Starting phenix.real_space_refine on Sun Mar 3 16:58:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqb_26686/03_2024/7uqb_26686_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqb_26686/03_2024/7uqb_26686.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqb_26686/03_2024/7uqb_26686_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqb_26686/03_2024/7uqb_26686_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqb_26686/03_2024/7uqb_26686_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqb_26686/03_2024/7uqb_26686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqb_26686/03_2024/7uqb_26686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqb_26686/03_2024/7uqb_26686_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uqb_26686/03_2024/7uqb_26686_updated.pdb" } resolution = 2.43 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= 0.014 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: 10 Type Number sf(0) Gaussians K 1 8.98 5 Zn 5 6.06 5 Al 1 5.89 5 P 3332 5.49 5 Mg 81 5.21 5 S 229 5.16 5 C 86384 2.51 5 N 28773 2.21 5 O 39139 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 157949 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: 64042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2991, 64042 Classifications: {'RNA': 2991} Modifications used: {'rna2p': 8, 'rna2p_pur': 309, 'rna2p_pyr': 207, 'rna3p': 40, 'rna3p_pur': 1343, 'rna3p_pyr': 1077} Link IDs: {'rna2p': 524, 'rna3p': 2466} Chain breaks: 14 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 96 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': 2, 'PTRANS': 12, '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: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 133 Unusual residues: {' MG': 76, 'B3P': 3} Classifications: {'undetermined': 79} Link IDs: {None: 78} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' K': 1, ' MG': 1, 'ALF': 1, 'GDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 340 Classifications: {'water': 340} Link IDs: {None: 339} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "m" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 90309 SG CYS I 51 186.477 152.505 140.976 1.00 32.03 S ATOM 90333 SG CYS I 54 184.879 149.079 139.855 1.00 32.25 S ATOM A0HOR SG CYS g 44 146.361 126.592 207.058 1.00 7.33 S ATOM A0HP9 SG CYS g 47 148.453 129.228 205.373 1.00 9.84 S ATOM A0HWB SG CYS g 81 149.961 127.136 208.259 1.00 6.65 S ATOM A0HWU SG CYS g 84 147.493 129.680 209.078 1.00 9.29 S ATOM A0JJM SG CYS j 19 109.075 104.018 168.629 1.00 13.67 S ATOM A0JKB SG CYS j 22 107.868 103.274 165.026 1.00 17.09 S ATOM A0JN3 SG CYS j 34 108.210 106.810 166.169 1.00 9.20 S ATOM A0JNL SG CYS j 37 105.539 104.700 167.773 1.00 9.00 S ATOM A0R2S SG CYS p 39 148.445 146.354 203.850 1.00 15.80 S ATOM A0R3F SG CYS p 42 151.877 145.233 204.622 1.00 16.06 S ATOM A0R6G SG CYS p 57 150.222 144.389 201.330 1.00 14.71 S ATOM A0R6Y SG CYS p 60 148.967 142.654 204.668 1.00 18.30 S ATOM A0W3G SG CYS u 6 186.725 136.976 115.870 1.00 6.50 S ATOM A0W47 SG CYS u 9 187.997 133.466 116.412 1.00 5.26 S ATOM A0W9C SG CYS u 32 185.229 134.049 113.889 1.00 6.57 S ATOM A0WA8 SG CYS u 36 184.762 134.223 117.765 1.00 6.52 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: 60.06, per 1000 atoms: 0.38 Number of scatterers: 157949 At special positions: 0 Unit cell: (230.688, 273.408, 306.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 5 29.99 K 1 19.00 S 229 16.00 P 3332 15.00 Al 1 13.00 Mg 81 11.99 F 4 9.00 O 39139 8.00 N 28773 7.00 C 86384 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 60.03 Conformation dependent library (CDL) restraints added in 12.2 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 54 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 51 " pdb=" ZN g 601 " pdb="ZN ZN g 601 " - pdb=" SG CYS g 47 " 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 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 22 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " 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: 380 helices and 104 sheets defined 45.1% alpha, 14.6% beta 1022 base pairs and 1643 stacking pairs defined. Time for finding SS restraints: 90.59 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 4.740A pdb=" N GLY A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 4.574A 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: 3.762A pdb=" N VAL A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.899A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.604A pdb=" N MET A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.158A 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: 3.593A 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: 3.724A pdb=" N LYS 5 98 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) Processing helix chain '5' and resid 100 through 114 removed outlier: 4.050A pdb=" N ARG 5 113 " --> pdb=" O ARG 5 109 " (cutoff:3.500A) removed outlier: 5.022A 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 removed outlier: 3.685A pdb=" N LYS 8 51 " --> pdb=" O ALA 8 47 " (cutoff:3.500A) Processing helix chain '8' and resid 76 through 86 removed outlier: 3.794A pdb=" N LYS 8 86 " --> pdb=" O ILE 8 82 " (cutoff:3.500A) Processing helix chain '8' and resid 105 through 118 removed outlier: 4.658A pdb=" N ASP 8 118 " --> pdb=" O ARG 8 114 " (cutoff:3.500A) Processing helix chain '8' and resid 124 through 140 Processing helix chain '8' and resid 147 through 158 Processing helix chain '9' and resid 10 through 34 removed outlier: 4.723A 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: 4.208A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.859A pdb=" N ALA B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 removed outlier: 5.908A pdb=" N ARG B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 4.197A 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: 3.787A 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 352 removed outlier: 3.828A pdb=" N LEU B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 23 through 29 removed outlier: 4.289A pdb=" N SER C 27 " --> pdb=" O PRO C 23 " (cutoff:3.500A) removed outlier: 3.761A 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: 3.870A pdb=" N ASN C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.841A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 5.581A 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: 4.214A pdb=" N SER C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.703A 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: 4.051A pdb=" N LYS C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.969A pdb=" N ARG C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.126A 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: 4.563A 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: 4.392A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.260A 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: 4.543A 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: 3.595A pdb=" N GLY D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.778A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.394A 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: 4.145A pdb=" N ALA D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 4.143A 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: 3.536A pdb=" N GLU D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N PHE D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 235 through 251 Proline residue: D 251 - end of helix Processing helix chain 'D' and resid 261 through 274 removed outlier: 3.745A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 5.365A 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: 3.953A pdb=" N VAL E 84 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.824A 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: 6.107A pdb=" N VAL E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 5.248A 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: 3.689A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 4.211A 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: 4.012A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 191 removed outlier: 4.080A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 removed outlier: 5.116A pdb=" N TRP F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 244 removed outlier: 4.923A pdb=" N ASN F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) removed outlier: 4.513A 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 81 removed outlier: 5.090A pdb=" N PHE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N THR G 81 " --> pdb=" O GLN G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 98 removed outlier: 3.881A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.649A pdb=" N LYS G 106 " --> pdb=" O ALA G 102 " (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: 5.174A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 233 removed outlier: 3.516A pdb=" N LYS G 230 " --> pdb=" O TYR G 226 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N TRP G 233 " --> pdb=" O VAL G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 226 through 233' Processing helix chain 'G' and resid 239 through 255 Processing helix chain 'H' and resid 61 through 84 Processing helix chain 'H' and resid 150 through 166 removed outlier: 4.161A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 4.937A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 9 Processing helix chain 'I' and resid 17 through 27 removed outlier: 4.407A pdb=" N THR I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 4.405A pdb=" N GLN I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 71 removed outlier: 3.843A pdb=" N GLY I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS I 71 " --> pdb=" O HIS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 82 removed outlier: 4.375A pdb=" N GLY I 82 " --> pdb=" O LYS I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 95 removed outlier: 3.977A pdb=" N SER I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 131 removed outlier: 3.995A pdb=" N VAL I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 5.083A 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 92 through 97 removed outlier: 4.456A pdb=" N PHE J 96 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER J 97 " --> pdb=" O ASP J 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 92 through 97' Processing helix chain 'J' and resid 136 through 141 removed outlier: 4.328A 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 108 through 113 removed outlier: 4.171A pdb=" N ASP J 111 " --> pdb=" O GLU J 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 50 removed outlier: 3.549A pdb=" N THR K 48 " --> pdb=" O LEU K 44 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS K 50 " --> pdb=" O LYS K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 77 removed outlier: 3.657A pdb=" N LYS K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS K 76 " --> pdb=" O GLU K 72 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (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: 6.096A pdb=" N THR K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL K 118 " --> pdb=" O SER K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 136 removed outlier: 4.565A pdb=" N LYS K 133 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS K 134 " --> pdb=" O SER K 130 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL K 135 " --> pdb=" O ASP K 131 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER K 136 " --> pdb=" O ILE K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 145 removed outlier: 4.141A 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: 3.971A pdb=" N GLN K 176 " --> pdb=" O ALA K 172 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 194 removed outlier: 4.888A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER K 189 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 3.838A 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: 4.020A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN K 200 " --> pdb=" O GLY K 196 " (cutoff:3.500A) removed outlier: 4.730A 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: 4.224A pdb=" N LEU K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) removed outlier: 5.615A 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: 3.790A pdb=" N LYS K 272 " --> pdb=" O GLU K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 302 removed outlier: 4.119A pdb=" N ASP K 299 " --> pdb=" O GLN K 295 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU K 300 " --> pdb=" O ASP K 296 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU K 301 " --> pdb=" O VAL K 297 " (cutoff:3.500A) removed outlier: 4.737A 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: 5.093A pdb=" N ASN K 338 " --> pdb=" O MET K 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.197A pdb=" N ARG L 21 " --> pdb=" O HIS L 17 " (cutoff:3.500A) removed outlier: 3.883A 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: 5.111A pdb=" N GLY L 181 " --> pdb=" O LYS L 177 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE L 182 " --> pdb=" O LYS L 178 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU L 194 " --> pdb=" O LYS L 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 64 removed outlier: 4.074A pdb=" N VAL M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 5.191A 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: 3.799A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 5.619A 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: 3.823A pdb=" N ALA M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 14 removed outlier: 4.598A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 4.769A 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: 4.584A pdb=" N CYS N 152 " --> pdb=" O TYR N 148 " (cutoff:3.500A) removed outlier: 4.118A 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: 3.714A 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: 5.355A pdb=" N ALA O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 3.781A 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: 3.664A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER O 89 " --> pdb=" O ARG O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 103 removed outlier: 3.567A pdb=" N ARG O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 116 removed outlier: 8.052A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LYS O 116 " --> pdb=" O TYR O 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 110 through 116' Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 151 through 183 Processing helix chain 'O' and resid 188 through 198 Processing helix chain 'P' and resid 10 through 15 removed outlier: 4.302A pdb=" N SER P 14 " --> pdb=" O ASN P 10 " (cutoff:3.500A) removed outlier: 5.160A 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: 4.859A pdb=" N LYS P 74 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 5.015A 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: 4.534A 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: 3.735A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 4.021A 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: 4.015A 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: 3.927A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 5.968A 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: 3.795A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 5.424A 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: 5.590A 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: 6.501A 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 137 through 145 removed outlier: 4.872A pdb=" N PHE S 143 " --> pdb=" O TYR S 139 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU S 144 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR S 145 " --> pdb=" O LYS S 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 97 removed outlier: 4.117A pdb=" N ILE T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.287A 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 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: 5.308A pdb=" N LYS V 71 " --> pdb=" O PRO V 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 127 Proline residue: V 127 - end of helix Processing helix chain 'V' and resid 128 through 133 Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.872A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 61 removed outlier: 3.676A 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: 4.643A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 3.576A 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: 5.108A pdb=" N VAL W 155 " --> pdb=" O ALA W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 167 removed outlier: 4.268A 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: 4.660A pdb=" N GLU X 64 " --> pdb=" O TYR X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 79 removed outlier: 3.658A pdb=" N LYS X 75 " --> pdb=" O THR X 71 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 3.983A 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: 3.535A 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: 3.664A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 4.451A 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: 3.652A pdb=" N LEU Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.065A 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: 3.882A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.692A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 5.335A 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: 3.730A pdb=" N VAL Z 96 " --> pdb=" O PHE Z 92 " (cutoff:3.500A) removed outlier: 5.039A 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: 3.707A pdb=" N GLU Z 102 " --> pdb=" O THR Z 98 " (cutoff:3.500A) removed outlier: 3.527A 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: 4.623A 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: 4.241A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 94 removed outlier: 3.552A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.143A 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 68 removed outlier: 3.532A pdb=" N PHE b 68 " --> pdb=" O ILE b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 86 Processing helix chain 'b' and resid 87 through 119 removed outlier: 4.332A pdb=" N PHE b 118 " --> pdb=" O ARG b 114 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY b 119 " --> pdb=" O LEU b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 144 removed outlier: 3.848A pdb=" N LEU b 143 " --> pdb=" O ILE b 139 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG b 144 " --> pdb=" O VAL b 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 160 removed outlier: 3.966A pdb=" N ARG b 159 " --> pdb=" O GLN b 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU b 160 " --> pdb=" O HIS b 156 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.856A 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: 4.422A pdb=" N ALA b 279 " --> pdb=" O LYS b 275 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 312 removed outlier: 4.054A pdb=" N VAL b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 351 removed outlier: 3.550A pdb=" N LYS b 349 " --> pdb=" O GLU b 345 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLN b 351 " --> pdb=" O LYS b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 353 through 362 removed outlier: 4.799A 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: 4.967A pdb=" N LYS b 419 " --> pdb=" O ASN b 415 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR b 420 " --> pdb=" O LEU b 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 415 through 420' Processing helix chain 'b' and resid 424 through 429 removed outlier: 4.245A pdb=" N LYS b 428 " --> pdb=" O ASP b 424 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN b 429 " --> pdb=" O ASP b 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 424 through 429' Processing helix chain 'b' and resid 440 through 445 removed outlier: 3.863A 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: 5.087A 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: 4.717A pdb=" N ARG b 557 " --> pdb=" O ALA b 553 " (cutoff:3.500A) Processing helix chain 'b' and resid 561 through 567 Processing helix chain 'b' and resid 595 through 617 removed outlier: 4.092A pdb=" N ARG b 611 " --> pdb=" O LYS b 607 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLU b 612 " --> pdb=" O MET b 608 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ARG b 613 " --> pdb=" O GLU b 609 " (cutoff:3.500A) Processing helix chain 'b' and resid 631 through 636 Processing helix chain 'c' and resid 9 through 20 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 82 Processing helix chain 'd' and resid 15 through 21 removed outlier: 3.919A pdb=" N ARG d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 45 removed outlier: 5.257A 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: 5.165A 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: 3.770A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU e 85 " --> pdb=" O ASP e 81 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR e 86 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N MET e 87 " --> pdb=" O GLU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.806A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 45 removed outlier: 4.266A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU f 45 " --> pdb=" O ALA f 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 66 removed outlier: 3.598A pdb=" N TYR g 62 " --> pdb=" O ARG g 58 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA g 63 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL g 65 " --> pdb=" O GLN g 61 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER g 66 " --> pdb=" O TYR g 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 58 through 66' Processing helix chain 'g' and resid 81 through 113 Processing helix chain 'h' and resid 5 through 13 removed outlier: 4.255A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS h 12 " --> pdb=" O GLU h 8 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 38 removed outlier: 3.652A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 71 removed outlier: 4.142A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 82 removed outlier: 5.414A 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 30 removed outlier: 4.412A pdb=" N LYS i 29 " --> pdb=" O LYS i 25 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS i 30 " --> pdb=" O ILE i 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 30' 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 99 Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.609A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS j 10 " --> pdb=" O PRO j 6 " (cutoff:3.500A) removed outlier: 4.458A 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: 5.509A pdb=" N HIS j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 4.862A 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: 5.414A pdb=" N ARG l 21 " --> pdb=" O LYS l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.189A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 3.745A 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: 4.302A pdb=" N TYR m 42 " --> pdb=" O PHE m 38 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR m 43 " --> pdb=" O LEU m 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 74 through 80 removed outlier: 4.544A pdb=" N PHE m 78 " --> pdb=" O ASP m 74 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY m 79 " --> pdb=" O ARG m 75 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN m 80 " --> pdb=" O ARG m 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 74 through 80' Processing helix chain 'm' and resid 85 through 99 removed outlier: 5.110A pdb=" N GLY m 97 " --> pdb=" O ARG m 93 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU m 98 " --> pdb=" O SER m 94 " (cutoff:3.500A) removed outlier: 3.647A 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: 4.171A 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 182 removed outlier: 4.296A pdb=" N LEU m 181 " --> pdb=" O LEU m 177 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 193 removed outlier: 3.681A pdb=" N ASP m 189 " --> pdb=" O GLY m 185 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS m 190 " --> pdb=" O ASN m 186 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU m 191 " --> pdb=" O GLN m 187 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN m 192 " --> pdb=" O GLU m 188 " (cutoff:3.500A) Processing helix chain 'm' and resid 200 through 205 removed outlier: 4.265A pdb=" N SER m 204 " --> pdb=" O GLU m 200 " (cutoff:3.500A) removed outlier: 3.801A 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: 4.329A 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: 3.658A pdb=" N LYS m 279 " --> pdb=" O LYS m 275 " (cutoff:3.500A) removed outlier: 4.496A 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: 3.792A pdb=" N GLY m 386 " --> pdb=" O ILE m 382 " (cutoff:3.500A) Processing helix chain 'm' and resid 395 through 407 removed outlier: 4.162A 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: 4.169A pdb=" N HIS n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU n 74 " --> pdb=" O TYR n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 97 Processing helix chain 'n' and resid 98 through 109 removed outlier: 4.125A 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: 4.861A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA n 135 " --> pdb=" O ASP n 131 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN n 144 " --> pdb=" O PHE n 140 " (cutoff:3.500A) removed outlier: 3.708A 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 258 through 263 removed outlier: 4.636A pdb=" N TYR n 262 " --> pdb=" O GLY n 258 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE n 263 " --> pdb=" O LEU n 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 258 through 263' Processing helix chain 'n' and resid 354 through 359 removed outlier: 6.667A 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 396 removed outlier: 3.665A pdb=" N MET n 393 " --> pdb=" O SER n 389 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP n 394 " --> pdb=" O GLU n 390 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLN n 395 " --> pdb=" O ALA n 391 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE n 396 " --> pdb=" O ALA n 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 389 through 396' Processing helix chain 'n' and resid 428 through 439 removed outlier: 4.312A pdb=" N ILE n 432 " --> pdb=" O GLN n 428 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE n 433 " --> pdb=" O PRO n 429 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 115 removed outlier: 4.140A pdb=" N GLN o 113 " --> pdb=" O LYS o 109 " (cutoff:3.500A) removed outlier: 4.188A 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 Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.696A pdb=" N LEU p 29 " --> pdb=" O GLN p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 Processing helix chain 'q' and resid 204 through 210 removed outlier: 4.212A pdb=" N ASP q 208 " --> pdb=" O PRO q 204 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE q 209 " --> pdb=" O SER q 205 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLU q 210 " --> pdb=" O THR q 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 204 through 210' Processing helix chain 'q' and resid 232 through 269 Processing helix chain 'q' and resid 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: 4.650A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 74 removed outlier: 3.994A pdb=" N LYS r 74 " --> pdb=" O GLN r 70 " (cutoff:3.500A) Processing helix chain 'r' and resid 129 through 134 Processing helix chain 'r' and resid 174 through 179 removed outlier: 3.626A pdb=" N ARG r 178 " --> pdb=" O PRO r 174 " (cutoff:3.500A) removed outlier: 5.874A 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 75 removed outlier: 3.776A pdb=" N GLU s 73 " --> pdb=" O MET s 69 " (cutoff:3.500A) Processing helix chain 't' and resid 15 through 52 removed outlier: 4.417A pdb=" N LEU t 19 " --> pdb=" O ASN t 15 " (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: 3.815A 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: 5.138A 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: 5.417A 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 72 removed outlier: 4.143A pdb=" N THR u 70 " --> pdb=" O ASP u 66 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE u 71 " --> pdb=" O SER u 67 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA u 72 " --> pdb=" O THR u 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 66 through 72' Processing helix chain 'u' and resid 82 through 131 removed outlier: 3.653A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLY u 114 " --> pdb=" O ASN u 110 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN u 115 " --> pdb=" O ARG u 111 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS u 116 " --> pdb=" O MET u 112 " (cutoff:3.500A) removed outlier: 7.225A 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: 5.457A 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: 4.163A pdb=" N PHE v 128 " --> pdb=" O LEU v 124 " (cutoff:3.500A) removed outlier: 4.332A 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: 4.327A 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 174 through 179 removed outlier: 3.981A pdb=" N LEU v 178 " --> pdb=" O ASP v 174 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLN v 179 " --> pdb=" O VAL v 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 174 through 179' Processing helix chain 'v' and resid 241 through 250 Processing helix chain 'v' and resid 281 through 286 removed outlier: 4.472A pdb=" N LEU v 285 " --> pdb=" O ASP v 281 " (cutoff:3.500A) removed outlier: 5.732A 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 'v' and resid 290 through 295 removed outlier: 3.864A pdb=" N LYS v 294 " --> pdb=" O MET v 290 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER v 295 " --> pdb=" O LYS v 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 290 through 295' Processing helix chain 'w' and resid 35 through 40 Processing helix chain 'w' and resid 45 through 68 Processing helix chain 'w' and resid 112 through 122 Processing helix chain 'w' and resid 149 through 157 removed outlier: 4.380A pdb=" N LYS w 153 " --> pdb=" O GLY w 149 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LEU w 154 " --> pdb=" O ALA w 150 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP w 155 " --> pdb=" O ASN w 151 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP w 156 " --> pdb=" O LYS w 152 " (cutoff:3.500A) Processing helix chain 'w' and resid 175 through 201 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: 5.041A pdb=" N LYS x 244 " --> pdb=" O ILE x 240 " (cutoff:3.500A) Processing helix chain 'x' and resid 330 through 337 Processing helix chain 'x' and resid 348 through 365 removed outlier: 3.919A pdb=" N ILE x 363 " --> pdb=" O ASN x 359 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 17 removed outlier: 3.728A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 43 removed outlier: 4.009A 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 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 133 Processing helix chain 'y' and resid 147 through 152 Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 197 Processing helix chain 'y' and resid 211 through 223 Processing helix chain 'y' and resid 232 through 244 removed outlier: 5.114A pdb=" N ASP y 238 " --> pdb=" O GLY y 234 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N THR y 239 " --> pdb=" O ASN y 235 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 56 removed outlier: 4.053A pdb=" N GLY z 20 " --> pdb=" O VAL z 16 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL z 21 " --> pdb=" O LYS z 17 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE z 22 " --> pdb=" O ARG z 18 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLN z 23 " --> pdb=" O ARG z 19 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) removed outlier: 3.643A 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: 4.292A pdb=" N GLN 4 78 " --> pdb=" O THR 4 74 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR 4 79 " --> pdb=" O ARG 4 75 " (cutoff:3.500A) removed outlier: 5.441A 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: 3.683A pdb=" N ALA 4 201 " --> pdb=" O LEU 4 197 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU 4 202 " --> pdb=" O LEU 4 198 " (cutoff:3.500A) removed outlier: 4.270A 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: 3.573A pdb=" N LYS 4 384 " --> pdb=" O THR 4 380 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN 4 385 " --> pdb=" O LYS 4 381 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY 4 386 " --> pdb=" O ILE 4 382 " (cutoff:3.500A) Processing helix chain '4' and resid 391 through 396 removed outlier: 4.041A pdb=" N LEU 4 395 " --> pdb=" O LYS 4 391 " (cutoff:3.500A) removed outlier: 4.164A 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: 3.896A pdb=" N SER 4 418 " --> pdb=" O LYS 4 414 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU 4 425 " --> pdb=" O LEU 4 421 " (cutoff:3.500A) Processing helix chain '4' and resid 444 through 451 removed outlier: 3.510A pdb=" N ILE 4 448 " --> pdb=" O PRO 4 444 " (cutoff:3.500A) Processing helix chain '4' and resid 466 through 472 removed outlier: 4.520A pdb=" N GLU 4 472 " --> pdb=" O LEU 4 468 " (cutoff:3.500A) Processing helix chain '4' and resid 481 through 493 removed outlier: 5.655A pdb=" N LYS 4 493 " --> pdb=" O MET 4 489 " (cutoff:3.500A) Processing helix chain '4' and resid 547 through 563 removed outlier: 5.373A pdb=" N LYS 4 563 " --> pdb=" O LEU 4 559 " (cutoff:3.500A) Processing helix chain '4' and resid 528 through 533 removed outlier: 4.213A 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: 3.851A pdb=" N GLN A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.246A 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: 4.164A pdb=" N THR A 111 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.527A 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: 4.155A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '8' and resid 11 through 16 removed outlier: 4.421A 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: 6.604A pdb=" N GLN B 182 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N HIS B 177 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL B 158 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.047A 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: 6.907A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 12.838A pdb=" N LYS B 333 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 11.274A pdb=" N LYS B 222 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 4.344A 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: 6.830A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.864A 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: 3.692A pdb=" N GLY B 288 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 5.358A 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: 4.386A 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: 5.324A 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: 5.236A 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: 6.666A 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: 4.134A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS E 50 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 133 through 138 removed outlier: 7.709A pdb=" N TYR F 133 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LYS F 82 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ASN F 112 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 152 through 155 removed outlier: 6.717A pdb=" N GLY F 152 " --> pdb=" O LEU F 163 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 176 through 181 Processing sheet with id= 20, first strand: chain 'H' and resid 5 through 12 removed outlier: 4.822A pdb=" N GLN H 51 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 17 through 20 removed outlier: 6.084A pdb=" N ARG H 23 " --> pdb=" O LEU H 38 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 100 through 105 removed outlier: 6.196A pdb=" N LYS H 110 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 132 through 137 removed outlier: 5.698A pdb=" N GLU H 143 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP H 142 " --> pdb=" O TYR H 92 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 49 through 52 removed outlier: 4.975A pdb=" N HIS I 49 " --> pdb=" O MET I 58 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 45 through 48 removed outlier: 3.974A pdb=" N ALA J 66 " --> pdb=" O SER J 48 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE J 65 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N SER J 22 " --> pdb=" O GLY J 124 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLY J 124 " --> pdb=" O SER J 22 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N MET J 131 " --> pdb=" O GLY J 100 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLY J 100 " --> pdb=" O MET J 131 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'K' and resid 97 through 101 Processing sheet with id= 27, first strand: chain 'K' and resid 122 through 126 Processing sheet with id= 28, first strand: chain 'K' and resid 242 through 248 removed outlier: 5.606A pdb=" N THR K 242 " --> pdb=" O ASN K 84 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU K 78 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'L' and resid 56 through 59 Processing sheet with id= 30, first strand: chain 'M' and resid 19 through 24 removed outlier: 4.414A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS M 31 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.625A pdb=" N VAL N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY N 58 " --> pdb=" O ASP N 136 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'N' and resid 117 through 121 removed outlier: 3.611A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 34, first strand: chain 'P' and resid 16 through 20 removed outlier: 6.447A pdb=" N LYS P 111 " --> pdb=" O LYS P 153 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'P' and resid 57 through 60 removed outlier: 5.435A pdb=" N LYS P 80 " --> pdb=" O PHE P 60 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'P' and resid 115 through 122 Processing sheet with id= 37, first strand: chain 'P' and resid 124 through 131 Processing sheet with id= 38, first strand: chain 'Q' and resid 79 through 83 Processing sheet with id= 39, first strand: chain 'S' and resid 24 through 31 removed outlier: 6.661A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'S' and resid 86 through 96 removed outlier: 6.604A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP S 82 " --> pdb=" O SER S 120 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N SER S 120 " --> pdb=" O ASP S 82 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'S' and resid 6 through 10 removed outlier: 4.584A pdb=" N GLU S 6 " --> pdb=" O ILE S 64 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'S' and resid 74 through 78 removed outlier: 5.004A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'T' and resid 39 through 43 removed outlier: 4.233A 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: 5.979A pdb=" N ASN U 101 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) removed outlier: 7.622A 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: 4.233A 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: 4.477A pdb=" N ASP V 56 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP V 97 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 3.554A 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 87 removed outlier: 3.591A 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: 6.104A pdb=" N VAL W 99 " --> pdb=" O LEU W 45 " (cutoff:3.500A) removed outlier: 6.878A 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 138 removed outlier: 6.553A pdb=" N PHE W 135 " --> pdb=" O VAL W 188 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'W' and resid 38 through 42 removed outlier: 8.427A pdb=" N ARG W 38 " --> pdb=" O ASN W 223 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'X' and resid 81 through 86 removed outlier: 3.694A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'Y' and resid 56 through 59 removed outlier: 4.409A pdb=" N GLN Y 66 " --> pdb=" O VAL Y 58 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'Y' and resid 72 through 75 Processing sheet with id= 55, first strand: chain 'Y' and resid 86 through 89 removed outlier: 4.222A pdb=" N ALA Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'Z' and resid 9 through 14 removed outlier: 4.285A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Z' and resid 42 through 45 Processing sheet with id= 58, first strand: chain 'a' and resid 99 through 102 Processing sheet with id= 59, first strand: chain 'b' and resid 204 through 210 removed outlier: 4.855A pdb=" N ARG b 168 " --> pdb=" O ARG b 215 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR b 221 " --> pdb=" O ILE b 172 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY b 174 " --> pdb=" O THR b 221 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU b 316 " --> pdb=" O VAL b 283 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.515A pdb=" N LYS c 22 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS c 66 " --> pdb=" O LYS c 40 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'd' and resid 48 through 51 removed outlier: 5.083A pdb=" N ASP d 48 " --> pdb=" O LEU d 89 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR d 9 " --> pdb=" O VAL d 109 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'e' and resid 71 through 77 Processing sheet with id= 63, first strand: chain 'f' and resid 10 through 14 removed outlier: 5.910A pdb=" N LYS f 10 " --> pdb=" O GLU f 33 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG f 82 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS f 47 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'f' and resid 8 through 14 removed outlier: 3.959A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.447A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'k' and resid 2 through 5 removed outlier: 4.507A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE k 27 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'm' and resid 291 through 294 removed outlier: 4.290A pdb=" N ASN m 292 " --> pdb=" O SER m 289 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N SER m 289 " --> pdb=" O ASN m 292 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS m 367 " --> pdb=" O PHE m 320 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY m 322 " --> pdb=" O CYS m 367 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE m 362 " --> pdb=" O LEU m 358 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'n' and resid 177 through 182 Processing sheet with id= 69, first strand: chain 'n' and resid 385 through 388 Processing sheet with id= 70, first strand: chain 'o' and resid 118 through 123 removed outlier: 3.717A pdb=" N GLU o 119 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'p' and resid 47 through 50 removed outlier: 6.921A pdb=" N ILE p 54 " --> pdb=" O GLY p 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'r' and resid 148 through 151 Processing sheet with id= 73, first strand: chain 'r' and resid 190 through 195 removed outlier: 3.801A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN r 256 " --> pdb=" O THR r 246 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TYR r 242 " --> pdb=" O LEU r 260 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR r 219 " --> pdb=" O VAL r 245 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 't' and resid 128 through 134 Processing sheet with id= 75, first strand: chain 't' and resid 193 through 198 removed outlier: 5.435A pdb=" N TYR t 193 " --> pdb=" O VAL t 147 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASN t 172 " --> pdb=" O LEU t 273 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'u' and resid 3 through 6 removed outlier: 4.686A pdb=" N SER u 11 " --> pdb=" O CYS u 6 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'u' and resid 18 through 22 Processing sheet with id= 78, first strand: chain 'v' and resid 56 through 60 removed outlier: 7.192A pdb=" N SER v 92 " --> pdb=" O GLY v 35 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N SER v 85 " --> pdb=" O THR v 105 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN v 98 " --> pdb=" O VAL v 118 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU v 115 " --> pdb=" O GLY v 235 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASP v 231 " --> pdb=" O ALA v 119 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'v' and resid 262 through 266 removed outlier: 5.979A pdb=" N ASN v 262 " --> pdb=" O ARG v 274 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP v 270 " --> pdb=" O ASP v 266 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'v' and resid 111 through 115 removed outlier: 9.004A pdb=" N TYR v 111 " --> pdb=" O PRO v 240 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'v' and resid 203 through 206 removed outlier: 6.941A pdb=" N VAL v 203 " --> pdb=" O ILE v 226 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'w' and resid 17 through 23 removed outlier: 5.712A pdb=" N SER w 31 " --> pdb=" O PRO w 18 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'w' and resid 69 through 72 Processing sheet with id= 84, first strand: chain 'x' and resid 48 through 52 removed outlier: 6.013A pdb=" N THR x 118 " --> pdb=" O THR x 82 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR x 82 " --> pdb=" O THR x 118 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N PHE x 79 " --> pdb=" O ILE x 97 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'x' and resid 136 through 140 removed outlier: 5.062A pdb=" N MET x 509 " --> pdb=" O GLY x 505 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY x 505 " --> pdb=" O MET x 509 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG x 500 " --> pdb=" O SER x 495 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'x' and resid 148 through 152 removed outlier: 6.401A pdb=" N ARG x 158 " --> pdb=" O ALA x 152 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER x 157 " --> pdb=" O CYS x 173 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR x 167 " --> pdb=" O ALA x 163 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE x 170 " --> pdb=" O MET x 179 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'x' and resid 191 through 195 removed outlier: 5.712A pdb=" N VAL x 200 " --> pdb=" O SER x 195 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR x 209 " --> pdb=" O SER x 205 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU x 212 " --> pdb=" O LEU x 221 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'x' and resid 233 through 238 removed outlier: 3.561A pdb=" N SER x 234 " --> pdb=" O SER x 254 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ARG x 250 " --> pdb=" O GLU x 238 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE x 262 " --> pdb=" O GLN x 271 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'x' and resid 283 through 287 removed outlier: 4.445A pdb=" N LEU x 291 " --> pdb=" O GLY x 287 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N GLY x 290 " --> pdb=" O ILE x 306 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'x' and resid 325 through 329 removed outlier: 6.806A pdb=" N MET x 373 " --> pdb=" O SER x 329 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR x 382 " --> pdb=" O SER x 378 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'x' and resid 406 through 411 removed outlier: 5.790A pdb=" N TYR x 416 " --> pdb=" O SER x 411 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'x' and resid 426 through 431 removed outlier: 6.474A pdb=" N ILE x 426 " --> pdb=" O THR x 439 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR x 439 " --> pdb=" O ILE x 426 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU x 428 " --> pdb=" O ILE x 437 " (cutoff:3.500A) removed outlier: 4.147A 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: 3.656A pdb=" N GLN x 449 " --> pdb=" O CYS x 462 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU x 458 " --> pdb=" O SER x 453 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ARG x 457 " --> pdb=" O VAL x 473 " (cutoff:3.500A) removed outlier: 4.185A 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: 3.903A pdb=" N TYR x 272 " --> pdb=" O ILE x 262 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'y' and resid 1 through 4 Processing sheet with id= 97, first strand: chain 'y' and resid 23 through 27 Processing sheet with id= 98, first strand: chain 'y' and resid 69 through 73 Processing sheet with id= 99, first strand: chain 'y' and resid 114 through 117 Processing sheet with id=100, first strand: chain 'y' and resid 158 through 162 Processing sheet with id=101, first strand: chain '4' and resid 93 through 97 removed outlier: 3.967A pdb=" N ASP 4 137 " --> pdb=" O ILE 4 160 " (cutoff:3.500A) removed outlier: 13.393A pdb=" N THR 4 151 " --> pdb=" O VAL 4 508 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N VAL 4 508 " --> pdb=" O THR 4 151 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU 4 153 " --> pdb=" O THR 4 506 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR 4 506 " --> pdb=" O GLU 4 153 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG 4 502 " --> pdb=" O THR 4 157 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N VAL 4 159 " --> pdb=" O VAL 4 500 " (cutoff:3.500A) removed outlier: 13.742A pdb=" N VAL 4 500 " --> pdb=" O VAL 4 159 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU 4 315 " --> pdb=" O LEU 4 509 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER 4 242 " --> pdb=" O TRP 4 269 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LYS 4 265 " --> pdb=" O ARG 4 246 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain '4' and resid 335 through 340 No H-bonds generated for sheet with id=102 Processing sheet with id=103, first strand: chain '4' and resid 568 through 572 Processing sheet with id=104, first strand: chain '4' and resid 506 through 511 removed outlier: 6.547A pdb=" N THR 4 506 " --> pdb=" O LEU 4 525 " (cutoff:3.500A) 3871 hydrogen bonds defined for protein. 11499 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2518 hydrogen bonds 4048 hydrogen bond angles 0 basepair planarities 1022 basepair parallelities 1643 stacking parallelities Total time for adding SS restraints: 270.89 Time building geometry restraints manager: 65.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 38289 1.34 - 1.46: 58511 1.46 - 1.59: 64350 1.59 - 1.72: 5926 1.72 - 1.84: 385 Bond restraints: 167461 Sorted by residual: bond pdb=" C2' A2M 1 876 " pdb=" C1' A2M 1 876 " ideal model delta sigma weight residual 1.305 1.572 -0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C2' A2M 12220 " pdb=" C1' A2M 12220 " ideal model delta sigma weight residual 1.305 1.569 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C2' A2M 11133 " pdb=" C1' A2M 11133 " ideal model delta sigma weight residual 1.305 1.569 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C2' A2M 1 807 " pdb=" C1' A2M 1 807 " ideal model delta sigma weight residual 1.305 1.569 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C2' A2M 1 649 " pdb=" C1' A2M 1 649 " ideal model delta sigma weight residual 1.305 1.560 -0.255 2.00e-02 2.50e+03 1.63e+02 ... (remaining 167456 not shown) Histogram of bond angle deviations from ideal: 86.31 - 104.47: 14820 104.47 - 122.64: 200321 122.64 - 140.80: 26988 140.80 - 158.96: 0 158.96 - 177.12: 2 Bond angle restraints: 242131 Sorted by residual: angle pdb=" F3 ALF m 802 " pdb="AL ALF m 802 " pdb=" F4 ALF m 802 " ideal model delta sigma weight residual 109.63 177.12 -67.49 3.00e+00 1.11e-01 5.06e+02 angle pdb=" F1 ALF m 802 " pdb="AL ALF m 802 " pdb=" F2 ALF m 802 " ideal model delta sigma weight residual 108.68 175.46 -66.78 3.00e+00 1.11e-01 4.95e+02 angle pdb=" C1' A2M 1 817 " pdb=" N9 A2M 1 817 " pdb=" C8 A2M 1 817 " ideal model delta sigma weight residual 88.50 128.88 -40.38 3.00e+00 1.11e-01 1.81e+02 angle pdb=" C1' A2M 1 807 " pdb=" N9 A2M 1 807 " pdb=" C8 A2M 1 807 " ideal model delta sigma weight residual 88.50 128.43 -39.93 3.00e+00 1.11e-01 1.77e+02 angle pdb=" C1' A2M 11449 " pdb=" N9 A2M 11449 " pdb=" C8 A2M 11449 " ideal model delta sigma weight residual 88.50 128.06 -39.56 3.00e+00 1.11e-01 1.74e+02 ... (remaining 242126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 97154 35.98 - 71.96: 7676 71.96 - 107.94: 842 107.94 - 143.92: 18 143.92 - 179.90: 45 Dihedral angle restraints: 105735 sinusoidal: 74356 harmonic: 31379 Sorted by residual: dihedral pdb=" C4' U 13283 " pdb=" C3' U 13283 " pdb=" C2' U 13283 " pdb=" C1' U 13283 " ideal model delta sinusoidal sigma weight residual -35.00 33.79 -68.79 1 8.00e+00 1.56e-02 9.57e+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 30.14 169.86 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 32.27 167.73 1 1.50e+01 4.44e-03 8.44e+01 ... (remaining 105732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 27547 0.071 - 0.142: 1969 0.142 - 0.214: 108 0.214 - 0.285: 8 0.285 - 0.356: 8 Chirality restraints: 29640 Sorted by residual: 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 -2.75 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C2' A2M 1 876 " pdb=" C3' A2M 1 876 " pdb=" O2' A2M 1 876 " pdb=" C1' A2M 1 876 " both_signs ideal model delta sigma weight residual False -2.39 -2.73 0.34 2.00e-01 2.50e+01 2.84e+00 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 -2.73 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 29637 not shown) Planarity restraints: 18333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12793 " 0.081 2.00e-02 2.50e+03 6.34e-01 9.05e+03 pdb=" C4' OMG 12793 " 0.466 2.00e-02 2.50e+03 pdb=" O4' OMG 12793 " 0.695 2.00e-02 2.50e+03 pdb=" C3' OMG 12793 " -0.588 2.00e-02 2.50e+03 pdb=" O3' OMG 12793 " -0.697 2.00e-02 2.50e+03 pdb=" C2' OMG 12793 " -0.167 2.00e-02 2.50e+03 pdb=" O2' OMG 12793 " 1.011 2.00e-02 2.50e+03 pdb=" C1' OMG 12793 " 0.195 2.00e-02 2.50e+03 pdb=" N9 OMG 12793 " -0.996 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 1MA 12142 " -0.891 2.00e-02 2.50e+03 5.88e-01 7.78e+03 pdb=" C4' 1MA 12142 " 0.194 2.00e-02 2.50e+03 pdb=" O4' 1MA 12142 " 0.827 2.00e-02 2.50e+03 pdb=" C3' 1MA 12142 " -0.267 2.00e-02 2.50e+03 pdb=" O3' 1MA 12142 " 0.817 2.00e-02 2.50e+03 pdb=" C2' 1MA 12142 " -0.594 2.00e-02 2.50e+03 pdb=" O2' 1MA 12142 " -0.535 2.00e-02 2.50e+03 pdb=" C1' 1MA 12142 " 0.468 2.00e-02 2.50e+03 pdb=" N9 1MA 12142 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 12197 " 0.850 2.00e-02 2.50e+03 5.73e-01 7.40e+03 pdb=" C4' OMC 12197 " -0.220 2.00e-02 2.50e+03 pdb=" O4' OMC 12197 " -0.687 2.00e-02 2.50e+03 pdb=" C3' OMC 12197 " 0.224 2.00e-02 2.50e+03 pdb=" O3' OMC 12197 " -0.887 2.00e-02 2.50e+03 pdb=" C2' OMC 12197 " 0.605 2.00e-02 2.50e+03 pdb=" O2' OMC 12197 " 0.565 2.00e-02 2.50e+03 pdb=" C1' OMC 12197 " -0.440 2.00e-02 2.50e+03 pdb=" N1 OMC 12197 " -0.010 2.00e-02 2.50e+03 ... (remaining 18330 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.59: 1825 2.59 - 3.23: 137373 3.23 - 3.86: 364482 3.86 - 4.50: 486283 4.50 - 5.14: 675107 Nonbonded interactions: 1665070 Sorted by model distance: nonbonded pdb=" OP2 C 1 893 " pdb="MG MG 13466 " model vdw 1.951 2.170 nonbonded pdb=" OP2 C 1 861 " pdb="MG MG 13465 " model vdw 1.965 2.170 nonbonded pdb=" OP2 C 1 863 " pdb="MG MG 13466 " model vdw 1.966 2.170 nonbonded pdb=" O ASN M 11 " pdb=" OD1 ASN M 11 " model vdw 1.970 3.040 nonbonded pdb=" OP1 A 12138 " pdb="MG MG 13429 " model vdw 1.972 2.170 ... (remaining 1665065 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: 4.550 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: 20.460 Check model and map are aligned: 1.750 Set scattering table: 1.170 Process input model: 627.060 Find NCS groups from input model: 4.000 Set up NCS constraints: 0.390 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 670.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 0.267 167461 Z= 0.310 Angle : 0.715 67.494 242131 Z= 0.332 Chirality : 0.038 0.356 29640 Planarity : 0.018 0.634 18333 Dihedral : 20.561 179.904 85419 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.43 % Allowed : 3.87 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 0.86 (0.08), residues: 10648 helix: 1.63 (0.08), residues: 4157 sheet: 0.26 (0.13), residues: 1535 loop : -0.17 (0.08), residues: 4956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP e 32 HIS 0.006 0.001 HIS P 145 PHE 0.035 0.002 PHE F 229 TYR 0.017 0.002 TYR C 194 ARG 0.007 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 1989 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1949 time to evaluate : 9.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASN cc_start: 0.7685 (m-40) cc_final: 0.7450 (m-40) REVERT: 9 32 ARG cc_start: 0.7068 (mtm-85) cc_final: 0.6643 (mtm-85) REVERT: 9 49 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 323 MET cc_start: 0.8150 (ttm) cc_final: 0.7875 (ttm) REVERT: B 335 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8271 (tp) REVERT: C 155 ASP cc_start: 0.7566 (m-30) cc_final: 0.7189 (m-30) REVERT: D 62 CYS cc_start: 0.8027 (m) cc_final: 0.7634 (m) REVERT: D 140 ARG cc_start: 0.7234 (mtt180) cc_final: 0.6992 (mtm-85) REVERT: D 152 ARG cc_start: 0.7169 (mmm-85) cc_final: 0.6890 (mmt90) REVERT: D 186 GLU cc_start: 0.3598 (mm-30) cc_final: 0.3283 (mm-30) REVERT: D 226 TYR cc_start: 0.4675 (m-80) cc_final: 0.4452 (m-10) REVERT: E 143 LYS cc_start: 0.7226 (ttmm) cc_final: 0.6832 (ttpp) REVERT: F 52 GLN cc_start: 0.8347 (tp40) cc_final: 0.8020 (mm-40) REVERT: G 54 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7458 (mt-10) REVERT: H 31 ARG cc_start: 0.8315 (mtp85) cc_final: 0.7922 (mtp85) REVERT: H 51 GLN cc_start: 0.8380 (mp10) cc_final: 0.8153 (mp10) REVERT: H 90 MET cc_start: 0.8818 (mtp) cc_final: 0.8600 (mtp) REVERT: H 129 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7760 (mtp85) REVERT: H 142 ASP cc_start: 0.7664 (m-30) cc_final: 0.7356 (m-30) REVERT: H 153 ASP cc_start: 0.7780 (m-30) cc_final: 0.7371 (m-30) REVERT: K 266 ILE cc_start: 0.5015 (mt) cc_final: 0.4802 (mm) REVERT: L 168 ARG cc_start: 0.7121 (ttt90) cc_final: 0.6854 (mmm160) REVERT: M 6 ILE cc_start: 0.8215 (tt) cc_final: 0.8010 (mp) REVERT: O 100 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7732 (mt-10) REVERT: P 43 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7947 (ttpp) REVERT: P 136 ILE cc_start: 0.8774 (mt) cc_final: 0.8571 (mt) REVERT: Q 7 SER cc_start: 0.7934 (p) cc_final: 0.7666 (p) REVERT: Q 124 LEU cc_start: 0.7949 (mt) cc_final: 0.7709 (mp) REVERT: Q 144 ARG cc_start: 0.6470 (mmt90) cc_final: 0.6054 (mmt180) REVERT: R 28 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7625 (mm-30) REVERT: S 34 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7497 (mt-10) REVERT: S 131 LYS cc_start: 0.7892 (mtpp) cc_final: 0.7683 (mtmt) REVERT: S 148 LEU cc_start: 0.8491 (tp) cc_final: 0.8131 (tp) REVERT: T 43 LYS cc_start: 0.7415 (tttp) cc_final: 0.7121 (tttp) REVERT: T 106 LEU cc_start: 0.7647 (mt) cc_final: 0.7422 (mm) REVERT: U 104 ARG cc_start: 0.8261 (ptt-90) cc_final: 0.8001 (ptm-80) REVERT: V 59 MET cc_start: 0.8893 (mmm) cc_final: 0.8680 (mmm) REVERT: W 35 ASP cc_start: 0.4878 (m-30) cc_final: 0.4660 (m-30) REVERT: W 183 ASP cc_start: 0.6421 (m-30) cc_final: 0.6217 (m-30) REVERT: X 58 ASP cc_start: 0.7991 (p0) cc_final: 0.7770 (p0) REVERT: Y 46 LYS cc_start: 0.7994 (tttt) cc_final: 0.7725 (tttm) REVERT: Y 114 ASP cc_start: 0.8380 (m-30) cc_final: 0.8149 (m-30) REVERT: Z 102 GLU cc_start: 0.6416 (mt-10) cc_final: 0.5917 (mt-10) REVERT: Z 116 LYS cc_start: 0.7989 (tttm) cc_final: 0.7648 (ttpm) REVERT: Z 119 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7362 (mm-30) REVERT: a 61 PHE cc_start: 0.7116 (t80) cc_final: 0.6821 (t80) REVERT: b 1 MET cc_start: 0.5852 (mtt) cc_final: 0.5482 (mpp) REVERT: b 47 MET cc_start: 0.9046 (mtt) cc_final: 0.8665 (mtp) REVERT: b 316 GLU cc_start: 0.5849 (tt0) cc_final: 0.5357 (tt0) REVERT: b 535 MET cc_start: 0.7623 (mmt) cc_final: 0.7419 (mmt) REVERT: b 561 ARG cc_start: 0.7025 (mtm-85) cc_final: 0.6526 (mtp85) REVERT: b 608 MET cc_start: 0.8595 (mtm) cc_final: 0.8100 (mtm) REVERT: c 36 GLN cc_start: 0.8144 (mt0) cc_final: 0.7905 (mt0) REVERT: d 97 LEU cc_start: 0.8368 (mt) cc_final: 0.8117 (mm) REVERT: d 102 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7522 (mtpp) REVERT: f 49 ILE cc_start: 0.8877 (mt) cc_final: 0.8516 (mt) REVERT: h 96 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8146 (mt-10) REVERT: h 105 ARG cc_start: 0.8070 (ttp80) cc_final: 0.7693 (ttt-90) REVERT: i 20 MET cc_start: 0.7887 (mtp) cc_final: 0.7505 (mtp) REVERT: j 55 ARG cc_start: 0.8476 (ttp-110) cc_final: 0.8255 (ttp-110) REVERT: j 68 LYS cc_start: 0.7748 (mtmt) cc_final: 0.7431 (mtmt) REVERT: k 77 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.7060 (mmm-85) REVERT: l 17 LYS cc_start: 0.8666 (tttp) cc_final: 0.8448 (tptm) REVERT: m 57 ARG cc_start: 0.7158 (ttp-170) cc_final: 0.6556 (ttp-110) REVERT: m 249 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6930 (mm-30) REVERT: m 346 ILE cc_start: 0.8596 (pt) cc_final: 0.8368 (mp) REVERT: m 360 LYS cc_start: 0.7881 (tptp) cc_final: 0.7649 (tppt) REVERT: m 417 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7337 (mm-30) REVERT: n 110 ASP cc_start: 0.6243 (p0) cc_final: 0.5891 (p0) REVERT: n 172 LYS cc_start: 0.7104 (tttm) cc_final: 0.6894 (tttt) REVERT: n 375 ILE cc_start: 0.6901 (mt) cc_final: 0.6658 (mm) REVERT: p 85 ARG cc_start: 0.7481 (ttp80) cc_final: 0.7270 (ttp-110) REVERT: q 249 GLU cc_start: 0.6204 (tp30) cc_final: 0.5398 (mm-30) REVERT: q 454 PHE cc_start: 0.8320 (t80) cc_final: 0.8018 (t80) REVERT: r 21 GLU cc_start: 0.7330 (mp0) cc_final: 0.6948 (mp0) REVERT: s 17 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7574 (mm-30) REVERT: t 33 ARG cc_start: 0.6021 (mtm180) cc_final: 0.5780 (mtm180) REVERT: t 316 SER cc_start: 0.6722 (p) cc_final: 0.6187 (t) REVERT: v 63 LYS cc_start: 0.6083 (mmtp) cc_final: 0.5530 (mtmp) REVERT: v 163 ASP cc_start: 0.7225 (t0) cc_final: 0.6915 (t70) REVERT: v 220 ARG cc_start: 0.7370 (tpt170) cc_final: 0.7125 (tpt90) REVERT: w 155 ASP cc_start: 0.6404 (m-30) cc_final: 0.6145 (m-30) REVERT: w 181 ARG cc_start: 0.6686 (mtm-85) cc_final: 0.6453 (mtm-85) REVERT: x 392 THR cc_start: 0.7196 (t) cc_final: 0.6884 (m) REVERT: y 1 MET cc_start: 0.5653 (mtt) cc_final: 0.5407 (mtt) REVERT: y 100 ARG cc_start: 0.7665 (tmm160) cc_final: 0.7325 (ttp80) REVERT: y 241 ILE cc_start: 0.6607 (mt) cc_final: 0.6287 (mp) REVERT: z 35 ASP cc_start: 0.8112 (m-30) cc_final: 0.7898 (m-30) REVERT: z 95 LYS cc_start: 0.7426 (ttmt) cc_final: 0.7028 (tmtt) REVERT: 4 94 THR cc_start: 0.7293 (m) cc_final: 0.7063 (p) REVERT: 4 255 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7215 (p0) REVERT: 4 322 LYS cc_start: 0.8190 (mttt) cc_final: 0.7927 (mttp) REVERT: 4 336 THR cc_start: 0.7501 (t) cc_final: 0.7139 (p) REVERT: 4 423 MET cc_start: 0.8301 (tpt) cc_final: 0.7776 (tpp) REVERT: 4 484 LYS cc_start: 0.8268 (tptt) cc_final: 0.7970 (tptm) REVERT: 4 502 ARG cc_start: 0.7847 (ttt180) cc_final: 0.7537 (ttp-170) REVERT: 4 546 GLN cc_start: 0.5495 (mm-40) cc_final: 0.5008 (tm-30) REVERT: 4 570 LYS cc_start: 0.6509 (tptt) cc_final: 0.6127 (mtmt) outliers start: 40 outliers final: 12 residues processed: 1978 average time/residue: 2.4812 time to fit residues: 6911.9051 Evaluate side-chains 1326 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1311 time to evaluate : 11.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain m residue 417 GLU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain v residue 267 ILE Chi-restraints excluded: chain x residue 75 VAL Chi-restraints excluded: chain 4 residue 108 ILE Chi-restraints excluded: chain 4 residue 255 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1169 optimal weight: 9.9990 chunk 1049 optimal weight: 2.9990 chunk 582 optimal weight: 6.9990 chunk 358 optimal weight: 30.0000 chunk 708 optimal weight: 7.9990 chunk 560 optimal weight: 10.0000 chunk 1085 optimal weight: 0.9990 chunk 420 optimal weight: 10.0000 chunk 660 optimal weight: 0.6980 chunk 807 optimal weight: 3.9990 chunk 1257 optimal weight: 20.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN 8 105 GLN 9 21 HIS B 109 HIS C 59 GLN C 160 GLN D 45 ASN G 24 ASN G 145 ASN H 9 GLN H 157 ASN ** K 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 ASN L 17 HIS N 11 GLN N 23 GLN O 55 HIS P 10 ASN P 179 GLN Q 73 GLN R 68 GLN R 92 GLN S 63 GLN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 223 ASN Y 81 GLN Y 120 GLN b 152 GLN h 34 GLN i 92 ASN m 40 ASN ** m 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 90 GLN m 156 ASN ** m 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 398 GLN n 69 GLN n 149 ASN n 157 ASN o 149 GLN q 228 ASN q 264 HIS r 179 GLN r 211 GLN t 157 ASN t 209 GLN t 303 ASN v 29 GLN v 156 GLN v 179 GLN v 191 GLN v 213 GLN w 57 ASN w 180 ASN w 194 GLN x 44 ASN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 180 HIS x 341 HIS 4 533 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 167461 Z= 0.189 Angle : 0.657 30.739 242131 Z= 0.346 Chirality : 0.037 0.280 29640 Planarity : 0.006 0.133 18333 Dihedral : 22.280 179.885 63393 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.42 % Allowed : 11.62 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 1.96 (0.08), residues: 4149 sheet: 0.27 (0.13), residues: 1530 loop : -0.08 (0.08), residues: 4969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP m 212 HIS 0.006 0.001 HIS 4 447 PHE 0.034 0.002 PHE F 229 TYR 0.018 0.002 TYR C 194 ARG 0.010 0.001 ARG w 46 *********************** 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 1567 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1342 time to evaluate : 9.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASN cc_start: 0.7697 (m-40) cc_final: 0.7466 (m-40) REVERT: 9 31 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6600 (tp30) REVERT: 9 32 ARG cc_start: 0.7175 (mtm-85) cc_final: 0.6735 (mtm-85) REVERT: B 19 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7747 (mtt-85) REVERT: B 323 MET cc_start: 0.8152 (ttm) cc_final: 0.7892 (ttm) REVERT: B 335 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8205 (tp) REVERT: C 155 ASP cc_start: 0.7607 (m-30) cc_final: 0.7224 (m-30) REVERT: D 62 CYS cc_start: 0.7966 (m) cc_final: 0.7544 (m) REVERT: D 72 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6886 (p0) REVERT: D 140 ARG cc_start: 0.7306 (mtt180) cc_final: 0.7033 (mtm-85) REVERT: D 152 ARG cc_start: 0.7153 (mmm-85) cc_final: 0.6857 (mmt90) REVERT: D 186 GLU cc_start: 0.3693 (mm-30) cc_final: 0.3453 (mm-30) REVERT: D 226 TYR cc_start: 0.4714 (m-80) cc_final: 0.4500 (m-10) REVERT: E 143 LYS cc_start: 0.7325 (ttmm) cc_final: 0.6945 (ttpp) REVERT: F 52 GLN cc_start: 0.8272 (tp40) cc_final: 0.7720 (tp-100) REVERT: G 43 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7901 (mptp) REVERT: G 172 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7957 (ttmt) REVERT: H 31 ARG cc_start: 0.8326 (mtp85) cc_final: 0.7982 (mtp85) REVERT: H 51 GLN cc_start: 0.8449 (mp10) cc_final: 0.8219 (mp10) REVERT: H 69 ARG cc_start: 0.7583 (tpp-160) cc_final: 0.7373 (tpp-160) REVERT: H 129 ARG cc_start: 0.7958 (mtp85) cc_final: 0.7726 (mtp85) REVERT: H 153 ASP cc_start: 0.7798 (m-30) cc_final: 0.7378 (m-30) REVERT: J 11 ASP cc_start: 0.5880 (OUTLIER) cc_final: 0.5448 (m-30) REVERT: M 59 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7814 (t0) REVERT: O 84 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7889 (tm) REVERT: O 134 LYS cc_start: 0.8326 (mmtt) cc_final: 0.8087 (mmtp) REVERT: P 136 ILE cc_start: 0.8831 (mt) cc_final: 0.8613 (mt) REVERT: P 154 GLU cc_start: 0.5762 (mp0) cc_final: 0.5387 (mp0) REVERT: Q 7 SER cc_start: 0.7951 (p) cc_final: 0.7699 (p) REVERT: Q 144 ARG cc_start: 0.6568 (mmt90) cc_final: 0.6277 (mmt180) REVERT: S 34 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7495 (mt-10) REVERT: S 61 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8737 (tt) REVERT: S 131 LYS cc_start: 0.7839 (mtpp) cc_final: 0.7626 (mtmt) REVERT: S 148 LEU cc_start: 0.8452 (tp) cc_final: 0.8151 (tp) REVERT: T 106 LEU cc_start: 0.7712 (mt) cc_final: 0.7425 (mm) REVERT: U 104 ARG cc_start: 0.8232 (ptt-90) cc_final: 0.7999 (ptm-80) REVERT: V 59 MET cc_start: 0.8890 (mmm) cc_final: 0.8569 (mmm) REVERT: V 70 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6737 (mtp180) REVERT: W 35 ASP cc_start: 0.5011 (m-30) cc_final: 0.4740 (m-30) REVERT: W 81 ARG cc_start: 0.5717 (mtp-110) cc_final: 0.5453 (mtp-110) REVERT: X 58 ASP cc_start: 0.7969 (p0) cc_final: 0.7748 (p0) REVERT: X 70 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.6600 (mm-30) REVERT: X 73 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7033 (mpp) REVERT: Y 46 LYS cc_start: 0.7988 (tttt) cc_final: 0.7711 (tttm) REVERT: Z 102 GLU cc_start: 0.6443 (mt-10) cc_final: 0.5964 (mt-10) REVERT: Z 116 LYS cc_start: 0.8025 (tttm) cc_final: 0.7688 (ttpm) REVERT: Z 119 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7363 (mm-30) REVERT: a 61 PHE cc_start: 0.7174 (t80) cc_final: 0.6868 (t80) REVERT: a 135 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: a 136 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: b 1 MET cc_start: 0.5888 (mtt) cc_final: 0.5442 (mpp) REVERT: b 59 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7009 (tt0) REVERT: b 365 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7379 (mm-40) REVERT: b 561 ARG cc_start: 0.7053 (mtm-85) cc_final: 0.6557 (mtp85) REVERT: b 573 LEU cc_start: 0.7794 (tt) cc_final: 0.7494 (tt) REVERT: b 608 MET cc_start: 0.8568 (mtm) cc_final: 0.8202 (mtm) REVERT: d 87 ASN cc_start: 0.6696 (OUTLIER) cc_final: 0.6473 (p0) REVERT: d 97 LEU cc_start: 0.8379 (mt) cc_final: 0.8163 (mm) REVERT: f 49 ILE cc_start: 0.8846 (mt) cc_final: 0.8513 (mt) REVERT: g 38 LEU cc_start: 0.8917 (mt) cc_final: 0.8679 (mt) REVERT: g 60 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7061 (tmt170) REVERT: h 69 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7253 (mt) REVERT: h 105 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7702 (ttt-90) REVERT: i 20 MET cc_start: 0.7808 (mtp) cc_final: 0.7424 (mtp) REVERT: j 68 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7511 (mtmt) REVERT: k 27 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7471 (mm) REVERT: k 30 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7470 (mtpt) REVERT: k 63 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6705 (mtpt) REVERT: k 77 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.7039 (mmm-85) REVERT: l 17 LYS cc_start: 0.8675 (tttp) cc_final: 0.8393 (tptm) REVERT: m 57 ARG cc_start: 0.7176 (ttp-170) cc_final: 0.6641 (ttp-110) REVERT: m 346 ILE cc_start: 0.8620 (pt) cc_final: 0.8370 (mp) REVERT: m 417 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7451 (mm-30) REVERT: n 110 ASP cc_start: 0.6224 (p0) cc_final: 0.5854 (p0) REVERT: n 160 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7077 (tp-100) REVERT: n 375 ILE cc_start: 0.6903 (mt) cc_final: 0.6701 (mm) REVERT: p 85 ARG cc_start: 0.7477 (ttp80) cc_final: 0.7266 (ttp-110) REVERT: q 249 GLU cc_start: 0.6230 (tp30) cc_final: 0.5992 (tp30) REVERT: q 454 PHE cc_start: 0.8342 (t80) cc_final: 0.8036 (t80) REVERT: s 17 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7583 (mm-30) REVERT: t 34 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: t 38 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6395 (tttp) REVERT: t 316 SER cc_start: 0.6780 (p) cc_final: 0.6197 (t) REVERT: v 63 LYS cc_start: 0.6093 (mmtp) cc_final: 0.5527 (mtmp) REVERT: v 220 ARG cc_start: 0.7377 (tpt170) cc_final: 0.7143 (tpt90) REVERT: v 290 MET cc_start: 0.8473 (mtm) cc_final: 0.8103 (mtm) REVERT: x 230 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6672 (mmmt) REVERT: x 332 TYR cc_start: 0.6896 (t80) cc_final: 0.6616 (t80) REVERT: x 371 GLU cc_start: 0.5613 (pt0) cc_final: 0.5397 (pm20) REVERT: x 392 THR cc_start: 0.7248 (t) cc_final: 0.6905 (m) REVERT: y 1 MET cc_start: 0.5682 (mtt) cc_final: 0.5461 (mtt) REVERT: y 62 MET cc_start: 0.8205 (mmm) cc_final: 0.7925 (mmm) REVERT: y 100 ARG cc_start: 0.7546 (tmm160) cc_final: 0.7332 (ttp80) REVERT: y 241 ILE cc_start: 0.6819 (mt) cc_final: 0.6486 (mp) REVERT: z 95 LYS cc_start: 0.7435 (ttmt) cc_final: 0.7054 (tmtt) REVERT: 4 49 SER cc_start: 0.8180 (m) cc_final: 0.7946 (t) REVERT: 4 94 THR cc_start: 0.7394 (m) cc_final: 0.7153 (p) REVERT: 4 423 MET cc_start: 0.8365 (tpt) cc_final: 0.7987 (tpp) REVERT: 4 484 LYS cc_start: 0.8279 (tptt) cc_final: 0.7896 (tptm) REVERT: 4 546 GLN cc_start: 0.5506 (mm-40) cc_final: 0.5028 (tm-30) REVERT: 4 570 LYS cc_start: 0.6514 (tptt) cc_final: 0.6125 (mtmt) outliers start: 225 outliers final: 99 residues processed: 1471 average time/residue: 2.4742 time to fit residues: 5192.4217 Evaluate side-chains 1388 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1262 time to evaluate : 9.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 9 residue 31 GLU Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 218 SER Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 182 ILE Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 70 ARG Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 229 GLU Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 292 ILE Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 87 ASN Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain k residue 27 ILE Chi-restraints excluded: chain k residue 30 LYS Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 63 LYS Chi-restraints excluded: chain k residue 74 LYS Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 169 THR Chi-restraints excluded: chain m residue 213 ASN Chi-restraints excluded: chain m residue 382 ILE Chi-restraints excluded: chain m residue 417 GLU Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 160 GLN Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 369 ARG Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 108 SER Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 34 GLN Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 75 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 276 GLU Chi-restraints excluded: chain u residue 138 GLU Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 73 SER Chi-restraints excluded: chain v residue 135 VAL Chi-restraints excluded: chain w residue 109 LYS Chi-restraints excluded: chain w residue 172 GLU Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 18 LEU Chi-restraints excluded: chain x residue 21 GLU Chi-restraints excluded: chain x residue 208 ASN Chi-restraints excluded: chain x residue 230 LYS Chi-restraints excluded: chain x residue 282 SER Chi-restraints excluded: chain x residue 336 ILE Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 108 ILE Chi-restraints excluded: chain 4 residue 134 ARG Chi-restraints excluded: chain 4 residue 464 SER Chi-restraints excluded: chain 4 residue 567 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 698 optimal weight: 1.9990 chunk 390 optimal weight: 6.9990 chunk 1046 optimal weight: 5.9990 chunk 856 optimal weight: 5.9990 chunk 346 optimal weight: 30.0000 chunk 1259 optimal weight: 0.0770 chunk 1361 optimal weight: 3.9990 chunk 1122 optimal weight: 8.9990 chunk 1249 optimal weight: 0.8980 chunk 429 optimal weight: 6.9990 chunk 1010 optimal weight: 20.0000 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN 9 21 HIS B 109 HIS D 45 ASN H 157 ASN H 163 GLN ** K 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 ASN L 17 HIS N 11 GLN N 23 GLN P 179 GLN R 68 GLN R 92 GLN S 63 GLN S 138 GLN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 GLN Y 120 GLN Z 123 GLN b 152 GLN h 34 GLN i 92 ASN m 40 ASN ** m 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 156 ASN ** m 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN n 149 ASN n 157 ASN o 149 GLN o 204 HIS q 228 ASN q 264 HIS r 179 GLN t 209 GLN v 156 GLN ** v 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 180 ASN w 194 GLN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 341 HIS 4 533 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 167461 Z= 0.162 Angle : 0.622 29.821 242131 Z= 0.332 Chirality : 0.036 0.269 29640 Planarity : 0.006 0.130 18333 Dihedral : 22.183 179.922 63387 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.73 % Allowed : 12.42 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 1.24 (0.08), residues: 10648 helix: 2.10 (0.08), residues: 4156 sheet: 0.25 (0.13), residues: 1530 loop : -0.03 (0.08), residues: 4962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP x 386 HIS 0.005 0.001 HIS O 55 PHE 0.030 0.001 PHE F 229 TYR 0.017 0.001 TYR C 194 ARG 0.007 0.000 ARG d 79 *********************** 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 1560 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1306 time to evaluate : 9.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASN cc_start: 0.7582 (m-40) cc_final: 0.7359 (m-40) REVERT: 9 31 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6590 (tp30) REVERT: 9 32 ARG cc_start: 0.7148 (mtm-85) cc_final: 0.6731 (mtm-85) REVERT: B 19 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7639 (mtt-85) REVERT: B 335 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8186 (tp) REVERT: C 155 ASP cc_start: 0.7608 (m-30) cc_final: 0.7238 (m-30) REVERT: C 260 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7514 (mt0) REVERT: D 62 CYS cc_start: 0.7945 (m) cc_final: 0.7522 (m) REVERT: D 72 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6910 (p0) REVERT: D 152 ARG cc_start: 0.7193 (mmm-85) cc_final: 0.6870 (mmt90) REVERT: D 186 GLU cc_start: 0.3684 (mm-30) cc_final: 0.3475 (mm-30) REVERT: D 226 TYR cc_start: 0.4725 (m-80) cc_final: 0.4501 (m-10) REVERT: E 143 LYS cc_start: 0.7309 (ttmm) cc_final: 0.6912 (ttpp) REVERT: F 52 GLN cc_start: 0.8248 (tp40) cc_final: 0.7707 (tp-100) REVERT: F 82 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.7964 (mttp) REVERT: G 43 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7875 (mptp) REVERT: G 106 LYS cc_start: 0.7522 (mttm) cc_final: 0.7250 (mttm) REVERT: G 172 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8042 (ttmt) REVERT: H 31 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7977 (mtp85) REVERT: H 51 GLN cc_start: 0.8452 (mp10) cc_final: 0.8222 (mp10) REVERT: H 69 ARG cc_start: 0.7572 (tpp-160) cc_final: 0.7357 (tpp-160) REVERT: H 153 ASP cc_start: 0.7788 (m-30) cc_final: 0.7362 (m-30) REVERT: I 36 ASN cc_start: 0.4275 (OUTLIER) cc_final: 0.4058 (m-40) REVERT: J 11 ASP cc_start: 0.5746 (OUTLIER) cc_final: 0.5327 (m-30) REVERT: J 55 ARG cc_start: 0.4036 (mpt-90) cc_final: 0.3527 (ttp-170) REVERT: J 133 ARG cc_start: 0.6076 (OUTLIER) cc_final: 0.5721 (mmm-85) REVERT: L 57 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8312 (t) REVERT: M 59 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7845 (t0) REVERT: P 136 ILE cc_start: 0.8837 (mt) cc_final: 0.8618 (mt) REVERT: Q 7 SER cc_start: 0.8010 (p) cc_final: 0.7721 (p) REVERT: S 34 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7506 (mt-10) REVERT: S 61 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8714 (tt) REVERT: S 131 LYS cc_start: 0.7809 (mtpp) cc_final: 0.7600 (mtmt) REVERT: S 148 LEU cc_start: 0.8449 (tp) cc_final: 0.8123 (tp) REVERT: U 104 ARG cc_start: 0.8239 (ptt-90) cc_final: 0.7997 (ptm-80) REVERT: V 32 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.7173 (mtm180) REVERT: V 59 MET cc_start: 0.8889 (mmm) cc_final: 0.8576 (mmm) REVERT: V 70 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6825 (mtp180) REVERT: W 35 ASP cc_start: 0.4967 (m-30) cc_final: 0.4733 (m-30) REVERT: X 58 ASP cc_start: 0.7936 (p0) cc_final: 0.7718 (p0) REVERT: Y 46 LYS cc_start: 0.7990 (tttt) cc_final: 0.7713 (tttm) REVERT: Z 102 GLU cc_start: 0.6425 (mt-10) cc_final: 0.5958 (mt-10) REVERT: Z 116 LYS cc_start: 0.8025 (tttm) cc_final: 0.7789 (ttpt) REVERT: Z 119 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7335 (mm-30) REVERT: a 61 PHE cc_start: 0.7171 (t80) cc_final: 0.6857 (t80) REVERT: a 135 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: a 136 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: b 1 MET cc_start: 0.6063 (mtt) cc_final: 0.5646 (mpp) REVERT: b 59 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: b 365 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7423 (mm-40) REVERT: b 396 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6511 (ptt90) REVERT: b 561 ARG cc_start: 0.7104 (mtm-85) cc_final: 0.6579 (mtp85) REVERT: b 608 MET cc_start: 0.8552 (mtm) cc_final: 0.8213 (mtm) REVERT: c 52 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7812 (tpp80) REVERT: d 87 ASN cc_start: 0.6697 (OUTLIER) cc_final: 0.6471 (p0) REVERT: d 97 LEU cc_start: 0.8333 (mt) cc_final: 0.8129 (mm) REVERT: f 49 ILE cc_start: 0.8849 (mt) cc_final: 0.8507 (mt) REVERT: g 60 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.6907 (tmt170) REVERT: h 69 LEU cc_start: 0.7490 (mt) cc_final: 0.7204 (mt) REVERT: h 96 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8116 (mt-10) REVERT: h 105 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7677 (ttt-90) REVERT: i 20 MET cc_start: 0.7770 (mtp) cc_final: 0.7382 (mtp) REVERT: j 68 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7516 (mtmt) REVERT: k 30 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7458 (mtpt) REVERT: k 77 ARG cc_start: 0.7393 (mmm-85) cc_final: 0.6952 (mmm-85) REVERT: l 17 LYS cc_start: 0.8663 (tttp) cc_final: 0.8427 (tptm) REVERT: m 23 ARG cc_start: 0.6892 (mtm-85) cc_final: 0.6686 (mtt90) REVERT: m 346 ILE cc_start: 0.8633 (pt) cc_final: 0.8387 (mp) REVERT: m 417 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7375 (mm-30) REVERT: n 110 ASP cc_start: 0.6247 (p0) cc_final: 0.5888 (p0) REVERT: n 160 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7122 (tp-100) REVERT: n 172 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6648 (tttt) REVERT: n 375 ILE cc_start: 0.6885 (mt) cc_final: 0.6681 (mm) REVERT: q 249 GLU cc_start: 0.6198 (tp30) cc_final: 0.5920 (tp30) REVERT: q 454 PHE cc_start: 0.8401 (t80) cc_final: 0.8078 (t80) REVERT: s 17 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7568 (mm-30) REVERT: t 34 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: t 82 GLU cc_start: 0.4443 (tp30) cc_final: 0.4216 (tp30) REVERT: t 316 SER cc_start: 0.6781 (p) cc_final: 0.6197 (t) REVERT: v 63 LYS cc_start: 0.6099 (mmtp) cc_final: 0.5535 (mtmp) REVERT: v 163 ASP cc_start: 0.7068 (t0) cc_final: 0.6704 (t70) REVERT: v 217 ARG cc_start: 0.6640 (OUTLIER) cc_final: 0.5894 (mmt180) REVERT: v 220 ARG cc_start: 0.7414 (tpt170) cc_final: 0.7159 (tpt90) REVERT: w 102 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6468 (pt0) REVERT: x 183 LYS cc_start: 0.5820 (OUTLIER) cc_final: 0.5571 (mtpt) REVERT: x 230 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6680 (mmmt) REVERT: x 332 TYR cc_start: 0.6942 (t80) cc_final: 0.6603 (t80) REVERT: x 392 THR cc_start: 0.7189 (t) cc_final: 0.6850 (m) REVERT: x 424 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8064 (m-40) REVERT: y 1 MET cc_start: 0.5682 (mtt) cc_final: 0.5453 (mtt) REVERT: y 100 ARG cc_start: 0.7569 (tmm160) cc_final: 0.7328 (ttp80) REVERT: y 241 ILE cc_start: 0.6880 (mt) cc_final: 0.6538 (mp) REVERT: z 95 LYS cc_start: 0.7441 (ttmt) cc_final: 0.7060 (tmtt) REVERT: 4 49 SER cc_start: 0.8171 (m) cc_final: 0.7962 (t) REVERT: 4 94 THR cc_start: 0.7357 (m) cc_final: 0.7136 (p) REVERT: 4 354 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8583 (mp) REVERT: 4 423 MET cc_start: 0.8356 (tpt) cc_final: 0.7954 (tpp) REVERT: 4 484 LYS cc_start: 0.8276 (tptt) cc_final: 0.7989 (tptm) REVERT: 4 502 ARG cc_start: 0.7795 (ttt180) cc_final: 0.7511 (mtp180) REVERT: 4 570 LYS cc_start: 0.6502 (tptt) cc_final: 0.6119 (mtmt) outliers start: 254 outliers final: 112 residues processed: 1458 average time/residue: 2.4869 time to fit residues: 5157.4690 Evaluate side-chains 1375 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1230 time to evaluate : 8.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 8 residue 15 LEU Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 139 VAL Chi-restraints excluded: chain 9 residue 31 GLU Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain 9 residue 110 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 218 SER Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 294 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 182 ILE Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 70 ARG Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 229 GLU Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 210 ASP Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 556 ASN Chi-restraints excluded: chain c residue 52 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 87 ASN Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain k residue 30 LYS Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain k residue 74 LYS Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 169 THR Chi-restraints excluded: chain m residue 213 ASN Chi-restraints excluded: chain m residue 382 ILE Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain m residue 417 GLU Chi-restraints excluded: chain m residue 443 GLU Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 160 GLN Chi-restraints excluded: chain n residue 172 LYS Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 220 THR Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 108 SER Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain q residue 392 GLU Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 34 GLN Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 276 GLU Chi-restraints excluded: chain t residue 303 ASN Chi-restraints excluded: chain u residue 138 GLU Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 135 VAL Chi-restraints excluded: chain v residue 217 ARG Chi-restraints excluded: chain w residue 102 GLU Chi-restraints excluded: chain w residue 109 LYS Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 18 LEU Chi-restraints excluded: chain x residue 75 VAL Chi-restraints excluded: chain x residue 120 LEU Chi-restraints excluded: chain x residue 183 LYS Chi-restraints excluded: chain x residue 208 ASN Chi-restraints excluded: chain x residue 230 LYS Chi-restraints excluded: chain x residue 282 SER Chi-restraints excluded: chain x residue 336 ILE Chi-restraints excluded: chain x residue 345 LYS Chi-restraints excluded: chain x residue 424 ASN Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 108 ILE Chi-restraints excluded: chain 4 residue 134 ARG Chi-restraints excluded: chain 4 residue 143 LEU Chi-restraints excluded: chain 4 residue 354 ILE Chi-restraints excluded: chain 4 residue 517 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1244 optimal weight: 10.0000 chunk 947 optimal weight: 0.9980 chunk 653 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 601 optimal weight: 0.8980 chunk 846 optimal weight: 10.0000 chunk 1264 optimal weight: 9.9990 chunk 1338 optimal weight: 0.1980 chunk 660 optimal weight: 9.9990 chunk 1198 optimal weight: 6.9990 chunk 360 optimal weight: 0.0670 overall best weight: 1.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN 9 21 HIS B 109 HIS D 45 ASN H 157 ASN K 42 ASN ** K 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 ASN L 17 HIS N 11 GLN N 23 GLN P 179 GLN R 92 GLN S 63 GLN S 138 GLN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 GLN Y 120 GLN b 152 GLN b 549 GLN h 34 GLN i 92 ASN m 40 ASN ** m 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 156 ASN ** m 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN n 149 ASN n 157 ASN o 149 GLN q 228 ASN q 264 HIS r 179 GLN v 156 GLN v 213 GLN w 180 ASN w 194 GLN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 341 HIS y 145 ASN 4 405 ASN 4 533 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 167461 Z= 0.133 Angle : 0.600 29.774 242131 Z= 0.321 Chirality : 0.035 0.267 29640 Planarity : 0.005 0.125 18333 Dihedral : 22.119 179.968 63385 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.62 % Allowed : 13.49 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 1.35 (0.08), residues: 10648 helix: 2.22 (0.08), residues: 4163 sheet: 0.29 (0.13), residues: 1516 loop : 0.00 (0.08), residues: 4969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP x 386 HIS 0.004 0.001 HIS B 163 PHE 0.026 0.001 PHE F 229 TYR 0.015 0.001 TYR W 221 ARG 0.008 0.000 ARG d 79 *********************** 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 1528 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1284 time to evaluate : 9.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASN cc_start: 0.7598 (m-40) cc_final: 0.7291 (m110) REVERT: 9 31 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6575 (tp30) REVERT: 9 32 ARG cc_start: 0.7152 (mtm-85) cc_final: 0.6571 (mtm-85) REVERT: B 19 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7599 (mtt-85) REVERT: B 335 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8185 (tp) REVERT: C 138 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.5939 (tmm160) REVERT: C 155 ASP cc_start: 0.7579 (m-30) cc_final: 0.7201 (m-30) REVERT: D 62 CYS cc_start: 0.7914 (m) cc_final: 0.7490 (m) REVERT: D 75 LEU cc_start: 0.7321 (tt) cc_final: 0.6830 (tp) REVERT: D 152 ARG cc_start: 0.7218 (mmm-85) cc_final: 0.6882 (mmt90) REVERT: D 163 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8025 (tp) REVERT: D 186 GLU cc_start: 0.3729 (mm-30) cc_final: 0.3496 (mm-30) REVERT: D 226 TYR cc_start: 0.4718 (m-80) cc_final: 0.4509 (m-10) REVERT: E 143 LYS cc_start: 0.7350 (ttmm) cc_final: 0.6929 (ttpp) REVERT: F 52 GLN cc_start: 0.8225 (tp40) cc_final: 0.7725 (tp40) REVERT: F 82 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.7951 (mttp) REVERT: G 43 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7846 (mptp) REVERT: G 106 LYS cc_start: 0.7511 (mttm) cc_final: 0.7259 (mttm) REVERT: G 172 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8047 (ttmt) REVERT: H 31 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7998 (mtp85) REVERT: H 69 ARG cc_start: 0.7552 (tpp-160) cc_final: 0.7335 (tpp-160) REVERT: H 132 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8080 (t) REVERT: H 153 ASP cc_start: 0.7835 (m-30) cc_final: 0.7415 (m-30) REVERT: I 36 ASN cc_start: 0.4239 (OUTLIER) cc_final: 0.4028 (m-40) REVERT: I 58 MET cc_start: 0.5641 (mmt) cc_final: 0.5149 (mmt) REVERT: J 11 ASP cc_start: 0.5722 (OUTLIER) cc_final: 0.5346 (m-30) REVERT: J 13 LYS cc_start: 0.6407 (pttp) cc_final: 0.6065 (pttm) REVERT: J 133 ARG cc_start: 0.6265 (OUTLIER) cc_final: 0.5184 (mmm-85) REVERT: K 272 LYS cc_start: 0.4686 (mttt) cc_final: 0.4336 (tmtp) REVERT: L 57 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8273 (t) REVERT: M 59 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7849 (t0) REVERT: O 84 LEU cc_start: 0.8259 (tm) cc_final: 0.7933 (mt) REVERT: P 136 ILE cc_start: 0.8792 (mt) cc_final: 0.8585 (mt) REVERT: P 154 GLU cc_start: 0.5694 (mp0) cc_final: 0.5475 (mt-10) REVERT: Q 7 SER cc_start: 0.8000 (p) cc_final: 0.7711 (p) REVERT: S 34 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7426 (mt-10) REVERT: S 61 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8740 (tt) REVERT: S 131 LYS cc_start: 0.7804 (mtpp) cc_final: 0.7590 (mtmt) REVERT: S 148 LEU cc_start: 0.8448 (tp) cc_final: 0.8127 (tp) REVERT: U 104 ARG cc_start: 0.8237 (ptt-90) cc_final: 0.7995 (ptm-80) REVERT: V 32 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.7139 (mtm180) REVERT: V 59 MET cc_start: 0.8868 (mmm) cc_final: 0.8551 (mmm) REVERT: V 64 LYS cc_start: 0.7289 (mttp) cc_final: 0.7033 (mtmm) REVERT: V 125 LEU cc_start: 0.8935 (tp) cc_final: 0.8730 (mt) REVERT: W 81 ARG cc_start: 0.5786 (mtp-110) cc_final: 0.5483 (mtp-110) REVERT: X 58 ASP cc_start: 0.7902 (p0) cc_final: 0.7680 (p0) REVERT: X 73 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7063 (mpp) REVERT: Y 46 LYS cc_start: 0.7989 (tttt) cc_final: 0.7698 (tttm) REVERT: Z 102 GLU cc_start: 0.6406 (mt-10) cc_final: 0.5944 (mt-10) REVERT: Z 116 LYS cc_start: 0.8017 (tttm) cc_final: 0.7789 (ttpt) REVERT: Z 119 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7311 (mm-30) REVERT: a 61 PHE cc_start: 0.7187 (t80) cc_final: 0.6855 (t80) REVERT: a 135 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: a 136 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: b 1 MET cc_start: 0.6094 (mtt) cc_final: 0.5679 (mpp) REVERT: b 59 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: b 365 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7403 (mm-40) REVERT: b 396 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6529 (ptt90) REVERT: b 561 ARG cc_start: 0.7059 (mtm-85) cc_final: 0.6561 (mtp85) REVERT: c 52 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7792 (tpp80) REVERT: d 79 ARG cc_start: 0.7571 (mtt-85) cc_final: 0.7344 (mmt-90) REVERT: d 87 ASN cc_start: 0.6722 (OUTLIER) cc_final: 0.6484 (p0) REVERT: d 97 LEU cc_start: 0.8311 (mt) cc_final: 0.8107 (mm) REVERT: f 49 ILE cc_start: 0.8850 (mt) cc_final: 0.8503 (mt) REVERT: g 60 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8248 (tpt170) REVERT: h 69 LEU cc_start: 0.7423 (mt) cc_final: 0.7155 (mt) REVERT: h 96 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8098 (mt-10) REVERT: h 105 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7663 (ttt-90) REVERT: i 20 MET cc_start: 0.7745 (mtp) cc_final: 0.7404 (mtp) REVERT: j 68 LYS cc_start: 0.7811 (mtmt) cc_final: 0.7485 (mtmt) REVERT: k 30 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7443 (mtpt) REVERT: m 346 ILE cc_start: 0.8616 (pt) cc_final: 0.8394 (mp) REVERT: n 110 ASP cc_start: 0.6257 (p0) cc_final: 0.5920 (p0) REVERT: n 172 LYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6637 (tttt) REVERT: n 375 ILE cc_start: 0.6893 (mt) cc_final: 0.6677 (mm) REVERT: q 249 GLU cc_start: 0.6192 (tp30) cc_final: 0.5926 (tp30) REVERT: q 454 PHE cc_start: 0.8304 (t80) cc_final: 0.7974 (t80) REVERT: r 53 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7829 (tppp) REVERT: s 17 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7590 (mm-30) REVERT: t 38 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6501 (tttp) REVERT: t 316 SER cc_start: 0.6769 (p) cc_final: 0.6199 (t) REVERT: v 56 ASP cc_start: 0.6414 (OUTLIER) cc_final: 0.6073 (m-30) REVERT: v 63 LYS cc_start: 0.5980 (mmtp) cc_final: 0.5482 (mtmp) REVERT: v 117 MET cc_start: 0.5401 (mpp) cc_final: 0.5092 (mpp) REVERT: v 217 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.5864 (mmt180) REVERT: v 220 ARG cc_start: 0.7463 (tpt170) cc_final: 0.7191 (tpt90) REVERT: w 39 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.5773 (mm) REVERT: w 102 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6430 (pt0) REVERT: x 183 LYS cc_start: 0.5821 (OUTLIER) cc_final: 0.5568 (mtpt) REVERT: x 230 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6668 (mmmt) REVERT: x 304 TRP cc_start: 0.7236 (OUTLIER) cc_final: 0.5933 (m100) REVERT: x 326 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8399 (pp) REVERT: x 332 TYR cc_start: 0.6940 (t80) cc_final: 0.6604 (t80) REVERT: x 392 THR cc_start: 0.7212 (t) cc_final: 0.6880 (m) REVERT: x 424 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.8044 (m-40) REVERT: y 1 MET cc_start: 0.5722 (mtt) cc_final: 0.5496 (mtt) REVERT: y 62 MET cc_start: 0.8220 (mmm) cc_final: 0.7810 (mmm) REVERT: y 100 ARG cc_start: 0.7565 (tmm160) cc_final: 0.7338 (ttp80) REVERT: y 241 ILE cc_start: 0.6908 (mt) cc_final: 0.6566 (mp) REVERT: z 95 LYS cc_start: 0.7442 (ttmt) cc_final: 0.7070 (tmtt) REVERT: 4 94 THR cc_start: 0.7329 (m) cc_final: 0.7078 (p) REVERT: 4 354 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8581 (mp) REVERT: 4 423 MET cc_start: 0.8355 (tpt) cc_final: 0.7965 (tpp) REVERT: 4 484 LYS cc_start: 0.8323 (tptt) cc_final: 0.8039 (tptm) REVERT: 4 570 LYS cc_start: 0.6477 (tptt) cc_final: 0.6097 (mtmt) outliers start: 244 outliers final: 122 residues processed: 1439 average time/residue: 2.4462 time to fit residues: 5034.1217 Evaluate side-chains 1368 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1210 time to evaluate : 9.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 8 residue 15 LEU Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 139 VAL Chi-restraints excluded: chain 9 residue 31 GLU Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain 9 residue 110 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 218 SER Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 294 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 149 LYS Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 229 GLU Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 210 ASP Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 556 ASN Chi-restraints excluded: chain c residue 52 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 87 ASN Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain k residue 30 LYS Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain k residue 74 LYS Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 208 SER Chi-restraints excluded: chain m residue 213 ASN Chi-restraints excluded: chain m residue 382 ILE Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain n residue 111 SER Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 172 LYS Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 220 THR Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 108 SER Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain q residue 392 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 276 GLU Chi-restraints excluded: chain t residue 303 ASN Chi-restraints excluded: chain u residue 138 GLU Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 116 LEU Chi-restraints excluded: chain v residue 134 THR Chi-restraints excluded: chain v residue 135 VAL Chi-restraints excluded: chain v residue 149 ASP Chi-restraints excluded: chain v residue 217 ARG Chi-restraints excluded: chain w residue 39 LEU Chi-restraints excluded: chain w residue 102 GLU Chi-restraints excluded: chain w residue 109 LYS Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 18 LEU Chi-restraints excluded: chain x residue 75 VAL Chi-restraints excluded: chain x residue 183 LYS Chi-restraints excluded: chain x residue 208 ASN Chi-restraints excluded: chain x residue 230 LYS Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 282 SER Chi-restraints excluded: chain x residue 304 TRP Chi-restraints excluded: chain x residue 326 LEU Chi-restraints excluded: chain x residue 336 ILE Chi-restraints excluded: chain x residue 342 THR Chi-restraints excluded: chain x residue 386 TRP Chi-restraints excluded: chain x residue 424 ASN Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 143 SER Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 108 ILE Chi-restraints excluded: chain 4 residue 134 ARG Chi-restraints excluded: chain 4 residue 143 LEU Chi-restraints excluded: chain 4 residue 354 ILE Chi-restraints excluded: chain 4 residue 464 SER Chi-restraints excluded: chain 4 residue 517 THR Chi-restraints excluded: chain 4 residue 567 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1114 optimal weight: 7.9990 chunk 759 optimal weight: 0.0040 chunk 19 optimal weight: 10.0000 chunk 996 optimal weight: 9.9990 chunk 552 optimal weight: 10.0000 chunk 1142 optimal weight: 0.9990 chunk 925 optimal weight: 6.9990 chunk 1 optimal weight: 0.0060 chunk 683 optimal weight: 10.0000 chunk 1201 optimal weight: 5.9990 chunk 337 optimal weight: 40.0000 overall best weight: 2.8014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN 9 21 HIS B 109 HIS D 45 ASN H 157 ASN K 42 ASN K 214 ASN ** K 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 ASN L 17 HIS N 11 GLN N 23 GLN P 179 GLN R 92 GLN S 63 GLN S 138 GLN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN Y 81 GLN Y 120 GLN b 152 GLN h 34 GLN i 92 ASN m 40 ASN ** m 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 156 ASN ** m 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN o 149 GLN q 228 ASN q 264 HIS r 179 GLN t 209 GLN v 156 GLN ** v 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 180 ASN x 314 ASN x 341 HIS y 145 ASN 4 455 ASN 4 533 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 167461 Z= 0.171 Angle : 0.624 29.759 242131 Z= 0.332 Chirality : 0.036 0.267 29640 Planarity : 0.005 0.129 18333 Dihedral : 22.113 179.940 63379 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.06 % Allowed : 13.49 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 1.31 (0.08), residues: 10648 helix: 2.16 (0.08), residues: 4172 sheet: 0.28 (0.13), residues: 1513 loop : 0.00 (0.09), residues: 4963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP x 386 HIS 0.005 0.001 HIS P 145 PHE 0.030 0.001 PHE F 229 TYR 0.017 0.001 TYR O 54 ARG 0.016 0.000 ARG 4 262 *********************** 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 1545 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1260 time to evaluate : 9.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASN cc_start: 0.7607 (m-40) cc_final: 0.7293 (m110) REVERT: 9 31 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6609 (tp30) REVERT: 9 32 ARG cc_start: 0.7158 (mtm-85) cc_final: 0.6545 (mtm-85) REVERT: B 19 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7652 (mtt-85) REVERT: B 335 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8183 (tp) REVERT: C 155 ASP cc_start: 0.7591 (m-30) cc_final: 0.7209 (m-30) REVERT: D 62 CYS cc_start: 0.7922 (m) cc_final: 0.7497 (m) REVERT: D 75 LEU cc_start: 0.7327 (tt) cc_final: 0.6865 (tp) REVERT: D 140 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.7057 (mtt180) REVERT: D 152 ARG cc_start: 0.7240 (mmm-85) cc_final: 0.6895 (mmt90) REVERT: D 163 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8044 (tp) REVERT: D 186 GLU cc_start: 0.3700 (mm-30) cc_final: 0.3491 (mm-30) REVERT: D 226 TYR cc_start: 0.4813 (m-80) cc_final: 0.4583 (m-10) REVERT: D 259 LYS cc_start: 0.4188 (OUTLIER) cc_final: 0.3723 (mmtt) REVERT: E 143 LYS cc_start: 0.7344 (ttmm) cc_final: 0.6929 (ttpp) REVERT: F 225 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: G 43 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7868 (mptp) REVERT: G 106 LYS cc_start: 0.7541 (mttm) cc_final: 0.7268 (mttm) REVERT: G 172 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8029 (ttmt) REVERT: H 31 ARG cc_start: 0.8312 (mtp85) cc_final: 0.8015 (mtp85) REVERT: H 69 ARG cc_start: 0.7581 (tpp-160) cc_final: 0.7361 (tpp-160) REVERT: H 132 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8130 (t) REVERT: H 153 ASP cc_start: 0.7859 (m-30) cc_final: 0.7426 (m-30) REVERT: J 11 ASP cc_start: 0.5825 (OUTLIER) cc_final: 0.5382 (m-30) REVERT: J 13 LYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5919 (pttm) REVERT: J 55 ARG cc_start: 0.3921 (mpt-90) cc_final: 0.3488 (mtp180) REVERT: J 91 LEU cc_start: 0.4273 (pt) cc_final: 0.4072 (pp) REVERT: J 133 ARG cc_start: 0.6331 (OUTLIER) cc_final: 0.5301 (mmm-85) REVERT: K 272 LYS cc_start: 0.4698 (mttt) cc_final: 0.4338 (tmtp) REVERT: L 57 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8318 (t) REVERT: M 59 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7972 (t0) REVERT: O 84 LEU cc_start: 0.8263 (tm) cc_final: 0.7954 (mt) REVERT: O 193 GLN cc_start: 0.8426 (mt0) cc_final: 0.8119 (mt0) REVERT: P 136 ILE cc_start: 0.8855 (mt) cc_final: 0.8638 (mt) REVERT: P 154 GLU cc_start: 0.5702 (mp0) cc_final: 0.5296 (mp0) REVERT: Q 7 SER cc_start: 0.8009 (p) cc_final: 0.7721 (p) REVERT: S 34 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7452 (mt-10) REVERT: S 61 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8744 (tt) REVERT: S 128 GLU cc_start: 0.7532 (tt0) cc_final: 0.7317 (tt0) REVERT: S 131 LYS cc_start: 0.7822 (mtpp) cc_final: 0.7594 (mtmt) REVERT: S 148 LEU cc_start: 0.8449 (tp) cc_final: 0.8132 (tp) REVERT: U 104 ARG cc_start: 0.8244 (ptt-90) cc_final: 0.7995 (ptm-80) REVERT: V 32 ARG cc_start: 0.7429 (mtm-85) cc_final: 0.7145 (mtm180) REVERT: V 59 MET cc_start: 0.8907 (mmm) cc_final: 0.8619 (mmm) REVERT: V 64 LYS cc_start: 0.7316 (mttp) cc_final: 0.7073 (mtmm) REVERT: V 125 LEU cc_start: 0.8973 (tp) cc_final: 0.8751 (mt) REVERT: W 81 ARG cc_start: 0.5870 (mtp-110) cc_final: 0.5561 (mtp-110) REVERT: X 58 ASP cc_start: 0.7956 (p0) cc_final: 0.7731 (p0) REVERT: X 73 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7088 (mpp) REVERT: Y 46 LYS cc_start: 0.7989 (tttt) cc_final: 0.7707 (tttm) REVERT: Z 102 GLU cc_start: 0.6375 (mt-10) cc_final: 0.5903 (mt-10) REVERT: Z 116 LYS cc_start: 0.8025 (tttm) cc_final: 0.7800 (ttpt) REVERT: Z 119 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7333 (mm-30) REVERT: a 61 PHE cc_start: 0.7208 (t80) cc_final: 0.6918 (t80) REVERT: a 135 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: a 136 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: b 1 MET cc_start: 0.6099 (mtt) cc_final: 0.5695 (mpp) REVERT: b 59 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6997 (tt0) REVERT: b 365 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7422 (mm-40) REVERT: b 396 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6689 (ptt90) REVERT: b 561 ARG cc_start: 0.7103 (mtm-85) cc_final: 0.6605 (mtp85) REVERT: c 18 ILE cc_start: 0.7890 (mm) cc_final: 0.7494 (mm) REVERT: c 52 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7819 (tpp80) REVERT: d 79 ARG cc_start: 0.7618 (mtt-85) cc_final: 0.7363 (mmt-90) REVERT: d 87 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.6547 (p0) REVERT: d 97 LEU cc_start: 0.8351 (mt) cc_final: 0.8132 (mm) REVERT: e 103 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8206 (ttmt) REVERT: f 49 ILE cc_start: 0.8858 (mt) cc_final: 0.8510 (mt) REVERT: g 60 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8279 (tpt170) REVERT: h 69 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7154 (mt) REVERT: h 96 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8115 (mt-10) REVERT: h 105 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7642 (ttt-90) REVERT: i 20 MET cc_start: 0.7763 (mtp) cc_final: 0.7432 (mtp) REVERT: k 30 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7444 (mtpt) REVERT: m 121 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7456 (mtpp) REVERT: m 346 ILE cc_start: 0.8649 (pt) cc_final: 0.8411 (mp) REVERT: n 110 ASP cc_start: 0.6247 (p0) cc_final: 0.5930 (p0) REVERT: n 160 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7101 (tp-100) REVERT: n 172 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6630 (tttt) REVERT: q 249 GLU cc_start: 0.6208 (tp30) cc_final: 0.5973 (tp30) REVERT: q 454 PHE cc_start: 0.8303 (t80) cc_final: 0.7975 (t80) REVERT: r 53 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7779 (tppp) REVERT: s 17 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7604 (mm-30) REVERT: s 59 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6813 (mmmm) REVERT: t 38 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6529 (tttp) REVERT: t 316 SER cc_start: 0.6783 (p) cc_final: 0.6209 (t) REVERT: v 56 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.6061 (m-30) REVERT: v 60 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6691 (m-10) REVERT: v 63 LYS cc_start: 0.5995 (mmtp) cc_final: 0.5495 (mtmp) REVERT: v 163 ASP cc_start: 0.7101 (t0) cc_final: 0.6751 (t70) REVERT: v 217 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.5872 (mmt180) REVERT: v 220 ARG cc_start: 0.7429 (tpt170) cc_final: 0.7146 (tpt90) REVERT: w 39 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.5852 (mm) REVERT: w 102 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6524 (pt0) REVERT: x 183 LYS cc_start: 0.5833 (OUTLIER) cc_final: 0.5594 (mtpt) REVERT: x 230 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6673 (mmmt) REVERT: x 326 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8403 (pp) REVERT: x 332 TYR cc_start: 0.6945 (t80) cc_final: 0.6610 (t80) REVERT: x 392 THR cc_start: 0.7143 (t) cc_final: 0.6840 (m) REVERT: x 424 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8097 (m-40) REVERT: y 1 MET cc_start: 0.5750 (mtt) cc_final: 0.5516 (mtt) REVERT: y 62 MET cc_start: 0.8221 (mmm) cc_final: 0.7906 (mmm) REVERT: y 100 ARG cc_start: 0.7612 (tmm160) cc_final: 0.7327 (ttp80) REVERT: y 241 ILE cc_start: 0.6788 (mt) cc_final: 0.6468 (mp) REVERT: z 95 LYS cc_start: 0.7431 (ttmt) cc_final: 0.7064 (tmtt) REVERT: 4 94 THR cc_start: 0.7398 (m) cc_final: 0.7163 (p) REVERT: 4 191 MET cc_start: 0.7690 (tpp) cc_final: 0.7428 (tpt) REVERT: 4 354 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8595 (mp) REVERT: 4 423 MET cc_start: 0.8361 (tpt) cc_final: 0.7953 (tpp) REVERT: 4 484 LYS cc_start: 0.8354 (tptt) cc_final: 0.8057 (tptm) REVERT: 4 502 ARG cc_start: 0.7780 (ttt180) cc_final: 0.7487 (mtp180) REVERT: 4 570 LYS cc_start: 0.6461 (tptt) cc_final: 0.6022 (mtmt) outliers start: 285 outliers final: 148 residues processed: 1439 average time/residue: 2.4275 time to fit residues: 4984.4063 Evaluate side-chains 1406 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1216 time to evaluate : 9.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 5 residue 67 GLU Chi-restraints excluded: chain 8 residue 15 LEU Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 139 VAL Chi-restraints excluded: chain 9 residue 31 GLU Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain 9 residue 110 LEU Chi-restraints excluded: chain 9 residue 142 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain D residue 140 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 218 SER Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 294 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 182 ILE Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 149 LYS Chi-restraints excluded: chain T residue 35 LYS Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 229 GLU Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 210 ASP Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 232 MET Chi-restraints excluded: chain b residue 292 ILE Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 52 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 87 ASN Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 103 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain k residue 30 LYS Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain k residue 74 LYS Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 121 LYS Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 169 THR Chi-restraints excluded: chain m residue 208 SER Chi-restraints excluded: chain m residue 213 ASN Chi-restraints excluded: chain m residue 359 MET Chi-restraints excluded: chain m residue 382 ILE Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain m residue 443 GLU Chi-restraints excluded: chain n residue 111 SER Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 160 GLN Chi-restraints excluded: chain n residue 172 LYS Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 220 THR Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 369 ARG Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 108 SER Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain q residue 392 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 59 LYS Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 276 GLU Chi-restraints excluded: chain t residue 303 ASN Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 138 GLU Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 60 PHE Chi-restraints excluded: chain v residue 116 LEU Chi-restraints excluded: chain v residue 134 THR Chi-restraints excluded: chain v residue 135 VAL Chi-restraints excluded: chain v residue 217 ARG Chi-restraints excluded: chain w residue 39 LEU Chi-restraints excluded: chain w residue 102 GLU Chi-restraints excluded: chain w residue 109 LYS Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 18 LEU Chi-restraints excluded: chain x residue 75 VAL Chi-restraints excluded: chain x residue 120 LEU Chi-restraints excluded: chain x residue 122 THR Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 183 LYS Chi-restraints excluded: chain x residue 208 ASN Chi-restraints excluded: chain x residue 230 LYS Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 282 SER Chi-restraints excluded: chain x residue 326 LEU Chi-restraints excluded: chain x residue 342 THR Chi-restraints excluded: chain x residue 345 LYS Chi-restraints excluded: chain x residue 386 TRP Chi-restraints excluded: chain x residue 424 ASN Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 143 SER Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 108 ILE Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 132 THR Chi-restraints excluded: chain 4 residue 134 ARG Chi-restraints excluded: chain 4 residue 143 LEU Chi-restraints excluded: chain 4 residue 354 ILE Chi-restraints excluded: chain 4 residue 464 SER Chi-restraints excluded: chain 4 residue 517 THR Chi-restraints excluded: chain 4 residue 567 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 450 optimal weight: 0.9990 chunk 1205 optimal weight: 7.9990 chunk 264 optimal weight: 10.0000 chunk 786 optimal weight: 2.9990 chunk 330 optimal weight: 10.0000 chunk 1340 optimal weight: 9.9990 chunk 1112 optimal weight: 5.9990 chunk 620 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 443 optimal weight: 9.9990 chunk 703 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN 9 21 HIS B 109 HIS D 45 ASN H 157 ASN K 42 ASN ** K 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN N 23 GLN O 182 ASN P 179 GLN R 92 GLN S 63 GLN S 138 GLN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN Y 81 GLN Y 120 GLN b 152 GLN b 327 ASN b 509 ASN h 34 GLN h 68 GLN i 92 ASN m 40 ASN ** m 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 276 HIS ** m 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN n 191 ASN q 228 ASN q 264 HIS r 179 GLN t 209 GLN v 156 GLN ** v 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 180 ASN w 194 GLN x 44 ASN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 341 HIS 4 455 ASN 4 533 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 167461 Z= 0.293 Angle : 0.735 30.419 242131 Z= 0.383 Chirality : 0.041 0.293 29640 Planarity : 0.007 0.139 18333 Dihedral : 22.251 179.987 63379 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.11 % Allowed : 13.91 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 1.85 (0.08), residues: 4175 sheet: 0.17 (0.13), residues: 1537 loop : -0.10 (0.08), residues: 4936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP m 212 HIS 0.008 0.001 HIS C 311 PHE 0.033 0.002 PHE F 229 TYR 0.027 0.002 TYR O 54 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 1521 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1232 time to evaluate : 9.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 31 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6649 (tp30) REVERT: 9 32 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.6702 (mtm-85) REVERT: B 19 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7707 (mtt-85) REVERT: B 335 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8486 (tp) REVERT: C 155 ASP cc_start: 0.7618 (m-30) cc_final: 0.7224 (m-30) REVERT: D 62 CYS cc_start: 0.7964 (m) cc_final: 0.7550 (m) REVERT: D 152 ARG cc_start: 0.7285 (mmm-85) cc_final: 0.6737 (mmt90) REVERT: D 163 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8121 (tp) REVERT: D 186 GLU cc_start: 0.3856 (mm-30) cc_final: 0.3422 (mm-30) REVERT: D 226 TYR cc_start: 0.4892 (m-80) cc_final: 0.4680 (m-10) REVERT: E 143 LYS cc_start: 0.7442 (ttmm) cc_final: 0.7033 (ttpp) REVERT: F 52 GLN cc_start: 0.8231 (tp40) cc_final: 0.7728 (tp40) REVERT: F 175 LYS cc_start: 0.7738 (pttt) cc_final: 0.7520 (pttt) REVERT: F 225 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: G 43 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8029 (mptp) REVERT: G 172 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8072 (ttmt) REVERT: G 245 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7269 (mtpm) REVERT: H 69 ARG cc_start: 0.7608 (tpp-160) cc_final: 0.7399 (tpp-160) REVERT: H 132 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8159 (t) REVERT: J 6 GLN cc_start: 0.2612 (OUTLIER) cc_final: 0.2385 (mp10) REVERT: J 11 ASP cc_start: 0.5811 (OUTLIER) cc_final: 0.5233 (m-30) REVERT: J 13 LYS cc_start: 0.6090 (OUTLIER) cc_final: 0.5814 (pttm) REVERT: J 55 ARG cc_start: 0.4079 (mpt-90) cc_final: 0.3591 (mtp180) REVERT: J 133 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.5279 (mmm-85) REVERT: L 57 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8417 (t) REVERT: O 193 GLN cc_start: 0.8385 (mt0) cc_final: 0.8059 (mt0) REVERT: P 136 ILE cc_start: 0.8841 (mt) cc_final: 0.8624 (mt) REVERT: P 154 GLU cc_start: 0.5670 (mp0) cc_final: 0.5245 (mp0) REVERT: Q 7 SER cc_start: 0.8026 (p) cc_final: 0.7726 (p) REVERT: S 34 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7538 (mt-10) REVERT: S 61 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8746 (tt) REVERT: S 96 ASP cc_start: 0.7667 (t0) cc_final: 0.7409 (t70) REVERT: S 123 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8557 (mm) REVERT: S 131 LYS cc_start: 0.7837 (mtpp) cc_final: 0.7628 (mtmt) REVERT: S 148 LEU cc_start: 0.8469 (tp) cc_final: 0.8167 (tp) REVERT: T 106 LEU cc_start: 0.7756 (mt) cc_final: 0.7469 (mm) REVERT: U 104 ARG cc_start: 0.8264 (ptt-90) cc_final: 0.7996 (ptt-90) REVERT: V 32 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.7145 (mtm180) REVERT: V 59 MET cc_start: 0.8889 (mmm) cc_final: 0.8597 (mmm) REVERT: V 64 LYS cc_start: 0.7385 (mttp) cc_final: 0.7128 (mtmm) REVERT: X 70 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: X 73 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7123 (mpp) REVERT: Y 46 LYS cc_start: 0.8033 (tttt) cc_final: 0.7730 (tttm) REVERT: Z 102 GLU cc_start: 0.6388 (mt-10) cc_final: 0.5923 (mt-10) REVERT: Z 116 LYS cc_start: 0.7919 (tttm) cc_final: 0.7610 (ttpm) REVERT: Z 119 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7342 (mm-30) REVERT: Z 121 ARG cc_start: 0.8390 (ttm-80) cc_final: 0.8096 (ttt90) REVERT: a 61 PHE cc_start: 0.7193 (t80) cc_final: 0.6888 (t80) REVERT: a 135 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: a 136 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: b 1 MET cc_start: 0.6139 (mtt) cc_final: 0.5736 (mpp) REVERT: b 59 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: b 117 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8093 (ttpp) REVERT: b 365 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7517 (mm-40) REVERT: b 396 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6579 (ptt90) REVERT: b 561 ARG cc_start: 0.7122 (mtm-85) cc_final: 0.6655 (mtp85) REVERT: c 52 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7933 (tpp80) REVERT: e 103 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8390 (ttmt) REVERT: f 49 ILE cc_start: 0.8850 (mt) cc_final: 0.8509 (mt) REVERT: g 60 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.6941 (tmt170) REVERT: h 69 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7310 (mt) REVERT: h 96 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8091 (mt-10) REVERT: i 20 MET cc_start: 0.7826 (mtp) cc_final: 0.7484 (mtp) REVERT: k 30 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7464 (mtpt) REVERT: m 121 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7503 (mtpp) REVERT: m 346 ILE cc_start: 0.8690 (pt) cc_final: 0.8416 (mp) REVERT: m 417 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7565 (mm-30) REVERT: n 160 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7164 (tp-100) REVERT: n 172 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6751 (tttt) REVERT: n 229 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7578 (tp) REVERT: n 375 ILE cc_start: 0.6977 (mt) cc_final: 0.6763 (mm) REVERT: o 93 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7193 (mp) REVERT: q 249 GLU cc_start: 0.6195 (tp30) cc_final: 0.5875 (tp30) REVERT: q 454 PHE cc_start: 0.8271 (t80) cc_final: 0.7973 (t80) REVERT: r 53 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7836 (tppp) REVERT: s 17 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7561 (mm-30) REVERT: t 38 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6558 (tttp) REVERT: t 316 SER cc_start: 0.6818 (p) cc_final: 0.6201 (t) REVERT: v 63 LYS cc_start: 0.6091 (mmtp) cc_final: 0.5519 (mtmp) REVERT: v 217 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.5911 (mmt180) REVERT: v 220 ARG cc_start: 0.7565 (tpt170) cc_final: 0.7303 (tpt90) REVERT: w 39 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5821 (mm) REVERT: x 183 LYS cc_start: 0.5843 (OUTLIER) cc_final: 0.5636 (mtpt) REVERT: x 230 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6719 (mmmt) REVERT: x 392 THR cc_start: 0.7162 (t) cc_final: 0.6861 (m) REVERT: y 1 MET cc_start: 0.5762 (mtt) cc_final: 0.5491 (mtt) REVERT: y 62 MET cc_start: 0.8213 (mmm) cc_final: 0.7828 (mmm) REVERT: y 100 ARG cc_start: 0.7669 (tmm160) cc_final: 0.7419 (ttp80) REVERT: y 241 ILE cc_start: 0.6813 (mt) cc_final: 0.6495 (mp) REVERT: z 95 LYS cc_start: 0.7390 (ttmt) cc_final: 0.6998 (tmtt) REVERT: 4 94 THR cc_start: 0.7455 (m) cc_final: 0.7229 (p) REVERT: 4 191 MET cc_start: 0.7740 (tpp) cc_final: 0.7426 (tpt) REVERT: 4 354 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8574 (mp) REVERT: 4 423 MET cc_start: 0.8359 (tpt) cc_final: 0.8021 (tpp) REVERT: 4 484 LYS cc_start: 0.8368 (tptt) cc_final: 0.8057 (tptm) REVERT: 4 570 LYS cc_start: 0.6492 (tptt) cc_final: 0.6086 (mtmt) outliers start: 289 outliers final: 170 residues processed: 1412 average time/residue: 2.4200 time to fit residues: 4868.7642 Evaluate side-chains 1411 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1201 time to evaluate : 9.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 5 residue 67 GLU Chi-restraints excluded: chain 8 residue 15 LEU Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 139 VAL Chi-restraints excluded: chain 9 residue 31 GLU Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain 9 residue 110 LEU Chi-restraints excluded: chain 9 residue 142 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 245 LYS Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 218 SER Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 294 ASN Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 149 LYS Chi-restraints excluded: chain T residue 35 LYS Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 229 GLU Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 210 ASP Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 232 MET Chi-restraints excluded: chain b residue 292 ILE Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 52 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 103 LYS Chi-restraints excluded: chain f residue 40 ASP Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain k residue 30 LYS Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 121 LYS Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 169 THR Chi-restraints excluded: chain m residue 208 SER Chi-restraints excluded: chain m residue 380 GLU Chi-restraints excluded: chain m residue 382 ILE Chi-restraints excluded: chain m residue 390 VAL Chi-restraints excluded: chain m residue 417 GLU Chi-restraints excluded: chain m residue 443 GLU Chi-restraints excluded: chain n residue 111 SER Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 160 GLN Chi-restraints excluded: chain n residue 172 LYS Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 220 THR Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 353 ASP Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 369 ARG Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain o residue 93 ILE Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 108 SER Chi-restraints excluded: chain o residue 194 LYS Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain q residue 392 GLU Chi-restraints excluded: chain q residue 422 LYS Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 69 MET Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 276 GLU Chi-restraints excluded: chain t residue 303 ASN Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain u residue 138 GLU Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 116 LEU Chi-restraints excluded: chain v residue 134 THR Chi-restraints excluded: chain v residue 135 VAL Chi-restraints excluded: chain v residue 217 ARG Chi-restraints excluded: chain w residue 39 LEU Chi-restraints excluded: chain w residue 102 GLU Chi-restraints excluded: chain w residue 109 LYS Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 18 LEU Chi-restraints excluded: chain x residue 75 VAL Chi-restraints excluded: chain x residue 120 LEU Chi-restraints excluded: chain x residue 122 THR Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 161 THR Chi-restraints excluded: chain x residue 183 LYS Chi-restraints excluded: chain x residue 208 ASN Chi-restraints excluded: chain x residue 230 LYS Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 282 SER Chi-restraints excluded: chain x residue 342 THR Chi-restraints excluded: chain x residue 345 LYS Chi-restraints excluded: chain x residue 386 TRP Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain x residue 486 LYS Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 143 SER Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain z residue 36 LYS Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 84 VAL Chi-restraints excluded: chain 4 residue 108 ILE Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 132 THR Chi-restraints excluded: chain 4 residue 143 LEU Chi-restraints excluded: chain 4 residue 354 ILE Chi-restraints excluded: chain 4 residue 464 SER Chi-restraints excluded: chain 4 residue 496 ILE Chi-restraints excluded: chain 4 residue 517 THR Chi-restraints excluded: chain 4 residue 543 LEU Chi-restraints excluded: chain 4 residue 567 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1291 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 763 optimal weight: 5.9990 chunk 978 optimal weight: 0.9990 chunk 758 optimal weight: 50.0000 chunk 1128 optimal weight: 9.9990 chunk 748 optimal weight: 6.9990 chunk 1334 optimal weight: 9.9990 chunk 835 optimal weight: 0.3980 chunk 813 optimal weight: 0.0980 chunk 616 optimal weight: 30.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 144 ASN 9 21 HIS B 109 HIS D 45 ASN G 191 ASN H 157 ASN K 42 ASN ** K 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 HIS N 11 GLN N 23 GLN P 179 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN S 63 GLN S 138 GLN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN Y 81 GLN Y 120 GLN Z 123 GLN b 152 GLN b 327 ASN b 362 HIS d 43 HIS i 92 ASN m 40 ASN ** m 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN o 149 GLN ** q 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 264 HIS r 179 GLN t 209 GLN v 156 GLN v 213 GLN w 180 ASN w 194 GLN x 44 ASN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 100 ASN x 341 HIS 4 455 ASN 4 533 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 167461 Z= 0.179 Angle : 0.643 29.863 242131 Z= 0.342 Chirality : 0.037 0.265 29640 Planarity : 0.006 0.131 18333 Dihedral : 22.166 179.949 63379 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.73 % Allowed : 14.71 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 2.01 (0.08), residues: 4177 sheet: 0.19 (0.13), residues: 1536 loop : -0.06 (0.09), residues: 4935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP w 114 HIS 0.007 0.001 HIS n 230 PHE 0.028 0.002 PHE F 229 TYR 0.018 0.002 TYR W 221 ARG 0.008 0.000 ARG y 68 *********************** 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 1495 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1241 time to evaluate : 9.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 31 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6615 (tp30) REVERT: 9 32 ARG cc_start: 0.7170 (mtm-85) cc_final: 0.6625 (mtm-85) REVERT: 9 142 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5779 (tp) REVERT: B 19 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7640 (mtt-85) REVERT: B 335 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8179 (tp) REVERT: C 155 ASP cc_start: 0.7617 (m-30) cc_final: 0.7225 (m-30) REVERT: D 62 CYS cc_start: 0.7918 (m) cc_final: 0.7489 (m) REVERT: D 140 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.7038 (mtt180) REVERT: D 152 ARG cc_start: 0.7261 (mmm-85) cc_final: 0.6922 (mmt90) REVERT: D 163 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8044 (tp) REVERT: D 186 GLU cc_start: 0.3816 (mm-30) cc_final: 0.3390 (mm-30) REVERT: D 259 LYS cc_start: 0.4219 (OUTLIER) cc_final: 0.3763 (mmtt) REVERT: E 143 LYS cc_start: 0.7360 (ttmm) cc_final: 0.6947 (ttpp) REVERT: F 52 GLN cc_start: 0.8169 (tp40) cc_final: 0.7692 (tp40) REVERT: F 225 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: G 43 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7914 (mptp) REVERT: G 172 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8033 (ttmt) REVERT: H 2 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.7029 (mptt) REVERT: H 69 ARG cc_start: 0.7568 (tpp-160) cc_final: 0.7349 (tpp-160) REVERT: H 132 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8184 (t) REVERT: J 6 GLN cc_start: 0.2491 (OUTLIER) cc_final: 0.2282 (mp10) REVERT: J 11 ASP cc_start: 0.5857 (OUTLIER) cc_final: 0.5354 (m-30) REVERT: J 13 LYS cc_start: 0.6204 (pttp) cc_final: 0.5929 (pttm) REVERT: J 55 ARG cc_start: 0.4011 (mpt-90) cc_final: 0.3537 (mtp180) REVERT: J 133 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5207 (mmm-85) REVERT: K 272 LYS cc_start: 0.4721 (mttt) cc_final: 0.4350 (tmtp) REVERT: L 57 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8361 (t) REVERT: O 80 PHE cc_start: 0.7926 (t80) cc_final: 0.7706 (t80) REVERT: O 193 GLN cc_start: 0.8417 (mt0) cc_final: 0.8116 (mt0) REVERT: P 136 ILE cc_start: 0.8798 (mt) cc_final: 0.8581 (mt) REVERT: P 154 GLU cc_start: 0.5743 (mp0) cc_final: 0.5322 (mp0) REVERT: Q 7 SER cc_start: 0.8006 (p) cc_final: 0.7717 (p) REVERT: S 34 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7461 (mt-10) REVERT: S 61 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8746 (tt) REVERT: S 131 LYS cc_start: 0.7807 (mtpp) cc_final: 0.7596 (mtmt) REVERT: S 148 LEU cc_start: 0.8437 (tp) cc_final: 0.8124 (tp) REVERT: T 106 LEU cc_start: 0.7737 (mt) cc_final: 0.7452 (mm) REVERT: U 104 ARG cc_start: 0.8248 (ptt-90) cc_final: 0.8029 (ptm-80) REVERT: V 32 ARG cc_start: 0.7422 (mtm-85) cc_final: 0.7124 (mtm180) REVERT: V 59 MET cc_start: 0.8862 (mmm) cc_final: 0.8581 (mmm) REVERT: V 64 LYS cc_start: 0.7348 (mttp) cc_final: 0.7114 (mtmm) REVERT: W 81 ARG cc_start: 0.5998 (mtp-110) cc_final: 0.5755 (mtp-110) REVERT: X 58 ASP cc_start: 0.7980 (p0) cc_final: 0.7733 (p0) REVERT: X 73 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7086 (mpp) REVERT: Y 46 LYS cc_start: 0.8106 (tttt) cc_final: 0.7838 (tttm) REVERT: Z 102 GLU cc_start: 0.6392 (mt-10) cc_final: 0.5927 (mt-10) REVERT: Z 116 LYS cc_start: 0.7934 (tttm) cc_final: 0.7617 (ttpm) REVERT: Z 119 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7354 (mm-30) REVERT: Z 121 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.8086 (ttt90) REVERT: a 61 PHE cc_start: 0.7203 (t80) cc_final: 0.6915 (t80) REVERT: a 135 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: a 136 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: b 1 MET cc_start: 0.6067 (mtt) cc_final: 0.5675 (mpp) REVERT: b 59 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6996 (tt0) REVERT: b 365 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7525 (mm-40) REVERT: b 396 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6652 (ptt90) REVERT: b 561 ARG cc_start: 0.7128 (mtm-85) cc_final: 0.6647 (mtp85) REVERT: c 52 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7827 (tpp80) REVERT: c 104 LEU cc_start: 0.3229 (OUTLIER) cc_final: 0.2775 (tp) REVERT: e 103 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8271 (ttmt) REVERT: f 49 ILE cc_start: 0.8863 (mt) cc_final: 0.8522 (mt) REVERT: g 60 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8272 (tpt170) REVERT: h 69 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7172 (mt) REVERT: h 96 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8099 (mt-10) REVERT: i 20 MET cc_start: 0.7816 (mtp) cc_final: 0.7461 (mtp) REVERT: j 55 ARG cc_start: 0.8510 (ttp-170) cc_final: 0.8309 (ttp-170) REVERT: k 30 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7420 (mtpt) REVERT: m 121 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7490 (mtpp) REVERT: m 346 ILE cc_start: 0.8670 (pt) cc_final: 0.8414 (mp) REVERT: m 417 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7448 (mm-30) REVERT: n 160 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7169 (tp-100) REVERT: n 172 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6710 (tttt) REVERT: n 218 MET cc_start: 0.7622 (mtm) cc_final: 0.7184 (mtm) REVERT: n 375 ILE cc_start: 0.6946 (mt) cc_final: 0.6732 (mm) REVERT: q 249 GLU cc_start: 0.6238 (tp30) cc_final: 0.5947 (tp30) REVERT: q 454 PHE cc_start: 0.8392 (t80) cc_final: 0.8085 (t80) REVERT: r 53 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7834 (tppp) REVERT: s 17 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7595 (mm-30) REVERT: s 59 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6759 (mmmm) REVERT: t 38 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6534 (tttp) REVERT: t 316 SER cc_start: 0.6789 (p) cc_final: 0.6191 (t) REVERT: v 63 LYS cc_start: 0.6074 (mmtp) cc_final: 0.5494 (mtmp) REVERT: v 72 MET cc_start: 0.5959 (OUTLIER) cc_final: 0.4694 (mmt) REVERT: v 217 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5908 (mmt180) REVERT: v 220 ARG cc_start: 0.7547 (tpt170) cc_final: 0.7265 (tpt90) REVERT: w 39 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.5877 (mm) REVERT: x 183 LYS cc_start: 0.5769 (OUTLIER) cc_final: 0.5540 (mtpt) REVERT: x 230 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6680 (mmmt) REVERT: x 332 TYR cc_start: 0.6918 (t80) cc_final: 0.6587 (t80) REVERT: x 345 LYS cc_start: 0.5207 (OUTLIER) cc_final: 0.4953 (mmtt) REVERT: x 392 THR cc_start: 0.7168 (t) cc_final: 0.6873 (m) REVERT: y 1 MET cc_start: 0.5746 (mtt) cc_final: 0.5484 (mtt) REVERT: y 62 MET cc_start: 0.8209 (mmm) cc_final: 0.7894 (mmm) REVERT: y 100 ARG cc_start: 0.7654 (tmm160) cc_final: 0.7366 (ttp80) REVERT: y 241 ILE cc_start: 0.6827 (mt) cc_final: 0.6500 (mp) REVERT: z 95 LYS cc_start: 0.7431 (ttmt) cc_final: 0.7054 (tmtt) REVERT: 4 94 THR cc_start: 0.7368 (m) cc_final: 0.7128 (p) REVERT: 4 191 MET cc_start: 0.7749 (tpp) cc_final: 0.7443 (tpt) REVERT: 4 354 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8565 (mp) REVERT: 4 423 MET cc_start: 0.8372 (tpt) cc_final: 0.7939 (tpp) REVERT: 4 484 LYS cc_start: 0.8360 (tptt) cc_final: 0.8051 (tptm) REVERT: 4 570 LYS cc_start: 0.6474 (tptt) cc_final: 0.6075 (mtmt) outliers start: 254 outliers final: 153 residues processed: 1403 average time/residue: 2.4352 time to fit residues: 4897.8907 Evaluate side-chains 1387 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1193 time to evaluate : 8.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 8 residue 15 LEU Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 139 VAL Chi-restraints excluded: chain 9 residue 31 GLU Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain 9 residue 110 LEU Chi-restraints excluded: chain 9 residue 142 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain D residue 140 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 218 SER Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 182 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 149 LYS Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 229 GLU Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 210 ASP Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 232 MET Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 530 LYS Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 52 ARG Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 103 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain k residue 30 LYS Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 121 LYS Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 169 THR Chi-restraints excluded: chain m residue 208 SER Chi-restraints excluded: chain m residue 380 GLU Chi-restraints excluded: chain m residue 382 ILE Chi-restraints excluded: chain m residue 390 VAL Chi-restraints excluded: chain m residue 417 GLU Chi-restraints excluded: chain m residue 443 GLU Chi-restraints excluded: chain n residue 111 SER Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 160 GLN Chi-restraints excluded: chain n residue 172 LYS Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 220 THR Chi-restraints excluded: chain n residue 353 ASP Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 369 ARG Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 108 SER Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain q residue 392 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 59 LYS Chi-restraints excluded: chain s residue 69 MET Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 276 GLU Chi-restraints excluded: chain t residue 303 ASN Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 138 GLU Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 72 MET Chi-restraints excluded: chain v residue 116 LEU Chi-restraints excluded: chain v residue 134 THR Chi-restraints excluded: chain v residue 135 VAL Chi-restraints excluded: chain v residue 217 ARG Chi-restraints excluded: chain w residue 39 LEU Chi-restraints excluded: chain w residue 102 GLU Chi-restraints excluded: chain w residue 109 LYS Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 18 LEU Chi-restraints excluded: chain x residue 41 THR Chi-restraints excluded: chain x residue 75 VAL Chi-restraints excluded: chain x residue 122 THR Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 183 LYS Chi-restraints excluded: chain x residue 208 ASN Chi-restraints excluded: chain x residue 230 LYS Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 282 SER Chi-restraints excluded: chain x residue 342 THR Chi-restraints excluded: chain x residue 345 LYS Chi-restraints excluded: chain x residue 386 TRP Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 143 SER Chi-restraints excluded: chain y residue 145 ASN Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain z residue 36 LYS Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 108 ILE Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 132 THR Chi-restraints excluded: chain 4 residue 143 LEU Chi-restraints excluded: chain 4 residue 354 ILE Chi-restraints excluded: chain 4 residue 464 SER Chi-restraints excluded: chain 4 residue 517 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 825 optimal weight: 10.0000 chunk 533 optimal weight: 9.9990 chunk 797 optimal weight: 0.9990 chunk 402 optimal weight: 10.0000 chunk 262 optimal weight: 20.0000 chunk 258 optimal weight: 40.0000 chunk 848 optimal weight: 9.9990 chunk 909 optimal weight: 20.0000 chunk 659 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 1049 optimal weight: 1.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN 9 21 HIS B 109 HIS D 45 ASN G 191 ASN H 157 ASN ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN N 23 GLN P 179 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN R 144 GLN S 63 GLN S 138 GLN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 GLN Y 81 GLN Y 120 GLN b 152 GLN ** b 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 327 ASN d 43 HIS h 68 GLN i 92 ASN m 40 ASN ** m 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 276 HIS ** m 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN ** n 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 149 GLN q 228 ASN q 264 HIS r 179 GLN t 209 GLN t 300 GLN u 110 ASN v 156 GLN ** v 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 249 HIS ** w 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 194 GLN x 44 ASN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 341 HIS 4 455 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 167461 Z= 0.335 Angle : 0.776 30.621 242131 Z= 0.402 Chirality : 0.043 0.297 29640 Planarity : 0.007 0.142 18333 Dihedral : 22.308 179.799 63379 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.89 % Allowed : 14.98 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 0.86 (0.08), residues: 10648 helix: 1.66 (0.08), residues: 4180 sheet: 0.08 (0.13), residues: 1534 loop : -0.15 (0.08), residues: 4934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP p 55 HIS 0.009 0.002 HIS C 311 PHE 0.034 0.003 PHE F 229 TYR 0.029 0.002 TYR O 54 ARG 0.010 0.001 ARG F 110 *********************** 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 1468 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1199 time to evaluate : 9.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 31 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6659 (tp30) REVERT: 9 32 ARG cc_start: 0.7075 (mtm-85) cc_final: 0.6667 (mtm-85) REVERT: 9 142 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5787 (tp) REVERT: B 19 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7722 (mtt-85) REVERT: B 197 GLU cc_start: 0.7349 (mp0) cc_final: 0.7072 (tp30) REVERT: D 62 CYS cc_start: 0.7974 (m) cc_final: 0.7556 (m) REVERT: D 152 ARG cc_start: 0.7211 (mmm-85) cc_final: 0.6665 (mmt90) REVERT: D 163 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8119 (tp) REVERT: D 186 GLU cc_start: 0.3938 (mm-30) cc_final: 0.3522 (mm-30) REVERT: D 259 LYS cc_start: 0.4247 (OUTLIER) cc_final: 0.3785 (mmtt) REVERT: E 59 GLU cc_start: 0.7507 (mp0) cc_final: 0.7226 (mp0) REVERT: E 143 LYS cc_start: 0.7438 (ttmm) cc_final: 0.7036 (ttpp) REVERT: G 43 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8063 (mptp) REVERT: G 172 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8029 (ttmt) REVERT: G 245 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7299 (mtpm) REVERT: H 2 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6918 (mptt) REVERT: H 69 ARG cc_start: 0.7617 (tpp-160) cc_final: 0.7406 (tpp-160) REVERT: H 90 MET cc_start: 0.8949 (mtp) cc_final: 0.8677 (mtp) REVERT: H 132 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8184 (t) REVERT: J 6 GLN cc_start: 0.2562 (OUTLIER) cc_final: 0.2329 (mp10) REVERT: J 13 LYS cc_start: 0.6086 (pttp) cc_final: 0.5801 (pttm) REVERT: J 55 ARG cc_start: 0.4073 (mpt-90) cc_final: 0.3585 (mtp180) REVERT: J 133 ARG cc_start: 0.6333 (OUTLIER) cc_final: 0.5236 (mmm-85) REVERT: O 80 PHE cc_start: 0.8080 (t80) cc_final: 0.7799 (t80) REVERT: O 193 GLN cc_start: 0.8382 (mt0) cc_final: 0.8065 (mt0) REVERT: P 136 ILE cc_start: 0.8837 (mt) cc_final: 0.8614 (mt) REVERT: P 154 GLU cc_start: 0.5661 (mp0) cc_final: 0.5230 (mp0) REVERT: Q 7 SER cc_start: 0.8038 (p) cc_final: 0.7736 (p) REVERT: R 13 SER cc_start: 0.8941 (t) cc_final: 0.8686 (t) REVERT: S 61 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8714 (tt) REVERT: S 123 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8591 (mm) REVERT: S 131 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7609 (mtmt) REVERT: T 106 LEU cc_start: 0.7777 (mt) cc_final: 0.7494 (mm) REVERT: U 104 ARG cc_start: 0.8282 (ptt-90) cc_final: 0.8049 (ptm-80) REVERT: V 32 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7149 (mtm180) REVERT: V 59 MET cc_start: 0.8878 (mmm) cc_final: 0.8593 (mmm) REVERT: W 81 ARG cc_start: 0.5936 (mtp-110) cc_final: 0.5729 (mtp-110) REVERT: W 155 VAL cc_start: 0.7539 (p) cc_final: 0.7316 (m) REVERT: X 73 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7157 (mpp) REVERT: Y 46 LYS cc_start: 0.8112 (tttt) cc_final: 0.7826 (tttm) REVERT: Z 102 GLU cc_start: 0.6446 (mt-10) cc_final: 0.5982 (mt-10) REVERT: Z 116 LYS cc_start: 0.7923 (tttm) cc_final: 0.7640 (ttpm) REVERT: Z 119 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7320 (mm-30) REVERT: Z 121 ARG cc_start: 0.8392 (ttm-80) cc_final: 0.8102 (ttt90) REVERT: a 120 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7518 (t0) REVERT: a 135 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: a 136 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: b 1 MET cc_start: 0.6139 (mtt) cc_final: 0.5771 (mpp) REVERT: b 59 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: b 117 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8105 (ttpp) REVERT: b 365 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7584 (mm-40) REVERT: b 396 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6609 (ptt90) REVERT: b 561 ARG cc_start: 0.7152 (mtm-85) cc_final: 0.6709 (mtp85) REVERT: c 52 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7925 (tpp80) REVERT: f 49 ILE cc_start: 0.8853 (mt) cc_final: 0.8521 (mt) REVERT: g 60 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.6794 (tmt170) REVERT: h 69 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7319 (mt) REVERT: h 96 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8114 (mt-10) REVERT: i 20 MET cc_start: 0.7908 (mtp) cc_final: 0.7599 (mtp) REVERT: k 30 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7408 (mtpt) REVERT: k 77 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6142 (mmm-85) REVERT: m 23 ARG cc_start: 0.6907 (mtm-85) cc_final: 0.6647 (mtt90) REVERT: m 121 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7497 (mtpp) REVERT: m 346 ILE cc_start: 0.8712 (pt) cc_final: 0.8409 (mp) REVERT: m 417 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: n 160 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7180 (tp-100) REVERT: n 218 MET cc_start: 0.7660 (mtm) cc_final: 0.7230 (mtm) REVERT: n 229 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7587 (tp) REVERT: q 249 GLU cc_start: 0.6114 (tp30) cc_final: 0.5794 (tp30) REVERT: q 454 PHE cc_start: 0.8285 (t80) cc_final: 0.7992 (t80) REVERT: r 53 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7839 (tppp) REVERT: s 17 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7640 (mm-30) REVERT: t 38 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6551 (tttp) REVERT: v 63 LYS cc_start: 0.6041 (mmtp) cc_final: 0.5471 (mtmp) REVERT: v 72 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.4834 (mmt) REVERT: v 217 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.5960 (mmt180) REVERT: v 220 ARG cc_start: 0.7601 (tpt170) cc_final: 0.7160 (tpt170) REVERT: w 39 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.5830 (mm) REVERT: x 230 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6700 (mmmt) REVERT: x 392 THR cc_start: 0.7180 (t) cc_final: 0.6872 (m) REVERT: y 1 MET cc_start: 0.5765 (mtt) cc_final: 0.5491 (mtt) REVERT: y 62 MET cc_start: 0.8215 (mmm) cc_final: 0.7748 (mmm) REVERT: y 100 ARG cc_start: 0.7664 (tmm160) cc_final: 0.7408 (ttp80) REVERT: y 241 ILE cc_start: 0.6823 (mt) cc_final: 0.6503 (mp) REVERT: z 95 LYS cc_start: 0.7386 (ttmt) cc_final: 0.6997 (tmtt) REVERT: 4 94 THR cc_start: 0.7461 (m) cc_final: 0.7255 (p) REVERT: 4 191 MET cc_start: 0.7755 (tpp) cc_final: 0.7498 (tpt) REVERT: 4 354 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8574 (mp) REVERT: 4 423 MET cc_start: 0.8393 (tpt) cc_final: 0.7982 (tpp) REVERT: 4 484 LYS cc_start: 0.8379 (tptt) cc_final: 0.8069 (tptm) outliers start: 269 outliers final: 176 residues processed: 1379 average time/residue: 2.3131 time to fit residues: 4533.0719 Evaluate side-chains 1398 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1186 time to evaluate : 8.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 5 residue 67 GLU Chi-restraints excluded: chain 8 residue 15 LEU Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 139 VAL Chi-restraints excluded: chain 9 residue 31 GLU Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain 9 residue 110 LEU Chi-restraints excluded: chain 9 residue 142 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 245 LYS Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 294 ASN Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 149 LYS Chi-restraints excluded: chain T residue 35 LYS Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 229 GLU Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 210 ASP Chi-restraints excluded: chain b residue 230 GLU Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 232 MET Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain c residue 52 ARG Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain k residue 30 LYS Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain k residue 77 ARG Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 121 LYS Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 169 THR Chi-restraints excluded: chain m residue 208 SER Chi-restraints excluded: chain m residue 380 GLU Chi-restraints excluded: chain m residue 382 ILE Chi-restraints excluded: chain m residue 390 VAL Chi-restraints excluded: chain m residue 417 GLU Chi-restraints excluded: chain m residue 443 GLU Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 111 SER Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 160 GLN Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 220 THR Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 353 ASP Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 369 ARG Chi-restraints excluded: chain n residue 387 VAL Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 108 SER Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain p residue 26 VAL 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 392 GLU Chi-restraints excluded: chain q residue 422 LYS Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 69 MET Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 276 GLU Chi-restraints excluded: chain t residue 303 ASN Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain u residue 138 GLU Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 72 MET Chi-restraints excluded: chain v residue 134 THR Chi-restraints excluded: chain v residue 135 VAL Chi-restraints excluded: chain v residue 217 ARG Chi-restraints excluded: chain w residue 39 LEU Chi-restraints excluded: chain w residue 102 GLU Chi-restraints excluded: chain w residue 109 LYS Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 18 LEU Chi-restraints excluded: chain x residue 21 GLU Chi-restraints excluded: chain x residue 41 THR Chi-restraints excluded: chain x residue 75 VAL Chi-restraints excluded: chain x residue 122 THR Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 161 THR Chi-restraints excluded: chain x residue 208 ASN Chi-restraints excluded: chain x residue 217 SER Chi-restraints excluded: chain x residue 230 LYS Chi-restraints excluded: chain x residue 255 SER Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 282 SER Chi-restraints excluded: chain x residue 342 THR Chi-restraints excluded: chain x residue 386 TRP Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain x residue 486 LYS Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 143 SER Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 84 VAL Chi-restraints excluded: chain 4 residue 108 ILE Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 132 THR Chi-restraints excluded: chain 4 residue 143 LEU Chi-restraints excluded: chain 4 residue 354 ILE Chi-restraints excluded: chain 4 residue 464 SER Chi-restraints excluded: chain 4 residue 496 ILE Chi-restraints excluded: chain 4 residue 517 THR Chi-restraints excluded: chain 4 residue 567 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1214 optimal weight: 8.9990 chunk 1278 optimal weight: 20.0000 chunk 1166 optimal weight: 6.9990 chunk 1243 optimal weight: 0.0570 chunk 748 optimal weight: 10.0000 chunk 541 optimal weight: 0.6980 chunk 976 optimal weight: 7.9990 chunk 381 optimal weight: 4.9990 chunk 1124 optimal weight: 8.9990 chunk 1176 optimal weight: 20.0000 chunk 1239 optimal weight: 4.9990 overall best weight: 3.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN 9 21 HIS B 109 HIS D 45 ASN G 191 ASN H 157 ASN K 42 ASN ** K 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 HIS N 11 GLN N 23 GLN P 179 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 63 GLN S 138 GLN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 26 GLN Y 81 GLN Y 120 GLN Z 123 GLN b 152 GLN b 327 ASN e 88 HIS h 68 GLN i 92 ASN m 40 ASN ** m 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN o 149 GLN ** q 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 264 HIS r 179 GLN t 209 GLN v 156 GLN ** v 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 194 GLN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 314 ASN x 341 HIS z 23 GLN 4 455 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 167461 Z= 0.205 Angle : 0.668 29.907 242131 Z= 0.353 Chirality : 0.038 0.271 29640 Planarity : 0.006 0.133 18333 Dihedral : 22.212 179.573 63379 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.37 % Allowed : 15.47 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 1.88 (0.08), residues: 4168 sheet: 0.09 (0.13), residues: 1537 loop : -0.09 (0.09), residues: 4943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP w 114 HIS 0.007 0.001 HIS n 230 PHE 0.029 0.002 PHE F 229 TYR 0.019 0.002 TYR O 54 ARG 0.008 0.001 ARG d 79 *********************** 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 1421 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1200 time to evaluate : 8.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 31 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6621 (tp30) REVERT: 9 32 ARG cc_start: 0.7197 (mtm-85) cc_final: 0.6682 (mtm-85) REVERT: 9 142 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5744 (tp) REVERT: B 19 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7691 (mtt-85) REVERT: B 335 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8177 (tp) REVERT: C 155 ASP cc_start: 0.7482 (m-30) cc_final: 0.7179 (m-30) REVERT: D 62 CYS cc_start: 0.7940 (m) cc_final: 0.7522 (m) REVERT: D 152 ARG cc_start: 0.7207 (mmm-85) cc_final: 0.6660 (mmt90) REVERT: D 186 GLU cc_start: 0.3927 (mm-30) cc_final: 0.3505 (mm-30) REVERT: D 259 LYS cc_start: 0.4219 (OUTLIER) cc_final: 0.3766 (mmtt) REVERT: E 143 LYS cc_start: 0.7402 (ttmm) cc_final: 0.6967 (ttpp) REVERT: F 52 GLN cc_start: 0.8252 (tp40) cc_final: 0.7786 (tp40) REVERT: G 43 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7982 (mptp) REVERT: G 172 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8032 (ttmt) REVERT: H 2 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6990 (mptt) REVERT: H 31 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7966 (mtp85) REVERT: H 69 ARG cc_start: 0.7571 (tpp-160) cc_final: 0.7353 (tpp-160) REVERT: H 132 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8121 (t) REVERT: J 13 LYS cc_start: 0.6062 (pttp) cc_final: 0.5788 (pttm) REVERT: J 55 ARG cc_start: 0.4099 (mpt-90) cc_final: 0.3581 (mtp180) REVERT: L 57 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8371 (t) REVERT: O 80 PHE cc_start: 0.7964 (t80) cc_final: 0.7723 (t80) REVERT: O 193 GLN cc_start: 0.8413 (mt0) cc_final: 0.8119 (mt0) REVERT: P 136 ILE cc_start: 0.8797 (mt) cc_final: 0.8575 (mt) REVERT: P 154 GLU cc_start: 0.5664 (mp0) cc_final: 0.5244 (mp0) REVERT: Q 7 SER cc_start: 0.8031 (p) cc_final: 0.7746 (p) REVERT: S 61 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8705 (tt) REVERT: S 131 LYS cc_start: 0.7802 (mtpp) cc_final: 0.7594 (mtmt) REVERT: T 106 LEU cc_start: 0.7788 (mt) cc_final: 0.7471 (mm) REVERT: U 104 ARG cc_start: 0.8251 (ptt-90) cc_final: 0.8013 (ptm-80) REVERT: V 32 ARG cc_start: 0.7433 (mtm-85) cc_final: 0.7141 (mtm180) REVERT: V 59 MET cc_start: 0.8868 (mmm) cc_final: 0.8595 (mmm) REVERT: W 155 VAL cc_start: 0.7486 (p) cc_final: 0.7241 (m) REVERT: X 58 ASP cc_start: 0.8000 (p0) cc_final: 0.7735 (p0) REVERT: X 73 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7119 (mpp) REVERT: Y 46 LYS cc_start: 0.8112 (tttt) cc_final: 0.7836 (tttm) REVERT: Z 102 GLU cc_start: 0.6418 (mt-10) cc_final: 0.5955 (mt-10) REVERT: Z 116 LYS cc_start: 0.7941 (tttm) cc_final: 0.7641 (ttpm) REVERT: Z 119 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7346 (mm-30) REVERT: Z 121 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.8088 (ttt90) REVERT: a 135 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: a 136 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: b 1 MET cc_start: 0.6108 (mtt) cc_final: 0.5704 (mpp) REVERT: b 59 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: b 365 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7557 (mm-40) REVERT: b 396 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6637 (ptt90) REVERT: b 561 ARG cc_start: 0.7153 (mtm-85) cc_final: 0.6702 (mtp85) REVERT: c 52 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7852 (tpp80) REVERT: f 49 ILE cc_start: 0.8867 (mt) cc_final: 0.8526 (mt) REVERT: g 60 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8286 (tpt170) REVERT: h 69 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7230 (mt) REVERT: h 96 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8080 (mt-10) REVERT: i 20 MET cc_start: 0.7883 (mtp) cc_final: 0.7559 (mtp) REVERT: k 77 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6123 (mmm-85) REVERT: m 121 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7485 (mtpp) REVERT: m 346 ILE cc_start: 0.8693 (pt) cc_final: 0.8406 (mp) REVERT: m 417 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: n 160 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7173 (tp-100) REVERT: n 218 MET cc_start: 0.7651 (mtm) cc_final: 0.7216 (mtm) REVERT: n 229 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7594 (tp) REVERT: q 249 GLU cc_start: 0.6202 (tp30) cc_final: 0.5928 (tp30) REVERT: q 454 PHE cc_start: 0.8345 (t80) cc_final: 0.8048 (t80) REVERT: r 53 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7843 (tppp) REVERT: s 17 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7617 (mm-30) REVERT: t 38 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6563 (tttp) REVERT: t 316 SER cc_start: 0.6800 (p) cc_final: 0.6177 (t) REVERT: v 63 LYS cc_start: 0.6037 (mmtp) cc_final: 0.5511 (mtmp) REVERT: v 217 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.5969 (mmt180) REVERT: w 39 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.5948 (mm) REVERT: x 230 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6655 (mmmt) REVERT: x 332 TYR cc_start: 0.6917 (t80) cc_final: 0.6591 (t80) REVERT: x 392 THR cc_start: 0.7179 (t) cc_final: 0.6874 (m) REVERT: y 1 MET cc_start: 0.5830 (mtt) cc_final: 0.5562 (mtt) REVERT: y 62 MET cc_start: 0.8221 (mmm) cc_final: 0.7915 (mmm) REVERT: y 100 ARG cc_start: 0.7664 (tmm160) cc_final: 0.7377 (ttp80) REVERT: y 241 ILE cc_start: 0.6830 (mt) cc_final: 0.6504 (mp) REVERT: z 95 LYS cc_start: 0.7412 (ttmt) cc_final: 0.7030 (tmtt) REVERT: 4 43 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8059 (m) REVERT: 4 94 THR cc_start: 0.7361 (m) cc_final: 0.7137 (p) REVERT: 4 191 MET cc_start: 0.7780 (tpp) cc_final: 0.7482 (tpt) REVERT: 4 354 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8561 (mp) REVERT: 4 423 MET cc_start: 0.8374 (tpt) cc_final: 0.7972 (tpp) REVERT: 4 484 LYS cc_start: 0.8381 (tptt) cc_final: 0.8079 (tptm) outliers start: 221 outliers final: 152 residues processed: 1342 average time/residue: 2.2504 time to fit residues: 4298.8873 Evaluate side-chains 1357 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1175 time to evaluate : 8.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 8 residue 15 LEU Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 139 VAL Chi-restraints excluded: chain 9 residue 31 GLU Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain 9 residue 110 LEU Chi-restraints excluded: chain 9 residue 142 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 294 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 182 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 149 LYS Chi-restraints excluded: chain T residue 35 LYS Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 229 GLU Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 210 ASP Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 292 ILE Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 52 ARG Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain k residue 77 ARG Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 121 LYS Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 169 THR Chi-restraints excluded: chain m residue 208 SER Chi-restraints excluded: chain m residue 359 MET Chi-restraints excluded: chain m residue 380 GLU Chi-restraints excluded: chain m residue 382 ILE Chi-restraints excluded: chain m residue 390 VAL Chi-restraints excluded: chain m residue 417 GLU Chi-restraints excluded: chain n residue 111 SER Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 160 GLN Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 220 THR Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 353 ASP Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 369 ARG Chi-restraints excluded: chain n residue 387 VAL Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 108 SER Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain q residue 392 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 276 GLU Chi-restraints excluded: chain t residue 303 ASN Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 138 GLU Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 57 MET Chi-restraints excluded: chain v residue 134 THR Chi-restraints excluded: chain v residue 135 VAL Chi-restraints excluded: chain v residue 217 ARG Chi-restraints excluded: chain w residue 39 LEU Chi-restraints excluded: chain w residue 102 GLU Chi-restraints excluded: chain w residue 109 LYS Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 18 LEU Chi-restraints excluded: chain x residue 21 GLU Chi-restraints excluded: chain x residue 41 THR Chi-restraints excluded: chain x residue 75 VAL Chi-restraints excluded: chain x residue 120 LEU Chi-restraints excluded: chain x residue 122 THR Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 208 ASN Chi-restraints excluded: chain x residue 230 LYS Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 282 SER Chi-restraints excluded: chain x residue 342 THR Chi-restraints excluded: chain x residue 386 TRP Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain x residue 486 LYS Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 143 SER Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 84 VAL Chi-restraints excluded: chain 4 residue 108 ILE Chi-restraints excluded: chain 4 residue 109 ASP Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 132 THR Chi-restraints excluded: chain 4 residue 143 LEU Chi-restraints excluded: chain 4 residue 354 ILE Chi-restraints excluded: chain 4 residue 464 SER Chi-restraints excluded: chain 4 residue 496 ILE Chi-restraints excluded: chain 4 residue 517 THR Chi-restraints excluded: chain 4 residue 567 LEU Chi-restraints excluded: chain 4 residue 570 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 816 optimal weight: 0.9980 chunk 1315 optimal weight: 20.0000 chunk 802 optimal weight: 9.9990 chunk 624 optimal weight: 5.9990 chunk 914 optimal weight: 10.0000 chunk 1379 optimal weight: 20.0000 chunk 1269 optimal weight: 9.9990 chunk 1098 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 848 optimal weight: 10.0000 chunk 673 optimal weight: 9.9990 overall best weight: 7.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN 9 21 HIS B 109 HIS D 45 ASN G 191 ASN H 157 ASN ** K 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 HIS N 11 GLN N 23 GLN P 179 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN S 63 GLN S 138 GLN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS Y 26 GLN Y 81 GLN Y 120 GLN Z 123 GLN b 152 GLN ** b 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 GLN i 92 ASN m 40 ASN ** m 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 276 HIS ** m 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN o 149 GLN q 228 ASN q 264 HIS r 179 GLN t 209 GLN t 230 ASN v 156 GLN ** v 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 194 GLN x 44 ASN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 341 HIS x 449 GLN z 23 GLN ** 4 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 455 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 167461 Z= 0.371 Angle : 0.809 30.572 242131 Z= 0.416 Chirality : 0.045 0.296 29640 Planarity : 0.007 0.144 18333 Dihedral : 22.349 179.741 63379 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.41 % Allowed : 15.66 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 0.72 (0.08), residues: 10648 helix: 1.53 (0.08), residues: 4178 sheet: 0.05 (0.13), residues: 1518 loop : -0.22 (0.08), residues: 4952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP p 55 HIS 0.009 0.002 HIS n 230 PHE 0.035 0.003 PHE w 117 TYR 0.030 0.003 TYR O 54 ARG 0.011 0.001 ARG W 81 ********************** 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 1412 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1188 time to evaluate : 8.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 31 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6666 (tp30) REVERT: 9 32 ARG cc_start: 0.7013 (mtm-85) cc_final: 0.6611 (mtm-85) REVERT: 9 142 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5784 (tp) REVERT: B 19 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7723 (mtt-85) REVERT: B 197 GLU cc_start: 0.7356 (mp0) cc_final: 0.7067 (tp30) REVERT: C 136 LEU cc_start: 0.8457 (mt) cc_final: 0.8073 (tp) REVERT: C 155 ASP cc_start: 0.7483 (m-30) cc_final: 0.7161 (m-30) REVERT: D 62 CYS cc_start: 0.7983 (m) cc_final: 0.7596 (m) REVERT: D 152 ARG cc_start: 0.7220 (mmm-85) cc_final: 0.6681 (mmt90) REVERT: D 186 GLU cc_start: 0.3989 (mm-30) cc_final: 0.3576 (mm-30) REVERT: D 259 LYS cc_start: 0.4232 (OUTLIER) cc_final: 0.3768 (mmtt) REVERT: E 59 GLU cc_start: 0.7526 (mp0) cc_final: 0.7290 (mp0) REVERT: E 143 LYS cc_start: 0.7517 (ttmm) cc_final: 0.7121 (ttpp) REVERT: F 52 GLN cc_start: 0.8287 (tp40) cc_final: 0.7828 (tp40) REVERT: G 43 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8090 (mptp) REVERT: G 172 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8028 (ttmt) REVERT: H 69 ARG cc_start: 0.7619 (tpp-160) cc_final: 0.7412 (tpp-160) REVERT: H 90 MET cc_start: 0.8956 (mtp) cc_final: 0.8664 (mtp) REVERT: J 13 LYS cc_start: 0.6094 (pttp) cc_final: 0.5811 (pttm) REVERT: J 133 ARG cc_start: 0.6239 (OUTLIER) cc_final: 0.5291 (mmm-85) REVERT: N 24 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7446 (mtp180) REVERT: O 80 PHE cc_start: 0.8087 (t80) cc_final: 0.7824 (t80) REVERT: O 187 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.5488 (pp20) REVERT: O 193 GLN cc_start: 0.8363 (mt0) cc_final: 0.8009 (mt0) REVERT: P 136 ILE cc_start: 0.8836 (mt) cc_final: 0.8612 (mt) REVERT: P 154 GLU cc_start: 0.5736 (mp0) cc_final: 0.5293 (mp0) REVERT: Q 7 SER cc_start: 0.8030 (p) cc_final: 0.7734 (p) REVERT: R 13 SER cc_start: 0.8946 (t) cc_final: 0.8691 (t) REVERT: S 61 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8732 (tt) REVERT: S 96 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7033 (t70) REVERT: S 131 LYS cc_start: 0.7816 (mtpp) cc_final: 0.7613 (mtmt) REVERT: T 106 LEU cc_start: 0.7923 (mt) cc_final: 0.7509 (mm) REVERT: U 104 ARG cc_start: 0.8249 (ptt-90) cc_final: 0.7979 (ptt-90) REVERT: V 59 MET cc_start: 0.8878 (mmm) cc_final: 0.8595 (mmm) REVERT: W 155 VAL cc_start: 0.7604 (p) cc_final: 0.7371 (m) REVERT: X 73 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7122 (mpp) REVERT: X 134 ASP cc_start: 0.7485 (m-30) cc_final: 0.7280 (m-30) REVERT: Y 46 LYS cc_start: 0.8142 (tttt) cc_final: 0.7844 (tttm) REVERT: Z 102 GLU cc_start: 0.6453 (mt-10) cc_final: 0.5990 (mt-10) REVERT: Z 116 LYS cc_start: 0.8031 (tttm) cc_final: 0.7734 (ttpm) REVERT: Z 119 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7325 (mm-30) REVERT: Z 121 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8099 (ttt90) REVERT: a 120 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7551 (t0) REVERT: a 135 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: a 136 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: b 1 MET cc_start: 0.6150 (mtt) cc_final: 0.5786 (mpp) REVERT: b 59 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7033 (tt0) REVERT: b 365 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7521 (mm-40) REVERT: b 396 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6597 (ptt90) REVERT: b 561 ARG cc_start: 0.7311 (mtm-85) cc_final: 0.6821 (mtp85) REVERT: c 52 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7897 (tpp80) REVERT: f 49 ILE cc_start: 0.8855 (mt) cc_final: 0.8528 (mt) REVERT: g 60 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.6755 (tmt170) REVERT: h 69 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7306 (mt) REVERT: h 96 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8125 (mt-10) REVERT: i 20 MET cc_start: 0.7893 (mtp) cc_final: 0.7599 (mtp) REVERT: k 77 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6186 (mmm-85) REVERT: m 121 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7506 (mtpp) REVERT: m 346 ILE cc_start: 0.8748 (pt) cc_final: 0.8454 (mp) REVERT: m 417 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: n 218 MET cc_start: 0.7618 (mtm) cc_final: 0.7085 (ttm) REVERT: n 229 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7601 (tp) REVERT: q 249 GLU cc_start: 0.6183 (tp30) cc_final: 0.5860 (tp30) REVERT: q 454 PHE cc_start: 0.8291 (t80) cc_final: 0.8000 (t80) REVERT: r 53 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7842 (tppp) REVERT: s 17 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7639 (mm-30) REVERT: t 38 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6542 (tttp) REVERT: v 63 LYS cc_start: 0.5967 (mmtp) cc_final: 0.5404 (mtmp) REVERT: v 217 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.5996 (mmt180) REVERT: w 39 LEU cc_start: 0.6296 (OUTLIER) cc_final: 0.5817 (mm) REVERT: x 230 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6706 (mmmt) REVERT: x 392 THR cc_start: 0.7184 (t) cc_final: 0.6870 (m) REVERT: y 1 MET cc_start: 0.5710 (mtt) cc_final: 0.5443 (mtt) REVERT: y 62 MET cc_start: 0.8204 (mmm) cc_final: 0.7902 (mmm) REVERT: y 241 ILE cc_start: 0.6812 (mt) cc_final: 0.6495 (mp) REVERT: z 95 LYS cc_start: 0.7403 (ttmt) cc_final: 0.7013 (tmtt) REVERT: 4 94 THR cc_start: 0.7484 (m) cc_final: 0.7278 (p) REVERT: 4 191 MET cc_start: 0.7769 (tpp) cc_final: 0.7503 (tpt) REVERT: 4 354 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8566 (mp) REVERT: 4 423 MET cc_start: 0.8398 (tpt) cc_final: 0.7994 (tpp) REVERT: 4 484 LYS cc_start: 0.8408 (tptt) cc_final: 0.8106 (tptm) outliers start: 224 outliers final: 157 residues processed: 1337 average time/residue: 2.2660 time to fit residues: 4307.3276 Evaluate side-chains 1362 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1176 time to evaluate : 8.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 5 residue 87 GLU Chi-restraints excluded: chain 8 residue 15 LEU Chi-restraints excluded: chain 8 residue 40 LYS Chi-restraints excluded: chain 8 residue 139 VAL Chi-restraints excluded: chain 9 residue 31 GLU Chi-restraints excluded: chain 9 residue 35 LEU Chi-restraints excluded: chain 9 residue 110 LEU Chi-restraints excluded: chain 9 residue 142 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 172 LYS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 294 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 182 ILE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 149 LYS Chi-restraints excluded: chain T residue 35 LYS Chi-restraints excluded: chain T residue 149 GLN Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 229 GLU Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 94 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 210 ASP Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 232 MET Chi-restraints excluded: chain b residue 292 ILE Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 574 THR Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 52 ARG Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain k residue 77 ARG Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 121 LYS Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 169 THR Chi-restraints excluded: chain m residue 208 SER Chi-restraints excluded: chain m residue 380 GLU Chi-restraints excluded: chain m residue 382 ILE Chi-restraints excluded: chain m residue 390 VAL Chi-restraints excluded: chain m residue 417 GLU Chi-restraints excluded: chain n residue 111 SER Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 195 GLU Chi-restraints excluded: chain n residue 220 THR Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 353 ASP Chi-restraints excluded: chain n residue 356 VAL Chi-restraints excluded: chain n residue 369 ARG Chi-restraints excluded: chain n residue 387 VAL Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 108 SER Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain q residue 392 GLU Chi-restraints excluded: chain q residue 422 LYS Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 223 VAL Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 38 LYS Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 173 THR Chi-restraints excluded: chain t residue 276 GLU Chi-restraints excluded: chain t residue 303 ASN Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 138 GLU Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 134 THR Chi-restraints excluded: chain v residue 135 VAL Chi-restraints excluded: chain v residue 217 ARG Chi-restraints excluded: chain w residue 39 LEU Chi-restraints excluded: chain w residue 102 GLU Chi-restraints excluded: chain w residue 109 LYS Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 21 GLU Chi-restraints excluded: chain x residue 41 THR Chi-restraints excluded: chain x residue 75 VAL Chi-restraints excluded: chain x residue 122 THR Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 161 THR Chi-restraints excluded: chain x residue 208 ASN Chi-restraints excluded: chain x residue 230 LYS Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 278 THR Chi-restraints excluded: chain x residue 282 SER Chi-restraints excluded: chain x residue 342 THR Chi-restraints excluded: chain x residue 386 TRP Chi-restraints excluded: chain x residue 454 SER Chi-restraints excluded: chain x residue 486 LYS Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 143 SER Chi-restraints excluded: chain y residue 145 ASN Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 84 VAL Chi-restraints excluded: chain 4 residue 108 ILE Chi-restraints excluded: chain 4 residue 109 ASP Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 132 THR Chi-restraints excluded: chain 4 residue 143 LEU Chi-restraints excluded: chain 4 residue 354 ILE Chi-restraints excluded: chain 4 residue 464 SER Chi-restraints excluded: chain 4 residue 517 THR Chi-restraints excluded: chain 4 residue 567 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 872 optimal weight: 1.9990 chunk 1170 optimal weight: 9.9990 chunk 336 optimal weight: 30.0000 chunk 1013 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 1100 optimal weight: 20.0000 chunk 460 optimal weight: 2.9990 chunk 1130 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 144 ASN 9 21 HIS B 109 HIS D 45 ASN G 191 ASN H 157 ASN ** K 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 HIS N 11 GLN N 23 GLN P 179 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 ASN S 63 GLN S 138 GLN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS Y 66 GLN Y 81 GLN Y 120 GLN Z 123 GLN b 152 GLN ** b 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 GLN i 92 ASN ** m 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 276 HIS ** m 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN o 149 GLN ** q 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 264 HIS r 179 GLN t 209 GLN t 230 ASN v 156 GLN ** v 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 194 GLN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 314 ASN x 341 HIS z 23 GLN 4 455 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.168797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.145652 restraints weight = 143425.323| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 0.44 r_work: 0.3386 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 167461 Z= 0.317 Angle : 0.767 30.348 242131 Z= 0.398 Chirality : 0.043 0.323 29640 Planarity : 0.007 0.140 18333 Dihedral : 22.334 179.895 63379 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.39 % Allowed : 15.85 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % 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: 0.69 (0.08), residues: 10648 helix: 1.52 (0.08), residues: 4179 sheet: -0.00 (0.13), residues: 1529 loop : -0.24 (0.08), residues: 4940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP p 55 HIS 0.009 0.001 HIS n 230 PHE 0.037 0.002 PHE w 117 TYR 0.031 0.002 TYR W 221 ARG 0.014 0.001 ARG q 436 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 64293.00 seconds wall clock time: 1110 minutes 28.24 seconds (66628.24 seconds total)