Starting phenix.real_space_refine on Sun Mar 3 16:03:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqz_26703/03_2024/7uqz_26703_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqz_26703/03_2024/7uqz_26703.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqz_26703/03_2024/7uqz_26703_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqz_26703/03_2024/7uqz_26703_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqz_26703/03_2024/7uqz_26703_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqz_26703/03_2024/7uqz_26703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqz_26703/03_2024/7uqz_26703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqz_26703/03_2024/7uqz_26703_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqz_26703/03_2024/7uqz_26703_updated.pdb" } resolution = 2.44 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s 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: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 134 Unusual residues: {' MG': 77, 'B3P': 3} Classifications: {'undetermined': 80} Link IDs: {None: 79} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "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: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 330 Classifications: {'water': 330} Link IDs: {None: 329} 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} 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 51 192.041 151.060 145.851 1.00 30.56 S ATOM 90229 SG CYS I 54 190.588 147.699 144.546 1.00 31.96 S ATOM A0HLV SG CYS g 44 145.801 125.272 208.725 1.00 4.74 S ATOM A0HMD SG CYS g 47 148.072 127.883 207.360 1.00 6.84 S ATOM A0HTF SG CYS g 81 149.268 125.614 210.280 1.00 4.81 S ATOM A0HTY SG CYS g 84 146.873 128.300 210.964 1.00 5.89 S ATOM A0JGQ SG CYS j 19 110.389 105.613 167.075 1.00 14.46 S ATOM A0JHF SG CYS j 22 109.080 104.843 163.495 1.00 14.48 S ATOM A0JK7 SG CYS j 34 109.798 108.424 164.685 1.00 14.46 S ATOM A0JKP SG CYS j 37 106.909 106.541 166.183 1.00 14.46 S ATOM A0QZW SG CYS p 39 149.136 145.058 206.165 1.00 11.58 S ATOM A0R0J SG CYS p 42 152.388 143.641 207.172 1.00 13.17 S ATOM A0R3K SG CYS p 57 150.989 143.016 203.735 1.00 11.87 S ATOM A0R42 SG CYS p 60 149.384 141.269 206.933 1.00 16.71 S ATOM A0W0K SG CYS u 6 193.115 136.080 120.565 1.00 5.65 S ATOM A0W1B SG CYS u 9 194.267 132.443 120.955 1.00 6.73 S ATOM A0W6G SG CYS u 32 191.675 133.254 118.375 1.00 6.40 S ATOM A0W7C SG CYS u 36 190.954 133.347 122.190 1.00 6.63 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: 60.04, per 1000 atoms: 0.38 Number of scatterers: 157839 At special positions: 0 Unit cell: (237.6, 278.64, 300.24, 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: 55.83 Conformation dependent library (CDL) restraints added in 12.6 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 84 " pdb="ZN ZN g 601 " - pdb=" SG CYS g 47 " pdb="ZN ZN g 601 " - pdb=" SG CYS g 44 " pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " 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 9 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 36 " 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: 383 helices and 105 sheets defined 45.3% alpha, 14.7% beta 1021 base pairs and 1619 stacking pairs defined. Time for finding SS restraints: 90.97 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 4.519A pdb=" N GLY A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 4.571A 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: 3.971A 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: 3.939A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.641A pdb=" N MET A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.093A 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 'A' and resid 173 through 178 removed outlier: 3.577A pdb=" N LYS A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain '5' and resid 42 through 99 removed outlier: 3.591A pdb=" N LYS 5 98 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) Processing helix chain '5' and resid 100 through 114 removed outlier: 3.745A pdb=" N ARG 5 113 " --> pdb=" O ARG 5 109 " (cutoff:3.500A) removed outlier: 4.474A 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: 3.632A pdb=" N LYS 8 86 " --> pdb=" O ILE 8 82 " (cutoff:3.500A) Processing helix chain '8' and resid 105 through 117 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: 4.826A 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: 4.352A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.890A pdb=" N ALA B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 removed outlier: 6.100A pdb=" N ARG B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 4.196A 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: 3.843A 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: 3.997A pdb=" N LEU B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 5.728A 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: 4.257A pdb=" N SER C 27 " --> pdb=" O PRO C 23 " (cutoff:3.500A) removed outlier: 3.739A 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: 3.732A pdb=" N ASN C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.885A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 5.583A 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 154 through 159 removed outlier: 4.278A pdb=" N SER C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 159' Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 185 removed outlier: 4.172A pdb=" N LYS C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 4.192A pdb=" N ARG C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.198A 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: 4.719A 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: 4.389A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.166A 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 320 through 328 Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.343A 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: 3.565A pdb=" N GLY D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.662A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.381A 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: 4.033A pdb=" N ALA D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 4.021A 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: 4.874A 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 234 through 251 removed outlier: 4.764A pdb=" N ASP D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Proline residue: D 251 - end of helix Processing helix chain 'D' and resid 261 through 274 removed outlier: 3.851A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 5.194A 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: 3.862A pdb=" N VAL E 84 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.985A 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: 6.439A pdb=" N VAL E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 5.160A 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: 3.735A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 4.080A 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: 4.097A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 191 removed outlier: 4.250A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 removed outlier: 5.080A pdb=" N TRP F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 244 removed outlier: 4.559A 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: 4.983A pdb=" N PHE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TYR G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 98 removed outlier: 3.938A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.906A pdb=" N LYS G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 4.049A 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 165 through 174 Processing helix chain 'G' and resid 182 through 191 Processing helix chain 'G' and resid 204 through 222 removed outlier: 4.941A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 232 removed outlier: 4.270A pdb=" N LYS G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N HIS G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) 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: 4.142A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 4.855A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 10 Processing helix chain 'I' and resid 17 through 27 removed outlier: 4.084A pdb=" N THR I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.883A pdb=" N GLN I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 71 removed outlier: 3.801A pdb=" N GLY I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LYS I 71 " --> pdb=" O HIS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 82 removed outlier: 3.634A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY I 82 " --> pdb=" O LYS I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 95 removed outlier: 4.080A pdb=" N SER I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 131 removed outlier: 3.725A pdb=" N VAL I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.786A 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 108 through 113 removed outlier: 4.477A pdb=" N LEU J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY J 113 " --> pdb=" O HIS J 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 108 through 113' Processing helix chain 'J' and resid 136 through 141 removed outlier: 4.332A 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: 3.545A pdb=" N ASN J 95 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE J 96 " --> pdb=" O ASP J 93 " (cutoff:3.500A) removed outlier: 5.132A 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 'K' and resid 33 through 50 removed outlier: 4.045A pdb=" N SER K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS K 50 " --> pdb=" O LYS K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 74 removed outlier: 4.544A pdb=" N GLU K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 118 Proline residue: K 109 - end of helix removed outlier: 4.069A pdb=" N ALA K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N THR K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ALA K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL K 118 " --> pdb=" O SER K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 136 removed outlier: 4.689A pdb=" N LYS K 133 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LYS K 134 " --> pdb=" O SER K 130 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL K 135 " --> pdb=" O ASP K 131 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N SER K 136 " --> pdb=" O ILE K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 144 removed outlier: 3.594A 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 177 removed outlier: 3.892A pdb=" N GLN K 176 " --> pdb=" O ALA K 172 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 194 removed outlier: 4.741A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER K 189 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 3.807A 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: 4.419A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN K 200 " --> pdb=" O GLY K 196 " (cutoff:3.500A) removed outlier: 4.573A 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: 3.689A pdb=" N LEU K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) removed outlier: 5.007A 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: 3.794A pdb=" N LYS K 272 " --> pdb=" O GLU K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 302 removed outlier: 4.016A pdb=" N ASP K 299 " --> pdb=" O GLN K 295 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU K 300 " --> pdb=" O ASP K 296 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU K 301 " --> pdb=" O VAL K 297 " (cutoff:3.500A) removed outlier: 4.876A 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 338 removed outlier: 5.003A pdb=" N ASN K 338 " --> pdb=" O MET K 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.160A pdb=" N ARG L 21 " --> pdb=" O HIS L 17 " (cutoff:3.500A) removed outlier: 3.904A 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: 5.169A pdb=" N GLY L 181 " --> pdb=" O LYS L 177 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE L 182 " --> pdb=" O LYS L 178 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG L 183 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU L 194 " --> pdb=" O LYS L 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 64 removed outlier: 4.031A pdb=" N VAL M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 5.193A 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: 3.613A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 5.562A 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: 3.816A pdb=" N LYS M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 14 removed outlier: 4.823A pdb=" N TYR N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 4.778A 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: 4.723A pdb=" N CYS N 152 " --> pdb=" O TYR N 148 " (cutoff:3.500A) removed outlier: 4.215A 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: 3.766A 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: 5.330A pdb=" N ALA O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 3.852A 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: 3.590A 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: 3.704A pdb=" N ARG O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 116 removed outlier: 7.901A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.545A 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 187 removed outlier: 4.296A pdb=" N ALA O 185 " --> pdb=" O ALA O 181 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA O 186 " --> pdb=" O ASN O 182 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLU O 187 " --> pdb=" O ALA O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 198 Processing helix chain 'P' and resid 10 through 15 removed outlier: 4.488A pdb=" N SER P 14 " --> pdb=" O ASN P 10 " (cutoff:3.500A) removed outlier: 5.314A 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: 4.827A pdb=" N LYS P 74 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 4.839A 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: 4.436A 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: 3.755A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.971A 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: 4.009A 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 18 through 23 removed outlier: 3.970A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TRP R 23 " --> pdb=" O LYS R 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 18 through 23' Processing helix chain 'R' and resid 28 through 36 removed outlier: 3.720A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 5.332A 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: 5.595A 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: 6.578A 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 113 Processing helix chain 'S' and resid 117 through 122 removed outlier: 5.248A pdb=" N HIS S 122 " --> pdb=" O PHE S 118 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 145 removed outlier: 4.999A pdb=" N PHE S 143 " --> pdb=" O TYR S 139 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU S 144 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR S 145 " --> pdb=" O LYS S 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 97 removed outlier: 4.072A pdb=" N ILE T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.498A 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: 3.781A 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: 4.974A 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: 4.072A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 61 removed outlier: 3.745A 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: 4.935A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 3.887A 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: 5.088A pdb=" N VAL W 155 " --> pdb=" O ALA W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 167 removed outlier: 4.280A 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: 4.647A pdb=" N GLU X 64 " --> pdb=" O TYR X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 79 removed outlier: 3.794A pdb=" N LYS X 75 " --> pdb=" O THR X 71 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 4.069A 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: 3.640A 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: 3.762A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 4.362A 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: 3.737A pdb=" N LEU Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.027A 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: 3.891A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.564A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 5.202A 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: 3.654A pdb=" N VAL Z 96 " --> pdb=" O PHE Z 92 " (cutoff:3.500A) removed outlier: 5.372A 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: 3.906A pdb=" N GLU Z 102 " --> pdb=" O THR Z 98 " (cutoff:3.500A) removed outlier: 3.665A 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: 4.378A 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: 4.282A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 94 removed outlier: 3.644A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.082A 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: 4.221A pdb=" N PHE b 118 " --> pdb=" O ARG b 114 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY b 119 " --> pdb=" O LEU b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 144 removed outlier: 3.893A pdb=" N LEU b 143 " --> pdb=" O ILE b 139 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG b 144 " --> pdb=" O VAL b 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 161 removed outlier: 4.061A pdb=" N ARG b 159 " --> pdb=" O GLN b 155 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU b 160 " --> pdb=" O HIS b 156 " (cutoff:3.500A) Proline residue: b 161 - end of helix Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.859A 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: 4.989A pdb=" N ALA b 279 " --> pdb=" O LYS b 275 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 312 removed outlier: 3.963A pdb=" N VAL b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 351 removed outlier: 3.593A pdb=" N LYS b 349 " --> pdb=" O GLU b 345 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLN b 351 " --> pdb=" O LYS b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 352 through 362 removed outlier: 5.370A pdb=" N ASN b 356 " --> pdb=" O SER b 352 " (cutoff:3.500A) removed outlier: 4.850A 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: 5.088A pdb=" N LYS b 419 " --> pdb=" O ASN b 415 " (cutoff:3.500A) removed outlier: 4.952A 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 440 through 445 removed outlier: 3.844A 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: 4.962A 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: 4.481A 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: 3.964A pdb=" N ARG b 611 " --> pdb=" O LYS b 607 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLU b 612 " --> pdb=" O MET b 608 " (cutoff:3.500A) removed outlier: 5.086A 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 'b' and resid 424 through 429 removed outlier: 3.575A pdb=" N LYS b 428 " --> pdb=" O ASP b 425 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN b 429 " --> pdb=" O GLU b 426 " (cutoff:3.500A) 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: 3.922A pdb=" N ARG d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 45 removed outlier: 5.270A 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: 5.117A 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: 3.680A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU e 85 " --> pdb=" O ASP e 81 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR e 86 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N MET e 87 " --> pdb=" O GLU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.663A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 45 removed outlier: 4.271A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU f 45 " --> pdb=" O ALA f 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 66 removed outlier: 3.573A pdb=" N TYR g 62 " --> pdb=" O ARG g 58 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA g 63 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL g 65 " --> pdb=" O GLN g 61 " (cutoff:3.500A) removed outlier: 5.848A 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: 3.921A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS h 12 " --> pdb=" O GLU h 8 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N SER h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 38 removed outlier: 3.787A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 41 through 71 removed outlier: 4.764A pdb=" N LYS h 45 " --> pdb=" O LEU h 41 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 82 removed outlier: 5.403A 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: 4.264A pdb=" N LYS i 29 " --> pdb=" O LYS i 25 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS i 30 " --> pdb=" O ILE i 26 " (cutoff:3.500A) removed outlier: 5.786A 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: 3.672A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS j 10 " --> pdb=" O PRO j 6 " (cutoff:3.500A) removed outlier: 4.533A 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: 5.415A pdb=" N HIS j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 4.854A 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: 5.417A pdb=" N ARG l 21 " --> pdb=" O LYS l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.250A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 3.882A 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 6 through 14 Processing helix chain 'm' and resid 32 through 44 removed outlier: 4.289A pdb=" N TYR m 42 " --> pdb=" O PHE m 38 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR m 43 " --> pdb=" O LEU m 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 74 through 80 removed outlier: 4.689A pdb=" N PHE m 78 " --> pdb=" O ASP m 74 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY m 79 " --> pdb=" O ARG m 75 " (cutoff:3.500A) removed outlier: 5.886A 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: 4.990A pdb=" N GLY m 97 " --> pdb=" O ARG m 93 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU m 98 " --> pdb=" O SER m 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR m 99 " --> pdb=" O ALA m 95 " (cutoff:3.500A) Processing helix chain 'm' and resid 114 through 119 Processing helix chain 'm' and resid 130 through 135 removed outlier: 4.588A 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: 4.135A pdb=" N LEU m 181 " --> pdb=" O LEU m 177 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU m 183 " --> pdb=" O ALA m 179 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N MET m 184 " --> pdb=" O THR m 180 " (cutoff:3.500A) Processing helix chain 'm' and resid 186 through 193 removed outlier: 3.968A pdb=" N LYS m 190 " --> pdb=" O ASN m 186 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU m 191 " --> pdb=" O GLN m 187 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN m 192 " --> pdb=" O GLU m 188 " (cutoff:3.500A) Processing helix chain 'm' and resid 200 through 205 removed outlier: 4.393A pdb=" N SER m 204 " --> pdb=" O GLU m 200 " (cutoff:3.500A) removed outlier: 3.968A 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: 4.320A 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: 3.720A pdb=" N LYS m 279 " --> pdb=" O LYS m 275 " (cutoff:3.500A) removed outlier: 4.366A 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: 3.959A pdb=" N GLY m 386 " --> pdb=" O ILE m 382 " (cutoff:3.500A) Processing helix chain 'm' and resid 395 through 407 removed outlier: 4.300A 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: 4.182A pdb=" N HIS n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) removed outlier: 4.413A 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: 3.997A 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: 4.858A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA n 135 " --> pdb=" O ASP n 131 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN n 144 " --> pdb=" O PHE n 140 " (cutoff:3.500A) removed outlier: 3.773A 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: 6.637A 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: 3.960A pdb=" N MET n 393 " --> pdb=" O SER n 389 " (cutoff:3.500A) removed outlier: 4.468A 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: 4.480A pdb=" N ILE n 432 " --> pdb=" O GLN n 428 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE n 433 " --> pdb=" O PRO n 429 " (cutoff:3.500A) Processing helix chain 'n' and resid 258 through 263 removed outlier: 3.637A pdb=" N TYR n 262 " --> pdb=" O LEU n 259 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE n 263 " --> pdb=" O SER n 260 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 115 removed outlier: 4.165A pdb=" N GLN o 113 " --> pdb=" O LYS o 109 " (cutoff:3.500A) removed outlier: 4.205A 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: 3.786A pdb=" N GLY o 215 " --> pdb=" O LEU o 211 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.630A 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 'p' and resid 9 through 14 removed outlier: 3.718A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 204 through 209 removed outlier: 4.495A pdb=" N ASP q 208 " --> pdb=" O PRO q 204 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE q 209 " --> pdb=" O SER q 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 204 through 209' Processing helix chain 'q' and resid 232 through 269 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: 4.678A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 74 removed outlier: 3.587A pdb=" N LYS r 74 " --> pdb=" O GLN r 70 " (cutoff:3.500A) Processing helix chain 'r' and resid 88 through 93 removed outlier: 5.697A 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: 3.645A pdb=" N ARG r 178 " --> pdb=" O PRO r 174 " (cutoff:3.500A) removed outlier: 5.748A 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: 3.878A pdb=" N GLU s 73 " --> pdb=" O MET s 69 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG s 75 " --> pdb=" O ASP s 71 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU s 76 " --> pdb=" O LEU s 72 " (cutoff:3.500A) Processing helix chain 't' and resid 15 through 52 removed outlier: 4.284A pdb=" N LEU t 19 " --> pdb=" O ASN t 15 " (cutoff:3.500A) removed outlier: 3.593A 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: 3.725A 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: 4.987A 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: 5.399A 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: 3.903A pdb=" N THR u 70 " --> pdb=" O ASP u 66 " (cutoff:3.500A) removed outlier: 4.576A 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: 3.662A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY u 114 " --> pdb=" O ASN u 110 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN u 115 " --> pdb=" O ARG u 111 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS u 116 " --> pdb=" O MET u 112 " (cutoff:3.500A) removed outlier: 7.349A 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: 5.511A 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: 4.284A pdb=" N PHE v 128 " --> pdb=" O LEU v 124 " (cutoff:3.500A) removed outlier: 4.170A 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: 4.339A 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: 4.564A pdb=" N LEU v 285 " --> pdb=" O ASP v 281 " (cutoff:3.500A) removed outlier: 5.728A 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: 3.522A 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: 4.366A pdb=" N LYS w 153 " --> pdb=" O GLY w 149 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU w 154 " --> pdb=" O ALA w 150 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP w 155 " --> pdb=" O ASN w 151 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP w 156 " --> pdb=" O LYS w 152 " (cutoff:3.500A) Processing helix chain 'w' and resid 163 through 168 removed outlier: 3.995A pdb=" N LYS w 167 " --> pdb=" O ASP w 163 " (cutoff:3.500A) removed outlier: 5.714A 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: 3.688A pdb=" N GLU w 172 " --> pdb=" O THR w 169 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU w 173 " --> pdb=" O ASP w 170 " (cutoff:3.500A) removed outlier: 3.581A 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: 5.143A 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: 4.008A pdb=" N ILE x 363 " --> pdb=" O ASN x 359 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 17 removed outlier: 3.673A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 43 removed outlier: 3.871A 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: 4.998A pdb=" N ASP y 238 " --> pdb=" O GLY y 234 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR y 239 " --> pdb=" O ASN y 235 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 56 removed outlier: 4.149A pdb=" N GLY z 20 " --> pdb=" O VAL z 16 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL z 21 " --> pdb=" O LYS z 17 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE z 22 " --> pdb=" O ARG z 18 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLN z 23 " --> pdb=" O ARG z 19 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN z 55 " --> pdb=" O LYS z 51 " (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: 4.350A pdb=" N GLN 4 78 " --> pdb=" O THR 4 74 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR 4 79 " --> pdb=" O ARG 4 75 " (cutoff:3.500A) removed outlier: 5.290A 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: 3.609A pdb=" N ALA 4 201 " --> pdb=" O LEU 4 197 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU 4 202 " --> pdb=" O LEU 4 198 " (cutoff:3.500A) removed outlier: 4.177A 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: 3.901A pdb=" N GLY 4 386 " --> pdb=" O ILE 4 382 " (cutoff:3.500A) Processing helix chain '4' and resid 391 through 396 removed outlier: 3.898A pdb=" N LEU 4 395 " --> pdb=" O LYS 4 391 " (cutoff:3.500A) removed outlier: 4.087A 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: 3.754A pdb=" N SER 4 418 " --> pdb=" O LYS 4 414 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU 4 425 " --> pdb=" O LEU 4 421 " (cutoff:3.500A) Processing helix chain '4' and resid 444 through 451 removed outlier: 3.605A pdb=" N ILE 4 448 " --> pdb=" O PRO 4 444 " (cutoff:3.500A) Processing helix chain '4' and resid 466 through 472 removed outlier: 4.554A pdb=" N GLU 4 472 " --> pdb=" O LEU 4 468 " (cutoff:3.500A) Processing helix chain '4' and resid 481 through 492 Processing helix chain '4' and resid 547 through 563 removed outlier: 5.106A pdb=" N LYS 4 563 " --> pdb=" O LEU 4 559 " (cutoff:3.500A) Processing helix chain '4' and resid 528 through 533 removed outlier: 3.882A 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: 3.790A pdb=" N GLN A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 110 through 114 removed outlier: 4.223A pdb=" N THR A 111 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.637A 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: 4.146A 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 17 removed outlier: 4.271A 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: 6.514A pdb=" N GLN B 182 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N HIS B 177 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL B 158 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS B 201 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 53 through 60 removed outlier: 6.894A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 12.783A pdb=" N LYS B 333 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 11.286A pdb=" N LYS B 222 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS B 273 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 98 through 102 removed outlier: 6.825A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 284 through 288 removed outlier: 3.780A pdb=" N GLY B 288 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASN B 319 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 76 through 80 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'B' and resid 88 through 93 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'B' and resid 213 through 216 removed outlier: 4.351A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 4 through 8 removed outlier: 5.308A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 224 through 230 removed outlier: 5.412A pdb=" N PHE C 247 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 72 through 75 removed outlier: 6.661A pdb=" N ILE D 64 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 38 through 43 removed outlier: 3.996A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS E 50 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 63 through 66 Processing sheet with id= 18, first strand: chain 'F' and resid 133 through 138 removed outlier: 7.787A pdb=" N TYR F 133 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LYS F 82 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 5.476A 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: 6.780A 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: 4.902A pdb=" N GLN H 51 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 17 through 20 removed outlier: 6.012A 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: 6.266A 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: 5.620A pdb=" N GLU H 143 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 5.578A 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: 4.994A 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: 4.285A pdb=" N ALA J 66 " --> pdb=" O SER J 48 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE J 65 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER J 22 " --> pdb=" O GLY J 124 " (cutoff:3.500A) removed outlier: 8.068A 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 122 through 126 Processing sheet with id= 29, first strand: chain 'K' and resid 242 through 248 removed outlier: 5.630A pdb=" N THR K 242 " --> pdb=" O ASN K 84 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU K 78 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP K 77 " --> pdb=" O ASN K 284 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE K 279 " --> pdb=" O PRO K 290 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE K 281 " --> pdb=" O VAL K 288 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL K 288 " --> pdb=" O ILE K 281 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR K 283 " --> pdb=" O SER K 286 " (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: 4.413A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS M 31 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 6.858A 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: 6.591A pdb=" N VAL N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY N 58 " --> pdb=" O ASP N 136 " (cutoff:3.500A) removed outlier: 6.897A 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: 3.650A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.910A 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: 6.426A pdb=" N VAL P 149 " --> pdb=" O SER P 115 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS P 111 " --> pdb=" O LYS P 153 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'P' and resid 57 through 60 removed outlier: 5.367A 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 'S' and resid 24 through 31 removed outlier: 6.628A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'S' and resid 87 through 96 removed outlier: 3.611A pdb=" N HIS S 88 " --> pdb=" O TYR S 81 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'S' and resid 6 through 10 removed outlier: 4.603A pdb=" N GLU S 6 " --> pdb=" O ILE S 64 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'T' and resid 40 through 43 removed outlier: 4.166A pdb=" N LYS T 60 " --> pdb=" O ILE T 42 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'T' and resid 72 through 79 Processing sheet with id= 45, first strand: chain 'U' and resid 54 through 58 removed outlier: 5.805A pdb=" N ASN U 101 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N TRP U 92 " --> pdb=" O TYR U 108 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'V' and resid 20 through 24 removed outlier: 4.289A pdb=" N ALA V 21 " --> pdb=" O ILE V 36 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 56 through 60 removed outlier: 4.370A pdb=" N ASP V 56 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP V 97 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA V 82 " --> pdb=" O ASP V 97 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 84 through 88 removed outlier: 3.684A pdb=" N VAL V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'W' and resid 63 through 67 removed outlier: 6.228A pdb=" N VAL W 99 " --> pdb=" O LEU W 45 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL W 42 " --> pdb=" O SER W 218 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'W' and resid 135 through 139 removed outlier: 6.703A pdb=" N PHE W 135 " --> pdb=" O VAL W 188 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU W 139 " --> pdb=" O SER W 184 " (cutoff:3.500A) removed outlier: 7.185A 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: 3.922A 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: 8.377A pdb=" N ARG W 38 " --> pdb=" O ASN W 223 " (cutoff:3.500A) removed outlier: 4.096A 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: 3.738A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 4.309A 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 85 through 88 removed outlier: 6.916A pdb=" N VAL Y 85 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Z' and resid 9 through 13 removed outlier: 4.239A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) removed outlier: 6.530A 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 203 through 210 removed outlier: 7.590A pdb=" N SER b 203 " --> pdb=" O PRO b 222 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ARG b 168 " --> pdb=" O ARG b 215 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR b 221 " --> pdb=" O ILE b 172 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY b 174 " --> pdb=" O THR b 221 " (cutoff:3.500A) removed outlier: 3.892A 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: 6.354A pdb=" N LYS c 22 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS c 66 " --> pdb=" O LYS c 40 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'd' and resid 48 through 51 removed outlier: 5.210A pdb=" N ASP d 48 " --> pdb=" O LEU d 89 " (cutoff:3.500A) removed outlier: 4.704A 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: 5.847A pdb=" N LYS f 10 " --> pdb=" O GLU f 33 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG f 82 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS f 47 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 4.374A 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: 4.045A 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: 4.621A 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: 4.618A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE k 27 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'm' and resid 291 through 294 removed outlier: 5.791A pdb=" N ILE m 290 " --> pdb=" O THR m 291 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N SER m 293 " --> pdb=" O ALA m 288 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA m 288 " --> pdb=" O SER m 293 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS m 367 " --> pdb=" O PHE m 320 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY m 322 " --> pdb=" O CYS m 367 " (cutoff:3.500A) removed outlier: 6.524A 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: 3.900A pdb=" N GLU o 119 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 5.161A 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: 6.928A pdb=" N ILE p 54 " --> pdb=" O GLY p 50 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 3.913A 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 195 removed outlier: 3.741A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (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: 4.227A pdb=" N THR r 219 " --> pdb=" O VAL r 245 " (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 194 through 198 removed outlier: 4.110A pdb=" N THR t 173 " --> pdb=" O ARG t 146 " (cutoff:3.500A) removed outlier: 5.983A 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: 3.627A pdb=" N TYR t 216 " --> pdb=" O HIS t 225 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'u' and resid 3 through 6 removed outlier: 4.619A 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: 4.173A 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: 7.239A pdb=" N SER v 92 " --> pdb=" O GLY v 35 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER v 85 " --> pdb=" O THR v 105 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N SER v 93 " --> pdb=" O LYS v 97 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ASN v 98 " --> pdb=" O VAL v 118 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU v 115 " --> pdb=" O GLY v 235 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP v 231 " --> pdb=" O ALA v 119 " (cutoff:3.500A) removed outlier: 6.853A 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: 6.030A pdb=" N ASN v 262 " --> pdb=" O ARG v 274 " (cutoff:3.500A) removed outlier: 4.582A 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: 8.984A 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 17 through 23 removed outlier: 5.576A pdb=" N SER w 31 " --> pdb=" O PRO w 18 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'x' and resid 48 through 52 removed outlier: 5.504A pdb=" N THR x 118 " --> pdb=" O THR x 82 " (cutoff:3.500A) removed outlier: 3.814A 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: 5.214A pdb=" N MET x 509 " --> pdb=" O GLY x 505 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY x 505 " --> pdb=" O MET x 509 " (cutoff:3.500A) removed outlier: 5.892A 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: 6.360A pdb=" N ARG x 158 " --> pdb=" O ALA x 152 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER x 157 " --> pdb=" O CYS x 173 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR x 167 " --> pdb=" O ALA x 163 " (cutoff:3.500A) removed outlier: 6.581A 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: 5.664A pdb=" N VAL x 200 " --> pdb=" O SER x 195 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR x 209 " --> pdb=" O SER x 205 " (cutoff:3.500A) removed outlier: 5.082A 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: 3.534A pdb=" N SER x 234 " --> pdb=" O SER x 254 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ARG x 250 " --> pdb=" O GLU x 238 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE x 262 " --> pdb=" O GLN x 271 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'x' and resid 283 through 287 removed outlier: 4.428A pdb=" N LEU x 291 " --> pdb=" O GLY x 287 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL x 303 " --> pdb=" O ILE x 313 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG x 311 " --> pdb=" O ASP x 305 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'x' and resid 324 through 329 removed outlier: 7.058A pdb=" N MET x 373 " --> pdb=" O SER x 329 " (cutoff:3.500A) removed outlier: 4.107A 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: 5.642A pdb=" N TYR x 416 " --> pdb=" O SER x 411 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER x 425 " --> pdb=" O SER x 421 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE x 426 " --> pdb=" O THR x 439 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR x 439 " --> pdb=" O ILE x 426 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU x 428 " --> pdb=" O ILE x 437 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS x 435 " --> pdb=" O ASP x 430 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'x' and resid 448 through 453 removed outlier: 3.684A pdb=" N GLN x 449 " --> pdb=" O CYS x 462 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU x 458 " --> pdb=" O SER x 453 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ARG x 457 " --> pdb=" O VAL x 473 " (cutoff:3.500A) removed outlier: 4.078A 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 259 through 262 removed outlier: 3.805A pdb=" N TYR x 272 " --> pdb=" O ILE x 262 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'x' and resid 300 through 303 Processing sheet with id= 97, first strand: chain 'y' and resid 1 through 4 Processing sheet with id= 98, first strand: chain 'y' and resid 23 through 27 Processing sheet with id= 99, first strand: chain 'y' and resid 69 through 73 Processing sheet with id=100, first strand: chain 'y' and resid 114 through 117 Processing sheet with id=101, first strand: chain 'y' and resid 158 through 162 Processing sheet with id=102, first strand: chain '4' and resid 93 through 97 removed outlier: 3.893A pdb=" N ASP 4 137 " --> pdb=" O ILE 4 160 " (cutoff:3.500A) removed outlier: 13.390A pdb=" N THR 4 151 " --> pdb=" O VAL 4 508 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N VAL 4 508 " --> pdb=" O THR 4 151 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU 4 153 " --> pdb=" O THR 4 506 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR 4 506 " --> pdb=" O GLU 4 153 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG 4 502 " --> pdb=" O THR 4 157 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N VAL 4 159 " --> pdb=" O VAL 4 500 " (cutoff:3.500A) removed outlier: 13.792A pdb=" N VAL 4 500 " --> pdb=" O VAL 4 159 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU 4 315 " --> pdb=" O LEU 4 509 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain '4' and resid 335 through 340 removed outlier: 4.947A pdb=" N ILE 4 437 " --> pdb=" O VAL 4 340 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain '4' and resid 568 through 572 Processing sheet with id=105, first strand: chain '4' and resid 506 through 511 removed outlier: 6.527A pdb=" N THR 4 506 " --> pdb=" O LEU 4 525 " (cutoff:3.500A) 3881 hydrogen bonds defined for protein. 11511 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2517 hydrogen bonds 4044 hydrogen bond angles 0 basepair planarities 1021 basepair parallelities 1619 stacking parallelities Total time for adding SS restraints: 225.75 Time building geometry restraints manager: 61.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 32597 1.33 - 1.46: 59526 1.46 - 1.58: 68210 1.58 - 1.71: 6627 1.71 - 1.83: 381 Bond restraints: 167341 Sorted by residual: bond pdb=" C2' A2M 11133 " pdb=" C1' A2M 11133 " ideal model delta sigma weight residual 1.305 1.575 -0.270 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C2' A2M 1 649 " pdb=" C1' A2M 1 649 " ideal model delta sigma weight residual 1.305 1.572 -0.267 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C2' A2M 12220 " pdb=" C1' A2M 12220 " ideal model delta sigma weight residual 1.305 1.571 -0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" N PRO y 229 " pdb=" CD PRO y 229 " ideal model delta sigma weight residual 1.473 1.658 -0.185 1.40e-02 5.10e+03 1.75e+02 bond pdb=" C2' A2M 1 807 " pdb=" C1' A2M 1 807 " ideal model delta sigma weight residual 1.305 1.565 -0.260 2.00e-02 2.50e+03 1.69e+02 ... (remaining 167336 not shown) Histogram of bond angle deviations from ideal: 97.96 - 105.67: 17850 105.67 - 113.38: 99877 113.38 - 121.09: 77802 121.09 - 128.80: 42595 128.80 - 136.50: 3820 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 88.50 128.66 -40.16 3.00e+00 1.11e-01 1.79e+02 angle pdb=" C1' A2M 1 807 " pdb=" N9 A2M 1 807 " pdb=" C8 A2M 1 807 " ideal model delta sigma weight residual 88.50 128.16 -39.66 3.00e+00 1.11e-01 1.75e+02 angle pdb=" C1' A2M 11449 " pdb=" N9 A2M 11449 " pdb=" C8 A2M 11449 " ideal model delta sigma weight residual 88.50 128.13 -39.63 3.00e+00 1.11e-01 1.75e+02 angle pdb=" C1' A2M 11133 " pdb=" N9 A2M 11133 " pdb=" C8 A2M 11133 " ideal model delta sigma weight residual 88.50 127.66 -39.16 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C1' A2M 1 876 " pdb=" N9 A2M 1 876 " pdb=" C8 A2M 1 876 " ideal model delta sigma weight residual 88.50 127.45 -38.95 3.00e+00 1.11e-01 1.69e+02 ... (remaining 241939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 97329 35.95 - 71.91: 7434 71.91 - 107.86: 834 107.86 - 143.82: 15 143.82 - 179.77: 42 Dihedral angle restraints: 105654 sinusoidal: 74275 harmonic: 31379 Sorted by residual: 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 29.63 170.37 1 1.50e+01 4.44e-03 8.47e+01 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 36.09 163.91 1 1.50e+01 4.44e-03 8.37e+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 36.38 163.62 1 1.50e+01 4.44e-03 8.36e+01 ... (remaining 105651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 27678 0.070 - 0.141: 1833 0.141 - 0.211: 95 0.211 - 0.282: 6 0.282 - 0.352: 5 Chirality restraints: 29617 Sorted by residual: chirality pdb=" C2' A2M 1 649 " pdb=" C3' A2M 1 649 " pdb=" O2' A2M 1 649 " pdb=" C1' A2M 1 649 " both_signs ideal model delta sigma weight residual False -2.39 -2.74 0.35 2.00e-01 2.50e+01 3.11e+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 -2.73 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C2' A2M 11133 " pdb=" C3' A2M 11133 " pdb=" O2' A2M 11133 " pdb=" C1' A2M 11133 " both_signs ideal model delta sigma weight residual False -2.39 -2.72 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 29614 not shown) Planarity restraints: 18328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12793 " 0.072 2.00e-02 2.50e+03 6.31e-01 8.96e+03 pdb=" C4' OMG 12793 " 0.469 2.00e-02 2.50e+03 pdb=" O4' OMG 12793 " 0.737 2.00e-02 2.50e+03 pdb=" C3' OMG 12793 " -0.588 2.00e-02 2.50e+03 pdb=" O3' OMG 12793 " -0.664 2.00e-02 2.50e+03 pdb=" C2' OMG 12793 " -0.188 2.00e-02 2.50e+03 pdb=" O2' OMG 12793 " 0.977 2.00e-02 2.50e+03 pdb=" C1' OMG 12793 " 0.187 2.00e-02 2.50e+03 pdb=" N9 OMG 12793 " -1.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 1MA 12142 " -0.913 2.00e-02 2.50e+03 5.96e-01 7.98e+03 pdb=" C4' 1MA 12142 " 0.190 2.00e-02 2.50e+03 pdb=" O4' 1MA 12142 " 0.831 2.00e-02 2.50e+03 pdb=" C3' 1MA 12142 " -0.261 2.00e-02 2.50e+03 pdb=" O3' 1MA 12142 " 0.831 2.00e-02 2.50e+03 pdb=" C2' 1MA 12142 " -0.593 2.00e-02 2.50e+03 pdb=" O2' 1MA 12142 " -0.549 2.00e-02 2.50e+03 pdb=" C1' 1MA 12142 " 0.470 2.00e-02 2.50e+03 pdb=" N9 1MA 12142 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12815 " -0.049 2.00e-02 2.50e+03 5.94e-01 7.93e+03 pdb=" C4' OMG 12815 " -0.441 2.00e-02 2.50e+03 pdb=" O4' OMG 12815 " -0.670 2.00e-02 2.50e+03 pdb=" C3' OMG 12815 " 0.596 2.00e-02 2.50e+03 pdb=" O3' OMG 12815 " 0.607 2.00e-02 2.50e+03 pdb=" C2' OMG 12815 " 0.201 2.00e-02 2.50e+03 pdb=" O2' OMG 12815 " -0.942 2.00e-02 2.50e+03 pdb=" C1' OMG 12815 " -0.214 2.00e-02 2.50e+03 pdb=" N9 OMG 12815 " 0.911 2.00e-02 2.50e+03 ... (remaining 18325 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.59: 1728 2.59 - 3.23: 136659 3.23 - 3.87: 359703 3.87 - 4.50: 481442 4.50 - 5.14: 670401 Nonbonded interactions: 1649933 Sorted by model distance: nonbonded pdb=" OP2 C 1 893 " pdb="MG MG 13463 " model vdw 1.953 2.170 nonbonded pdb=" OP1 A2M 1 817 " pdb="MG MG 13447 " model vdw 1.966 2.170 nonbonded pdb=" OP1 A 12138 " pdb="MG MG 13426 " model vdw 1.975 2.170 nonbonded pdb=" OP2 C 1 863 " pdb="MG MG 13463 " model vdw 1.980 2.170 nonbonded pdb=" OE1 GLN j 30 " pdb="MG MG 13447 " model vdw 1.990 2.170 ... (remaining 1649928 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: 4.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 18.300 Check model and map are aligned: 1.580 Set scattering table: 0.950 Process input model: 580.510 Find NCS groups from input model: 4.460 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 621.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 0.005 0.270 167341 Z= 0.298 Angle : 0.652 40.160 241944 Z= 0.305 Chirality : 0.036 0.352 29617 Planarity : 0.018 0.631 18328 Dihedral : 20.221 179.769 85338 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.33 % Allowed : 3.13 % Favored : 96.54 % 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: 0.96 (0.08), residues: 10648 helix: 1.78 (0.08), residues: 4189 sheet: 0.37 (0.13), residues: 1592 loop : -0.22 (0.08), residues: 4867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP e 32 HIS 0.005 0.001 HIS P 145 PHE 0.031 0.001 PHE F 229 TYR 0.017 0.001 TYR C 194 ARG 0.005 0.000 ARG l 21 *********************** 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 2149 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 2118 time to evaluate : 9.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8461 (tp) cc_final: 0.8175 (tt) REVERT: A 70 ARG cc_start: 0.8171 (ptt180) cc_final: 0.7896 (ptt180) REVERT: 5 68 LYS cc_start: 0.5524 (tttm) cc_final: 0.5314 (tttp) REVERT: 8 59 THR cc_start: 0.7746 (m) cc_final: 0.7124 (p) REVERT: 8 111 GLU cc_start: 0.6896 (tp30) cc_final: 0.6653 (tp30) REVERT: 9 26 LYS cc_start: 0.8333 (mtmm) cc_final: 0.8075 (mtpm) REVERT: 9 30 ARG cc_start: 0.7751 (mtm180) cc_final: 0.7287 (mtp180) REVERT: 9 98 GLU cc_start: 0.7142 (tt0) cc_final: 0.6907 (tt0) REVERT: B 71 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7891 (mt-10) REVERT: B 145 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6937 (mm-30) REVERT: B 335 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8576 (tp) REVERT: B 336 VAL cc_start: 0.8993 (m) cc_final: 0.8792 (p) REVERT: C 93 MET cc_start: 0.8769 (pmm) cc_final: 0.8534 (pmm) REVERT: C 99 MET cc_start: 0.8779 (ptm) cc_final: 0.8480 (ptm) REVERT: D 130 GLU cc_start: 0.5009 (mm-30) cc_final: 0.4783 (mm-30) REVERT: D 163 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7128 (tm) REVERT: D 253 PHE cc_start: 0.6551 (t80) cc_final: 0.6302 (t80) REVERT: E 60 ASP cc_start: 0.8366 (p0) cc_final: 0.8129 (p0) REVERT: G 54 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8067 (mt-10) REVERT: G 66 SER cc_start: 0.7041 (p) cc_final: 0.6766 (m) REVERT: G 156 ASP cc_start: 0.8085 (p0) cc_final: 0.7674 (p0) REVERT: G 161 GLU cc_start: 0.8047 (mp0) cc_final: 0.7798 (mp0) REVERT: G 207 ASP cc_start: 0.7925 (m-30) cc_final: 0.7678 (m-30) REVERT: G 230 LYS cc_start: 0.6419 (ptpt) cc_final: 0.6017 (pttt) REVERT: H 9 GLN cc_start: 0.7904 (mt0) cc_final: 0.7402 (mt0) REVERT: K 173 PHE cc_start: 0.7527 (t80) cc_final: 0.7190 (t80) REVERT: K 225 ASN cc_start: 0.6003 (m-40) cc_final: 0.5777 (m110) REVERT: K 329 PHE cc_start: 0.4184 (t80) cc_final: 0.3941 (t80) REVERT: K 333 LEU cc_start: 0.7452 (mt) cc_final: 0.7226 (mt) REVERT: L 102 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8078 (mm110) REVERT: N 10 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8346 (tp) REVERT: N 17 ASP cc_start: 0.7679 (m-30) cc_final: 0.7378 (m-30) REVERT: N 145 ASP cc_start: 0.8189 (t0) cc_final: 0.7988 (t0) REVERT: O 84 LEU cc_start: 0.7978 (mt) cc_final: 0.7772 (tm) REVERT: O 126 VAL cc_start: 0.8688 (m) cc_final: 0.8407 (p) REVERT: O 150 GLU cc_start: 0.8091 (tt0) cc_final: 0.7857 (tt0) REVERT: Q 22 ASP cc_start: 0.7656 (m-30) cc_final: 0.7373 (m-30) REVERT: R 72 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7140 (mt-10) REVERT: S 45 LEU cc_start: 0.8014 (tp) cc_final: 0.7809 (tp) REVERT: S 66 GLU cc_start: 0.8555 (tp30) cc_final: 0.8050 (tp30) REVERT: S 90 MET cc_start: 0.8302 (ttm) cc_final: 0.7993 (ttm) REVERT: T 38 ASP cc_start: 0.6272 (m-30) cc_final: 0.6039 (m-30) REVERT: T 87 LYS cc_start: 0.6993 (mtpp) cc_final: 0.6705 (mmmm) REVERT: U 39 ASP cc_start: 0.7857 (m-30) cc_final: 0.7642 (m-30) REVERT: U 76 LEU cc_start: 0.8987 (tp) cc_final: 0.8693 (tp) REVERT: V 133 SER cc_start: 0.8506 (m) cc_final: 0.8276 (t) REVERT: W 35 ASP cc_start: 0.5618 (m-30) cc_final: 0.5404 (m-30) REVERT: W 41 TRP cc_start: 0.7808 (m100) cc_final: 0.7591 (m100) REVERT: W 67 MET cc_start: 0.7553 (mmm) cc_final: 0.7231 (mtt) REVERT: W 194 LYS cc_start: 0.6903 (ttmm) cc_final: 0.6668 (tppt) REVERT: Z 88 ASP cc_start: 0.7069 (t70) cc_final: 0.6684 (t0) REVERT: a 60 TYR cc_start: 0.6769 (m-80) cc_final: 0.6523 (m-80) REVERT: a 68 PHE cc_start: 0.5949 (p90) cc_final: 0.5628 (p90) REVERT: a 135 GLU cc_start: 0.8034 (tt0) cc_final: 0.7757 (tt0) REVERT: b 3 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6643 (mp) REVERT: b 215 ARG cc_start: 0.8492 (tpp80) cc_final: 0.8160 (tpp80) REVERT: b 254 MET cc_start: 0.7151 (mtt) cc_final: 0.6827 (mmm) REVERT: b 514 LYS cc_start: 0.7687 (tttm) cc_final: 0.7456 (pttp) REVERT: b 615 ARG cc_start: 0.8275 (ttp80) cc_final: 0.8049 (ttt180) REVERT: b 646 PHE cc_start: 0.7509 (p90) cc_final: 0.7302 (p90) REVERT: c 42 ILE cc_start: 0.8252 (pt) cc_final: 0.7983 (pt) REVERT: c 57 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8178 (mt-10) REVERT: d 62 ARG cc_start: 0.8499 (mtm180) cc_final: 0.8212 (mtm110) REVERT: d 68 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7765 (mm-30) REVERT: d 97 LEU cc_start: 0.8171 (mt) cc_final: 0.7919 (mt) REVERT: f 67 MET cc_start: 0.9132 (mtp) cc_final: 0.8742 (mtm) REVERT: i 71 LYS cc_start: 0.7390 (ttmt) cc_final: 0.7065 (mttt) REVERT: m 308 GLN cc_start: 0.7755 (tp40) cc_final: 0.7408 (tp40) REVERT: n 5 LYS cc_start: 0.7648 (mmtt) cc_final: 0.7365 (mtmm) REVERT: n 106 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7771 (tm-30) REVERT: n 138 MET cc_start: 0.7595 (tpp) cc_final: 0.7307 (ttm) REVERT: n 191 ASN cc_start: 0.6727 (t0) cc_final: 0.6425 (t0) REVERT: n 366 TYR cc_start: 0.6250 (t80) cc_final: 0.5934 (t80) REVERT: o 110 TYR cc_start: 0.8261 (t80) cc_final: 0.7993 (t80) REVERT: o 152 MET cc_start: 0.7582 (mmm) cc_final: 0.7100 (mmm) REVERT: p 70 THR cc_start: 0.8295 (p) cc_final: 0.8090 (t) REVERT: q 249 GLU cc_start: 0.4303 (tp30) cc_final: 0.3894 (tp30) REVERT: s 60 ILE cc_start: 0.7481 (mm) cc_final: 0.7272 (mt) REVERT: t 38 LYS cc_start: 0.6622 (tttp) cc_final: 0.6228 (mtpt) REVERT: t 82 GLU cc_start: 0.5317 (mm-30) cc_final: 0.5032 (pt0) REVERT: t 297 ARG cc_start: 0.5628 (ttp-170) cc_final: 0.5167 (mtp180) REVERT: u 76 ASN cc_start: 0.8965 (m-40) cc_final: 0.8610 (m-40) REVERT: v 179 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6777 (mm-40) REVERT: v 249 HIS cc_start: 0.8066 (m90) cc_final: 0.7804 (m90) REVERT: v 268 MET cc_start: 0.8819 (mmm) cc_final: 0.8418 (mmm) REVERT: v 277 MET cc_start: 0.8381 (mmm) cc_final: 0.7954 (mmm) REVERT: w 32 ASN cc_start: 0.6186 (m-40) cc_final: 0.5929 (m-40) REVERT: w 40 ASP cc_start: 0.5407 (t0) cc_final: 0.5150 (p0) REVERT: y 39 GLU cc_start: 0.8124 (tt0) cc_final: 0.7922 (tt0) REVERT: y 112 ASP cc_start: 0.8314 (m-30) cc_final: 0.8081 (m-30) REVERT: z 99 LYS cc_start: 0.7391 (mttm) cc_final: 0.7073 (mtpt) REVERT: z 105 ARG cc_start: 0.7673 (mtt-85) cc_final: 0.7421 (mtt180) REVERT: 4 81 LYS cc_start: 0.5434 (ttmt) cc_final: 0.4577 (pttt) REVERT: 4 167 LYS cc_start: 0.4868 (mmtt) cc_final: 0.4590 (tptt) REVERT: 4 232 ARG cc_start: 0.6452 (ttp-110) cc_final: 0.6114 (ttp80) REVERT: 4 272 SER cc_start: 0.7692 (p) cc_final: 0.7201 (t) REVERT: 4 373 LYS cc_start: 0.7911 (ttpp) cc_final: 0.7631 (ttmt) REVERT: 4 404 GLU cc_start: 0.5417 (mt-10) cc_final: 0.5093 (tp30) REVERT: 4 489 MET cc_start: 0.7254 (ttm) cc_final: 0.6885 (ttp) REVERT: 4 555 GLN cc_start: 0.4797 (mt0) cc_final: 0.4143 (tt0) REVERT: 4 568 LEU cc_start: 0.5528 (tp) cc_final: 0.5226 (mt) outliers start: 31 outliers final: 12 residues processed: 2140 average time/residue: 2.5172 time to fit residues: 7527.4606 Evaluate side-chains 1368 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1352 time to evaluate : 9.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain n residue 259 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain 4 residue 370 LEU Chi-restraints excluded: chain 4 residue 401 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 1168 optimal weight: 5.9990 chunk 1049 optimal weight: 9.9990 chunk 582 optimal weight: 20.0000 chunk 358 optimal weight: 20.0000 chunk 707 optimal weight: 10.0000 chunk 560 optimal weight: 9.9990 chunk 1084 optimal weight: 7.9990 chunk 419 optimal weight: 0.9980 chunk 659 optimal weight: 0.9990 chunk 807 optimal weight: 20.0000 chunk 1256 optimal weight: 0.6980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 115 GLN C 307 GLN E 138 GLN G 77 GLN G 221 ASN H 5 GLN H 102 ASN H 157 ASN ** K 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN L 114 GLN N 34 ASN N 182 ASN N 195 ASN P 92 GLN P 137 ASN Q 73 GLN R 34 GLN S 46 GLN S 89 ASN ** S 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN T 131 GLN W 22 ASN Y 66 GLN Z 123 GLN b 107 GLN b 152 GLN b 208 HIS b 619 GLN e 71 HIS g 3 GLN i 91 ASN m 165 ASN m 227 HIS m 452 GLN n 409 HIS n 456 HIS q 228 ASN q 424 GLN r 179 GLN t 25 ASN t 230 ASN v 213 GLN w 43 ASN w 63 ASN w 83 GLN y 145 ASN z 31 GLN 4 447 HIS 4 546 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 167341 Z= 0.187 Angle : 0.636 18.076 241944 Z= 0.338 Chirality : 0.037 0.349 29617 Planarity : 0.006 0.135 18328 Dihedral : 22.156 179.745 63314 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.74 % Allowed : 11.29 % Favored : 85.97 % 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: 1.16 (0.08), residues: 10648 helix: 2.06 (0.08), residues: 4184 sheet: 0.35 (0.13), residues: 1574 loop : -0.17 (0.08), residues: 4890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP m 212 HIS 0.006 0.001 HIS C 311 PHE 0.028 0.002 PHE F 229 TYR 0.018 0.002 TYR C 194 ARG 0.007 0.001 ARG O 125 *********************** 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 1629 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1374 time to evaluate : 9.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8487 (tp) cc_final: 0.8229 (tt) REVERT: A 119 LYS cc_start: 0.8058 (mttt) cc_final: 0.7654 (mttp) REVERT: 5 68 LYS cc_start: 0.5547 (tttm) cc_final: 0.5276 (tttt) REVERT: 8 59 THR cc_start: 0.7684 (m) cc_final: 0.7253 (p) REVERT: 9 26 LYS cc_start: 0.8352 (mtmm) cc_final: 0.8087 (mtpm) REVERT: 9 30 ARG cc_start: 0.7759 (mtm180) cc_final: 0.7467 (mtp180) REVERT: B 71 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7970 (mt-10) REVERT: B 308 MET cc_start: 0.8480 (mmm) cc_final: 0.8241 (mmm) REVERT: B 336 VAL cc_start: 0.9002 (m) cc_final: 0.8794 (p) REVERT: C 99 MET cc_start: 0.8840 (ptm) cc_final: 0.8531 (ptm) REVERT: D 130 GLU cc_start: 0.5120 (mm-30) cc_final: 0.4869 (mm-30) REVERT: D 253 PHE cc_start: 0.6612 (t80) cc_final: 0.6315 (t80) REVERT: E 136 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6645 (mm-30) REVERT: F 125 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: G 66 SER cc_start: 0.7157 (p) cc_final: 0.6780 (m) REVERT: G 145 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7343 (m110) REVERT: G 156 ASP cc_start: 0.8151 (p0) cc_final: 0.7779 (p0) REVERT: G 207 ASP cc_start: 0.8018 (m-30) cc_final: 0.7735 (m-30) REVERT: G 230 LYS cc_start: 0.6515 (ptpt) cc_final: 0.6155 (pttt) REVERT: H 9 GLN cc_start: 0.7906 (mt0) cc_final: 0.7494 (mt0) REVERT: H 177 ASP cc_start: 0.8027 (m-30) cc_final: 0.7656 (m-30) REVERT: I 56 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.6069 (ttpp) REVERT: K 173 PHE cc_start: 0.7542 (t80) cc_final: 0.7118 (t80) REVERT: K 225 ASN cc_start: 0.6072 (m-40) cc_final: 0.5853 (m110) REVERT: K 228 LYS cc_start: 0.5746 (OUTLIER) cc_final: 0.5175 (mttm) REVERT: K 329 PHE cc_start: 0.4267 (t80) cc_final: 0.4043 (t80) REVERT: K 333 LEU cc_start: 0.7479 (mt) cc_final: 0.7229 (mt) REVERT: L 107 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: N 5 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6776 (tmtm) REVERT: N 10 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8486 (tp) REVERT: N 71 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7746 (ttt-90) REVERT: N 145 ASP cc_start: 0.8228 (t0) cc_final: 0.8007 (t0) REVERT: O 130 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7438 (ttmt) REVERT: Q 22 ASP cc_start: 0.7682 (m-30) cc_final: 0.7386 (m-30) REVERT: R 72 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7183 (mt-10) REVERT: S 66 GLU cc_start: 0.8574 (tp30) cc_final: 0.8042 (tp30) REVERT: S 120 SER cc_start: 0.6264 (p) cc_final: 0.6033 (m) REVERT: T 91 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7723 (mp) REVERT: T 149 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: U 39 ASP cc_start: 0.7939 (m-30) cc_final: 0.7661 (m-30) REVERT: U 76 LEU cc_start: 0.9023 (tp) cc_final: 0.8725 (tp) REVERT: W 21 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5800 (mp0) REVERT: W 35 ASP cc_start: 0.5671 (m-30) cc_final: 0.5424 (m-30) REVERT: W 194 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6637 (tppt) REVERT: Y 69 LYS cc_start: 0.8467 (ttmt) cc_final: 0.8203 (tttt) REVERT: Z 88 ASP cc_start: 0.7046 (t70) cc_final: 0.6724 (t0) REVERT: a 68 PHE cc_start: 0.6021 (p90) cc_final: 0.5609 (p90) REVERT: b 3 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6183 (tp) REVERT: b 254 MET cc_start: 0.7298 (mtt) cc_final: 0.6872 (mmm) REVERT: b 550 ASN cc_start: 0.6406 (m-40) cc_final: 0.6117 (m-40) REVERT: b 615 ARG cc_start: 0.8383 (ttp80) cc_final: 0.8129 (ttt180) REVERT: b 646 PHE cc_start: 0.7576 (p90) cc_final: 0.7339 (p90) REVERT: c 42 ILE cc_start: 0.8322 (pt) cc_final: 0.8065 (pt) REVERT: c 57 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8189 (mt-10) REVERT: d 62 ARG cc_start: 0.8515 (mtm180) cc_final: 0.8177 (mtm110) REVERT: d 68 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7791 (mm-30) REVERT: d 97 LEU cc_start: 0.8231 (mt) cc_final: 0.7976 (mt) REVERT: f 67 MET cc_start: 0.9169 (mtp) cc_final: 0.8855 (mtm) REVERT: h 107 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7943 (mtpt) REVERT: i 56 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6890 (ttp-110) REVERT: i 71 LYS cc_start: 0.7451 (ttmt) cc_final: 0.7105 (mttt) REVERT: k 16 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6296 (mtp-110) REVERT: m 184 MET cc_start: 0.3196 (ppp) cc_final: 0.1946 (ppp) REVERT: m 314 LYS cc_start: 0.7855 (mmtm) cc_final: 0.7459 (mttt) REVERT: m 429 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6879 (tp30) REVERT: n 5 LYS cc_start: 0.7672 (mmtt) cc_final: 0.7357 (mtmm) REVERT: n 72 MET cc_start: 0.7161 (tpp) cc_final: 0.6560 (tpp) REVERT: n 138 MET cc_start: 0.7542 (tpp) cc_final: 0.7315 (ttm) REVERT: n 174 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6565 (mtp180) REVERT: n 191 ASN cc_start: 0.6733 (t0) cc_final: 0.6405 (t0) REVERT: n 366 TYR cc_start: 0.6355 (t80) cc_final: 0.5929 (t80) REVERT: n 376 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7558 (mp) REVERT: n 388 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.6146 (mm) REVERT: n 390 GLU cc_start: 0.5587 (OUTLIER) cc_final: 0.5086 (tt0) REVERT: o 105 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6734 (pttp) REVERT: o 110 TYR cc_start: 0.8288 (t80) cc_final: 0.7953 (t80) REVERT: o 121 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6428 (mtp180) REVERT: o 152 MET cc_start: 0.7474 (mmm) cc_final: 0.7097 (mmm) REVERT: q 210 GLU cc_start: 0.6570 (mm-30) cc_final: 0.6186 (mm-30) REVERT: q 215 LYS cc_start: 0.6377 (ttpt) cc_final: 0.5189 (ttpt) REVERT: q 249 GLU cc_start: 0.4725 (tp30) cc_final: 0.4209 (tp30) REVERT: q 259 LYS cc_start: 0.6391 (mmpt) cc_final: 0.5936 (mppt) REVERT: s 60 ILE cc_start: 0.7539 (mm) cc_final: 0.7312 (mt) REVERT: t 82 GLU cc_start: 0.5351 (mm-30) cc_final: 0.5020 (pt0) REVERT: t 158 LYS cc_start: 0.7049 (ttmt) cc_final: 0.6481 (mptt) REVERT: t 292 ARG cc_start: 0.6637 (mtt90) cc_final: 0.6360 (mtm-85) REVERT: t 297 ARG cc_start: 0.5639 (ttp-170) cc_final: 0.5274 (mtp180) REVERT: u 76 ASN cc_start: 0.8989 (m-40) cc_final: 0.8646 (m-40) REVERT: v 19 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.5835 (mtt90) REVERT: v 39 ASN cc_start: 0.5159 (OUTLIER) cc_final: 0.4685 (m110) REVERT: v 179 GLN cc_start: 0.7132 (mm-40) cc_final: 0.6849 (mm-40) REVERT: v 268 MET cc_start: 0.8853 (mmm) cc_final: 0.8449 (mmm) REVERT: v 277 MET cc_start: 0.8482 (mmm) cc_final: 0.8056 (mmm) REVERT: v 284 LYS cc_start: 0.7788 (mtpp) cc_final: 0.7439 (mmmt) REVERT: w 40 ASP cc_start: 0.5294 (t0) cc_final: 0.5078 (p0) REVERT: w 184 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.5996 (ttm110) REVERT: x 289 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7441 (mt0) REVERT: x 397 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6831 (ttt180) REVERT: y 1 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.4642 (ttt) REVERT: y 39 GLU cc_start: 0.8193 (tt0) cc_final: 0.7939 (tt0) REVERT: y 112 ASP cc_start: 0.8344 (m-30) cc_final: 0.8111 (m-30) REVERT: z 99 LYS cc_start: 0.7418 (mttm) cc_final: 0.7077 (mtpt) REVERT: z 105 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7491 (mtt180) REVERT: 4 167 LYS cc_start: 0.4942 (mmtt) cc_final: 0.4646 (tptt) REVERT: 4 232 ARG cc_start: 0.6541 (ttp-110) cc_final: 0.6202 (ttm110) REVERT: 4 272 SER cc_start: 0.7747 (p) cc_final: 0.7245 (t) REVERT: 4 373 LYS cc_start: 0.7919 (ttpp) cc_final: 0.7611 (ttmt) REVERT: 4 404 GLU cc_start: 0.5463 (mt-10) cc_final: 0.5180 (tp30) REVERT: 4 489 MET cc_start: 0.7315 (ttm) cc_final: 0.6873 (ttp) REVERT: 4 555 GLN cc_start: 0.4841 (mt0) cc_final: 0.4268 (tt0) REVERT: 4 568 LEU cc_start: 0.5632 (tp) cc_final: 0.5299 (mt) outliers start: 255 outliers final: 103 residues processed: 1512 average time/residue: 2.5170 time to fit residues: 5353.6057 Evaluate side-chains 1424 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1293 time to evaluate : 9.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 338 ASN Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 98 SER Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain W residue 21 GLU Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 184 SER Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain a residue 86 LYS Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain b residue 461 GLU Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain c residue 98 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain h residue 107 LYS Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 259 LEU Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 361 SER Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 386 ASN Chi-restraints excluded: chain n residue 388 ILE Chi-restraints excluded: chain n residue 390 GLU Chi-restraints excluded: chain n residue 417 LEU Chi-restraints excluded: chain n residue 445 ASN Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 121 ARG Chi-restraints excluded: chain o residue 146 MET Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain r residue 66 LYS Chi-restraints excluded: chain r residue 119 SER Chi-restraints excluded: chain s residue 16 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 206 SER Chi-restraints excluded: chain t residue 215 ILE Chi-restraints excluded: chain t residue 296 SER Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 112 MET Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 39 ASN Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 114 ILE Chi-restraints excluded: chain v residue 120 ASP Chi-restraints excluded: chain v residue 208 SER Chi-restraints excluded: chain v residue 224 VAL Chi-restraints excluded: chain w residue 155 ASP Chi-restraints excluded: chain w residue 184 ARG Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 289 GLN Chi-restraints excluded: chain x residue 336 ILE Chi-restraints excluded: chain x residue 389 LEU Chi-restraints excluded: chain x residue 392 THR Chi-restraints excluded: chain x residue 397 ARG Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 145 ASN Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 175 SER Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 45 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 307 ASP Chi-restraints excluded: chain 4 residue 330 THR Chi-restraints excluded: chain 4 residue 367 THR Chi-restraints excluded: chain 4 residue 370 LEU Chi-restraints excluded: chain 4 residue 517 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 698 optimal weight: 5.9990 chunk 390 optimal weight: 8.9990 chunk 1046 optimal weight: 0.9980 chunk 855 optimal weight: 9.9990 chunk 346 optimal weight: 9.9990 chunk 1259 optimal weight: 20.0000 chunk 1360 optimal weight: 4.9990 chunk 1121 optimal weight: 9.9990 chunk 1248 optimal weight: 9.9990 chunk 429 optimal weight: 6.9990 chunk 1010 optimal weight: 2.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 114 ASN C 5 GLN C 307 GLN G 61 GLN G 221 ASN H 5 GLN H 102 ASN H 157 ASN J 90 GLN ** K 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN N 182 ASN N 195 ASN R 34 GLN S 89 ASN ** S 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 131 GLN Y 66 GLN Z 123 GLN b 152 GLN g 3 GLN i 91 ASN n 69 GLN n 456 HIS q 228 ASN r 179 GLN t 230 ASN t 303 ASN v 213 GLN w 63 ASN w 83 GLN w 201 ASN x 176 GLN x 449 GLN 4 116 ASN 4 546 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 167341 Z= 0.230 Angle : 0.677 18.730 241944 Z= 0.360 Chirality : 0.039 0.319 29617 Planarity : 0.006 0.135 18328 Dihedral : 22.170 179.768 63305 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.26 % Allowed : 12.16 % Favored : 84.58 % 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: 1.93 (0.08), residues: 4184 sheet: 0.28 (0.12), residues: 1580 loop : -0.26 (0.08), residues: 4884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP e 32 HIS 0.008 0.001 HIS C 311 PHE 0.031 0.002 PHE F 229 TYR 0.022 0.002 TYR C 194 ARG 0.007 0.001 ARG l 21 *********************** 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 1643 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1340 time to evaluate : 9.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.8065 (mttt) cc_final: 0.7662 (mttp) REVERT: 8 59 THR cc_start: 0.7705 (m) cc_final: 0.7287 (p) REVERT: 9 21 HIS cc_start: 0.7155 (OUTLIER) cc_final: 0.6537 (m90) REVERT: 9 26 LYS cc_start: 0.8278 (mtmm) cc_final: 0.8078 (mtpm) REVERT: 9 30 ARG cc_start: 0.7889 (mtm180) cc_final: 0.7422 (mtp180) REVERT: B 71 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8002 (mt-10) REVERT: B 308 MET cc_start: 0.8450 (mmm) cc_final: 0.8226 (mmm) REVERT: B 336 VAL cc_start: 0.9076 (m) cc_final: 0.8840 (p) REVERT: C 99 MET cc_start: 0.8935 (ptm) cc_final: 0.8658 (ptm) REVERT: C 143 GLU cc_start: 0.7036 (mp0) cc_final: 0.6807 (mp0) REVERT: C 345 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6147 (tt0) REVERT: D 72 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6527 (p0) REVERT: D 130 GLU cc_start: 0.5167 (mm-30) cc_final: 0.4911 (mm-30) REVERT: D 163 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7145 (tp) REVERT: D 258 LYS cc_start: 0.5045 (OUTLIER) cc_final: 0.4057 (tptt) REVERT: E 136 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6607 (mm-30) REVERT: F 125 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: G 66 SER cc_start: 0.7239 (p) cc_final: 0.6831 (m) REVERT: G 70 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7734 (mtpp) REVERT: G 145 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7354 (m110) REVERT: G 171 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7521 (tptm) REVERT: G 207 ASP cc_start: 0.8023 (m-30) cc_final: 0.7774 (m-30) REVERT: G 230 LYS cc_start: 0.6500 (ptpt) cc_final: 0.6162 (pttt) REVERT: H 9 GLN cc_start: 0.7932 (mt0) cc_final: 0.7558 (mt0) REVERT: H 177 ASP cc_start: 0.8128 (m-30) cc_final: 0.7910 (m-30) REVERT: I 41 GLU cc_start: 0.4521 (OUTLIER) cc_final: 0.4089 (mm-30) REVERT: K 173 PHE cc_start: 0.7561 (t80) cc_final: 0.7198 (t80) REVERT: K 329 PHE cc_start: 0.4439 (t80) cc_final: 0.4111 (t80) REVERT: L 136 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6349 (mp0) REVERT: N 5 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6814 (tmtm) REVERT: N 10 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8580 (tp) REVERT: N 145 ASP cc_start: 0.8201 (t0) cc_final: 0.7971 (t0) REVERT: N 189 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8156 (tttm) REVERT: O 84 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7715 (mt) REVERT: O 89 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8389 (p) REVERT: O 130 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7511 (ttmt) REVERT: Q 22 ASP cc_start: 0.7704 (m-30) cc_final: 0.7375 (m-30) REVERT: R 72 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7235 (mt-10) REVERT: S 66 GLU cc_start: 0.8560 (tp30) cc_final: 0.8127 (tp30) REVERT: T 91 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7736 (mp) REVERT: T 149 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7749 (pt0) REVERT: U 39 ASP cc_start: 0.7933 (m-30) cc_final: 0.7657 (m-30) REVERT: W 21 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5990 (mp0) REVERT: W 194 LYS cc_start: 0.6869 (ttmm) cc_final: 0.6551 (tppt) REVERT: W 214 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7432 (mtmm) REVERT: Y 69 LYS cc_start: 0.8503 (ttmt) cc_final: 0.8267 (tttt) REVERT: Y 90 VAL cc_start: 0.7602 (OUTLIER) cc_final: 0.7354 (m) REVERT: Z 88 ASP cc_start: 0.7130 (t70) cc_final: 0.6681 (t0) REVERT: a 68 PHE cc_start: 0.6094 (p90) cc_final: 0.5684 (p90) REVERT: b 3 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6393 (tp) REVERT: b 316 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5614 (mm-30) REVERT: b 550 ASN cc_start: 0.6461 (m-40) cc_final: 0.6199 (m-40) REVERT: b 646 PHE cc_start: 0.7693 (p90) cc_final: 0.7450 (p90) REVERT: c 57 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8290 (mt-10) REVERT: d 62 ARG cc_start: 0.8567 (mtm180) cc_final: 0.8037 (mtm-85) REVERT: d 68 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7662 (mm-30) REVERT: e 34 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7674 (tmtm) REVERT: f 67 MET cc_start: 0.9198 (mtp) cc_final: 0.8755 (mtm) REVERT: h 107 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7880 (mtpt) REVERT: i 56 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6969 (ttp-110) REVERT: i 71 LYS cc_start: 0.7486 (ttmt) cc_final: 0.7154 (mttt) REVERT: k 16 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6691 (mtp-110) REVERT: l 11 GLN cc_start: 0.8471 (tt0) cc_final: 0.8252 (tt0) REVERT: m 63 ASP cc_start: 0.7800 (t0) cc_final: 0.7556 (t70) REVERT: m 124 ASP cc_start: 0.6253 (p0) cc_final: 0.5893 (p0) REVERT: m 125 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6213 (pm20) REVERT: m 314 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7539 (mttt) REVERT: m 429 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6971 (tp30) REVERT: n 5 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7370 (mtmm) REVERT: n 72 MET cc_start: 0.6964 (tpp) cc_final: 0.6578 (tpp) REVERT: n 150 GLN cc_start: 0.7040 (mt0) cc_final: 0.6727 (mt0) REVERT: n 174 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6490 (mtp180) REVERT: n 198 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6611 (ttp80) REVERT: n 252 LYS cc_start: 0.7652 (mtmt) cc_final: 0.7425 (mtmt) REVERT: n 366 TYR cc_start: 0.6324 (t80) cc_final: 0.5932 (t80) REVERT: n 376 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7645 (mp) REVERT: n 388 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6301 (mm) REVERT: n 390 GLU cc_start: 0.5838 (OUTLIER) cc_final: 0.5139 (tt0) REVERT: n 440 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5967 (mt-10) REVERT: o 105 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6741 (pttp) REVERT: o 110 TYR cc_start: 0.8318 (t80) cc_final: 0.7979 (t80) REVERT: o 121 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6467 (mtp180) REVERT: o 152 MET cc_start: 0.7494 (mmm) cc_final: 0.7113 (mmm) REVERT: q 210 GLU cc_start: 0.6582 (mm-30) cc_final: 0.6347 (mt-10) REVERT: q 249 GLU cc_start: 0.4679 (tp30) cc_final: 0.4247 (tp30) REVERT: q 259 LYS cc_start: 0.6784 (mmpt) cc_final: 0.6529 (mmmt) REVERT: q 412 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5259 (mp0) REVERT: r 54 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7397 (mmm160) REVERT: s 60 ILE cc_start: 0.7588 (mm) cc_final: 0.7336 (mt) REVERT: t 82 GLU cc_start: 0.5680 (mm-30) cc_final: 0.5020 (pt0) REVERT: t 297 ARG cc_start: 0.5747 (ttp-170) cc_final: 0.5197 (mtm-85) REVERT: u 76 ASN cc_start: 0.8995 (m-40) cc_final: 0.8660 (m-40) REVERT: v 39 ASN cc_start: 0.5471 (OUTLIER) cc_final: 0.5235 (m-40) REVERT: v 113 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6444 (mtm) REVERT: v 268 MET cc_start: 0.8841 (mmm) cc_final: 0.8473 (mmm) REVERT: v 277 MET cc_start: 0.8595 (mmm) cc_final: 0.8089 (mmm) REVERT: v 284 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7536 (mmmt) REVERT: x 289 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7394 (mt0) REVERT: x 365 LYS cc_start: 0.4575 (tppt) cc_final: 0.4041 (tttp) REVERT: x 397 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6775 (ttt180) REVERT: y 1 MET cc_start: 0.5514 (OUTLIER) cc_final: 0.4663 (ttt) REVERT: y 39 GLU cc_start: 0.8232 (tt0) cc_final: 0.7977 (tt0) REVERT: y 112 ASP cc_start: 0.8369 (m-30) cc_final: 0.8123 (m-30) REVERT: z 99 LYS cc_start: 0.7531 (mttm) cc_final: 0.7201 (mtpt) REVERT: z 105 ARG cc_start: 0.7789 (mtt-85) cc_final: 0.7566 (mtt180) REVERT: 4 167 LYS cc_start: 0.5050 (mmtt) cc_final: 0.4720 (tptt) REVERT: 4 232 ARG cc_start: 0.6634 (ttp-110) cc_final: 0.6304 (ttm110) REVERT: 4 272 SER cc_start: 0.7749 (p) cc_final: 0.7339 (t) REVERT: 4 373 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7780 (ttmt) REVERT: 4 404 GLU cc_start: 0.5652 (mt-10) cc_final: 0.5342 (tp30) REVERT: 4 489 MET cc_start: 0.7399 (ttm) cc_final: 0.6899 (ttp) REVERT: 4 568 LEU cc_start: 0.5577 (tp) cc_final: 0.5299 (mt) outliers start: 303 outliers final: 146 residues processed: 1508 average time/residue: 2.5041 time to fit residues: 5311.9727 Evaluate side-chains 1431 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1240 time to evaluate : 9.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 124 THR Chi-restraints excluded: chain 9 residue 19 LYS Chi-restraints excluded: chain 9 residue 21 HIS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 338 ASN Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain L residue 176 GLU Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain W residue 21 GLU Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 214 LYS Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 108 GLU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain b residue 461 GLU Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain c residue 98 SER Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 38 ILE Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 113 LYS Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain h residue 107 LYS Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 125 GLU Chi-restraints excluded: chain m residue 170 LYS Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain m residue 422 LYS Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain m residue 447 SER Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 198 ARG Chi-restraints excluded: chain n residue 259 LEU Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 386 ASN Chi-restraints excluded: chain n residue 388 ILE Chi-restraints excluded: chain n residue 390 GLU Chi-restraints excluded: chain n residue 440 GLU Chi-restraints excluded: chain n residue 442 VAL Chi-restraints excluded: chain n residue 445 ASN Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 121 ARG Chi-restraints excluded: chain o residue 146 MET Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 412 GLU Chi-restraints excluded: chain r residue 54 ARG Chi-restraints excluded: chain r residue 66 LYS Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain s residue 16 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 GLU Chi-restraints excluded: chain s residue 35 LYS Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain t residue 40 LYS Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 206 SER Chi-restraints excluded: chain t residue 296 SER Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 112 MET Chi-restraints excluded: chain v residue 39 ASN Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 113 MET Chi-restraints excluded: chain v residue 114 ILE Chi-restraints excluded: chain v residue 120 ASP Chi-restraints excluded: chain v residue 190 PHE Chi-restraints excluded: chain v residue 208 SER Chi-restraints excluded: chain v residue 224 VAL Chi-restraints excluded: chain v residue 226 ILE Chi-restraints excluded: chain v residue 237 ILE Chi-restraints excluded: chain w residue 155 ASP Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 145 THR Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 289 GLN Chi-restraints excluded: chain x residue 336 ILE Chi-restraints excluded: chain x residue 389 LEU Chi-restraints excluded: chain x residue 392 THR Chi-restraints excluded: chain x residue 397 ARG Chi-restraints excluded: chain x residue 398 MET Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 175 SER Chi-restraints excluded: chain y residue 185 THR Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 45 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 307 ASP Chi-restraints excluded: chain 4 residue 330 THR Chi-restraints excluded: chain 4 residue 370 LEU Chi-restraints excluded: chain 4 residue 517 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: 5.9990 chunk 653 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 600 optimal weight: 5.9990 chunk 845 optimal weight: 7.9990 chunk 1263 optimal weight: 0.0010 chunk 1337 optimal weight: 9.9990 chunk 660 optimal weight: 9.9990 chunk 1197 optimal weight: 3.9990 chunk 360 optimal weight: 0.0040 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN 9 106 GLN C 307 GLN D 57 ASN E 138 GLN F 194 HIS G 221 ASN H 5 GLN H 102 ASN H 157 ASN J 90 GLN ** K 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN N 182 ASN N 195 ASN O 182 ASN P 92 GLN R 34 GLN S 89 ASN ** S 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN Y 66 GLN Z 123 GLN b 152 GLN g 3 GLN i 91 ASN n 69 GLN n 456 HIS q 228 ASN r 179 GLN t 230 ASN ** v 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 63 ASN w 201 ASN x 17 GLN y 145 ASN 4 546 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 167341 Z= 0.180 Angle : 0.628 17.694 241944 Z= 0.338 Chirality : 0.037 0.321 29617 Planarity : 0.006 0.130 18328 Dihedral : 22.104 179.456 63305 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.12 % Allowed : 13.14 % Favored : 83.74 % 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: 1.12 (0.08), residues: 10648 helix: 2.05 (0.08), residues: 4183 sheet: 0.28 (0.12), residues: 1582 loop : -0.21 (0.08), residues: 4883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 32 HIS 0.007 0.001 HIS C 311 PHE 0.026 0.002 PHE F 229 TYR 0.019 0.002 TYR C 194 ARG 0.007 0.000 ARG t 292 *********************** 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 1568 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1278 time to evaluate : 9.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8434 (tp) cc_final: 0.8180 (tt) REVERT: A 119 LYS cc_start: 0.8060 (mttt) cc_final: 0.7665 (mttp) REVERT: 8 59 THR cc_start: 0.7689 (m) cc_final: 0.7278 (p) REVERT: 8 146 LYS cc_start: 0.6125 (OUTLIER) cc_final: 0.5777 (mtpp) REVERT: 9 21 HIS cc_start: 0.7152 (OUTLIER) cc_final: 0.6549 (m90) REVERT: 9 26 LYS cc_start: 0.8274 (mtmm) cc_final: 0.8065 (mtpm) REVERT: 9 30 ARG cc_start: 0.7894 (mtm180) cc_final: 0.7436 (mtp180) REVERT: B 71 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7984 (mt-10) REVERT: B 336 VAL cc_start: 0.9056 (m) cc_final: 0.8833 (p) REVERT: C 99 MET cc_start: 0.8896 (ptm) cc_final: 0.8621 (ptm) REVERT: C 143 GLU cc_start: 0.6967 (mp0) cc_final: 0.6702 (mp0) REVERT: D 130 GLU cc_start: 0.5197 (mm-30) cc_final: 0.4944 (mm-30) REVERT: D 163 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7169 (tp) REVERT: D 218 ARG cc_start: 0.6160 (mtp85) cc_final: 0.5632 (mmt-90) REVERT: D 258 LYS cc_start: 0.5134 (OUTLIER) cc_final: 0.4178 (tptt) REVERT: E 136 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6711 (mm-30) REVERT: F 125 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: G 66 SER cc_start: 0.7211 (p) cc_final: 0.6813 (m) REVERT: G 70 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7707 (mtpp) REVERT: G 145 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7340 (m110) REVERT: G 161 GLU cc_start: 0.8088 (mp0) cc_final: 0.7805 (mp0) REVERT: G 207 ASP cc_start: 0.8067 (m-30) cc_final: 0.7716 (m-30) REVERT: G 230 LYS cc_start: 0.6481 (ptpt) cc_final: 0.6153 (pttt) REVERT: H 9 GLN cc_start: 0.7909 (mt0) cc_final: 0.7528 (mt0) REVERT: H 177 ASP cc_start: 0.7970 (m-30) cc_final: 0.7750 (m-30) REVERT: I 41 GLU cc_start: 0.4536 (OUTLIER) cc_final: 0.4072 (mm-30) REVERT: K 173 PHE cc_start: 0.7580 (t80) cc_final: 0.7219 (t80) REVERT: K 329 PHE cc_start: 0.4666 (t80) cc_final: 0.4457 (t80) REVERT: L 68 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7757 (ptpt) REVERT: L 136 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6317 (mp0) REVERT: N 5 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6711 (tmtm) REVERT: N 10 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8552 (tp) REVERT: N 145 ASP cc_start: 0.8204 (t0) cc_final: 0.7988 (t0) REVERT: O 84 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7796 (mt) REVERT: O 130 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7544 (ttmt) REVERT: Q 22 ASP cc_start: 0.7663 (m-30) cc_final: 0.7320 (m-30) REVERT: R 5 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7608 (ttm170) REVERT: S 46 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6995 (tt0) REVERT: S 66 GLU cc_start: 0.8559 (tp30) cc_final: 0.8024 (tp30) REVERT: T 52 MET cc_start: 0.4981 (OUTLIER) cc_final: 0.3972 (tpp) REVERT: T 91 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7738 (mp) REVERT: T 149 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7733 (pt0) REVERT: U 39 ASP cc_start: 0.7892 (m-30) cc_final: 0.7586 (m-30) REVERT: U 88 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.6867 (mt0) REVERT: W 194 LYS cc_start: 0.6677 (ttmm) cc_final: 0.6433 (tppt) REVERT: W 214 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7393 (mtmm) REVERT: Y 84 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7516 (mmtm) REVERT: Y 90 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7515 (m) REVERT: Z 88 ASP cc_start: 0.7140 (t70) cc_final: 0.6714 (t0) REVERT: a 68 PHE cc_start: 0.6076 (p90) cc_final: 0.5663 (p90) REVERT: a 96 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6938 (tppp) REVERT: b 247 ARG cc_start: 0.6632 (ptt90) cc_final: 0.6334 (ptt90) REVERT: b 646 PHE cc_start: 0.7680 (p90) cc_final: 0.7451 (p90) REVERT: c 57 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8287 (mt-10) REVERT: d 62 ARG cc_start: 0.8532 (mtm180) cc_final: 0.8010 (mtm-85) REVERT: d 68 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7734 (mm-30) REVERT: e 34 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7587 (tmtm) REVERT: e 120 THR cc_start: 0.8290 (m) cc_final: 0.7913 (p) REVERT: f 67 MET cc_start: 0.9191 (mtp) cc_final: 0.8799 (mtm) REVERT: h 107 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7867 (mtpt) REVERT: i 56 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6924 (ttp-110) REVERT: i 71 LYS cc_start: 0.7471 (ttmt) cc_final: 0.7126 (mttt) REVERT: j 55 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7508 (ttp-170) REVERT: k 16 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6358 (mtp180) REVERT: l 11 GLN cc_start: 0.8529 (tt0) cc_final: 0.8309 (tt0) REVERT: m 314 LYS cc_start: 0.7896 (mmtm) cc_final: 0.7510 (mttt) REVERT: m 429 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6798 (tp30) REVERT: n 5 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7325 (mtmm) REVERT: n 72 MET cc_start: 0.7020 (tpp) cc_final: 0.6540 (tpp) REVERT: n 150 GLN cc_start: 0.7003 (mt0) cc_final: 0.6683 (mt0) REVERT: n 174 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6526 (mtp180) REVERT: n 198 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6557 (ttp80) REVERT: n 366 TYR cc_start: 0.6298 (t80) cc_final: 0.5977 (t80) REVERT: n 376 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7634 (mp) REVERT: n 388 ILE cc_start: 0.6673 (OUTLIER) cc_final: 0.6226 (mm) REVERT: n 390 GLU cc_start: 0.5816 (OUTLIER) cc_final: 0.5083 (tt0) REVERT: n 440 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.5970 (mt-10) REVERT: o 105 LYS cc_start: 0.6933 (OUTLIER) cc_final: 0.6689 (pttp) REVERT: o 110 TYR cc_start: 0.8260 (t80) cc_final: 0.7960 (t80) REVERT: o 121 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6449 (mtp180) REVERT: o 152 MET cc_start: 0.7423 (mmm) cc_final: 0.7059 (mmm) REVERT: q 249 GLU cc_start: 0.4705 (tp30) cc_final: 0.4160 (tp30) REVERT: q 259 LYS cc_start: 0.6790 (mmpt) cc_final: 0.6533 (mmmt) REVERT: q 412 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.5509 (mp0) REVERT: s 60 ILE cc_start: 0.7577 (mm) cc_final: 0.7317 (mt) REVERT: t 82 GLU cc_start: 0.5691 (mm-30) cc_final: 0.5032 (pt0) REVERT: t 292 ARG cc_start: 0.6729 (mtt90) cc_final: 0.6347 (mtm-85) REVERT: t 297 ARG cc_start: 0.5683 (ttp-170) cc_final: 0.5188 (mtm-85) REVERT: u 76 ASN cc_start: 0.8997 (m-40) cc_final: 0.8671 (m-40) REVERT: v 268 MET cc_start: 0.8843 (mmm) cc_final: 0.8444 (mmm) REVERT: v 277 MET cc_start: 0.8582 (mmm) cc_final: 0.8095 (mmm) REVERT: v 284 LYS cc_start: 0.7854 (mtpp) cc_final: 0.7596 (mmmt) REVERT: w 32 ASN cc_start: 0.5838 (m-40) cc_final: 0.5608 (m-40) REVERT: w 55 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.5621 (tmm160) REVERT: w 186 ARG cc_start: 0.7674 (ttp80) cc_final: 0.7405 (ttp80) REVERT: x 379 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: x 397 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6861 (ttt180) REVERT: y 1 MET cc_start: 0.5595 (OUTLIER) cc_final: 0.4762 (ttt) REVERT: y 39 GLU cc_start: 0.8227 (tt0) cc_final: 0.7971 (tt0) REVERT: y 112 ASP cc_start: 0.8326 (m-30) cc_final: 0.8107 (m-30) REVERT: z 99 LYS cc_start: 0.7527 (mttm) cc_final: 0.7192 (mtpt) REVERT: z 105 ARG cc_start: 0.7780 (mtt-85) cc_final: 0.7558 (mtt180) REVERT: 4 167 LYS cc_start: 0.4983 (mmtt) cc_final: 0.4642 (tptt) REVERT: 4 232 ARG cc_start: 0.6598 (ttp-110) cc_final: 0.6288 (ttm110) REVERT: 4 272 SER cc_start: 0.7724 (p) cc_final: 0.7321 (t) REVERT: 4 373 LYS cc_start: 0.8042 (ttpp) cc_final: 0.7756 (ttmt) REVERT: 4 404 GLU cc_start: 0.5689 (mt-10) cc_final: 0.5361 (tp30) REVERT: 4 489 MET cc_start: 0.7354 (ttm) cc_final: 0.6917 (ttp) REVERT: 4 568 LEU cc_start: 0.5680 (tp) cc_final: 0.5376 (mt) outliers start: 290 outliers final: 137 residues processed: 1442 average time/residue: 2.5106 time to fit residues: 5098.3829 Evaluate side-chains 1408 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1228 time to evaluate : 9.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 8 residue 85 LEU Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 146 LYS Chi-restraints excluded: chain 9 residue 19 LYS Chi-restraints excluded: chain 9 residue 21 HIS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain K residue 338 ASN Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain L residue 176 GLU Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 153 LYS Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 46 GLN Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 88 GLN Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 214 LYS Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 108 GLU Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 265 GLU Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain b residue 461 GLU Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain c residue 98 SER Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 113 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 67 LYS Chi-restraints excluded: chain h residue 107 LYS Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain j residue 55 ARG Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain m residue 170 LYS Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain m residue 422 LYS Chi-restraints excluded: chain m residue 447 SER Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 198 ARG Chi-restraints excluded: chain n residue 259 LEU Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 386 ASN Chi-restraints excluded: chain n residue 388 ILE Chi-restraints excluded: chain n residue 390 GLU Chi-restraints excluded: chain n residue 440 GLU Chi-restraints excluded: chain n residue 445 ASN Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 121 ARG Chi-restraints excluded: chain o residue 146 MET Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 412 GLU Chi-restraints excluded: chain r residue 66 LYS Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain s residue 3 VAL Chi-restraints excluded: chain s residue 16 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 GLU Chi-restraints excluded: chain s residue 35 LYS Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain t residue 40 LYS Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 206 SER Chi-restraints excluded: chain t residue 296 SER Chi-restraints excluded: chain t residue 310 ILE Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 120 ASP Chi-restraints excluded: chain v residue 208 SER Chi-restraints excluded: chain w residue 55 ARG Chi-restraints excluded: chain w residue 155 ASP Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 166 ASN Chi-restraints excluded: chain x residue 183 LYS Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 336 ILE Chi-restraints excluded: chain x residue 379 ASP Chi-restraints excluded: chain x residue 389 LEU Chi-restraints excluded: chain x residue 392 THR Chi-restraints excluded: chain x residue 397 ARG Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 175 SER Chi-restraints excluded: chain y residue 185 THR Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 45 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 170 LEU Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 307 ASP Chi-restraints excluded: chain 4 residue 330 THR Chi-restraints excluded: chain 4 residue 370 LEU Chi-restraints excluded: chain 4 residue 517 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 1114 optimal weight: 0.0010 chunk 759 optimal weight: 0.0570 chunk 19 optimal weight: 9.9990 chunk 996 optimal weight: 10.0000 chunk 551 optimal weight: 10.0000 chunk 1141 optimal weight: 9.9990 chunk 924 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 683 optimal weight: 5.9990 chunk 1200 optimal weight: 0.7980 chunk 337 optimal weight: 30.0000 overall best weight: 1.5708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN C 18 ASN C 304 GLN C 307 GLN G 24 ASN G 61 GLN G 221 ASN H 5 GLN H 102 ASN H 157 ASN ** K 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN M 41 GLN N 182 ASN N 195 ASN P 92 GLN P 179 GLN R 34 GLN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN T 131 GLN Y 66 GLN Z 123 GLN b 152 GLN g 3 GLN i 91 ASN n 48 ASN n 69 GLN n 456 HIS t 230 ASN ** v 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 63 ASN w 201 ASN x 176 GLN y 145 ASN 4 546 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 167341 Z= 0.128 Angle : 0.592 17.089 241944 Z= 0.321 Chirality : 0.035 0.326 29617 Planarity : 0.005 0.125 18328 Dihedral : 22.050 179.784 63303 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.70 % Allowed : 14.09 % Favored : 83.22 % 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: 1.28 (0.08), residues: 10648 helix: 2.22 (0.08), residues: 4182 sheet: 0.34 (0.12), residues: 1580 loop : -0.15 (0.08), residues: 4886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP e 32 HIS 0.006 0.001 HIS S 122 PHE 0.021 0.001 PHE F 229 TYR 0.022 0.001 TYR q 387 ARG 0.007 0.000 ARG b 100 *********************** 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 1531 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1280 time to evaluate : 8.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8412 (tp) cc_final: 0.8161 (tt) REVERT: A 119 LYS cc_start: 0.7943 (mttt) cc_final: 0.7647 (mttp) REVERT: 8 59 THR cc_start: 0.7713 (m) cc_final: 0.7300 (p) REVERT: 8 111 GLU cc_start: 0.7013 (tp30) cc_final: 0.6781 (tp30) REVERT: 9 21 HIS cc_start: 0.7145 (OUTLIER) cc_final: 0.6536 (m90) REVERT: 9 30 ARG cc_start: 0.7842 (mtm180) cc_final: 0.7305 (mtp180) REVERT: B 71 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7903 (mt-10) REVERT: B 336 VAL cc_start: 0.9043 (m) cc_final: 0.8831 (p) REVERT: C 99 MET cc_start: 0.8862 (ptm) cc_final: 0.8564 (ptm) REVERT: D 130 GLU cc_start: 0.5190 (mm-30) cc_final: 0.4950 (mm-30) REVERT: D 163 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7181 (tp) REVERT: D 218 ARG cc_start: 0.6071 (mtp85) cc_final: 0.5611 (mmt-90) REVERT: D 258 LYS cc_start: 0.5094 (OUTLIER) cc_final: 0.4277 (tptt) REVERT: E 136 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6708 (mm-30) REVERT: F 125 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: G 66 SER cc_start: 0.7100 (p) cc_final: 0.6715 (m) REVERT: G 145 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7339 (m110) REVERT: G 161 GLU cc_start: 0.8030 (mp0) cc_final: 0.7742 (mp0) REVERT: G 171 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7449 (tptm) REVERT: G 230 LYS cc_start: 0.6471 (ptpt) cc_final: 0.6199 (pttm) REVERT: H 1 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.5335 (tmm) REVERT: H 9 GLN cc_start: 0.7896 (mt0) cc_final: 0.7491 (mt0) REVERT: H 161 LEU cc_start: 0.8564 (tp) cc_final: 0.8301 (tm) REVERT: H 177 ASP cc_start: 0.7931 (m-30) cc_final: 0.7712 (m-30) REVERT: I 41 GLU cc_start: 0.4365 (OUTLIER) cc_final: 0.3906 (mm-30) REVERT: I 56 LYS cc_start: 0.6334 (OUTLIER) cc_final: 0.6108 (tttt) REVERT: I 122 LEU cc_start: 0.5360 (mt) cc_final: 0.5104 (mm) REVERT: J 14 ILE cc_start: 0.5172 (OUTLIER) cc_final: 0.4708 (pp) REVERT: K 173 PHE cc_start: 0.7586 (t80) cc_final: 0.7235 (t80) REVERT: K 329 PHE cc_start: 0.4556 (t80) cc_final: 0.4346 (t80) REVERT: L 136 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6349 (mp0) REVERT: N 10 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8473 (tp) REVERT: N 145 ASP cc_start: 0.8197 (t0) cc_final: 0.7972 (t0) REVERT: O 106 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: O 130 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7541 (ttmt) REVERT: Q 22 ASP cc_start: 0.7639 (m-30) cc_final: 0.7319 (m-30) REVERT: R 5 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7496 (ttm170) REVERT: S 66 GLU cc_start: 0.8558 (tp30) cc_final: 0.8023 (tp30) REVERT: T 91 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7675 (mp) REVERT: T 149 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7743 (pt0) REVERT: U 39 ASP cc_start: 0.7879 (m-30) cc_final: 0.7568 (m-30) REVERT: U 76 LEU cc_start: 0.9010 (tp) cc_final: 0.8737 (tp) REVERT: U 88 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.6912 (mt0) REVERT: W 168 LYS cc_start: 0.7940 (tttt) cc_final: 0.7733 (tttp) REVERT: W 194 LYS cc_start: 0.6819 (ttmm) cc_final: 0.6570 (tppt) REVERT: W 214 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7379 (mtmm) REVERT: Y 84 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7494 (mmtm) REVERT: Z 88 ASP cc_start: 0.7129 (t70) cc_final: 0.6691 (t0) REVERT: a 68 PHE cc_start: 0.6083 (p90) cc_final: 0.5667 (p90) REVERT: a 96 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6952 (tppp) REVERT: b 88 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7319 (ttmm) REVERT: b 247 ARG cc_start: 0.6597 (ptt90) cc_final: 0.6294 (ptt90) REVERT: b 316 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.5636 (mm-30) REVERT: b 526 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7551 (ttpt) REVERT: b 646 PHE cc_start: 0.7647 (p90) cc_final: 0.7391 (p90) REVERT: c 57 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8288 (mt-10) REVERT: d 42 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7784 (tp) REVERT: d 62 ARG cc_start: 0.8507 (mtm180) cc_final: 0.8070 (mtm-85) REVERT: d 68 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7812 (mm-30) REVERT: e 34 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7519 (tmtm) REVERT: e 120 THR cc_start: 0.8292 (m) cc_final: 0.8030 (p) REVERT: f 67 MET cc_start: 0.9181 (mtp) cc_final: 0.8790 (mtm) REVERT: i 56 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6896 (ttp-110) REVERT: i 71 LYS cc_start: 0.7403 (ttmt) cc_final: 0.7097 (mttt) REVERT: j 55 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7511 (ttp-170) REVERT: k 16 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6267 (mtp-110) REVERT: m 314 LYS cc_start: 0.7877 (mmtm) cc_final: 0.7509 (mttt) REVERT: m 429 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6858 (tp30) REVERT: n 5 LYS cc_start: 0.7664 (mmtt) cc_final: 0.7330 (mtmm) REVERT: n 72 MET cc_start: 0.7065 (tpp) cc_final: 0.6638 (tpp) REVERT: n 150 GLN cc_start: 0.7001 (mt0) cc_final: 0.6679 (mt0) REVERT: n 174 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6514 (mtp180) REVERT: n 198 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6557 (ttp80) REVERT: n 366 TYR cc_start: 0.6257 (t80) cc_final: 0.5964 (t80) REVERT: n 376 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7566 (mp) REVERT: n 390 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.4923 (tt0) REVERT: n 440 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5955 (mt-10) REVERT: o 110 TYR cc_start: 0.8227 (t80) cc_final: 0.7956 (t80) REVERT: o 121 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6416 (mtp180) REVERT: o 152 MET cc_start: 0.7349 (mmm) cc_final: 0.6906 (mmm) REVERT: q 249 GLU cc_start: 0.4669 (tp30) cc_final: 0.4113 (tp30) REVERT: q 259 LYS cc_start: 0.6769 (mmpt) cc_final: 0.6495 (mmmt) REVERT: s 60 ILE cc_start: 0.7553 (mm) cc_final: 0.7300 (mt) REVERT: t 82 GLU cc_start: 0.5637 (mm-30) cc_final: 0.5037 (pt0) REVERT: t 213 ARG cc_start: 0.7139 (mtp85) cc_final: 0.6879 (mmm-85) REVERT: t 292 ARG cc_start: 0.6721 (mtt90) cc_final: 0.6272 (mtm-85) REVERT: t 297 ARG cc_start: 0.5667 (ttp-170) cc_final: 0.5171 (mtm-85) REVERT: u 76 ASN cc_start: 0.8990 (m-40) cc_final: 0.8620 (m-40) REVERT: u 98 GLU cc_start: 0.7184 (tt0) cc_final: 0.6966 (tt0) REVERT: v 57 MET cc_start: 0.7257 (tmm) cc_final: 0.7032 (tmm) REVERT: v 184 MET cc_start: 0.7264 (mtp) cc_final: 0.7029 (mtp) REVERT: v 251 LYS cc_start: 0.7041 (mmtp) cc_final: 0.6352 (mmtp) REVERT: v 268 MET cc_start: 0.8827 (mmm) cc_final: 0.8404 (mmm) REVERT: v 277 MET cc_start: 0.8520 (mmm) cc_final: 0.7919 (mmm) REVERT: v 284 LYS cc_start: 0.7835 (mtpp) cc_final: 0.7602 (mmmt) REVERT: w 32 ASN cc_start: 0.5822 (m-40) cc_final: 0.5599 (m-40) REVERT: w 128 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.4942 (ptm160) REVERT: w 186 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7415 (ttp80) REVERT: x 289 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7325 (mt0) REVERT: x 365 LYS cc_start: 0.4574 (tppt) cc_final: 0.4324 (tttp) REVERT: x 397 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.7061 (ttt180) REVERT: y 1 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.4791 (ttt) REVERT: y 112 ASP cc_start: 0.8319 (m-30) cc_final: 0.8117 (m-30) REVERT: z 99 LYS cc_start: 0.7481 (mttm) cc_final: 0.7137 (mtpt) REVERT: z 105 ARG cc_start: 0.7762 (mtt-85) cc_final: 0.7537 (mtt180) REVERT: 4 167 LYS cc_start: 0.4924 (mmtt) cc_final: 0.4598 (tptt) REVERT: 4 232 ARG cc_start: 0.6593 (ttp-110) cc_final: 0.6292 (ttm110) REVERT: 4 272 SER cc_start: 0.7696 (p) cc_final: 0.7292 (t) REVERT: 4 373 LYS cc_start: 0.7986 (ttpp) cc_final: 0.7709 (ttmt) REVERT: 4 404 GLU cc_start: 0.5668 (mt-10) cc_final: 0.5341 (tp30) REVERT: 4 489 MET cc_start: 0.7349 (ttm) cc_final: 0.6914 (ttp) REVERT: 4 568 LEU cc_start: 0.5644 (tp) cc_final: 0.5365 (mt) outliers start: 251 outliers final: 120 residues processed: 1429 average time/residue: 2.4787 time to fit residues: 4996.4147 Evaluate side-chains 1403 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1244 time to evaluate : 9.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 9 residue 19 LYS Chi-restraints excluded: chain 9 residue 21 HIS Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 338 ASN Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 106 GLU Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 88 GLN Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 184 SER Chi-restraints excluded: chain W residue 214 LYS Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 88 LYS Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 265 GLU Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain b residue 461 GLU Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 54 LYS Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain j residue 55 ARG Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 45 VAL Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain m residue 124 ASP Chi-restraints excluded: chain m residue 170 LYS Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain m residue 422 LYS Chi-restraints excluded: chain m residue 447 SER Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 198 ARG Chi-restraints excluded: chain n residue 259 LEU Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 386 ASN Chi-restraints excluded: chain n residue 390 GLU Chi-restraints excluded: chain n residue 440 GLU Chi-restraints excluded: chain n residue 442 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 121 ARG Chi-restraints excluded: chain o residue 146 MET Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 235 SER Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain s residue 16 LYS Chi-restraints excluded: chain s residue 30 GLU Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain t residue 40 LYS Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 206 SER Chi-restraints excluded: chain t residue 296 SER Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain v residue 208 SER Chi-restraints excluded: chain v residue 226 ILE Chi-restraints excluded: chain w residue 128 ARG Chi-restraints excluded: chain w residue 155 ASP Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 183 LYS Chi-restraints excluded: chain x residue 191 CYS Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 289 GLN Chi-restraints excluded: chain x residue 389 LEU Chi-restraints excluded: chain x residue 392 THR Chi-restraints excluded: chain x residue 397 ARG Chi-restraints excluded: chain x residue 398 MET Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 145 ASN Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 175 SER Chi-restraints excluded: chain y residue 185 THR Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 45 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 170 LEU Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 307 ASP Chi-restraints excluded: chain 4 residue 330 THR Chi-restraints excluded: chain 4 residue 466 LEU Chi-restraints excluded: chain 4 residue 517 THR Chi-restraints excluded: chain 4 residue 521 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 450 optimal weight: 9.9990 chunk 1204 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 chunk 785 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 1339 optimal weight: 0.0070 chunk 1111 optimal weight: 2.9990 chunk 619 optimal weight: 9.9990 chunk 111 optimal weight: 30.0000 chunk 442 optimal weight: 9.9990 chunk 702 optimal weight: 9.9990 overall best weight: 5.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN C 18 ASN C 304 GLN C 307 GLN G 24 ASN G 61 GLN G 221 ASN H 5 GLN H 157 ASN J 90 GLN L 114 GLN N 182 ASN N 195 ASN P 10 ASN P 179 GLN R 34 GLN S 46 GLN ** S 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN T 131 GLN X 65 GLN b 152 GLN g 3 GLN h 104 GLN i 91 ASN ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS q 228 ASN t 230 ASN ** v 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 63 ASN w 83 GLN w 201 ASN x 176 GLN 4 471 HIS 4 546 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 167341 Z= 0.286 Angle : 0.730 19.247 241944 Z= 0.384 Chirality : 0.041 0.346 29617 Planarity : 0.007 0.139 18328 Dihedral : 22.194 179.946 63300 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.47 % Allowed : 13.78 % Favored : 82.75 % 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: 0.91 (0.08), residues: 10648 helix: 1.85 (0.08), residues: 4175 sheet: 0.19 (0.12), residues: 1564 loop : -0.30 (0.08), residues: 4909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP e 32 HIS 0.009 0.002 HIS C 311 PHE 0.033 0.002 PHE F 229 TYR 0.024 0.002 TYR C 194 ARG 0.008 0.001 ARG l 21 *********************** 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 1589 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 1266 time to evaluate : 9.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.8059 (mttt) cc_final: 0.7663 (mttp) REVERT: 8 59 THR cc_start: 0.7655 (m) cc_final: 0.7259 (p) REVERT: 8 146 LYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5784 (mtpp) REVERT: 9 30 ARG cc_start: 0.7941 (mtm180) cc_final: 0.7373 (mtp180) REVERT: B 71 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8026 (mt-10) REVERT: B 336 VAL cc_start: 0.9083 (m) cc_final: 0.8841 (p) REVERT: C 143 GLU cc_start: 0.7113 (mp0) cc_final: 0.6870 (mp0) REVERT: D 163 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7165 (tp) REVERT: D 258 LYS cc_start: 0.5207 (OUTLIER) cc_final: 0.4089 (tptt) REVERT: E 136 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6592 (mm-30) REVERT: F 125 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: G 66 SER cc_start: 0.7300 (p) cc_final: 0.6839 (m) REVERT: G 70 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7805 (mtpp) REVERT: G 145 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7372 (m110) REVERT: G 161 GLU cc_start: 0.8038 (mp0) cc_final: 0.7734 (mp0) REVERT: G 230 LYS cc_start: 0.6501 (ptpt) cc_final: 0.6151 (pttt) REVERT: H 9 GLN cc_start: 0.7948 (mt0) cc_final: 0.7581 (mt0) REVERT: H 177 ASP cc_start: 0.8081 (m-30) cc_final: 0.7866 (m-30) REVERT: I 78 LYS cc_start: 0.6706 (tttt) cc_final: 0.6410 (tttm) REVERT: K 170 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6723 (ttm170) REVERT: K 173 PHE cc_start: 0.7486 (t80) cc_final: 0.7131 (t80) REVERT: N 5 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6911 (tmtm) REVERT: N 10 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8650 (tp) REVERT: N 23 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8507 (tm130) REVERT: N 145 ASP cc_start: 0.8236 (t0) cc_final: 0.8019 (t0) REVERT: O 130 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7573 (ttmt) REVERT: P 152 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7479 (mt-10) REVERT: Q 22 ASP cc_start: 0.7617 (m-30) cc_final: 0.7262 (m-30) REVERT: R 5 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.7547 (ttm170) REVERT: S 66 GLU cc_start: 0.8552 (tp30) cc_final: 0.8099 (tp30) REVERT: T 38 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6546 (m-30) REVERT: T 91 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7598 (mp) REVERT: T 149 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7678 (pt0) REVERT: U 39 ASP cc_start: 0.7887 (m-30) cc_final: 0.7567 (m-30) REVERT: W 194 LYS cc_start: 0.6785 (ttmm) cc_final: 0.6530 (tppt) REVERT: W 214 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7448 (mtmm) REVERT: Y 54 ASP cc_start: 0.7853 (p0) cc_final: 0.6624 (p0) REVERT: Y 90 VAL cc_start: 0.7709 (OUTLIER) cc_final: 0.7430 (m) REVERT: Z 88 ASP cc_start: 0.7220 (t70) cc_final: 0.6735 (t0) REVERT: a 68 PHE cc_start: 0.6086 (p90) cc_final: 0.5666 (p90) REVERT: b 247 ARG cc_start: 0.6700 (ptt90) cc_final: 0.6405 (ptt90) REVERT: b 448 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5521 (pm20) REVERT: b 646 PHE cc_start: 0.7710 (p90) cc_final: 0.7472 (p90) REVERT: c 36 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7302 (mt0) REVERT: c 57 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8285 (mt-10) REVERT: d 62 ARG cc_start: 0.8533 (mtm180) cc_final: 0.8066 (mtm-85) REVERT: d 68 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7738 (mm-30) REVERT: e 34 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7731 (tmtm) REVERT: f 67 MET cc_start: 0.9210 (mtp) cc_final: 0.8722 (mtm) REVERT: g 79 SER cc_start: 0.8140 (p) cc_final: 0.7815 (t) REVERT: h 107 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7899 (mtpt) REVERT: i 56 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6892 (ttp-110) REVERT: i 71 LYS cc_start: 0.7469 (ttmt) cc_final: 0.7134 (mttt) REVERT: i 80 PHE cc_start: 0.7604 (t80) cc_final: 0.7387 (t80) REVERT: j 55 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7442 (ttp-170) REVERT: k 16 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6764 (mtp-110) REVERT: m 63 ASP cc_start: 0.7818 (t0) cc_final: 0.7500 (t70) REVERT: m 314 LYS cc_start: 0.7939 (mmtm) cc_final: 0.7572 (mttt) REVERT: m 443 GLU cc_start: 0.6508 (mm-30) cc_final: 0.5835 (tp30) REVERT: n 72 MET cc_start: 0.7017 (tpp) cc_final: 0.6563 (tpp) REVERT: n 150 GLN cc_start: 0.7307 (mt0) cc_final: 0.6786 (mt0) REVERT: n 174 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6515 (mtp180) REVERT: n 198 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6583 (ttp80) REVERT: n 366 TYR cc_start: 0.6320 (t80) cc_final: 0.6009 (t80) REVERT: n 388 ILE cc_start: 0.6866 (OUTLIER) cc_final: 0.6584 (mm) REVERT: n 390 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.5134 (tt0) REVERT: n 440 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6248 (mt-10) REVERT: o 100 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.7290 (m170) REVERT: o 105 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6758 (pttp) REVERT: o 110 TYR cc_start: 0.8327 (t80) cc_final: 0.7978 (t80) REVERT: o 121 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6776 (mtt-85) REVERT: o 143 GLU cc_start: 0.6193 (mt-10) cc_final: 0.5277 (pt0) REVERT: o 152 MET cc_start: 0.7568 (mmm) cc_final: 0.7038 (mmm) REVERT: o 172 LYS cc_start: 0.4532 (pttp) cc_final: 0.4327 (tptp) REVERT: q 232 LYS cc_start: 0.6549 (tmmt) cc_final: 0.6129 (tptp) REVERT: q 249 GLU cc_start: 0.4948 (tp30) cc_final: 0.4376 (tp30) REVERT: q 412 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.5713 (mp0) REVERT: q 442 LYS cc_start: 0.6697 (mtpt) cc_final: 0.6493 (mtpp) REVERT: r 54 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7373 (mmm160) REVERT: s 20 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8197 (mtpt) REVERT: s 60 ILE cc_start: 0.7643 (mm) cc_final: 0.7373 (mt) REVERT: t 82 GLU cc_start: 0.5808 (mm-30) cc_final: 0.5005 (pt0) REVERT: t 297 ARG cc_start: 0.5681 (ttp-170) cc_final: 0.5412 (mtp180) REVERT: v 113 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.6502 (mtm) REVERT: v 251 LYS cc_start: 0.7133 (mmtp) cc_final: 0.6434 (mmtp) REVERT: v 268 MET cc_start: 0.8836 (mmm) cc_final: 0.8477 (mmm) REVERT: v 277 MET cc_start: 0.8640 (mmm) cc_final: 0.8144 (mmm) REVERT: w 55 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.5260 (tmm160) REVERT: w 56 ASP cc_start: 0.4873 (m-30) cc_final: 0.4632 (m-30) REVERT: w 128 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.5674 (ptm160) REVERT: w 186 ARG cc_start: 0.7701 (ttp80) cc_final: 0.7438 (ttp80) REVERT: x 289 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.7214 (mt0) REVERT: x 379 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: x 397 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7157 (ttt180) REVERT: y 1 MET cc_start: 0.5632 (OUTLIER) cc_final: 0.4840 (ttt) REVERT: z 99 LYS cc_start: 0.7619 (mttm) cc_final: 0.7256 (mtpt) REVERT: 4 167 LYS cc_start: 0.5081 (mmtt) cc_final: 0.4697 (tptt) REVERT: 4 232 ARG cc_start: 0.6688 (ttp-110) cc_final: 0.6301 (mtm110) REVERT: 4 272 SER cc_start: 0.7766 (p) cc_final: 0.7348 (t) REVERT: 4 373 LYS cc_start: 0.8114 (ttpp) cc_final: 0.7866 (ttmt) REVERT: 4 404 GLU cc_start: 0.5691 (mt-10) cc_final: 0.5427 (mt-10) REVERT: 4 489 MET cc_start: 0.7420 (ttm) cc_final: 0.6978 (ttp) outliers start: 323 outliers final: 178 residues processed: 1467 average time/residue: 2.6007 time to fit residues: 5395.0666 Evaluate side-chains 1462 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1242 time to evaluate : 9.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 85 LEU Chi-restraints excluded: chain 8 residue 98 VAL Chi-restraints excluded: chain 8 residue 115 GLN Chi-restraints excluded: chain 8 residue 124 THR Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 146 LYS Chi-restraints excluded: chain 9 residue 19 LYS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain K residue 338 ASN Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 153 LYS Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 38 ASP Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain T residue 151 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 184 SER Chi-restraints excluded: chain W residue 214 LYS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 265 GLU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain b residue 448 GLU Chi-restraints excluded: chain b residue 461 GLU Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain c residue 36 GLN Chi-restraints excluded: chain c residue 98 SER Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 38 ILE Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 113 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain h residue 107 LYS Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain i residue 88 GLU Chi-restraints excluded: chain j residue 55 ARG Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain m residue 101 LYS Chi-restraints excluded: chain m residue 124 ASP Chi-restraints excluded: chain m residue 170 LYS Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain m residue 422 LYS Chi-restraints excluded: chain m residue 447 SER Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 127 ASP Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 198 ARG Chi-restraints excluded: chain n residue 259 LEU Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 386 ASN Chi-restraints excluded: chain n residue 388 ILE Chi-restraints excluded: chain n residue 390 GLU Chi-restraints excluded: chain n residue 440 GLU Chi-restraints excluded: chain n residue 442 VAL Chi-restraints excluded: chain n residue 445 ASN Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 121 ARG Chi-restraints excluded: chain o residue 146 MET Chi-restraints excluded: chain o residue 169 LYS Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 235 SER Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 412 GLU Chi-restraints excluded: chain r residue 54 ARG Chi-restraints excluded: chain r residue 66 LYS Chi-restraints excluded: chain s residue 16 LYS Chi-restraints excluded: chain s residue 20 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 GLU Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain t residue 40 LYS Chi-restraints excluded: chain t residue 97 LYS Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 206 SER Chi-restraints excluded: chain t residue 296 SER Chi-restraints excluded: chain t residue 310 ILE Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 113 MET Chi-restraints excluded: chain v residue 120 ASP Chi-restraints excluded: chain v residue 190 PHE Chi-restraints excluded: chain v residue 208 SER Chi-restraints excluded: chain v residue 224 VAL Chi-restraints excluded: chain v residue 226 ILE Chi-restraints excluded: chain w residue 55 ARG Chi-restraints excluded: chain w residue 128 ARG Chi-restraints excluded: chain w residue 155 ASP Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 145 THR Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 289 GLN Chi-restraints excluded: chain x residue 379 ASP Chi-restraints excluded: chain x residue 389 LEU Chi-restraints excluded: chain x residue 392 THR Chi-restraints excluded: chain x residue 397 ARG Chi-restraints excluded: chain x residue 398 MET Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 175 SER Chi-restraints excluded: chain y residue 185 THR Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 45 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 307 ASP Chi-restraints excluded: chain 4 residue 330 THR Chi-restraints excluded: chain 4 residue 370 LEU Chi-restraints excluded: chain 4 residue 453 ASN Chi-restraints excluded: chain 4 residue 511 ASP Chi-restraints excluded: chain 4 residue 517 THR Chi-restraints excluded: chain 4 residue 521 GLU 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: 6.9990 chunk 977 optimal weight: 0.7980 chunk 757 optimal weight: 5.9990 chunk 1127 optimal weight: 9.9990 chunk 747 optimal weight: 3.9990 chunk 1333 optimal weight: 6.9990 chunk 834 optimal weight: 0.4980 chunk 813 optimal weight: 5.9990 chunk 615 optimal weight: 0.7980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN 9 106 GLN C 58 HIS C 307 GLN G 24 ASN G 192 GLN G 221 ASN H 5 GLN H 102 ASN H 157 ASN I 48 GLN J 90 GLN K 250 ASN L 114 GLN N 182 ASN N 195 ASN O 50 ASN P 92 GLN P 179 GLN R 34 GLN S 46 GLN ** S 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN T 131 GLN Y 66 GLN b 152 GLN g 3 GLN i 91 ASN ** n 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS q 228 ASN t 230 ASN v 213 GLN w 63 ASN w 201 ASN x 176 GLN y 145 ASN 4 546 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 167341 Z= 0.151 Angle : 0.611 17.480 241944 Z= 0.331 Chirality : 0.036 0.314 29617 Planarity : 0.005 0.127 18328 Dihedral : 22.077 179.460 63300 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.94 % Allowed : 14.87 % Favored : 82.18 % 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: 1.15 (0.08), residues: 10648 helix: 2.11 (0.08), residues: 4181 sheet: 0.29 (0.12), residues: 1567 loop : -0.22 (0.08), residues: 4900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 106 HIS 0.006 0.001 HIS C 311 PHE 0.023 0.001 PHE F 229 TYR 0.019 0.001 TYR c 27 ARG 0.009 0.000 ARG t 292 *********************** 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 1558 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1284 time to evaluate : 9.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.7959 (mttt) cc_final: 0.7663 (mttp) REVERT: 8 59 THR cc_start: 0.7696 (m) cc_final: 0.7304 (p) REVERT: 8 146 LYS cc_start: 0.6156 (OUTLIER) cc_final: 0.5804 (mtpp) REVERT: 9 30 ARG cc_start: 0.7910 (mtm180) cc_final: 0.7439 (mtp180) REVERT: B 71 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 336 VAL cc_start: 0.9053 (m) cc_final: 0.8835 (p) REVERT: C 143 GLU cc_start: 0.6992 (mp0) cc_final: 0.6717 (mp0) REVERT: D 163 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7172 (tp) REVERT: D 258 LYS cc_start: 0.5145 (OUTLIER) cc_final: 0.4062 (tptt) REVERT: E 136 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6697 (mm-30) REVERT: F 125 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: G 70 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7708 (mtpp) REVERT: G 145 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7339 (m110) REVERT: G 161 GLU cc_start: 0.8075 (mp0) cc_final: 0.7753 (mp0) REVERT: G 230 LYS cc_start: 0.6477 (ptpt) cc_final: 0.6163 (pttt) REVERT: H 9 GLN cc_start: 0.7848 (mt0) cc_final: 0.7456 (mt0) REVERT: H 177 ASP cc_start: 0.8018 (m-30) cc_final: 0.7792 (m-30) REVERT: J 14 ILE cc_start: 0.5128 (OUTLIER) cc_final: 0.4699 (pp) REVERT: K 173 PHE cc_start: 0.7523 (t80) cc_final: 0.7156 (t80) REVERT: L 134 GLU cc_start: 0.5241 (OUTLIER) cc_final: 0.4829 (tm-30) REVERT: N 5 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6699 (tmtm) REVERT: N 10 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8565 (tp) REVERT: N 145 ASP cc_start: 0.8203 (t0) cc_final: 0.7978 (t0) REVERT: O 130 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7553 (ttmt) REVERT: Q 22 ASP cc_start: 0.7647 (m-30) cc_final: 0.7325 (m-30) REVERT: R 5 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7563 (ttm170) REVERT: S 66 GLU cc_start: 0.8554 (tp30) cc_final: 0.8015 (tp30) REVERT: T 52 MET cc_start: 0.5336 (OUTLIER) cc_final: 0.4357 (tpp) REVERT: T 91 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7583 (mp) REVERT: T 149 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7717 (pt0) REVERT: U 39 ASP cc_start: 0.7859 (m-30) cc_final: 0.7543 (m-30) REVERT: U 88 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.6880 (mt0) REVERT: W 79 GLU cc_start: 0.5735 (mp0) cc_final: 0.5461 (pm20) REVERT: W 194 LYS cc_start: 0.6736 (ttmm) cc_final: 0.6456 (tppt) REVERT: W 214 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7397 (mtmm) REVERT: X 6 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7295 (ttpt) REVERT: Y 84 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7558 (mmtm) REVERT: Y 90 VAL cc_start: 0.7723 (OUTLIER) cc_final: 0.7486 (m) REVERT: Z 88 ASP cc_start: 0.7178 (t70) cc_final: 0.6711 (t0) REVERT: Z 120 GLU cc_start: 0.6982 (pt0) cc_final: 0.6772 (pt0) REVERT: a 68 PHE cc_start: 0.6041 (p90) cc_final: 0.5607 (p90) REVERT: a 96 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7025 (tppp) REVERT: b 3 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6889 (mp) REVERT: b 247 ARG cc_start: 0.6640 (ptt90) cc_final: 0.6343 (ptt90) REVERT: b 526 LYS cc_start: 0.7923 (mtpp) cc_final: 0.7587 (ttpt) REVERT: b 646 PHE cc_start: 0.7650 (p90) cc_final: 0.7392 (p90) REVERT: c 57 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8293 (mt-10) REVERT: d 42 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7746 (tp) REVERT: d 62 ARG cc_start: 0.8514 (mtm180) cc_final: 0.8064 (mtm-85) REVERT: d 68 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7819 (mm-30) REVERT: e 34 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7579 (tmtm) REVERT: e 120 THR cc_start: 0.8346 (m) cc_final: 0.7991 (p) REVERT: f 67 MET cc_start: 0.9189 (mtp) cc_final: 0.8763 (mtm) REVERT: g 87 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: h 107 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7856 (mtpt) REVERT: i 56 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6881 (ttp-110) REVERT: i 71 LYS cc_start: 0.7425 (ttmt) cc_final: 0.7078 (mttt) REVERT: i 80 PHE cc_start: 0.7464 (t80) cc_final: 0.7231 (t80) REVERT: j 55 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7499 (ttp-170) REVERT: k 16 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6523 (mtp-110) REVERT: m 63 ASP cc_start: 0.7687 (t0) cc_final: 0.7445 (t70) REVERT: m 125 GLU cc_start: 0.6662 (pm20) cc_final: 0.6417 (pm20) REVERT: m 314 LYS cc_start: 0.7900 (mmtm) cc_final: 0.7525 (mttt) REVERT: m 429 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: n 72 MET cc_start: 0.6922 (tpp) cc_final: 0.6498 (tpp) REVERT: n 150 GLN cc_start: 0.7205 (mt0) cc_final: 0.6683 (mt0) REVERT: n 174 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6518 (mtp180) REVERT: n 198 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6423 (ttp80) REVERT: n 366 TYR cc_start: 0.6274 (t80) cc_final: 0.5989 (t80) REVERT: n 376 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7577 (mp) REVERT: n 388 ILE cc_start: 0.6745 (OUTLIER) cc_final: 0.6317 (mm) REVERT: n 390 GLU cc_start: 0.5673 (OUTLIER) cc_final: 0.4930 (tt0) REVERT: n 440 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.6204 (mt-10) REVERT: o 105 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6672 (pttp) REVERT: o 110 TYR cc_start: 0.8234 (t80) cc_final: 0.7961 (t80) REVERT: o 121 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6785 (mtt-85) REVERT: o 143 GLU cc_start: 0.6082 (mt-10) cc_final: 0.5143 (pt0) REVERT: o 152 MET cc_start: 0.7324 (mmm) cc_final: 0.6876 (mmm) REVERT: q 249 GLU cc_start: 0.4951 (tp30) cc_final: 0.4355 (tp30) REVERT: r 54 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7425 (mmm160) REVERT: s 60 ILE cc_start: 0.7598 (mm) cc_final: 0.7335 (mt) REVERT: t 38 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6847 (ttmt) REVERT: t 82 GLU cc_start: 0.5646 (mm-30) cc_final: 0.4924 (pt0) REVERT: t 213 ARG cc_start: 0.7155 (mtp85) cc_final: 0.6906 (mmm-85) REVERT: t 292 ARG cc_start: 0.6745 (mtt90) cc_final: 0.6320 (mtm-85) REVERT: t 297 ARG cc_start: 0.5716 (ttp-170) cc_final: 0.5397 (mtp180) REVERT: v 36 GLN cc_start: 0.6617 (tp40) cc_final: 0.6326 (mm-40) REVERT: v 57 MET cc_start: 0.7440 (tmm) cc_final: 0.7233 (tmm) REVERT: v 113 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6476 (mtm) REVERT: v 251 LYS cc_start: 0.7112 (mmtp) cc_final: 0.6408 (mmtp) REVERT: v 268 MET cc_start: 0.8839 (mmm) cc_final: 0.8434 (mmm) REVERT: v 277 MET cc_start: 0.8557 (mmm) cc_final: 0.8050 (mmm) REVERT: v 284 LYS cc_start: 0.7789 (mtpp) cc_final: 0.7554 (mmmt) REVERT: w 32 ASN cc_start: 0.5844 (m-40) cc_final: 0.5577 (m-40) REVERT: w 128 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.5084 (ptm160) REVERT: w 186 ARG cc_start: 0.7691 (ttp80) cc_final: 0.7443 (ttp80) REVERT: x 179 MET cc_start: 0.6694 (mtm) cc_final: 0.6356 (mtm) REVERT: x 379 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: x 397 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7161 (ttt180) REVERT: y 1 MET cc_start: 0.5567 (OUTLIER) cc_final: 0.4800 (ttt) REVERT: z 99 LYS cc_start: 0.7545 (mttm) cc_final: 0.7194 (mtpt) REVERT: 4 167 LYS cc_start: 0.4977 (mmtt) cc_final: 0.4629 (tptt) REVERT: 4 232 ARG cc_start: 0.6644 (ttp-110) cc_final: 0.6275 (mtm110) REVERT: 4 272 SER cc_start: 0.7709 (p) cc_final: 0.7305 (t) REVERT: 4 373 LYS cc_start: 0.8048 (ttpp) cc_final: 0.7769 (ttmt) REVERT: 4 404 GLU cc_start: 0.5699 (mt-10) cc_final: 0.5451 (mt-10) REVERT: 4 489 MET cc_start: 0.7336 (ttm) cc_final: 0.6908 (ttp) outliers start: 274 outliers final: 146 residues processed: 1453 average time/residue: 2.4711 time to fit residues: 5064.9350 Evaluate side-chains 1432 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1240 time to evaluate : 9.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 85 LEU Chi-restraints excluded: chain 8 residue 124 THR Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 146 LYS Chi-restraints excluded: chain 9 residue 19 LYS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 231 LYS Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain K residue 338 ASN Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 88 GLN Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 184 SER Chi-restraints excluded: chain W residue 214 LYS Chi-restraints excluded: chain X residue 6 LYS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain a residue 86 LYS Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 265 GLU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain b residue 461 GLU Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain c residue 98 SER Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 38 ILE Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain h residue 107 LYS Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain j residue 55 ARG Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain m residue 124 ASP Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain m residue 422 LYS Chi-restraints excluded: chain m residue 429 GLU Chi-restraints excluded: chain m residue 447 SER Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 127 ASP Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 198 ARG Chi-restraints excluded: chain n residue 259 LEU Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 386 ASN Chi-restraints excluded: chain n residue 388 ILE Chi-restraints excluded: chain n residue 390 GLU Chi-restraints excluded: chain n residue 440 GLU Chi-restraints excluded: chain n residue 442 VAL Chi-restraints excluded: chain n residue 445 ASN Chi-restraints excluded: chain n residue 457 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 121 ARG Chi-restraints excluded: chain o residue 146 MET Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 235 SER Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain r residue 54 ARG Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain r residue 230 MET Chi-restraints excluded: chain s residue 16 LYS Chi-restraints excluded: chain s residue 30 GLU Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 40 LYS Chi-restraints excluded: chain t residue 80 ILE Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 206 SER Chi-restraints excluded: chain t residue 296 SER Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 113 MET Chi-restraints excluded: chain v residue 120 ASP Chi-restraints excluded: chain v residue 208 SER Chi-restraints excluded: chain v residue 226 ILE Chi-restraints excluded: chain w residue 128 ARG Chi-restraints excluded: chain w residue 155 ASP Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 183 LYS Chi-restraints excluded: chain x residue 190 LEU Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 379 ASP Chi-restraints excluded: chain x residue 389 LEU Chi-restraints excluded: chain x residue 392 THR Chi-restraints excluded: chain x residue 397 ARG Chi-restraints excluded: chain x residue 398 MET Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 145 ASN Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 175 SER Chi-restraints excluded: chain y residue 185 THR Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 45 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 307 ASP Chi-restraints excluded: chain 4 residue 330 THR Chi-restraints excluded: chain 4 residue 370 LEU Chi-restraints excluded: chain 4 residue 517 THR Chi-restraints excluded: chain 4 residue 521 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 825 optimal weight: 8.9990 chunk 532 optimal weight: 9.9990 chunk 796 optimal weight: 2.9990 chunk 401 optimal weight: 9.9990 chunk 262 optimal weight: 20.0000 chunk 258 optimal weight: 30.0000 chunk 848 optimal weight: 5.9990 chunk 908 optimal weight: 5.9990 chunk 659 optimal weight: 0.0670 chunk 124 optimal weight: 10.0000 chunk 1048 optimal weight: 1.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN C 58 HIS C 307 GLN E 138 GLN G 24 ASN G 221 ASN H 5 GLN H 102 ASN H 157 ASN L 114 GLN N 23 GLN N 182 ASN N 195 ASN P 92 GLN P 179 GLN R 34 GLN S 46 GLN ** S 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN T 131 GLN X 65 GLN Y 66 GLN b 152 GLN c 11 ASN g 3 GLN h 68 GLN i 91 ASN m 213 ASN n 456 HIS q 228 ASN t 230 ASN u 24 ASN ** v 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 63 ASN w 201 ASN x 176 GLN y 145 ASN 4 546 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 167341 Z= 0.190 Angle : 0.641 18.035 241944 Z= 0.344 Chirality : 0.037 0.317 29617 Planarity : 0.006 0.130 18328 Dihedral : 22.077 179.585 63300 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.80 % Allowed : 15.25 % Favored : 81.95 % 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: 1.10 (0.08), residues: 10648 helix: 2.06 (0.08), residues: 4177 sheet: 0.24 (0.12), residues: 1580 loop : -0.24 (0.08), residues: 4891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP e 32 HIS 0.008 0.001 HIS S 122 PHE 0.026 0.002 PHE F 229 TYR 0.022 0.002 TYR S 43 ARG 0.008 0.000 ARG t 292 *********************** 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 1516 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1255 time to evaluate : 9.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.7934 (mttt) cc_final: 0.7632 (mttp) REVERT: 8 59 THR cc_start: 0.7666 (m) cc_final: 0.7269 (p) REVERT: 8 146 LYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5772 (mtpp) REVERT: 9 30 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7450 (mtp180) REVERT: B 71 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8015 (mt-10) REVERT: B 336 VAL cc_start: 0.9058 (m) cc_final: 0.8835 (p) REVERT: C 143 GLU cc_start: 0.7092 (mp0) cc_final: 0.6846 (mp0) REVERT: C 345 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.6155 (tt0) REVERT: D 163 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7182 (tp) REVERT: D 258 LYS cc_start: 0.5196 (OUTLIER) cc_final: 0.4116 (tptt) REVERT: E 136 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6680 (mm-30) REVERT: F 125 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: F 234 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: G 70 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7737 (mtpp) REVERT: G 145 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7365 (m110) REVERT: G 161 GLU cc_start: 0.8015 (mp0) cc_final: 0.7746 (mp0) REVERT: G 230 LYS cc_start: 0.6484 (ptpt) cc_final: 0.6159 (pttt) REVERT: H 9 GLN cc_start: 0.7907 (mt0) cc_final: 0.7534 (mt0) REVERT: H 161 LEU cc_start: 0.8602 (tp) cc_final: 0.8313 (tm) REVERT: H 177 ASP cc_start: 0.8042 (m-30) cc_final: 0.7817 (m-30) REVERT: J 14 ILE cc_start: 0.5117 (OUTLIER) cc_final: 0.4684 (pp) REVERT: L 134 GLU cc_start: 0.5316 (OUTLIER) cc_final: 0.4902 (tm-30) REVERT: N 5 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6748 (tmtm) REVERT: N 10 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8604 (tp) REVERT: N 145 ASP cc_start: 0.8236 (t0) cc_final: 0.8021 (t0) REVERT: O 130 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7563 (ttmt) REVERT: Q 22 ASP cc_start: 0.7652 (m-30) cc_final: 0.7339 (m-30) REVERT: R 5 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7531 (ttm170) REVERT: S 66 GLU cc_start: 0.8551 (tp30) cc_final: 0.8018 (tp30) REVERT: T 52 MET cc_start: 0.5482 (OUTLIER) cc_final: 0.5163 (mmt) REVERT: T 91 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7583 (mp) REVERT: T 149 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7741 (pt0) REVERT: U 39 ASP cc_start: 0.7868 (m-30) cc_final: 0.7548 (m-30) REVERT: U 76 LEU cc_start: 0.9041 (tp) cc_final: 0.8788 (tp) REVERT: U 88 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.6949 (mt0) REVERT: W 79 GLU cc_start: 0.5771 (mp0) cc_final: 0.5477 (pm20) REVERT: W 194 LYS cc_start: 0.6761 (ttmm) cc_final: 0.6482 (tppt) REVERT: W 214 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7401 (mtmm) REVERT: X 6 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7288 (ttpt) REVERT: Y 90 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7449 (m) REVERT: Z 88 ASP cc_start: 0.7198 (t70) cc_final: 0.6721 (t0) REVERT: a 68 PHE cc_start: 0.6044 (p90) cc_final: 0.5616 (p90) REVERT: a 96 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7034 (tppp) REVERT: b 3 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7036 (mp) REVERT: b 247 ARG cc_start: 0.6660 (ptt90) cc_final: 0.6373 (ptt90) REVERT: b 526 LYS cc_start: 0.7936 (mtpp) cc_final: 0.7609 (ttpt) REVERT: b 550 ASN cc_start: 0.6323 (m-40) cc_final: 0.6120 (m-40) REVERT: b 646 PHE cc_start: 0.7651 (p90) cc_final: 0.7411 (p90) REVERT: c 57 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8283 (mt-10) REVERT: d 62 ARG cc_start: 0.8504 (mtm180) cc_final: 0.8089 (mtm-85) REVERT: d 68 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7822 (mm-30) REVERT: e 34 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7589 (tmtm) REVERT: e 120 THR cc_start: 0.8293 (m) cc_final: 0.8025 (p) REVERT: f 67 MET cc_start: 0.9182 (mtp) cc_final: 0.8792 (mtm) REVERT: g 87 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: h 107 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7857 (mtpt) REVERT: i 56 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6884 (ttp-110) REVERT: i 71 LYS cc_start: 0.7437 (ttmt) cc_final: 0.7105 (mttt) REVERT: i 80 PHE cc_start: 0.7504 (t80) cc_final: 0.7285 (t80) REVERT: j 55 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7514 (ttp-170) REVERT: k 16 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6544 (mtp-110) REVERT: m 63 ASP cc_start: 0.7720 (t0) cc_final: 0.7488 (t70) REVERT: m 125 GLU cc_start: 0.6666 (pm20) cc_final: 0.6423 (pm20) REVERT: m 314 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7551 (mttt) REVERT: m 429 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6878 (tm-30) REVERT: m 443 GLU cc_start: 0.6423 (mm-30) cc_final: 0.5752 (tp30) REVERT: n 72 MET cc_start: 0.6984 (tpp) cc_final: 0.6558 (tpp) REVERT: n 174 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6524 (mtp180) REVERT: n 198 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6518 (ttp80) REVERT: n 366 TYR cc_start: 0.6294 (t80) cc_final: 0.6003 (t80) REVERT: n 376 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7585 (mp) REVERT: n 388 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6388 (mm) REVERT: n 390 GLU cc_start: 0.5723 (OUTLIER) cc_final: 0.4949 (tt0) REVERT: n 440 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6169 (mt-10) REVERT: o 105 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6722 (pttp) REVERT: o 110 TYR cc_start: 0.8258 (t80) cc_final: 0.7974 (t80) REVERT: o 121 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6834 (mtt-85) REVERT: o 143 GLU cc_start: 0.6102 (mt-10) cc_final: 0.5191 (pt0) REVERT: o 152 MET cc_start: 0.7408 (mmm) cc_final: 0.6923 (mmm) REVERT: o 184 LEU cc_start: 0.3308 (OUTLIER) cc_final: 0.3073 (tt) REVERT: q 232 LYS cc_start: 0.6584 (tmmt) cc_final: 0.6121 (tptp) REVERT: q 249 GLU cc_start: 0.4910 (tp30) cc_final: 0.4212 (tp30) REVERT: q 412 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.5470 (mp0) REVERT: r 54 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7423 (mmm160) REVERT: s 60 ILE cc_start: 0.7610 (mm) cc_final: 0.7359 (mt) REVERT: t 38 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6782 (ttmt) REVERT: t 82 GLU cc_start: 0.5797 (mm-30) cc_final: 0.5010 (pt0) REVERT: t 213 ARG cc_start: 0.7197 (mtp85) cc_final: 0.6955 (mmm-85) REVERT: t 297 ARG cc_start: 0.5658 (ttp-170) cc_final: 0.5392 (mtp180) REVERT: v 251 LYS cc_start: 0.7110 (mmtp) cc_final: 0.6411 (mmtp) REVERT: v 268 MET cc_start: 0.8840 (mmm) cc_final: 0.8435 (mmm) REVERT: v 277 MET cc_start: 0.8563 (mmm) cc_final: 0.8052 (mmm) REVERT: v 284 LYS cc_start: 0.7871 (mtpp) cc_final: 0.7620 (mmmt) REVERT: w 128 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.5317 (ptm160) REVERT: w 186 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7480 (ttp80) REVERT: x 179 MET cc_start: 0.6660 (mtm) cc_final: 0.6334 (mtm) REVERT: x 379 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: x 389 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6021 (tm) REVERT: x 397 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7172 (ttt180) REVERT: y 1 MET cc_start: 0.5597 (OUTLIER) cc_final: 0.4827 (ttt) REVERT: z 99 LYS cc_start: 0.7580 (mttm) cc_final: 0.7222 (mtpt) REVERT: 4 167 LYS cc_start: 0.4980 (mmtt) cc_final: 0.4631 (tptt) REVERT: 4 232 ARG cc_start: 0.6656 (ttp-110) cc_final: 0.6289 (mtm110) REVERT: 4 272 SER cc_start: 0.7722 (p) cc_final: 0.7314 (t) REVERT: 4 373 LYS cc_start: 0.8066 (ttpp) cc_final: 0.7789 (ttmt) REVERT: 4 404 GLU cc_start: 0.5718 (mt-10) cc_final: 0.5432 (mt-10) REVERT: 4 489 MET cc_start: 0.7352 (ttm) cc_final: 0.6927 (ttp) outliers start: 261 outliers final: 158 residues processed: 1415 average time/residue: 2.4425 time to fit residues: 4870.9544 Evaluate side-chains 1436 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1230 time to evaluate : 8.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 85 LEU Chi-restraints excluded: chain 8 residue 124 THR Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 146 LYS Chi-restraints excluded: chain 9 residue 19 LYS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 231 LYS Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain K residue 338 ASN Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 88 GLN Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain W residue 86 LYS Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 184 SER Chi-restraints excluded: chain W residue 214 LYS Chi-restraints excluded: chain X residue 6 LYS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain a residue 86 LYS Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 265 GLU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 317 ILE Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain b residue 461 GLU Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain c residue 98 SER Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 38 ILE Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain h residue 107 LYS Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain j residue 55 ARG Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain m residue 124 ASP Chi-restraints excluded: chain m residue 170 LYS Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain m residue 422 LYS Chi-restraints excluded: chain m residue 429 GLU Chi-restraints excluded: chain m residue 447 SER Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 127 ASP Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 198 ARG Chi-restraints excluded: chain n residue 259 LEU Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 386 ASN Chi-restraints excluded: chain n residue 388 ILE Chi-restraints excluded: chain n residue 390 GLU Chi-restraints excluded: chain n residue 440 GLU Chi-restraints excluded: chain n residue 442 VAL Chi-restraints excluded: chain n residue 445 ASN Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 121 ARG Chi-restraints excluded: chain o residue 146 MET Chi-restraints excluded: chain o residue 184 LEU Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain q residue 206 THR Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 235 SER Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 412 GLU Chi-restraints excluded: chain r residue 54 ARG Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain s residue 3 VAL Chi-restraints excluded: chain s residue 16 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 GLU Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 40 LYS Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 206 SER Chi-restraints excluded: chain t residue 296 SER Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 120 ASP Chi-restraints excluded: chain v residue 208 SER Chi-restraints excluded: chain v residue 224 VAL Chi-restraints excluded: chain v residue 226 ILE Chi-restraints excluded: chain w residue 128 ARG Chi-restraints excluded: chain w residue 155 ASP Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 145 THR Chi-restraints excluded: chain x residue 190 LEU Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 379 ASP Chi-restraints excluded: chain x residue 389 LEU Chi-restraints excluded: chain x residue 392 THR Chi-restraints excluded: chain x residue 397 ARG Chi-restraints excluded: chain x residue 398 MET Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 175 SER Chi-restraints excluded: chain y residue 185 THR Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 45 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 307 ASP Chi-restraints excluded: chain 4 residue 330 THR Chi-restraints excluded: chain 4 residue 370 LEU Chi-restraints excluded: chain 4 residue 517 THR Chi-restraints excluded: chain 4 residue 521 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 1213 optimal weight: 6.9990 chunk 1277 optimal weight: 20.0000 chunk 1165 optimal weight: 0.6980 chunk 1243 optimal weight: 20.0000 chunk 748 optimal weight: 20.0000 chunk 541 optimal weight: 20.0000 chunk 976 optimal weight: 9.9990 chunk 381 optimal weight: 7.9990 chunk 1123 optimal weight: 0.1980 chunk 1175 optimal weight: 1.9990 chunk 1238 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN C 58 HIS C 307 GLN G 24 ASN G 221 ASN H 5 GLN H 102 ASN H 157 ASN L 17 HIS L 114 GLN M 62 GLN N 182 ASN N 195 ASN P 179 GLN R 34 GLN S 46 GLN ** S 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN T 131 GLN Y 66 GLN b 152 GLN g 3 GLN h 68 GLN h 104 GLN i 91 ASN m 213 ASN n 456 HIS q 228 ASN t 230 ASN ** v 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 63 ASN w 201 ASN x 176 GLN x 297 HIS y 145 ASN 4 546 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 167341 Z= 0.167 Angle : 0.622 17.711 241944 Z= 0.336 Chirality : 0.037 0.312 29617 Planarity : 0.005 0.128 18328 Dihedral : 22.063 179.396 63300 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.74 % Allowed : 15.52 % Favored : 81.74 % 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: 1.15 (0.08), residues: 10648 helix: 2.11 (0.08), residues: 4182 sheet: 0.26 (0.12), residues: 1582 loop : -0.21 (0.08), residues: 4884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP W 41 HIS 0.011 0.001 HIS S 122 PHE 0.024 0.001 PHE F 229 TYR 0.022 0.001 TYR c 27 ARG 0.011 0.000 ARG t 292 *********************** 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 1514 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1259 time to evaluate : 8.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.7961 (mttt) cc_final: 0.7661 (mttp) REVERT: 8 59 THR cc_start: 0.7661 (m) cc_final: 0.7262 (p) REVERT: 8 146 LYS cc_start: 0.6160 (OUTLIER) cc_final: 0.5805 (mtpp) REVERT: 9 21 HIS cc_start: 0.7047 (OUTLIER) cc_final: 0.6575 (m90) REVERT: 9 30 ARG cc_start: 0.7922 (mtm180) cc_final: 0.7367 (mtp180) REVERT: 9 84 ILE cc_start: 0.7404 (mm) cc_final: 0.7146 (tp) REVERT: B 71 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 336 VAL cc_start: 0.9058 (m) cc_final: 0.8835 (p) REVERT: C 143 GLU cc_start: 0.7083 (mp0) cc_final: 0.6840 (mp0) REVERT: D 163 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7181 (tp) REVERT: D 258 LYS cc_start: 0.5178 (OUTLIER) cc_final: 0.4088 (tptt) REVERT: E 136 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6687 (mm-30) REVERT: F 125 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: F 234 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: G 70 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7726 (mtpp) REVERT: G 145 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7337 (m110) REVERT: G 161 GLU cc_start: 0.8049 (mp0) cc_final: 0.7758 (mp0) REVERT: G 230 LYS cc_start: 0.6474 (ptpt) cc_final: 0.6149 (pttt) REVERT: H 9 GLN cc_start: 0.7905 (mt0) cc_final: 0.7532 (mt0) REVERT: H 177 ASP cc_start: 0.8016 (m-30) cc_final: 0.7788 (m-30) REVERT: I 65 LYS cc_start: 0.6931 (ttpm) cc_final: 0.6194 (tttt) REVERT: J 14 ILE cc_start: 0.5114 (OUTLIER) cc_final: 0.4697 (pp) REVERT: L 134 GLU cc_start: 0.5249 (OUTLIER) cc_final: 0.4846 (tm-30) REVERT: N 5 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6723 (tmtm) REVERT: N 10 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8581 (tp) REVERT: N 145 ASP cc_start: 0.8206 (t0) cc_final: 0.7979 (t0) REVERT: O 130 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7562 (ttmt) REVERT: Q 22 ASP cc_start: 0.7606 (m-30) cc_final: 0.7305 (m-30) REVERT: R 5 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7593 (ttm170) REVERT: S 66 GLU cc_start: 0.8550 (tp30) cc_final: 0.8022 (tp30) REVERT: S 141 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8290 (mtmt) REVERT: T 52 MET cc_start: 0.5357 (OUTLIER) cc_final: 0.5016 (mmt) REVERT: T 91 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7567 (mp) REVERT: T 149 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7735 (pt0) REVERT: U 39 ASP cc_start: 0.7840 (m-30) cc_final: 0.7532 (m-30) REVERT: U 76 LEU cc_start: 0.9030 (tp) cc_final: 0.8776 (tp) REVERT: U 88 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.6903 (mt0) REVERT: W 79 GLU cc_start: 0.5769 (mp0) cc_final: 0.5492 (pm20) REVERT: W 214 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7422 (mtmm) REVERT: X 6 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7297 (ttpt) REVERT: Y 84 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7216 (mmmm) REVERT: Y 90 VAL cc_start: 0.7724 (OUTLIER) cc_final: 0.7441 (m) REVERT: Z 88 ASP cc_start: 0.7186 (t70) cc_final: 0.6713 (t0) REVERT: a 68 PHE cc_start: 0.6045 (p90) cc_final: 0.5599 (p90) REVERT: a 96 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7041 (tppp) REVERT: b 3 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6955 (mp) REVERT: b 247 ARG cc_start: 0.6685 (ptt90) cc_final: 0.6394 (ptt90) REVERT: b 526 LYS cc_start: 0.7879 (mtpp) cc_final: 0.7549 (ttpt) REVERT: b 550 ASN cc_start: 0.6316 (m-40) cc_final: 0.6113 (m-40) REVERT: b 646 PHE cc_start: 0.7647 (p90) cc_final: 0.7408 (p90) REVERT: c 36 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: c 57 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8285 (mt-10) REVERT: d 62 ARG cc_start: 0.8487 (mtm180) cc_final: 0.8071 (mtm-85) REVERT: d 68 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7820 (mm-30) REVERT: e 34 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7560 (tmtm) REVERT: e 120 THR cc_start: 0.8325 (m) cc_final: 0.7974 (p) REVERT: f 67 MET cc_start: 0.9189 (mtp) cc_final: 0.8759 (mtm) REVERT: g 87 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: h 107 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7850 (mtpt) REVERT: i 56 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6880 (ttp-110) REVERT: i 71 LYS cc_start: 0.7434 (ttmt) cc_final: 0.7107 (mttt) REVERT: i 80 PHE cc_start: 0.7483 (t80) cc_final: 0.7265 (t80) REVERT: j 55 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7506 (ttp-170) REVERT: k 16 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6548 (mtp-110) REVERT: m 63 ASP cc_start: 0.7691 (t0) cc_final: 0.7471 (t70) REVERT: m 125 GLU cc_start: 0.6660 (pm20) cc_final: 0.6420 (pm20) REVERT: m 314 LYS cc_start: 0.7903 (mmtm) cc_final: 0.7543 (mttt) REVERT: m 429 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6831 (tm-30) REVERT: n 72 MET cc_start: 0.6938 (tpp) cc_final: 0.6514 (tpp) REVERT: n 174 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6519 (mtp180) REVERT: n 198 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6581 (ttp80) REVERT: n 366 TYR cc_start: 0.6285 (t80) cc_final: 0.6000 (t80) REVERT: n 376 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7585 (mp) REVERT: n 388 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6364 (mm) REVERT: n 390 GLU cc_start: 0.5704 (OUTLIER) cc_final: 0.4944 (tt0) REVERT: n 440 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6159 (mt-10) REVERT: o 105 LYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6680 (pttp) REVERT: o 110 TYR cc_start: 0.8242 (t80) cc_final: 0.7974 (t80) REVERT: o 119 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5590 (mp0) REVERT: o 121 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6843 (mtt-85) REVERT: o 143 GLU cc_start: 0.6082 (mt-10) cc_final: 0.5145 (pt0) REVERT: o 152 MET cc_start: 0.7307 (mmm) cc_final: 0.6882 (mmm) REVERT: q 232 LYS cc_start: 0.6609 (tmmt) cc_final: 0.6143 (tptp) REVERT: q 249 GLU cc_start: 0.4964 (tp30) cc_final: 0.4267 (tp30) REVERT: q 412 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.5467 (mp0) REVERT: r 54 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7439 (mmm160) REVERT: s 60 ILE cc_start: 0.7596 (mm) cc_final: 0.7331 (mt) REVERT: t 38 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6760 (ttmt) REVERT: t 82 GLU cc_start: 0.5630 (mm-30) cc_final: 0.5078 (pt0) REVERT: t 213 ARG cc_start: 0.7210 (mtp85) cc_final: 0.6973 (mmm-85) REVERT: t 297 ARG cc_start: 0.5656 (ttp-170) cc_final: 0.5388 (mtp180) REVERT: v 251 LYS cc_start: 0.7099 (mmtp) cc_final: 0.6403 (mmtp) REVERT: v 268 MET cc_start: 0.8841 (mmm) cc_final: 0.8427 (mmm) REVERT: v 277 MET cc_start: 0.8541 (mmm) cc_final: 0.8040 (mmm) REVERT: v 284 LYS cc_start: 0.7852 (mtpp) cc_final: 0.7606 (mmmt) REVERT: w 128 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.5201 (ptm160) REVERT: w 186 ARG cc_start: 0.7711 (ttp80) cc_final: 0.7470 (ttp80) REVERT: x 179 MET cc_start: 0.6606 (mtm) cc_final: 0.6280 (mtm) REVERT: x 379 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7856 (m-30) REVERT: x 389 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6027 (tm) REVERT: x 397 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7166 (ttt180) REVERT: y 1 MET cc_start: 0.5588 (OUTLIER) cc_final: 0.4817 (ttt) REVERT: z 99 LYS cc_start: 0.7498 (mttm) cc_final: 0.7166 (mtpt) REVERT: 4 167 LYS cc_start: 0.4963 (mmtt) cc_final: 0.4616 (tptt) REVERT: 4 232 ARG cc_start: 0.6641 (ttp-110) cc_final: 0.6278 (mtm110) REVERT: 4 272 SER cc_start: 0.7710 (p) cc_final: 0.7307 (t) REVERT: 4 373 LYS cc_start: 0.8053 (ttpp) cc_final: 0.7763 (ttmt) REVERT: 4 404 GLU cc_start: 0.5722 (mt-10) cc_final: 0.5436 (mt-10) REVERT: 4 489 MET cc_start: 0.7334 (ttm) cc_final: 0.6911 (ttp) outliers start: 255 outliers final: 165 residues processed: 1419 average time/residue: 2.3099 time to fit residues: 4626.7723 Evaluate side-chains 1447 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1231 time to evaluate : 8.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 85 LEU Chi-restraints excluded: chain 8 residue 124 THR Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 146 LYS Chi-restraints excluded: chain 9 residue 19 LYS Chi-restraints excluded: chain 9 residue 21 HIS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 231 LYS Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain K residue 338 ASN Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 153 LYS Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 88 GLN Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain W residue 86 LYS Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 184 SER Chi-restraints excluded: chain W residue 214 LYS Chi-restraints excluded: chain X residue 6 LYS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain a residue 86 LYS Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 265 GLU Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 317 ILE Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain b residue 461 GLU Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain c residue 36 GLN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain c residue 98 SER Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 38 ILE Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain h residue 107 LYS Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain j residue 55 ARG Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain m residue 124 ASP Chi-restraints excluded: chain m residue 170 LYS Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain m residue 422 LYS Chi-restraints excluded: chain m residue 429 GLU Chi-restraints excluded: chain m residue 447 SER Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 127 ASP Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 198 ARG Chi-restraints excluded: chain n residue 259 LEU Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 386 ASN Chi-restraints excluded: chain n residue 388 ILE Chi-restraints excluded: chain n residue 390 GLU Chi-restraints excluded: chain n residue 440 GLU Chi-restraints excluded: chain n residue 442 VAL Chi-restraints excluded: chain n residue 445 ASN Chi-restraints excluded: chain n residue 457 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 119 GLU Chi-restraints excluded: chain o residue 121 ARG Chi-restraints excluded: chain o residue 146 MET Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain q residue 206 THR Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 235 SER Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 412 GLU Chi-restraints excluded: chain r residue 54 ARG Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain s residue 3 VAL Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 GLU Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 40 LYS Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 206 SER Chi-restraints excluded: chain t residue 296 SER Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 120 ASP Chi-restraints excluded: chain v residue 208 SER Chi-restraints excluded: chain v residue 226 ILE Chi-restraints excluded: chain w residue 128 ARG Chi-restraints excluded: chain w residue 155 ASP Chi-restraints excluded: chain w residue 164 ASP Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 145 THR Chi-restraints excluded: chain x residue 183 LYS Chi-restraints excluded: chain x residue 190 LEU Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 379 ASP Chi-restraints excluded: chain x residue 389 LEU Chi-restraints excluded: chain x residue 392 THR Chi-restraints excluded: chain x residue 397 ARG Chi-restraints excluded: chain x residue 398 MET Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 145 ASN Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 175 SER Chi-restraints excluded: chain y residue 185 THR Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 45 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 307 ASP Chi-restraints excluded: chain 4 residue 330 THR Chi-restraints excluded: chain 4 residue 370 LEU Chi-restraints excluded: chain 4 residue 517 THR Chi-restraints excluded: chain 4 residue 521 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 816 optimal weight: 10.0000 chunk 1314 optimal weight: 9.9990 chunk 802 optimal weight: 10.0000 chunk 623 optimal weight: 10.0000 chunk 913 optimal weight: 7.9990 chunk 1378 optimal weight: 10.0000 chunk 1269 optimal weight: 8.9990 chunk 1097 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 848 optimal weight: 6.9990 chunk 673 optimal weight: 8.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN 9 64 ASN C 18 ASN C 58 HIS C 307 GLN D 264 GLN G 24 ASN G 221 ASN H 5 GLN H 157 ASN J 90 GLN K 79 GLN L 17 HIS L 114 GLN N 182 ASN N 195 ASN P 179 GLN R 34 GLN S 46 GLN ** S 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN T 131 GLN W 74 GLN Y 66 GLN b 152 GLN b 616 HIS g 3 GLN h 68 GLN h 104 GLN ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 213 ASN ** n 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS o 100 HIS q 228 ASN t 44 GLN t 230 ASN w 63 ASN w 201 ASN x 176 GLN 4 377 GLN 4 447 HIS 4 546 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 167341 Z= 0.403 Angle : 0.854 20.602 241944 Z= 0.439 Chirality : 0.047 0.434 29617 Planarity : 0.008 0.145 18328 Dihedral : 22.337 179.117 63300 Min Nonbonded Distance : 1.598 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.65 % Allowed : 15.68 % Favored : 81.67 % 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: 0.55 (0.08), residues: 10648 helix: 1.49 (0.08), residues: 4166 sheet: 0.08 (0.12), residues: 1567 loop : -0.46 (0.08), residues: 4915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP e 32 HIS 0.014 0.002 HIS C 311 PHE 0.040 0.003 PHE F 229 TYR 0.029 0.003 TYR C 194 ARG 0.012 0.001 ARG 4 524 ********************** 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 1473 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1226 time to evaluate : 8.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.8069 (mttt) cc_final: 0.7495 (mttp) REVERT: 5 78 MET cc_start: 0.4515 (ttp) cc_final: 0.4289 (tmm) REVERT: 8 59 THR cc_start: 0.7779 (m) cc_final: 0.7377 (p) REVERT: 8 146 LYS cc_start: 0.6274 (OUTLIER) cc_final: 0.5950 (mtpp) REVERT: 9 30 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7376 (mtp180) REVERT: 9 84 ILE cc_start: 0.7613 (mm) cc_final: 0.7394 (tp) REVERT: B 37 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7242 (mpt180) REVERT: B 71 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7985 (mt-10) REVERT: B 336 VAL cc_start: 0.9191 (m) cc_final: 0.8872 (p) REVERT: C 143 GLU cc_start: 0.7205 (mp0) cc_final: 0.6865 (mp0) REVERT: D 163 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7180 (tp) REVERT: D 258 LYS cc_start: 0.5275 (OUTLIER) cc_final: 0.3966 (tptt) REVERT: E 136 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6598 (mm-30) REVERT: F 125 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: F 234 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: G 70 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7871 (mtpp) REVERT: G 230 LYS cc_start: 0.6500 (ptpt) cc_final: 0.6164 (pttt) REVERT: H 9 GLN cc_start: 0.7974 (mt0) cc_final: 0.7685 (mt0) REVERT: N 5 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7126 (tmtm) REVERT: N 10 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8635 (tp) REVERT: N 145 ASP cc_start: 0.8223 (t0) cc_final: 0.8016 (t0) REVERT: O 130 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7609 (ttmt) REVERT: Q 22 ASP cc_start: 0.7600 (m-30) cc_final: 0.7235 (m-30) REVERT: S 141 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8326 (mtmt) REVERT: T 38 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6709 (m-30) REVERT: T 52 MET cc_start: 0.5553 (OUTLIER) cc_final: 0.5041 (mmt) REVERT: T 91 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7561 (mp) REVERT: U 39 ASP cc_start: 0.7887 (m-30) cc_final: 0.7529 (m-30) REVERT: V 7 GLN cc_start: 0.8928 (tp40) cc_final: 0.8592 (tp40) REVERT: W 135 PHE cc_start: 0.7580 (t80) cc_final: 0.7325 (t80) REVERT: W 214 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7419 (mtmm) REVERT: X 6 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7297 (ttpt) REVERT: Y 54 ASP cc_start: 0.7963 (p0) cc_final: 0.6764 (p0) REVERT: Y 90 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.7556 (m) REVERT: Z 88 ASP cc_start: 0.7235 (t70) cc_final: 0.6765 (t0) REVERT: a 68 PHE cc_start: 0.6043 (p90) cc_final: 0.5598 (p90) REVERT: a 96 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7000 (tppp) REVERT: b 3 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7197 (mp) REVERT: b 247 ARG cc_start: 0.6769 (ptt90) cc_final: 0.6507 (ptt90) REVERT: b 425 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7313 (t0) REVERT: b 646 PHE cc_start: 0.7684 (p90) cc_final: 0.7453 (p90) REVERT: c 36 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7342 (mt0) REVERT: c 57 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8236 (mt-10) REVERT: d 68 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7778 (mm-30) REVERT: e 34 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7706 (tmtm) REVERT: f 67 MET cc_start: 0.9220 (mtp) cc_final: 0.8705 (mtm) REVERT: g 79 SER cc_start: 0.8192 (p) cc_final: 0.7915 (t) REVERT: g 87 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: h 107 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7909 (mtpt) REVERT: i 56 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6914 (ttp-110) REVERT: i 71 LYS cc_start: 0.7503 (ttmt) cc_final: 0.7132 (mttt) REVERT: j 55 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7554 (ttp-170) REVERT: k 16 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6938 (mtp-110) REVERT: m 63 ASP cc_start: 0.7910 (t0) cc_final: 0.7620 (t70) REVERT: m 314 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7549 (mttt) REVERT: m 429 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6877 (tm-30) REVERT: n 72 MET cc_start: 0.7028 (tpp) cc_final: 0.6612 (tpp) REVERT: n 174 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6697 (mtt180) REVERT: n 198 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6694 (ttp80) REVERT: n 366 TYR cc_start: 0.6331 (t80) cc_final: 0.6014 (t80) REVERT: n 388 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6794 (mm) REVERT: n 390 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5472 (tt0) REVERT: o 105 LYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6734 (pttp) REVERT: o 110 TYR cc_start: 0.8327 (t80) cc_final: 0.8018 (t80) REVERT: o 121 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6748 (mtt-85) REVERT: o 152 MET cc_start: 0.7712 (mmm) cc_final: 0.7300 (mmm) REVERT: o 172 LYS cc_start: 0.4196 (pttp) cc_final: 0.3877 (tptp) REVERT: q 412 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.5549 (mp0) REVERT: q 442 LYS cc_start: 0.6727 (mtpt) cc_final: 0.6481 (mtpp) REVERT: r 54 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7467 (mmm160) REVERT: s 60 ILE cc_start: 0.7597 (mm) cc_final: 0.7326 (mt) REVERT: t 38 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6777 (ttmt) REVERT: t 82 GLU cc_start: 0.5834 (mm-30) cc_final: 0.4803 (pt0) REVERT: v 117 MET cc_start: 0.6366 (mtt) cc_final: 0.6100 (mtt) REVERT: v 268 MET cc_start: 0.8830 (mmm) cc_final: 0.8526 (mmm) REVERT: v 277 MET cc_start: 0.8701 (mmm) cc_final: 0.8208 (mmm) REVERT: v 284 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7477 (mmmt) REVERT: w 128 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.5803 (ptm160) REVERT: w 186 ARG cc_start: 0.7764 (ttp80) cc_final: 0.7507 (ttp80) REVERT: x 179 MET cc_start: 0.6605 (mtm) cc_final: 0.6305 (mtm) REVERT: x 379 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: x 397 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7202 (ttt180) REVERT: z 99 LYS cc_start: 0.7627 (mttm) cc_final: 0.7275 (mtpt) REVERT: 4 167 LYS cc_start: 0.4868 (mmtt) cc_final: 0.4480 (tptt) REVERT: 4 232 ARG cc_start: 0.6834 (ttp-110) cc_final: 0.6348 (mtm110) REVERT: 4 272 SER cc_start: 0.7784 (p) cc_final: 0.7375 (t) REVERT: 4 373 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7890 (ttmt) REVERT: 4 404 GLU cc_start: 0.5983 (mt-10) cc_final: 0.5677 (tt0) REVERT: 4 489 MET cc_start: 0.7422 (ttm) cc_final: 0.6975 (ttp) outliers start: 247 outliers final: 163 residues processed: 1386 average time/residue: 2.2910 time to fit residues: 4468.9840 Evaluate side-chains 1387 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1183 time to evaluate : 8.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 85 LEU Chi-restraints excluded: chain 8 residue 124 THR Chi-restraints excluded: chain 8 residue 125 LEU Chi-restraints excluded: chain 8 residue 146 LYS Chi-restraints excluded: chain 9 residue 19 LYS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 231 LYS Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain K residue 338 ASN Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 176 GLU Chi-restraints excluded: chain L residue 182 ILE Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 130 LYS Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 38 ASP Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain W residue 86 LYS Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 184 SER Chi-restraints excluded: chain W residue 214 LYS Chi-restraints excluded: chain X residue 6 LYS Chi-restraints excluded: chain X residue 71 THR Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 71 SER Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain a residue 86 LYS Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 265 GLU Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 317 ILE Chi-restraints excluded: chain b residue 425 ASP Chi-restraints excluded: chain b residue 461 GLU Chi-restraints excluded: chain b residue 525 THR Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain c residue 36 GLN Chi-restraints excluded: chain c residue 98 SER Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 38 ILE Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain h residue 107 LYS Chi-restraints excluded: chain i residue 56 ARG Chi-restraints excluded: chain j residue 55 ARG Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain m residue 124 ASP Chi-restraints excluded: chain m residue 170 LYS Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain m residue 422 LYS Chi-restraints excluded: chain m residue 429 GLU Chi-restraints excluded: chain m residue 447 SER Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 127 ASP Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 198 ARG Chi-restraints excluded: chain n residue 259 LEU Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 386 ASN Chi-restraints excluded: chain n residue 388 ILE Chi-restraints excluded: chain n residue 390 GLU Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain n residue 442 VAL Chi-restraints excluded: chain n residue 445 ASN Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 121 ARG Chi-restraints excluded: chain o residue 146 MET Chi-restraints excluded: chain o residue 200 MET Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain q residue 206 THR Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 412 GLU Chi-restraints excluded: chain r residue 54 ARG Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 GLU Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 40 LYS Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 206 SER Chi-restraints excluded: chain t residue 296 SER Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain v residue 93 SER Chi-restraints excluded: chain v residue 120 ASP Chi-restraints excluded: chain v residue 208 SER Chi-restraints excluded: chain v residue 224 VAL Chi-restraints excluded: chain v residue 226 ILE Chi-restraints excluded: chain w residue 128 ARG Chi-restraints excluded: chain w residue 155 ASP Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 145 THR Chi-restraints excluded: chain x residue 183 LYS Chi-restraints excluded: chain x residue 190 LEU Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 379 ASP Chi-restraints excluded: chain x residue 389 LEU Chi-restraints excluded: chain x residue 392 THR Chi-restraints excluded: chain x residue 397 ARG Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 153 SER Chi-restraints excluded: chain y residue 175 SER Chi-restraints excluded: chain y residue 185 THR Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 45 LYS Chi-restraints excluded: chain z residue 97 SER Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 307 ASP Chi-restraints excluded: chain 4 residue 330 THR Chi-restraints excluded: chain 4 residue 370 LEU Chi-restraints excluded: chain 4 residue 517 THR Chi-restraints excluded: chain 4 residue 521 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1384 random chunks: chunk 872 optimal weight: 10.0000 chunk 1169 optimal weight: 9.9990 chunk 336 optimal weight: 30.0000 chunk 1012 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 1099 optimal weight: 7.9990 chunk 460 optimal weight: 8.9990 chunk 1129 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN C 307 GLN G 38 GLN H 5 GLN H 157 ASN K 79 GLN L 17 HIS L 114 GLN N 182 ASN N 195 ASN P 179 GLN R 34 GLN S 46 GLN ** S 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 ASN T 131 GLN Y 66 GLN b 152 GLN f 106 ASN g 3 GLN h 68 GLN h 104 GLN i 91 ASN m 213 ASN n 150 GLN ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 456 HIS q 228 ASN t 230 ASN w 63 ASN w 201 ASN x 176 GLN ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 546 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.161552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.132083 restraints weight = 154353.178| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 0.54 r_work: 0.3203 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work: 0.3028 rms_B_bonded: 4.55 restraints_weight: 0.1250 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 167341 Z= 0.328 Angle : 0.773 18.868 241944 Z= 0.404 Chirality : 0.044 0.371 29617 Planarity : 0.007 0.140 18328 Dihedral : 22.298 179.801 63300 Min Nonbonded Distance : 1.616 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.58 % Allowed : 16.01 % Favored : 81.41 % 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: 0.52 (0.08), residues: 10648 helix: 1.49 (0.08), residues: 4180 sheet: 0.04 (0.12), residues: 1593 loop : -0.51 (0.08), residues: 4875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP e 32 HIS 0.011 0.002 HIS C 311 PHE 0.036 0.002 PHE F 229 TYR 0.026 0.002 TYR c 27 ARG 0.011 0.001 ARG L 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 68549.28 seconds wall clock time: 1181 minutes 7.10 seconds (70867.10 seconds total)