tpt) REVERT: H 78 MET cc_start: 0.8547 (mtp) cc_final: 0.8069 (mtm) REVERT: H 150 SER cc_start: 0.8252 (t) cc_final: 0.7906 (t) REVERT: I 62 ILE cc_start: 0.7249 (tp) cc_final: 0.6815 (tp) REVERT: J 131 MET cc_start: 0.5420 (mmt) cc_final: 0.4862 (mpp) REVERT: J 173 ASP cc_start: 0.2754 (OUTLIER) cc_final: 0.2017 (t0) REVERT: K 153 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.5344 (tp30) REVERT: K 170 ARG cc_start: 0.7424 (ttp-170) cc_final: 0.6961 (ttp-110) REVERT: L 104 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6471 (mtt90) REVERT: M 6 ILE cc_start: 0.8116 (tt) cc_final: 0.7733 (tt) REVERT: M 8 LYS cc_start: 0.6642 (mmmt) cc_final: 0.6392 (mtpt) REVERT: O 40 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6883 (mt-10) REVERT: O 134 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7958 (mttt) REVERT: P 67 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7665 (mp) REVERT: Q 136 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7126 (m-40) REVERT: S 13 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6805 (ttm110) REVERT: T 89 LEU cc_start: 0.8045 (mp) cc_final: 0.7841 (mm) REVERT: T 140 ILE cc_start: 0.8250 (mt) cc_final: 0.7936 (mp) REVERT: T 142 SER cc_start: 0.7941 (t) cc_final: 0.7639 (m) REVERT: U 91 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: V 70 ARG cc_start: 0.7065 (mtt180) cc_final: 0.6523 (mtm-85) REVERT: W 29 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6476 (mt-10) REVERT: W 179 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6955 (mtpt) REVERT: X 70 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: X 142 ILE cc_start: 0.5425 (OUTLIER) cc_final: 0.4589 (mt) REVERT: a 70 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7459 (ttpp) REVERT: a 120 ASN cc_start: 0.7097 (m-40) cc_final: 0.6817 (t0) REVERT: b 343 ARG cc_start: 0.6800 (mtp180) cc_final: 0.6357 (ttt-90) REVERT: b 532 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6610 (tp30) REVERT: b 613 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7789 (mtp-110) REVERT: b 643 LYS cc_start: 0.6144 (tptm) cc_final: 0.5268 (mtpp) REVERT: c 53 LYS cc_start: 0.8220 (ttpp) cc_final: 0.8001 (ttmt) REVERT: c 55 GLU cc_start: 0.7806 (tt0) cc_final: 0.7351 (tt0) REVERT: e 21 HIS cc_start: 0.9029 (OUTLIER) cc_final: 0.8037 (m-70) REVERT: e 128 LEU cc_start: 0.3854 (OUTLIER) cc_final: 0.3640 (tm) REVERT: f 49 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8510 (mt) REVERT: g 102 LYS cc_start: 0.7270 (mtmt) cc_final: 0.6547 (tttm) REVERT: k 8 ILE cc_start: 0.6996 (mp) cc_final: 0.6731 (mt) REVERT: k 64 LYS cc_start: 0.5941 (mttm) cc_final: 0.5354 (mmtm) REVERT: l 8 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.8206 (ttm-80) REVERT: m 162 LYS cc_start: 0.7342 (ptmm) cc_final: 0.6853 (ptmt) REVERT: m 184 MET cc_start: 0.1034 (pmm) cc_final: 0.0791 (pmm) REVERT: m 210 ARG cc_start: 0.7259 (ttp80) cc_final: 0.6867 (tmm160) REVERT: m 246 MET cc_start: 0.8180 (mtp) cc_final: 0.7935 (mtp) REVERT: m 397 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: n 1 MET cc_start: 0.7510 (ttm) cc_final: 0.7053 (ttp) REVERT: n 66 LYS cc_start: 0.7410 (mtmt) cc_final: 0.7187 (mmmt) REVERT: n 107 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5704 (mm-30) REVERT: n 157 ASN cc_start: 0.6918 (m110) cc_final: 0.6677 (m-40) REVERT: n 173 GLU cc_start: 0.6702 (mm-30) cc_final: 0.6368 (mm-30) REVERT: n 381 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.6052 (tp) REVERT: n 448 LEU cc_start: 0.6335 (mt) cc_final: 0.5678 (tt) REVERT: o 102 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7563 (t80) REVERT: o 109 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7446 (tmtt) REVERT: o 152 MET cc_start: 0.7383 (mmm) cc_final: 0.7168 (mmm) REVERT: o 200 MET cc_start: 0.3378 (OUTLIER) cc_final: 0.2889 (ppp) REVERT: q 242 TYR cc_start: 0.5591 (t80) cc_final: 0.5324 (t80) REVERT: q 244 GLU cc_start: 0.4988 (mt-10) cc_final: 0.4743 (mm-30) REVERT: q 249 GLU cc_start: 0.6056 (mp0) cc_final: 0.5597 (mp0) REVERT: q 257 LYS cc_start: 0.6217 (ttpt) cc_final: 0.6001 (tmmm) REVERT: q 381 HIS cc_start: 0.6852 (m90) cc_final: 0.6632 (m-70) REVERT: q 436 ARG cc_start: 0.6103 (ttt90) cc_final: 0.5504 (mtm180) REVERT: r 141 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7331 (mttt) REVERT: r 250 ASP cc_start: 0.8072 (p0) cc_final: 0.7785 (p0) REVERT: r 252 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8070 (p0) REVERT: s 14 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7793 (ttmm) REVERT: t 30 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.4803 (tmm-80) REVERT: t 129 ILE cc_start: 0.5413 (OUTLIER) cc_final: 0.4942 (mm) REVERT: t 162 ILE cc_start: 0.7833 (mt) cc_final: 0.7459 (mp) REVERT: t 236 GLU cc_start: 0.4797 (OUTLIER) cc_final: 0.4505 (tm-30) REVERT: u 4 TYR cc_start: 0.8517 (m-80) cc_final: 0.8306 (m-80) REVERT: u 84 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6315 (pt0) REVERT: u 93 MET cc_start: 0.8437 (mtp) cc_final: 0.8096 (mtp) REVERT: u 118 LYS cc_start: 0.7678 (mmtp) cc_final: 0.7213 (mtpt) REVERT: v 22 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6040 (mptp) REVERT: v 50 SER cc_start: 0.6672 (p) cc_final: 0.6395 (m) REVERT: v 54 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6727 (ttpp) REVERT: v 71 ASP cc_start: 0.5213 (t0) cc_final: 0.4849 (m-30) REVERT: v 73 SER cc_start: 0.5291 (OUTLIER) cc_final: 0.4713 (t) REVERT: v 140 MET cc_start: 0.7700 (mtm) cc_final: 0.7323 (mpp) REVERT: v 279 LYS cc_start: 0.6595 (tppt) cc_final: 0.6215 (tptt) REVERT: w 70 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.5925 (mtt) REVERT: x 104 SER cc_start: 0.5925 (m) cc_final: 0.5544 (p) REVERT: x 139 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7133 (mp) REVERT: x 176 GLN cc_start: 0.6802 (mp10) cc_final: 0.6422 (mt0) REVERT: x 474 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6408 (ttm110) REVERT: x 477 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7805 (ptpt) REVERT: x 500 ARG cc_start: 0.7613 (mtt90) cc_final: 0.7378 (mtt180) REVERT: x 509 MET cc_start: 0.8171 (mmt) cc_final: 0.7924 (mmt) REVERT: y 62 MET cc_start: 0.8141 (mmm) cc_final: 0.7904 (mmm) REVERT: y 98 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5292 (mm-30) REVERT: y 171 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6377 (mt-10) REVERT: z 95 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7236 (ttpt) REVERT: z 98 LYS cc_start: 0.6786 (tptp) cc_final: 0.6318 (tttp) REVERT: 4 29 ARG cc_start: 0.6609 (ttm110) cc_final: 0.6189 (ttp-110) REVERT: 4 72 ILE cc_start: 0.7821 (mt) cc_final: 0.7506 (mt) REVERT: 4 77 GLU cc_start: 0.5981 (tp30) cc_final: 0.5386 (mt-10) REVERT: 4 99 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6698 (pm20) REVERT: 4 119 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6906 (pttt) REVERT: 4 170 LEU cc_start: 0.4261 (OUTLIER) cc_final: 0.3968 (mp) REVERT: 4 173 THR cc_start: 0.5678 (p) cc_final: 0.5365 (m) REVERT: 4 205 GLU cc_start: 0.3651 (pm20) cc_final: 0.3349 (mp0) REVERT: 4 425 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: 4 434 GLU cc_start: 0.6294 (mt-10) cc_final: 0.5888 (pt0) REVERT: 4 446 ASP cc_start: 0.5986 (p0) cc_final: 0.5709 (p0) REVERT: 4 468 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5454 (mp) REVERT: 4 496 ILE cc_start: 0.7533 (pt) cc_final: 0.7311 (pt) outliers start: 318 outliers final: 203 residues processed: 1577 average time/residue: 2.3312 time to fit residues: 5211.9209 Evaluate side-chains 1614 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1353 time to evaluate : 8.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain 5 residue 99 MET Chi-restraints excluded: chain 5 residue 104 VAL Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 8 residue 42 VAL Chi-restraints excluded: chain 8 residue 58 VAL Chi-restraints excluded: chain 8 residue 153 GLU Chi-restraints excluded: chain 9 residue 41 SER Chi-restraints excluded: chain 9 residue 43 VAL Chi-restraints excluded: chain 9 residue 141 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 150 LYS Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 215 LYS Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 104 ARG Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 14 LYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain W residue 21 GLU Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 158 ILE Chi-restraints excluded: chain W residue 179 LYS Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 190 THR Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 227 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 49 LYS Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 482 GLU Chi-restraints excluded: chain b residue 512 SER Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 532 GLU Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain b residue 613 ARG Chi-restraints excluded: chain b residue 622 SER Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 44 ILE Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 164 THR Chi-restraints excluded: chain m residue 169 THR Chi-restraints excluded: chain m residue 247 LYS Chi-restraints excluded: chain m residue 390 VAL Chi-restraints excluded: chain m residue 393 VAL Chi-restraints excluded: chain m residue 397 GLU Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 107 GLU Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 381 LEU Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 109 LYS Chi-restraints excluded: chain o residue 146 MET Chi-restraints excluded: chain o residue 150 GLU Chi-restraints excluded: chain o residue 158 MET Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain q residue 194 THR Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 141 LYS Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 14 LYS Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 50 ILE Chi-restraints excluded: chain t residue 30 ARG Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 39 LYS Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 79 SER Chi-restraints excluded: chain t residue 82 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 234 ILE Chi-restraints excluded: chain t residue 236 GLU Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain t residue 262 SER Chi-restraints excluded: chain t residue 275 ARG Chi-restraints excluded: chain t residue 278 SER Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain u residue 109 LYS Chi-restraints excluded: chain u residue 141 ILE Chi-restraints excluded: chain v residue 20 GLU Chi-restraints excluded: chain v residue 22 LYS Chi-restraints excluded: chain v residue 39 ASN Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 54 LYS Chi-restraints excluded: chain v residue 57 MET Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 89 LEU Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 129 LYS Chi-restraints excluded: chain v residue 160 LEU Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 256 GLU Chi-restraints excluded: chain v residue 259 THR Chi-restraints excluded: chain w residue 70 MET Chi-restraints excluded: chain w residue 75 GLU Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain w residue 199 MET Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 18 LEU Chi-restraints excluded: chain x residue 136 SER Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 195 SER Chi-restraints excluded: chain x residue 225 LEU Chi-restraints excluded: chain x residue 283 CYS Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 347 SER Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain x residue 474 ARG Chi-restraints excluded: chain x residue 477 LYS Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 98 GLU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 10 HIS Chi-restraints excluded: chain z residue 95 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 99 GLN Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 4 residue 170 LEU Chi-restraints excluded: chain 4 residue 255 ASN Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 336 THR Chi-restraints excluded: chain 4 residue 373 LYS Chi-restraints excluded: chain 4 residue 416 LEU Chi-restraints excluded: chain 4 residue 425 GLU Chi-restraints excluded: chain 4 residue 466 LEU Chi-restraints excluded: chain 4 residue 468 LEU Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 531 THR Chi-restraints excluded: chain 4 residue 543 LEU Chi-restraints excluded: chain 4 residue 558 THR Chi-restraints excluded: chain 4 residue 572 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 825 optimal weight: 0.7980 chunk 532 optimal weight: 9.9990 chunk 796 optimal weight: 7.9990 chunk 401 optimal weight: 6.9990 chunk 262 optimal weight: 30.0000 chunk 258 optimal weight: 40.0000 chunk 848 optimal weight: 0.7980 chunk 908 optimal weight: 10.0000 chunk 659 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 1048 optimal weight: 8.9990 overall best weight: 5.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 24 ASN B 198 HIS C 175 HIS F 157 ASN G 192 GLN H 9 GLN H 100 ASN H 102 ASN H 163 GLN K 101 ASN M 11 ASN N 15 GLN N 23 GLN O 122 GLN R 34 GLN S 122 HIS W 205 GLN Y 4 GLN Y 26 GLN b 152 GLN b 429 ASN e 88 HIS ** g 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN k 76 ASN ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN n 144 ASN p 25 GLN w 25 ASN x 12 GLN 4 398 ASN 4 544 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 167341 Z= 0.220 Angle : 0.694 18.005 241944 Z= 0.370 Chirality : 0.040 0.345 29617 Planarity : 0.006 0.135 18328 Dihedral : 22.139 179.931 63297 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.11 % Allowed : 16.04 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % 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: 0.89 (0.08), residues: 10648 helix: 1.79 (0.08), residues: 4178 sheet: 0.04 (0.13), residues: 1581 loop : -0.22 (0.08), residues: 4889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP m 212 HIS 0.007 0.001 HIS O 55 PHE 0.028 0.002 PHE O 48 TYR 0.033 0.002 TYR N 53 ARG 0.011 0.001 ARG b 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1662 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1373 time to evaluate : 8.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8375 (pttm) cc_final: 0.7619 (mttm) REVERT: A 72 ARG cc_start: 0.7886 (mmm160) cc_final: 0.7546 (mmm160) REVERT: A 74 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8212 (mm-30) REVERT: A 191 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8323 (mm) REVERT: 5 84 GLU cc_start: 0.4498 (mm-30) cc_final: 0.4127 (mt-10) REVERT: 5 103 LYS cc_start: 0.2442 (pttm) cc_final: 0.2088 (mttp) REVERT: 5 104 VAL cc_start: 0.4715 (OUTLIER) cc_final: 0.4316 (m) REVERT: 8 146 LYS cc_start: 0.5689 (mmmm) cc_final: 0.5336 (mtmm) REVERT: B 248 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7549 (mtmt) REVERT: C 63 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7145 (pp20) REVERT: C 212 ASP cc_start: 0.7934 (t0) cc_final: 0.7588 (t0) REVERT: D 48 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.6659 (mtpp) REVERT: D 198 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.4980 (t80) REVERT: E 90 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.5923 (ttpt) REVERT: F 46 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7030 (tp30) REVERT: F 64 GLN cc_start: 0.8120 (tp40) cc_final: 0.7758 (tp40) REVERT: F 182 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: F 234 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: G 100 GLU cc_start: 0.6662 (tt0) cc_final: 0.6160 (tt0) REVERT: G 208 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6989 (tp30) REVERT: G 230 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.5929 (mtpm) REVERT: H 1 MET cc_start: 0.5794 (OUTLIER) cc_final: 0.4248 (tpt) REVERT: H 78 MET cc_start: 0.8503 (mtp) cc_final: 0.8048 (mtm) REVERT: H 150 SER cc_start: 0.8244 (t) cc_final: 0.7885 (t) REVERT: I 62 ILE cc_start: 0.7246 (tp) cc_final: 0.6812 (tp) REVERT: J 131 MET cc_start: 0.5403 (mmt) cc_final: 0.4812 (mpp) REVERT: K 153 GLU cc_start: 0.5795 (OUTLIER) cc_final: 0.5336 (tp30) REVERT: K 170 ARG cc_start: 0.7421 (ttp-170) cc_final: 0.6958 (ttp-110) REVERT: K 215 LYS cc_start: 0.5222 (OUTLIER) cc_final: 0.4271 (tptp) REVERT: L 16 LYS cc_start: 0.7862 (mttt) cc_final: 0.7513 (mttt) REVERT: L 104 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6450 (mtt90) REVERT: M 6 ILE cc_start: 0.8124 (tt) cc_final: 0.7741 (tt) REVERT: O 40 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6796 (mt-10) REVERT: O 134 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7941 (mttt) REVERT: P 67 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7679 (mp) REVERT: Q 136 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.7110 (m-40) REVERT: S 13 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6806 (ttm110) REVERT: T 89 LEU cc_start: 0.8038 (mp) cc_final: 0.7836 (mm) REVERT: T 140 ILE cc_start: 0.8240 (mt) cc_final: 0.7927 (mp) REVERT: T 142 SER cc_start: 0.7946 (t) cc_final: 0.7637 (m) REVERT: U 35 LYS cc_start: 0.7831 (tptm) cc_final: 0.7617 (tppt) REVERT: U 91 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: V 70 ARG cc_start: 0.7067 (mtt180) cc_final: 0.6530 (mtm-85) REVERT: W 29 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6475 (mt-10) REVERT: W 179 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6960 (mtpt) REVERT: X 70 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: X 142 ILE cc_start: 0.5377 (OUTLIER) cc_final: 0.4546 (mt) REVERT: a 70 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7449 (ttpp) REVERT: a 120 ASN cc_start: 0.7085 (m-40) cc_final: 0.6872 (t0) REVERT: b 343 ARG cc_start: 0.6780 (mtp180) cc_final: 0.6343 (ttt-90) REVERT: b 613 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7710 (mtp-110) REVERT: b 643 LYS cc_start: 0.6139 (tptm) cc_final: 0.5241 (mtpp) REVERT: c 53 LYS cc_start: 0.8214 (ttpp) cc_final: 0.8000 (ttmt) REVERT: c 55 GLU cc_start: 0.7787 (tt0) cc_final: 0.7326 (tt0) REVERT: e 21 HIS cc_start: 0.9026 (OUTLIER) cc_final: 0.7939 (m-70) REVERT: e 128 LEU cc_start: 0.3830 (OUTLIER) cc_final: 0.3604 (tm) REVERT: f 49 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8503 (mt) REVERT: g 102 LYS cc_start: 0.7265 (mtmt) cc_final: 0.6542 (tttm) REVERT: k 8 ILE cc_start: 0.6826 (mp) cc_final: 0.6591 (mt) REVERT: k 64 LYS cc_start: 0.5954 (mttm) cc_final: 0.5365 (mmtm) REVERT: l 8 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.8178 (ttm-80) REVERT: m 8 LYS cc_start: 0.6749 (mttt) cc_final: 0.6455 (mttm) REVERT: m 162 LYS cc_start: 0.7301 (ptmm) cc_final: 0.6809 (ptmt) REVERT: m 184 MET cc_start: 0.1086 (pmm) cc_final: 0.0811 (pmm) REVERT: m 210 ARG cc_start: 0.7235 (ttp80) cc_final: 0.6851 (tmm160) REVERT: m 246 MET cc_start: 0.8153 (mtp) cc_final: 0.7901 (mtp) REVERT: n 1 MET cc_start: 0.7496 (ttm) cc_final: 0.7034 (ttp) REVERT: n 66 LYS cc_start: 0.7368 (mtmt) cc_final: 0.7148 (mmmt) REVERT: n 107 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5701 (mm-30) REVERT: n 157 ASN cc_start: 0.6902 (m110) cc_final: 0.6659 (m-40) REVERT: n 173 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6364 (mm-30) REVERT: n 381 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6026 (tp) REVERT: n 448 LEU cc_start: 0.6335 (mt) cc_final: 0.5677 (tt) REVERT: o 102 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7537 (t80) REVERT: o 109 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7366 (tmtt) REVERT: o 158 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6362 (mtt) REVERT: o 200 MET cc_start: 0.3369 (OUTLIER) cc_final: 0.2905 (ppp) REVERT: q 242 TYR cc_start: 0.5821 (t80) cc_final: 0.5408 (t80) REVERT: q 244 GLU cc_start: 0.5102 (mt-10) cc_final: 0.4798 (mm-30) REVERT: q 249 GLU cc_start: 0.6051 (mp0) cc_final: 0.5629 (mp0) REVERT: q 257 LYS cc_start: 0.6210 (ttpt) cc_final: 0.6000 (tmmm) REVERT: q 381 HIS cc_start: 0.6871 (m90) cc_final: 0.6656 (m-70) REVERT: q 436 ARG cc_start: 0.6102 (ttt90) cc_final: 0.5499 (mtm180) REVERT: r 141 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7040 (mttt) REVERT: r 250 ASP cc_start: 0.8034 (p0) cc_final: 0.7744 (p0) REVERT: r 252 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8051 (p0) REVERT: s 14 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7789 (ttmm) REVERT: t 129 ILE cc_start: 0.5408 (OUTLIER) cc_final: 0.4938 (mm) REVERT: t 162 ILE cc_start: 0.7823 (mt) cc_final: 0.7422 (mp) REVERT: t 201 LEU cc_start: 0.6206 (tp) cc_final: 0.5878 (tp) REVERT: t 311 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5569 (mp0) REVERT: u 4 TYR cc_start: 0.8502 (m-80) cc_final: 0.8232 (m-80) REVERT: u 25 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.7058 (p0) REVERT: u 84 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6338 (pt0) REVERT: u 93 MET cc_start: 0.8418 (mtp) cc_final: 0.8044 (mtp) REVERT: u 118 LYS cc_start: 0.7681 (mmtp) cc_final: 0.7251 (mtpt) REVERT: v 22 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6174 (mptp) REVERT: v 50 SER cc_start: 0.6602 (p) cc_final: 0.6333 (m) REVERT: v 54 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6711 (ttpp) REVERT: v 63 LYS cc_start: 0.5924 (mmtm) cc_final: 0.5449 (mmtt) REVERT: v 71 ASP cc_start: 0.5209 (t0) cc_final: 0.4852 (m-30) REVERT: v 73 SER cc_start: 0.5207 (OUTLIER) cc_final: 0.4662 (t) REVERT: v 140 MET cc_start: 0.7706 (mtm) cc_final: 0.7325 (mpp) REVERT: v 279 LYS cc_start: 0.6587 (tppt) cc_final: 0.6209 (tptt) REVERT: w 70 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.5861 (mtt) REVERT: x 104 SER cc_start: 0.5916 (m) cc_final: 0.5542 (p) REVERT: x 139 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.7116 (mp) REVERT: x 176 GLN cc_start: 0.6804 (mp10) cc_final: 0.6438 (mt0) REVERT: x 474 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6404 (ttm110) REVERT: x 477 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7767 (ptpt) REVERT: x 500 ARG cc_start: 0.7605 (mtt90) cc_final: 0.7374 (mtt180) REVERT: x 509 MET cc_start: 0.8163 (mmt) cc_final: 0.7921 (mmt) REVERT: y 62 MET cc_start: 0.8125 (mmm) cc_final: 0.7885 (mmm) REVERT: y 98 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5287 (mm-30) REVERT: y 171 GLU cc_start: 0.6580 (mm-30) cc_final: 0.6339 (mt-10) REVERT: z 95 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7230 (ttpt) REVERT: z 98 LYS cc_start: 0.6786 (tptp) cc_final: 0.6314 (tttp) REVERT: 4 29 ARG cc_start: 0.6608 (ttm110) cc_final: 0.6194 (ttp-110) REVERT: 4 72 ILE cc_start: 0.7805 (mt) cc_final: 0.7517 (mt) REVERT: 4 77 GLU cc_start: 0.5971 (tp30) cc_final: 0.5378 (mt-10) REVERT: 4 119 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6878 (pttt) REVERT: 4 170 LEU cc_start: 0.4410 (OUTLIER) cc_final: 0.4107 (mp) REVERT: 4 173 THR cc_start: 0.5673 (p) cc_final: 0.5362 (m) REVERT: 4 205 GLU cc_start: 0.3645 (pm20) cc_final: 0.3357 (mp0) REVERT: 4 425 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: 4 434 GLU cc_start: 0.6275 (mt-10) cc_final: 0.5875 (pt0) REVERT: 4 446 ASP cc_start: 0.6045 (p0) cc_final: 0.5777 (p0) REVERT: 4 468 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5453 (mp) REVERT: 4 496 ILE cc_start: 0.7528 (pt) cc_final: 0.7309 (pt) outliers start: 289 outliers final: 202 residues processed: 1549 average time/residue: 2.2543 time to fit residues: 4953.5409 Evaluate side-chains 1617 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1362 time to evaluate : 8.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain 5 residue 104 VAL Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 8 residue 42 VAL Chi-restraints excluded: chain 8 residue 58 VAL Chi-restraints excluded: chain 8 residue 153 GLU Chi-restraints excluded: chain 9 residue 41 SER Chi-restraints excluded: chain 9 residue 43 VAL Chi-restraints excluded: chain 9 residue 141 THR Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 150 LYS Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 215 LYS Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 104 ARG Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 14 LYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 138 GLN Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain W residue 21 GLU Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 158 ILE Chi-restraints excluded: chain W residue 179 LYS Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 190 THR Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 51 LYS Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 482 GLU Chi-restraints excluded: chain b residue 512 SER Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain b residue 613 ARG Chi-restraints excluded: chain b residue 622 SER Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 44 ILE Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 124 ASP Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 164 THR Chi-restraints excluded: chain m residue 247 LYS Chi-restraints excluded: chain m residue 390 VAL Chi-restraints excluded: chain m residue 393 VAL Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 6 LYS Chi-restraints excluded: chain n residue 107 GLU Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 381 LEU Chi-restraints excluded: chain n residue 408 THR Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 109 LYS Chi-restraints excluded: chain o residue 146 MET Chi-restraints excluded: chain o residue 150 GLU Chi-restraints excluded: chain o residue 158 MET Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain q residue 194 THR Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain r residue 73 VAL Chi-restraints excluded: chain r residue 141 LYS Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 14 LYS Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 50 ILE Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 39 LYS Chi-restraints excluded: chain t residue 40 LYS Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 79 SER Chi-restraints excluded: chain t residue 82 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 153 VAL Chi-restraints excluded: chain t residue 234 ILE Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain t residue 262 SER Chi-restraints excluded: chain t residue 275 ARG Chi-restraints excluded: chain t residue 278 SER Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain t residue 311 GLU Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain v residue 20 GLU Chi-restraints excluded: chain v residue 22 LYS Chi-restraints excluded: chain v residue 39 ASN Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 54 LYS Chi-restraints excluded: chain v residue 57 MET Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 89 LEU Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 129 LYS Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 256 GLU Chi-restraints excluded: chain v residue 259 THR Chi-restraints excluded: chain w residue 70 MET Chi-restraints excluded: chain w residue 75 GLU Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain x residue 18 LEU Chi-restraints excluded: chain x residue 71 SER Chi-restraints excluded: chain x residue 122 THR Chi-restraints excluded: chain x residue 136 SER Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 195 SER Chi-restraints excluded: chain x residue 225 LEU Chi-restraints excluded: chain x residue 283 CYS Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 347 SER Chi-restraints excluded: chain x residue 379 ASP Chi-restraints excluded: chain x residue 395 ILE Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain x residue 474 ARG Chi-restraints excluded: chain x residue 477 LYS Chi-restraints excluded: chain y residue 98 GLU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 10 HIS Chi-restraints excluded: chain z residue 95 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 4 residue 170 LEU Chi-restraints excluded: chain 4 residue 255 ASN Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 336 THR Chi-restraints excluded: chain 4 residue 373 LYS Chi-restraints excluded: chain 4 residue 416 LEU Chi-restraints excluded: chain 4 residue 425 GLU Chi-restraints excluded: chain 4 residue 468 LEU Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 531 THR Chi-restraints excluded: chain 4 residue 543 LEU Chi-restraints excluded: chain 4 residue 558 THR Chi-restraints excluded: chain 4 residue 572 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 1213 optimal weight: 0.0670 chunk 1277 optimal weight: 20.0000 chunk 1165 optimal weight: 9.9990 chunk 1243 optimal weight: 0.9990 chunk 748 optimal weight: 4.9990 chunk 541 optimal weight: 20.0000 chunk 976 optimal weight: 4.9990 chunk 381 optimal weight: 5.9990 chunk 1123 optimal weight: 8.9990 chunk 1175 optimal weight: 20.0000 chunk 1238 optimal weight: 8.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 24 ASN B 198 HIS C 175 HIS F 157 ASN G 192 GLN H 9 GLN H 100 ASN H 102 ASN H 163 GLN K 101 ASN M 11 ASN N 15 GLN N 23 GLN O 122 GLN R 34 GLN S 122 HIS W 205 GLN Y 4 GLN Y 26 GLN b 152 GLN b 429 ASN ** g 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN k 76 ASN ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN n 144 ASN p 25 GLN 4 99 GLN 4 398 ASN 4 544 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 167341 Z= 0.171 Angle : 0.648 17.539 241944 Z= 0.350 Chirality : 0.038 0.356 29617 Planarity : 0.006 0.131 18328 Dihedral : 22.096 179.872 63297 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.84 % Allowed : 16.44 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % 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: 1.02 (0.08), residues: 10648 helix: 1.94 (0.08), residues: 4180 sheet: 0.07 (0.13), residues: 1574 loop : -0.17 (0.09), residues: 4894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP w 114 HIS 0.007 0.001 HIS J 68 PHE 0.028 0.002 PHE D 219 TYR 0.030 0.002 TYR N 53 ARG 0.012 0.000 ARG b 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1652 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1388 time to evaluate : 8.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8367 (pttm) cc_final: 0.7615 (mttm) REVERT: A 72 ARG cc_start: 0.7878 (mmm160) cc_final: 0.7549 (mmm160) REVERT: A 74 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8200 (mm-30) REVERT: A 191 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8303 (mm) REVERT: 5 84 GLU cc_start: 0.4492 (mm-30) cc_final: 0.4064 (mm-30) REVERT: 5 103 LYS cc_start: 0.2457 (OUTLIER) cc_final: 0.2126 (mttp) REVERT: 5 104 VAL cc_start: 0.4747 (OUTLIER) cc_final: 0.4327 (m) REVERT: 8 146 LYS cc_start: 0.5679 (mmmm) cc_final: 0.5323 (mtmm) REVERT: 9 35 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7265 (mp) REVERT: B 248 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7538 (mtmt) REVERT: C 63 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7073 (pp20) REVERT: C 212 ASP cc_start: 0.7895 (t0) cc_final: 0.7542 (t0) REVERT: D 48 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.6681 (mtpp) REVERT: D 198 TYR cc_start: 0.6925 (OUTLIER) cc_final: 0.4957 (t80) REVERT: E 90 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.5909 (ttpt) REVERT: F 46 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7004 (tp30) REVERT: F 64 GLN cc_start: 0.8101 (tp40) cc_final: 0.7414 (tp40) REVERT: F 182 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7379 (m-30) REVERT: F 234 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: G 100 GLU cc_start: 0.6575 (tt0) cc_final: 0.6080 (tt0) REVERT: G 208 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6793 (tp30) REVERT: G 230 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.5945 (mtpm) REVERT: H 1 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.4107 (tpt) REVERT: H 78 MET cc_start: 0.8451 (mtp) cc_final: 0.8003 (ttm) REVERT: H 150 SER cc_start: 0.8259 (t) cc_final: 0.7888 (t) REVERT: I 62 ILE cc_start: 0.7205 (tp) cc_final: 0.6732 (tp) REVERT: J 125 MET cc_start: 0.3518 (pmm) cc_final: 0.2081 (pmm) REVERT: K 106 PHE cc_start: 0.5236 (t80) cc_final: 0.4999 (t80) REVERT: K 153 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.5306 (tp30) REVERT: K 170 ARG cc_start: 0.7433 (ttp-170) cc_final: 0.6974 (ttp-110) REVERT: K 215 LYS cc_start: 0.5217 (OUTLIER) cc_final: 0.4275 (tptp) REVERT: L 104 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.6441 (mtt90) REVERT: M 6 ILE cc_start: 0.8105 (tt) cc_final: 0.7721 (tt) REVERT: N 14 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7346 (tttp) REVERT: O 40 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6817 (mt-10) REVERT: P 67 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7676 (mm) REVERT: P 179 GLN cc_start: 0.7849 (mt0) cc_final: 0.7617 (mt0) REVERT: Q 136 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.7101 (m-40) REVERT: S 13 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6755 (ttm110) REVERT: T 140 ILE cc_start: 0.8229 (mt) cc_final: 0.7924 (mp) REVERT: T 142 SER cc_start: 0.7938 (t) cc_final: 0.7615 (m) REVERT: U 91 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: V 70 ARG cc_start: 0.7052 (mtt180) cc_final: 0.6513 (mtm-85) REVERT: W 29 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6472 (mt-10) REVERT: W 113 LYS cc_start: 0.7336 (mttm) cc_final: 0.7094 (mtpt) REVERT: W 179 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6991 (mtpt) REVERT: X 70 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: X 142 ILE cc_start: 0.5280 (OUTLIER) cc_final: 0.4961 (pt) REVERT: a 70 LYS cc_start: 0.8001 (ttpt) cc_final: 0.7459 (ttpp) REVERT: a 120 ASN cc_start: 0.7025 (m-40) cc_final: 0.6760 (t0) REVERT: b 343 ARG cc_start: 0.6780 (mtp180) cc_final: 0.6420 (ttt-90) REVERT: b 613 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7666 (mtp-110) REVERT: b 643 LYS cc_start: 0.6126 (tptm) cc_final: 0.5238 (mtpp) REVERT: c 53 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7990 (ttmt) REVERT: c 55 GLU cc_start: 0.7758 (tt0) cc_final: 0.7321 (tt0) REVERT: e 21 HIS cc_start: 0.9017 (OUTLIER) cc_final: 0.7925 (m-70) REVERT: f 49 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8511 (mt) REVERT: g 102 LYS cc_start: 0.7181 (mtmt) cc_final: 0.6419 (tttm) REVERT: k 8 ILE cc_start: 0.6729 (mp) cc_final: 0.6482 (mt) REVERT: k 64 LYS cc_start: 0.5958 (mttm) cc_final: 0.5364 (mmtm) REVERT: l 8 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.8141 (ttm-80) REVERT: m 8 LYS cc_start: 0.6715 (mttt) cc_final: 0.6427 (mttm) REVERT: m 162 LYS cc_start: 0.7293 (ptmm) cc_final: 0.6797 (ptmt) REVERT: m 184 MET cc_start: 0.1290 (pmm) cc_final: 0.1049 (pmm) REVERT: m 210 ARG cc_start: 0.7234 (ttp80) cc_final: 0.6854 (tmm160) REVERT: m 246 MET cc_start: 0.8143 (mtp) cc_final: 0.7886 (mtp) REVERT: m 397 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: n 1 MET cc_start: 0.7582 (ttm) cc_final: 0.7138 (ttp) REVERT: n 66 LYS cc_start: 0.7371 (mtmt) cc_final: 0.7144 (mmmt) REVERT: n 107 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5626 (mm-30) REVERT: n 157 ASN cc_start: 0.6869 (m110) cc_final: 0.6648 (m-40) REVERT: n 173 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6408 (mm-30) REVERT: n 381 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5966 (tp) REVERT: n 448 LEU cc_start: 0.6352 (mt) cc_final: 0.5695 (tt) REVERT: o 102 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7525 (t80) REVERT: o 109 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7383 (tmtt) REVERT: o 200 MET cc_start: 0.3358 (OUTLIER) cc_final: 0.2954 (ppp) REVERT: p 61 LYS cc_start: 0.7724 (mmtm) cc_final: 0.7375 (mmtp) REVERT: p 88 GLU cc_start: 0.6397 (mt-10) cc_final: 0.5845 (pt0) REVERT: q 242 TYR cc_start: 0.5824 (t80) cc_final: 0.5396 (t80) REVERT: q 244 GLU cc_start: 0.5088 (mt-10) cc_final: 0.4789 (mm-30) REVERT: q 249 GLU cc_start: 0.6047 (mp0) cc_final: 0.5606 (mp0) REVERT: q 381 HIS cc_start: 0.6860 (m90) cc_final: 0.6654 (m-70) REVERT: q 436 ARG cc_start: 0.6071 (ttt90) cc_final: 0.5480 (mtm180) REVERT: r 250 ASP cc_start: 0.8060 (p0) cc_final: 0.7753 (p0) REVERT: r 252 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7970 (p0) REVERT: s 14 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7760 (ttmm) REVERT: t 129 ILE cc_start: 0.5383 (OUTLIER) cc_final: 0.4914 (mm) REVERT: t 162 ILE cc_start: 0.7847 (mt) cc_final: 0.7453 (mp) REVERT: t 201 LEU cc_start: 0.6198 (tp) cc_final: 0.5869 (tp) REVERT: u 25 ASP cc_start: 0.7121 (p0) cc_final: 0.6887 (p0) REVERT: u 84 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6082 (pt0) REVERT: u 93 MET cc_start: 0.8403 (mtp) cc_final: 0.8072 (mtp) REVERT: u 118 LYS cc_start: 0.7702 (mmtp) cc_final: 0.7266 (mtpt) REVERT: v 22 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6136 (mptp) REVERT: v 50 SER cc_start: 0.6524 (p) cc_final: 0.6292 (m) REVERT: v 54 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6713 (ttpp) REVERT: v 63 LYS cc_start: 0.5900 (mmtm) cc_final: 0.5248 (mmtp) REVERT: v 71 ASP cc_start: 0.5208 (t0) cc_final: 0.4855 (m-30) REVERT: v 73 SER cc_start: 0.5172 (OUTLIER) cc_final: 0.4637 (t) REVERT: v 140 MET cc_start: 0.7710 (mtm) cc_final: 0.7324 (mpp) REVERT: v 279 LYS cc_start: 0.6582 (tppt) cc_final: 0.6204 (tptt) REVERT: w 70 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.5850 (mtt) REVERT: x 104 SER cc_start: 0.5929 (m) cc_final: 0.5551 (p) REVERT: x 139 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.7139 (mp) REVERT: x 176 GLN cc_start: 0.6805 (mp10) cc_final: 0.6464 (mt0) REVERT: x 216 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.5964 (mppt) REVERT: x 459 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8349 (tt) REVERT: x 474 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6247 (ttm170) REVERT: x 477 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7810 (ptpt) REVERT: x 500 ARG cc_start: 0.7589 (mtt90) cc_final: 0.7346 (mtt180) REVERT: x 509 MET cc_start: 0.8159 (mmt) cc_final: 0.7894 (mmt) REVERT: y 62 MET cc_start: 0.8094 (mmm) cc_final: 0.7865 (mmm) REVERT: y 98 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5269 (mm-30) REVERT: y 171 GLU cc_start: 0.6540 (mm-30) cc_final: 0.6306 (mt-10) REVERT: z 95 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7722 (ttpt) REVERT: 4 29 ARG cc_start: 0.6602 (ttm110) cc_final: 0.6202 (ttp-110) REVERT: 4 72 ILE cc_start: 0.7801 (mt) cc_final: 0.7514 (mt) REVERT: 4 77 GLU cc_start: 0.5960 (tp30) cc_final: 0.5366 (mt-10) REVERT: 4 119 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6898 (pttt) REVERT: 4 170 LEU cc_start: 0.4405 (OUTLIER) cc_final: 0.4103 (mp) REVERT: 4 173 THR cc_start: 0.5808 (p) cc_final: 0.5501 (m) REVERT: 4 205 GLU cc_start: 0.3759 (pm20) cc_final: 0.3453 (mp0) REVERT: 4 371 LYS cc_start: 0.6991 (mmtt) cc_final: 0.6530 (mmtt) REVERT: 4 425 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: 4 434 GLU cc_start: 0.6254 (mt-10) cc_final: 0.5852 (pt0) REVERT: 4 446 ASP cc_start: 0.6008 (p0) cc_final: 0.5755 (p0) REVERT: 4 496 ILE cc_start: 0.7519 (pt) cc_final: 0.7314 (pt) REVERT: 4 555 GLN cc_start: 0.5548 (mt0) cc_final: 0.4930 (mm-40) outliers start: 264 outliers final: 176 residues processed: 1548 average time/residue: 2.3060 time to fit residues: 5069.2931 Evaluate side-chains 1591 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1362 time to evaluate : 8.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain 5 residue 103 LYS Chi-restraints excluded: chain 5 residue 104 VAL Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 8 residue 58 VAL Chi-restraints excluded: chain 8 residue 153 GLU Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain 9 residue 43 VAL Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 150 LYS Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 215 LYS Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 104 ARG Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 14 LYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain W residue 21 GLU Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 158 ILE Chi-restraints excluded: chain W residue 179 LYS Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 190 THR Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 51 LYS Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 482 GLU Chi-restraints excluded: chain b residue 512 SER Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain b residue 613 ARG Chi-restraints excluded: chain b residue 622 SER Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 247 LYS Chi-restraints excluded: chain m residue 390 VAL Chi-restraints excluded: chain m residue 393 VAL Chi-restraints excluded: chain m residue 397 GLU Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 107 GLU Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 381 LEU Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 109 LYS Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain q residue 194 THR Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 14 LYS Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 39 LYS Chi-restraints excluded: chain t residue 40 LYS Chi-restraints excluded: chain t residue 79 SER Chi-restraints excluded: chain t residue 82 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 234 ILE Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain t residue 275 ARG Chi-restraints excluded: chain t residue 278 SER Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain u residue 141 ILE Chi-restraints excluded: chain v residue 20 GLU Chi-restraints excluded: chain v residue 22 LYS Chi-restraints excluded: chain v residue 39 ASN Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 54 LYS Chi-restraints excluded: chain v residue 57 MET Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 89 LEU Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 256 GLU Chi-restraints excluded: chain v residue 259 THR Chi-restraints excluded: chain w residue 70 MET Chi-restraints excluded: chain w residue 75 GLU Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain x residue 18 LEU Chi-restraints excluded: chain x residue 71 SER Chi-restraints excluded: chain x residue 122 THR Chi-restraints excluded: chain x residue 136 SER Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 195 SER Chi-restraints excluded: chain x residue 216 LYS Chi-restraints excluded: chain x residue 225 LEU Chi-restraints excluded: chain x residue 283 CYS Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 347 SER Chi-restraints excluded: chain x residue 379 ASP Chi-restraints excluded: chain x residue 395 ILE Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain x residue 459 LEU Chi-restraints excluded: chain x residue 474 ARG Chi-restraints excluded: chain x residue 477 LYS Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 98 GLU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 10 HIS Chi-restraints excluded: chain z residue 95 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 99 GLN Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 4 residue 170 LEU Chi-restraints excluded: chain 4 residue 255 ASN Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 336 THR Chi-restraints excluded: chain 4 residue 373 LYS Chi-restraints excluded: chain 4 residue 416 LEU Chi-restraints excluded: chain 4 residue 425 GLU Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 526 THR Chi-restraints excluded: chain 4 residue 531 THR Chi-restraints excluded: chain 4 residue 543 LEU Chi-restraints excluded: chain 4 residue 558 THR Chi-restraints excluded: chain 4 residue 572 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 816 optimal weight: 30.0000 chunk 1314 optimal weight: 8.9990 chunk 802 optimal weight: 6.9990 chunk 623 optimal weight: 6.9990 chunk 913 optimal weight: 10.0000 chunk 1378 optimal weight: 0.9980 chunk 1269 optimal weight: 10.0000 chunk 1097 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 848 optimal weight: 5.9990 chunk 673 optimal weight: 10.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 24 ASN B 198 HIS C 175 HIS F 157 ASN G 192 GLN H 9 GLN H 100 ASN H 102 ASN H 163 GLN J 90 GLN K 101 ASN M 11 ASN N 15 GLN N 23 GLN O 122 GLN R 34 GLN W 205 GLN Y 4 GLN Y 26 GLN b 152 GLN ** g 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN k 76 ASN ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN n 144 ASN p 25 GLN t 209 GLN ** v 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 25 ASN 4 398 ASN 4 533 GLN 4 544 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 167341 Z= 0.248 Angle : 0.719 18.485 241944 Z= 0.381 Chirality : 0.041 0.363 29617 Planarity : 0.006 0.137 18328 Dihedral : 22.132 179.755 63297 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.73 % Allowed : 16.68 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % 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: 0.88 (0.08), residues: 10648 helix: 1.78 (0.08), residues: 4176 sheet: 0.03 (0.13), residues: 1573 loop : -0.22 (0.08), residues: 4899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP m 212 HIS 0.008 0.001 HIS O 55 PHE 0.029 0.002 PHE F 229 TYR 0.032 0.002 TYR N 53 ARG 0.011 0.001 ARG b 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1377 time to evaluate : 8.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8373 (pttm) cc_final: 0.7626 (mttm) REVERT: A 72 ARG cc_start: 0.7890 (mmm160) cc_final: 0.7553 (mmm160) REVERT: A 74 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8159 (mm-30) REVERT: A 191 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8331 (mm) REVERT: 5 84 GLU cc_start: 0.4501 (mm-30) cc_final: 0.4136 (mt-10) REVERT: 5 104 VAL cc_start: 0.4733 (OUTLIER) cc_final: 0.4336 (m) REVERT: 8 146 LYS cc_start: 0.5705 (mmmm) cc_final: 0.5352 (mtmm) REVERT: B 21 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8105 (mtm-85) REVERT: B 248 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7548 (mtmt) REVERT: C 63 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7140 (pp20) REVERT: C 212 ASP cc_start: 0.7929 (t0) cc_final: 0.7586 (t0) REVERT: D 48 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.6660 (mtpp) REVERT: D 198 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.4991 (t80) REVERT: E 90 LYS cc_start: 0.6603 (OUTLIER) cc_final: 0.5926 (ttpt) REVERT: F 46 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: F 64 GLN cc_start: 0.7985 (tp40) cc_final: 0.7581 (tp40) REVERT: F 182 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: G 92 LYS cc_start: 0.8160 (ttmp) cc_final: 0.7850 (mtmt) REVERT: G 100 GLU cc_start: 0.6668 (tt0) cc_final: 0.6167 (tt0) REVERT: G 208 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6998 (tp30) REVERT: G 230 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6138 (mtpm) REVERT: H 1 MET cc_start: 0.5801 (OUTLIER) cc_final: 0.4340 (tpt) REVERT: H 78 MET cc_start: 0.8487 (mtp) cc_final: 0.8055 (mtm) REVERT: H 150 SER cc_start: 0.8249 (t) cc_final: 0.7893 (t) REVERT: I 62 ILE cc_start: 0.7208 (tp) cc_final: 0.6746 (tp) REVERT: J 32 ARG cc_start: 0.3010 (mtt90) cc_final: 0.2721 (mtt-85) REVERT: J 125 MET cc_start: 0.3505 (pmm) cc_final: 0.2279 (pmm) REVERT: K 153 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.5343 (tp30) REVERT: K 170 ARG cc_start: 0.7418 (ttp-170) cc_final: 0.6918 (ttp-110) REVERT: K 215 LYS cc_start: 0.5230 (OUTLIER) cc_final: 0.4277 (tptp) REVERT: L 104 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6554 (mtt90) REVERT: M 6 ILE cc_start: 0.8121 (tt) cc_final: 0.7733 (tt) REVERT: O 40 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: P 67 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7724 (mp) REVERT: Q 136 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.7116 (m-40) REVERT: S 13 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6806 (ttm110) REVERT: S 130 GLU cc_start: 0.6353 (mm-30) cc_final: 0.6007 (mm-30) REVERT: T 140 ILE cc_start: 0.8243 (mt) cc_final: 0.7927 (mp) REVERT: T 142 SER cc_start: 0.7958 (t) cc_final: 0.7645 (m) REVERT: U 91 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7714 (m-30) REVERT: V 70 ARG cc_start: 0.7046 (mtt180) cc_final: 0.6511 (mtm-85) REVERT: W 29 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6439 (mt-10) REVERT: W 113 LYS cc_start: 0.7342 (mttm) cc_final: 0.7109 (mtpt) REVERT: W 179 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6929 (mtpt) REVERT: X 70 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: X 142 ILE cc_start: 0.5357 (OUTLIER) cc_final: 0.4544 (mt) REVERT: a 70 LYS cc_start: 0.7998 (ttpt) cc_final: 0.7446 (ttpp) REVERT: a 92 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6357 (tmmm) REVERT: a 120 ASN cc_start: 0.7094 (m-40) cc_final: 0.6846 (t0) REVERT: b 168 ARG cc_start: 0.7757 (mtt90) cc_final: 0.7341 (mtt180) REVERT: b 343 ARG cc_start: 0.6770 (mtp180) cc_final: 0.6340 (ttt-90) REVERT: b 613 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7776 (mtp-110) REVERT: b 643 LYS cc_start: 0.6134 (tptm) cc_final: 0.5243 (mtpp) REVERT: c 53 LYS cc_start: 0.8218 (ttpp) cc_final: 0.8003 (ttmt) REVERT: c 55 GLU cc_start: 0.7798 (tt0) cc_final: 0.7330 (tt0) REVERT: e 21 HIS cc_start: 0.9027 (OUTLIER) cc_final: 0.8037 (m-70) REVERT: f 49 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8505 (mt) REVERT: g 102 LYS cc_start: 0.7174 (mtmt) cc_final: 0.6409 (tttm) REVERT: k 8 ILE cc_start: 0.6806 (mp) cc_final: 0.6559 (mt) REVERT: k 64 LYS cc_start: 0.5968 (mttm) cc_final: 0.5371 (mmtm) REVERT: m 8 LYS cc_start: 0.6629 (mttt) cc_final: 0.6345 (mttm) REVERT: m 162 LYS cc_start: 0.7336 (ptmm) cc_final: 0.6842 (ptmt) REVERT: m 184 MET cc_start: 0.1315 (pmm) cc_final: 0.1073 (pmm) REVERT: m 210 ARG cc_start: 0.7231 (ttp80) cc_final: 0.6838 (tmm160) REVERT: m 246 MET cc_start: 0.8173 (mtp) cc_final: 0.7911 (mtp) REVERT: m 397 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: n 1 MET cc_start: 0.7481 (ttm) cc_final: 0.7017 (ttp) REVERT: n 66 LYS cc_start: 0.7428 (mtmt) cc_final: 0.7194 (mmmt) REVERT: n 107 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5690 (mm-30) REVERT: n 157 ASN cc_start: 0.6899 (m110) cc_final: 0.6660 (m-40) REVERT: n 173 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6366 (mm-30) REVERT: n 381 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.6036 (tp) REVERT: n 448 LEU cc_start: 0.6339 (mt) cc_final: 0.5665 (tt) REVERT: o 102 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7409 (t80) REVERT: o 109 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7365 (tmtt) REVERT: o 158 MET cc_start: 0.6920 (mtt) cc_final: 0.6132 (mmm) REVERT: o 200 MET cc_start: 0.3374 (OUTLIER) cc_final: 0.2915 (ppp) REVERT: p 88 GLU cc_start: 0.6436 (mt-10) cc_final: 0.5827 (pt0) REVERT: q 242 TYR cc_start: 0.5881 (t80) cc_final: 0.5475 (t80) REVERT: q 244 GLU cc_start: 0.5105 (mt-10) cc_final: 0.4792 (mm-30) REVERT: q 249 GLU cc_start: 0.6051 (mp0) cc_final: 0.5619 (mp0) REVERT: q 266 MET cc_start: 0.5601 (ttm) cc_final: 0.5318 (mmm) REVERT: q 436 ARG cc_start: 0.6147 (ttt90) cc_final: 0.5533 (mtm180) REVERT: r 141 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6990 (mttt) REVERT: r 250 ASP cc_start: 0.8039 (p0) cc_final: 0.7754 (p0) REVERT: r 252 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8068 (p0) REVERT: s 14 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7792 (ttmm) REVERT: t 101 LEU cc_start: 0.6557 (tp) cc_final: 0.6355 (tm) REVERT: t 129 ILE cc_start: 0.5393 (OUTLIER) cc_final: 0.4918 (mm) REVERT: t 162 ILE cc_start: 0.7859 (mt) cc_final: 0.7461 (mp) REVERT: t 201 LEU cc_start: 0.6226 (tp) cc_final: 0.5885 (tp) REVERT: t 311 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5570 (mp0) REVERT: u 84 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6362 (pt0) REVERT: u 93 MET cc_start: 0.8421 (mtp) cc_final: 0.8136 (mtp) REVERT: u 118 LYS cc_start: 0.7679 (mmtp) cc_final: 0.7248 (mtpt) REVERT: v 22 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6059 (ptpt) REVERT: v 50 SER cc_start: 0.6623 (p) cc_final: 0.6337 (m) REVERT: v 54 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6720 (ttpp) REVERT: v 63 LYS cc_start: 0.5811 (mmtm) cc_final: 0.5301 (mmtp) REVERT: v 65 ASP cc_start: 0.5360 (p0) cc_final: 0.5140 (m-30) REVERT: v 71 ASP cc_start: 0.5139 (t0) cc_final: 0.4804 (m-30) REVERT: v 73 SER cc_start: 0.4980 (OUTLIER) cc_final: 0.4627 (t) REVERT: v 140 MET cc_start: 0.7699 (mtm) cc_final: 0.7319 (mpp) REVERT: v 279 LYS cc_start: 0.6679 (tppt) cc_final: 0.6236 (tptt) REVERT: w 70 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.5859 (mtt) REVERT: w 193 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6866 (tttt) REVERT: x 104 SER cc_start: 0.5854 (m) cc_final: 0.5477 (p) REVERT: x 139 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.7101 (mp) REVERT: x 176 GLN cc_start: 0.6804 (mp10) cc_final: 0.6464 (mt0) REVERT: x 216 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.5975 (mppt) REVERT: x 459 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8360 (tt) REVERT: x 474 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6406 (ttm110) REVERT: x 477 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7759 (ptpt) REVERT: x 500 ARG cc_start: 0.7606 (mtt90) cc_final: 0.7367 (mtt180) REVERT: x 509 MET cc_start: 0.8186 (mmt) cc_final: 0.7959 (mmt) REVERT: y 62 MET cc_start: 0.8139 (mmm) cc_final: 0.7899 (mmm) REVERT: y 98 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5291 (mm-30) REVERT: y 171 GLU cc_start: 0.6579 (mm-30) cc_final: 0.6339 (mt-10) REVERT: z 95 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7817 (ttpt) REVERT: z 98 LYS cc_start: 0.6779 (tptp) cc_final: 0.6313 (tttp) REVERT: 4 29 ARG cc_start: 0.6612 (ttm110) cc_final: 0.6195 (ttp-110) REVERT: 4 72 ILE cc_start: 0.7811 (mt) cc_final: 0.7509 (mt) REVERT: 4 77 GLU cc_start: 0.5964 (tp30) cc_final: 0.5373 (mt-10) REVERT: 4 119 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6902 (pttt) REVERT: 4 170 LEU cc_start: 0.4412 (OUTLIER) cc_final: 0.4110 (mp) REVERT: 4 173 THR cc_start: 0.5702 (p) cc_final: 0.5390 (m) REVERT: 4 205 GLU cc_start: 0.3621 (pm20) cc_final: 0.3061 (mp0) REVERT: 4 425 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: 4 434 GLU cc_start: 0.6265 (mt-10) cc_final: 0.5866 (pt0) REVERT: 4 446 ASP cc_start: 0.6023 (p0) cc_final: 0.5755 (p0) REVERT: 4 468 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5449 (mp) REVERT: 4 496 ILE cc_start: 0.7537 (pt) cc_final: 0.7319 (pt) REVERT: 4 555 GLN cc_start: 0.5488 (mt0) cc_final: 0.4911 (mm-40) outliers start: 254 outliers final: 185 residues processed: 1532 average time/residue: 2.2292 time to fit residues: 4833.9709 Evaluate side-chains 1599 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1359 time to evaluate : 8.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain 5 residue 103 LYS Chi-restraints excluded: chain 5 residue 104 VAL Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 8 residue 58 VAL Chi-restraints excluded: chain 8 residue 153 GLU Chi-restraints excluded: chain 9 residue 43 VAL Chi-restraints excluded: chain 9 residue 141 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 150 LYS Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 215 LYS Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 104 ARG Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 14 LYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 40 GLU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 136 ASN Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain W residue 21 GLU Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 158 ILE Chi-restraints excluded: chain W residue 179 LYS Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 190 THR Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain a residue 92 LYS Chi-restraints excluded: chain b residue 51 LYS Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 482 GLU Chi-restraints excluded: chain b residue 512 SER Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain b residue 613 ARG Chi-restraints excluded: chain b residue 622 SER Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 107 VAL Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 28 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 124 ASP Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 247 LYS Chi-restraints excluded: chain m residue 390 VAL Chi-restraints excluded: chain m residue 393 VAL Chi-restraints excluded: chain m residue 397 GLU Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 107 GLU Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 381 LEU Chi-restraints excluded: chain n residue 408 THR Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 109 LYS Chi-restraints excluded: chain o residue 150 GLU Chi-restraints excluded: chain o residue 167 LEU Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain q residue 194 THR Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain r residue 141 LYS Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 14 LYS Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 39 LYS Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain t residue 79 SER Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 234 ILE Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain t residue 262 SER Chi-restraints excluded: chain t residue 275 ARG Chi-restraints excluded: chain t residue 278 SER Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 288 LYS Chi-restraints excluded: chain t residue 311 GLU Chi-restraints excluded: chain u residue 84 GLU Chi-restraints excluded: chain u residue 141 ILE Chi-restraints excluded: chain v residue 20 GLU Chi-restraints excluded: chain v residue 22 LYS Chi-restraints excluded: chain v residue 39 ASN Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 54 LYS Chi-restraints excluded: chain v residue 57 MET Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 89 LEU Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 181 VAL Chi-restraints excluded: chain v residue 256 GLU Chi-restraints excluded: chain v residue 259 THR Chi-restraints excluded: chain w residue 70 MET Chi-restraints excluded: chain w residue 75 GLU Chi-restraints excluded: chain w residue 80 THR Chi-restraints excluded: chain w residue 84 SER Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 187 LEU Chi-restraints excluded: chain w residue 193 LYS Chi-restraints excluded: chain x residue 18 LEU Chi-restraints excluded: chain x residue 71 SER Chi-restraints excluded: chain x residue 122 THR Chi-restraints excluded: chain x residue 136 SER Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 195 SER Chi-restraints excluded: chain x residue 216 LYS Chi-restraints excluded: chain x residue 225 LEU Chi-restraints excluded: chain x residue 283 CYS Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 347 SER Chi-restraints excluded: chain x residue 379 ASP Chi-restraints excluded: chain x residue 395 ILE Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain x residue 459 LEU Chi-restraints excluded: chain x residue 474 ARG Chi-restraints excluded: chain x residue 477 LYS Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 98 GLU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain z residue 10 HIS Chi-restraints excluded: chain z residue 95 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 4 residue 170 LEU Chi-restraints excluded: chain 4 residue 255 ASN Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 336 THR Chi-restraints excluded: chain 4 residue 373 LYS Chi-restraints excluded: chain 4 residue 416 LEU Chi-restraints excluded: chain 4 residue 425 GLU Chi-restraints excluded: chain 4 residue 468 LEU Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 526 THR Chi-restraints excluded: chain 4 residue 531 THR Chi-restraints excluded: chain 4 residue 543 LEU Chi-restraints excluded: chain 4 residue 558 THR Chi-restraints excluded: chain 4 residue 572 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 872 optimal weight: 8.9990 chunk 1169 optimal weight: 30.0000 chunk 336 optimal weight: 50.0000 chunk 1012 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 305 optimal weight: 20.0000 chunk 1099 optimal weight: 8.9990 chunk 460 optimal weight: 30.0000 chunk 1129 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS C 175 HIS F 157 ASN G 192 GLN H 9 GLN H 100 ASN H 102 ASN H 163 GLN K 101 ASN M 11 ASN N 15 GLN N 23 GLN O 122 GLN ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 205 GLN Y 4 GLN Y 26 GLN b 152 GLN ** g 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN k 76 ASN ** l 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN n 144 ASN n 165 GLN p 25 GLN q 424 GLN ** v 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 25 ASN 4 533 GLN 4 544 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.182530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.148321 restraints weight = 131607.362| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.17 r_work: 0.3276 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 167341 Z= 0.322 Angle : 0.811 19.466 241944 Z= 0.422 Chirality : 0.044 0.317 29617 Planarity : 0.007 0.143 18328 Dihedral : 22.247 179.869 63297 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.88 % Allowed : 16.65 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.61 (0.08), residues: 10648 helix: 1.49 (0.08), residues: 4173 sheet: -0.05 (0.12), residues: 1579 loop : -0.32 (0.08), residues: 4896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP m 212 HIS 0.009 0.002 HIS C 175 PHE 0.037 0.003 PHE i 80 TYR 0.036 0.003 TYR N 53 ARG 0.011 0.001 ARG b 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 69757.63 seconds wall clock time: 1202 minutes 36.91 seconds (72156.91 seconds total)