Starting phenix.real_space_refine on Sun Mar 3 17:51:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoo_26651/03_2024/7uoo_26651_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoo_26651/03_2024/7uoo_26651.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoo_26651/03_2024/7uoo_26651_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoo_26651/03_2024/7uoo_26651_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoo_26651/03_2024/7uoo_26651_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoo_26651/03_2024/7uoo_26651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoo_26651/03_2024/7uoo_26651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoo_26651/03_2024/7uoo_26651_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoo_26651/03_2024/7uoo_26651_updated.pdb" } resolution = 2.34 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 5 6.06 5 P 3333 5.49 5 Mg 81 5.21 5 S 229 5.16 5 C 86385 2.51 5 N 28773 2.21 5 O 39140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 157947 Number of models: 1 Model: "" Number of chains: 83 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: 64043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2991, 64043 Classifications: {'RNA': 2991} Modifications used: {'rna2p': 8, 'rna2p_pur': 309, 'rna2p_pyr': 206, 'rna3p': 41, 'rna3p_pur': 1342, 'rna3p_pyr': 1078} Link IDs: {'rna2p': 523, 'rna3p': 2467} Chain breaks: 14 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 18 Chain: "2" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 16, 'rna3p': 1, 'rna3p_pur': 60, 'rna3p_pyr': 63} Link IDs: {'rna2p': 33, 'rna3p': 124} Chain: "3" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p': 1, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 107} Chain: "5" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 645 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "6" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1227 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 13, 'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna2p': 21, 'rna3p': 36} Chain breaks: 3 Chain: "8" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1196 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain: "9" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain breaks: 3 Chain: "B" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3081 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 371} Chain: "C" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2749 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain: "D" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2180 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Chain: "E" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1230 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 146} Chain breaks: 1 Chain: "F" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1761 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "G" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 211} Chain breaks: 1 Chain: "H" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain: "I" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "J" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1368 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "K" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2155 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 11, 'TRANS': 256} Chain breaks: 2 Chain: "L" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1438 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 171} Chain: "M" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1059 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "N" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1620 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1388 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Chain breaks: 1 Chain: "Q" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1136 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 7, 'TRANS': 139} Chain: "R" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1258 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "S" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "T" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 905 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain breaks: 1 Chain: "U" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 844 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "V" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "W" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1887 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain: "X" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1088 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "Y" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "a" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 731 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "b" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5185 Classifications: {'peptide': 642} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 616} Chain breaks: 1 Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "d" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 873 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 771 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "j" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 665 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 81} Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "l" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "m" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3754 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 1 Chain: "n" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3014 Classifications: {'peptide': 369} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 347} Chain breaks: 2 Chain: "o" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "p" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "q" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1298 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain breaks: 1 Chain: "r" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1860 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "s" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 602 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain breaks: 1 Chain: "t" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2306 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 1 Chain: "u" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1265 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "v" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2366 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 279} Chain: "w" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "x" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3927 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 25, 'TRANS': 478} Chain breaks: 1 Chain: "y" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1849 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain: "z" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 714 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain breaks: 1 Chain: "4" Number of atoms: 4166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4166 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 511} Chain breaks: 1 Chain: "1" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 134 Unusual residues: {' MG': 77, 'B3P': 3} Classifications: {'undetermined': 80} Link IDs: {None: 79} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' K': 1, ' MG': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 346 Classifications: {'water': 346} Link IDs: {None: 345} Chain: "2" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} 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 90310 SG CYS I 51 185.451 153.872 140.524 1.00 18.28 S ATOM 90334 SG CYS I 54 184.474 150.329 139.246 1.00 18.01 S ATOM A0HOR SG CYS g 44 146.990 125.130 207.040 1.00 4.00 S ATOM A0HP9 SG CYS g 47 148.994 127.854 205.497 1.00 8.09 S ATOM A0HWB SG CYS g 81 150.582 125.848 208.382 1.00 2.73 S ATOM A0HWU SG CYS g 84 147.969 128.145 209.255 1.00 4.82 S ATOM A0JJM SG CYS j 19 110.037 101.520 168.480 1.00 11.37 S ATOM A0JKB SG CYS j 22 108.519 100.795 165.102 1.00 12.65 S ATOM A0JN3 SG CYS j 34 109.080 104.426 166.249 1.00 12.65 S ATOM A0JNL SG CYS j 37 106.402 102.289 167.924 1.00 12.65 S ATOM A0R2S SG CYS p 39 148.259 145.172 204.120 1.00 10.67 S ATOM A0R3F SG CYS p 42 151.749 144.034 204.881 1.00 10.29 S ATOM A0R6G SG CYS p 57 150.047 143.190 201.577 1.00 10.46 S ATOM A0R6Y SG CYS p 60 148.905 141.466 204.911 1.00 14.50 S ATOM A0W3G SG CYS u 6 186.034 138.448 115.131 1.00 5.18 S ATOM A0W47 SG CYS u 9 187.575 135.000 115.562 1.00 5.34 S ATOM A0W9C SG CYS u 32 184.680 135.509 113.189 1.00 5.72 S ATOM A0WA8 SG CYS u 36 184.254 135.639 117.053 1.00 7.97 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: 58.39, per 1000 atoms: 0.37 Number of scatterers: 157947 At special positions: 0 Unit cell: (230.04, 271.08, 307.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 5 29.99 K 1 19.00 S 229 16.00 P 3333 15.00 Mg 81 11.99 O 39140 8.00 N 28773 7.00 C 86385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 56.90 Conformation dependent library (CDL) restraints added in 11.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 67 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 73 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 54 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 51 " pdb=" ZN g 601 " pdb="ZN ZN g 601 " - pdb=" SG CYS g 81 " pdb="ZN ZN g 601 " - pdb=" SG CYS g 47 " pdb="ZN ZN g 601 " - pdb=" SG CYS g 84 " pdb="ZN ZN g 601 " - pdb=" SG CYS g 44 " pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb=" ZN p 501 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 39 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 57 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 60 " pdb=" ZN u 201 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 9 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 36 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 6 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 32 " 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: 381 helices and 106 sheets defined 45.1% alpha, 14.9% beta 1011 base pairs and 1606 stacking pairs defined. Time for finding SS restraints: 87.02 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 4.711A pdb=" N GLY A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 4.489A 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 181 through 193 removed outlier: 3.904A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.591A pdb=" N MET A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain '5' and resid 42 through 99 removed outlier: 3.658A pdb=" N LYS 5 98 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) Processing helix chain '5' and resid 100 through 114 removed outlier: 4.105A pdb=" N ARG 5 113 " --> pdb=" O ARG 5 109 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN 5 114 " --> pdb=" O ARG 5 110 " (cutoff:3.500A) Processing helix chain '8' and resid 25 through 30 removed outlier: 3.666A pdb=" N ALA 8 29 " --> pdb=" O SER 8 25 " (cutoff:3.500A) Proline residue: 8 30 - end of helix No H-bonds generated for 'chain '8' and resid 25 through 30' Processing helix chain '8' and resid 31 through 36 removed outlier: 4.355A pdb=" N LEU 8 35 " --> pdb=" O LYS 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 38 through 51 removed outlier: 3.582A pdb=" N LYS 8 51 " --> pdb=" O ALA 8 47 " (cutoff:3.500A) Processing helix chain '8' and resid 76 through 86 removed outlier: 3.686A pdb=" N LYS 8 86 " --> pdb=" O ILE 8 82 " (cutoff:3.500A) Processing helix chain '8' and resid 105 through 117 Processing helix chain '8' and resid 124 through 140 Processing helix chain '8' and resid 147 through 158 Processing helix chain '9' and resid 10 through 34 removed outlier: 4.735A 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 13 through 18 removed outlier: 4.525A pdb=" N LEU B 17 " --> pdb=" O HIS B 13 " (cutoff:3.500A) Proline residue: B 18 - end of helix No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 111 through 120 removed outlier: 4.121A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 removed outlier: 4.174A pdb=" N ALA B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 removed outlier: 6.035A pdb=" N ARG B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 4.293A 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: 3.825A 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: 3.805A 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 28 removed outlier: 4.422A pdb=" N SER C 27 " --> pdb=" O PRO C 23 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 28' Processing helix chain 'C' and resid 31 through 46 removed outlier: 3.713A pdb=" N ASN C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.905A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 5.649A 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: 4.260A pdb=" N SER C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.756A 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: 4.050A pdb=" N LYS C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.983A pdb=" N ARG C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.042A 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: 4.653A 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: 4.522A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.219A 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: 4.331A 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: 3.622A 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: 4.511A 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: 4.302A pdb=" N ALA D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 4.276A 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: 3.777A pdb=" N GLU D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 4.949A 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: 3.802A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 5.625A 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: 3.967A pdb=" N VAL E 84 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.836A 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: 6.309A pdb=" N VAL E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 5.290A 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: 3.831A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.964A 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: 4.050A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 191 removed outlier: 4.215A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 removed outlier: 5.052A pdb=" N TRP F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 244 removed outlier: 4.918A pdb=" N ASN F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) removed outlier: 4.367A 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: 5.191A pdb=" N PHE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLN G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR G 81 " --> pdb=" O GLN G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 98 removed outlier: 3.973A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.603A pdb=" N GLU G 107 " --> pdb=" O ALA G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 146 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 191 Processing helix chain 'G' and resid 204 through 222 removed outlier: 5.100A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 232 removed outlier: 4.469A pdb=" N LYS G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 255 Processing helix chain 'H' and resid 61 through 84 Processing helix chain 'H' and resid 150 through 166 removed outlier: 4.059A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 4.724A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 10 Processing helix chain 'I' and resid 17 through 27 removed outlier: 3.936A pdb=" N THR I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.865A pdb=" N GLN I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 71 removed outlier: 3.848A pdb=" N GLY I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LYS I 71 " --> pdb=" O HIS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 82 removed outlier: 3.854A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLY I 82 " --> pdb=" O LYS I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 95 removed outlier: 3.998A pdb=" N SER I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 131 removed outlier: 3.929A pdb=" N VAL I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY I 113 " --> pdb=" O THR I 109 " (cutoff:3.500A) Proline residue: I 114 - end of helix Processing helix chain 'J' and resid 27 through 42 Processing helix chain 'J' and resid 73 through 88 Processing helix chain 'J' and resid 108 through 113 removed outlier: 4.764A pdb=" N LEU J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY J 113 " --> pdb=" O HIS J 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 108 through 113' Processing helix chain 'J' and resid 136 through 141 removed outlier: 4.291A 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 'K' and resid 33 through 50 removed outlier: 3.759A pdb=" N THR K 48 " --> pdb=" O LEU K 44 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS K 50 " --> pdb=" O LYS K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 76 removed outlier: 4.896A pdb=" N GLU K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LYS K 76 " --> pdb=" O GLU K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 118 Proline residue: K 109 - end of helix removed outlier: 4.138A pdb=" N ALA K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N THR K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL K 118 " --> pdb=" O SER K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 136 removed outlier: 5.129A pdb=" N LYS K 133 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LYS K 134 " --> pdb=" O SER K 130 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL K 135 " --> pdb=" O ASP K 131 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER K 136 " --> pdb=" O ILE K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 145 removed outlier: 4.524A pdb=" N GLN K 143 " --> pdb=" O ASP K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 163 removed outlier: 3.630A pdb=" N LEU K 160 " --> pdb=" O CYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 177 removed outlier: 4.014A pdb=" N GLN K 176 " --> pdb=" O ALA K 172 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 194 removed outlier: 4.523A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER K 189 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 3.710A 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: 4.291A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN K 200 " --> pdb=" O GLY K 196 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS K 201 " --> pdb=" O LYS K 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 195 through 201' Processing helix chain 'K' and resid 218 through 232 Processing helix chain 'K' and resid 250 through 255 removed outlier: 3.715A pdb=" N LEU K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) removed outlier: 5.156A 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: 4.097A pdb=" N LYS K 272 " --> pdb=" O GLU K 268 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA K 273 " --> pdb=" O GLN K 269 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR K 274 " --> pdb=" O LEU K 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 300 removed outlier: 4.338A pdb=" N ASP K 299 " --> pdb=" O GLN K 295 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLU K 300 " --> pdb=" O ASP K 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 295 through 300' Processing helix chain 'K' and resid 327 through 338 removed outlier: 5.065A pdb=" N ASN K 338 " --> pdb=" O MET K 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.332A pdb=" N ARG L 21 " --> pdb=" O HIS L 17 " (cutoff:3.500A) removed outlier: 3.939A 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: 5.238A pdb=" N GLY L 181 " --> pdb=" O LYS L 177 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE L 182 " --> pdb=" O LYS L 178 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG L 183 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU L 194 " --> pdb=" O LYS L 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 64 removed outlier: 4.049A pdb=" N VAL M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 5.104A 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: 3.697A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 5.581A 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 136 Processing helix chain 'N' and resid 2 through 14 removed outlier: 4.630A pdb=" N TYR N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 4.854A 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: 4.531A pdb=" N CYS N 152 " --> pdb=" O TYR N 148 " (cutoff:3.500A) removed outlier: 4.220A 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: 3.804A 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: 5.384A pdb=" N ALA O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 3.826A 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: 3.947A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER O 89 " --> pdb=" O ARG O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 103 removed outlier: 3.621A pdb=" N ARG O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 116 removed outlier: 8.003A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.409A 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: 4.284A pdb=" N SER P 14 " --> pdb=" O ASN P 10 " (cutoff:3.500A) removed outlier: 5.395A 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 84 through 106 Processing helix chain 'P' and resid 169 through 184 removed outlier: 4.583A pdb=" N ALA P 184 " --> pdb=" O LYS P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 76 removed outlier: 3.583A pdb=" N GLY P 73 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 42 through 54 removed outlier: 3.756A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 60 Proline residue: Q 60 - end of helix Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.864A pdb=" N GLN Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 118 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 36 removed outlier: 3.639A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 5.405A 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: 6.617A pdb=" N VAL R 93 " --> pdb=" O LEU R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 Processing helix chain 'R' and resid 134 through 157 Processing helix chain 'S' and resid 33 through 49 Processing helix chain 'S' and resid 98 through 113 Processing helix chain 'S' and resid 117 through 122 removed outlier: 5.293A pdb=" N HIS S 122 " --> pdb=" O PHE S 118 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 145 removed outlier: 5.073A pdb=" N PHE S 143 " --> pdb=" O TYR S 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU S 144 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR S 145 " --> pdb=" O LYS S 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 97 removed outlier: 4.060A pdb=" N ILE T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS T 97 " --> pdb=" O VAL T 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 92 through 97' Processing helix chain 'T' and resid 102 through 123 removed outlier: 3.869A pdb=" N GLY T 123 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 26 Processing helix chain 'U' and resid 29 through 41 Processing helix chain 'U' and resid 72 through 88 Processing helix chain 'V' and resid 66 through 71 removed outlier: 5.200A 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: 3.942A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 61 removed outlier: 3.786A 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: 4.674A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 3.731A 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: 5.065A pdb=" N VAL W 155 " --> pdb=" O ALA W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 167 removed outlier: 4.394A 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: 4.576A pdb=" N GLU X 64 " --> pdb=" O TYR X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 79 removed outlier: 3.664A pdb=" N LYS X 75 " --> pdb=" O THR X 71 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 3.992A 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: 3.582A 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: 3.820A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 4.396A 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: 3.728A pdb=" N LEU Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.046A 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: 3.953A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.776A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 5.300A 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: 3.858A pdb=" N VAL Z 96 " --> pdb=" O PHE Z 92 " (cutoff:3.500A) removed outlier: 5.161A 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: 3.849A pdb=" N GLU Z 102 " --> pdb=" O THR Z 98 " (cutoff:3.500A) removed outlier: 3.748A 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: 4.482A 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: 4.346A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 94 removed outlier: 3.776A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN a 89 " --> pdb=" O ASP a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 108 Processing helix chain 'a' and resid 131 through 142 Processing helix chain 'b' and resid 13 through 29 Processing helix chain 'b' and resid 38 through 66 Processing helix chain 'b' and resid 70 through 75 removed outlier: 6.015A pdb=" N HIS b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 86 Processing helix chain 'b' and resid 87 through 119 removed outlier: 4.275A pdb=" N PHE b 118 " --> pdb=" O ARG b 114 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY b 119 " --> pdb=" O LEU b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 144 removed outlier: 3.973A pdb=" N LEU b 143 " --> pdb=" O ILE b 139 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG b 144 " --> pdb=" O VAL b 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 161 removed outlier: 4.038A pdb=" N ARG b 159 " --> pdb=" O GLN b 155 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU b 160 " --> pdb=" O HIS b 156 " (cutoff:3.500A) Proline residue: b 161 - end of helix Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.822A 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: 4.967A pdb=" N ALA b 279 " --> pdb=" O LYS b 275 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 312 removed outlier: 4.095A pdb=" N VAL b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 350 removed outlier: 4.047A pdb=" N LYS b 349 " --> pdb=" O GLU b 345 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 353 through 362 removed outlier: 5.009A pdb=" N VAL b 357 " --> pdb=" O ARG b 353 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS b 360 " --> pdb=" O ASN b 356 " (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: 4.963A pdb=" N LYS b 419 " --> pdb=" O ASN b 415 " (cutoff:3.500A) removed outlier: 4.550A 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: 4.323A pdb=" N LYS b 428 " --> pdb=" O ASP b 424 " (cutoff:3.500A) removed outlier: 5.166A 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: 3.809A 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 512 removed outlier: 5.473A pdb=" N SER b 512 " --> pdb=" O ARG b 508 " (cutoff:3.500A) Processing helix chain 'b' and resid 520 through 525 removed outlier: 4.925A 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: 4.592A 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: 4.042A pdb=" N ARG b 611 " --> pdb=" O LYS b 607 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLU b 612 " --> pdb=" O MET b 608 " (cutoff:3.500A) removed outlier: 5.124A 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: 4.016A pdb=" N ARG d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 45 removed outlier: 5.367A 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: 5.141A 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: 3.673A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU e 85 " --> pdb=" O ASP e 81 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR e 86 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N MET e 87 " --> pdb=" O GLU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.807A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 45 removed outlier: 4.396A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU f 45 " --> pdb=" O ALA f 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 66 removed outlier: 3.694A pdb=" N TYR g 62 " --> pdb=" O ARG g 58 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA g 63 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL g 65 " --> pdb=" O GLN g 61 " (cutoff:3.500A) removed outlier: 5.709A 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 removed outlier: 3.591A pdb=" N ALA g 111 " --> pdb=" O GLU g 107 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 13 removed outlier: 4.055A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS h 12 " --> pdb=" O GLU h 8 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 38 removed outlier: 3.776A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 71 removed outlier: 4.078A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 82 removed outlier: 5.315A pdb=" N ALA h 82 " --> pdb=" O LYS h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 91 Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 25 through 31 removed outlier: 4.402A pdb=" N LYS i 29 " --> pdb=" O LYS i 25 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS i 30 " --> pdb=" O ILE i 26 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLY i 31 " --> pdb=" O SER i 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 31' Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 64 Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 98 Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.622A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS j 10 " --> pdb=" O PRO j 6 " (cutoff:3.500A) removed outlier: 4.437A 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: 5.534A pdb=" N HIS j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 5.029A 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: 5.433A pdb=" N ARG l 21 " --> pdb=" O LYS l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.219A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 3.888A 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 removed outlier: 3.536A pdb=" N ILE m 12 " --> pdb=" O LYS m 8 " (cutoff:3.500A) Processing helix chain 'm' and resid 32 through 44 removed outlier: 4.287A pdb=" N TYR m 42 " --> pdb=" O PHE m 38 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR m 43 " --> pdb=" O LEU m 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 74 through 80 removed outlier: 4.735A pdb=" N PHE m 78 " --> pdb=" O ASP m 74 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY m 79 " --> pdb=" O ARG m 75 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN m 80 " --> pdb=" O ARG m 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 74 through 80' Processing helix chain 'm' and resid 85 through 99 removed outlier: 4.925A pdb=" N GLY m 97 " --> pdb=" O ARG m 93 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU m 98 " --> pdb=" O SER m 94 " (cutoff:3.500A) removed outlier: 3.678A 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: 4.305A pdb=" N THR m 134 " --> pdb=" O ARG m 130 " (cutoff:3.500A) Processing helix chain 'm' and resid 136 through 141 Processing helix chain 'm' and resid 156 through 185 removed outlier: 4.129A pdb=" N LEU m 181 " --> pdb=" O LEU m 177 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU m 183 " --> pdb=" O ALA m 179 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N MET m 184 " --> pdb=" O THR m 180 " (cutoff:3.500A) Processing helix chain 'm' and resid 186 through 193 removed outlier: 3.893A pdb=" N LYS m 190 " --> pdb=" O ASN m 186 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU m 191 " --> pdb=" O GLN m 187 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN m 192 " --> pdb=" O GLU m 188 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY m 193 " --> pdb=" O ASP m 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 186 through 193' Processing helix chain 'm' and resid 200 through 205 removed outlier: 4.416A pdb=" N SER m 204 " --> pdb=" O GLU m 200 " (cutoff:3.500A) removed outlier: 4.266A 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 removed outlier: 3.604A pdb=" N ARG m 238 " --> pdb=" O PRO m 234 " (cutoff:3.500A) Processing helix chain 'm' and resid 239 through 249 Processing helix chain 'm' and resid 261 through 266 removed outlier: 4.318A 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: 3.702A pdb=" N LYS m 279 " --> pdb=" O LYS m 275 " (cutoff:3.500A) removed outlier: 4.408A 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: 3.759A pdb=" N GLY m 386 " --> pdb=" O ILE m 382 " (cutoff:3.500A) Processing helix chain 'm' and resid 395 through 407 removed outlier: 4.283A 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 removed outlier: 3.551A pdb=" N PHE n 15 " --> pdb=" O ASN n 11 " (cutoff:3.500A) 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: 4.159A pdb=" N HIS n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU n 74 " --> pdb=" O TYR n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 97 Processing helix chain 'n' and resid 98 through 109 removed outlier: 3.935A 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: 4.789A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA n 135 " --> pdb=" O ASP n 131 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN n 144 " --> pdb=" O PHE n 140 " (cutoff:3.500A) removed outlier: 3.684A 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: 4.646A pdb=" N TYR n 262 " --> pdb=" O GLY n 258 " (cutoff:3.500A) removed outlier: 5.546A 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: 6.615A pdb=" N SER n 358 " --> pdb=" O SER n 354 " (cutoff:3.500A) Processing helix chain 'n' and resid 372 through 384 Processing helix chain 'n' and resid 389 through 394 removed outlier: 4.184A pdb=" N MET n 393 " --> pdb=" O SER n 389 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP n 394 " --> pdb=" O GLU n 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 389 through 394' Processing helix chain 'n' and resid 428 through 439 removed outlier: 4.368A pdb=" N ILE n 432 " --> pdb=" O GLN n 428 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE n 433 " --> pdb=" O PRO n 429 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 115 removed outlier: 4.220A pdb=" N GLN o 113 " --> pdb=" O LYS o 109 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE o 114 " --> pdb=" O TYR o 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 141 through 153 Processing helix chain 'o' and resid 192 through 215 removed outlier: 3.650A pdb=" N GLY o 215 " --> pdb=" O LEU o 211 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.636A pdb=" N LEU p 29 " --> pdb=" O GLN p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 Processing helix chain 'p' and resid 9 through 14 removed outlier: 3.680A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 204 through 209 removed outlier: 4.468A pdb=" N ASP q 208 " --> pdb=" O PRO q 204 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE q 209 " --> pdb=" O SER q 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 204 through 209' Processing helix chain 'q' and resid 232 through 269 Processing helix chain 'q' and resid 414 through 427 Processing helix chain 'q' and resid 448 through 454 Processing helix chain 'r' and resid 5 through 14 Processing helix chain 'r' and resid 19 through 42 removed outlier: 4.640A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 74 removed outlier: 3.702A 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: 3.554A pdb=" N ARG r 178 " --> pdb=" O PRO r 174 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLN r 179 " --> pdb=" O SER r 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 174 through 179' Processing helix chain 'r' and resid 206 through 213 Processing helix chain 'r' and resid 248 through 253 Processing helix chain 's' and resid 12 through 37 Processing helix chain 's' and resid 56 through 77 removed outlier: 4.010A pdb=" N GLU s 73 " --> pdb=" O MET s 69 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG s 75 " --> pdb=" O ASP s 71 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU s 76 " --> pdb=" O LEU s 72 " (cutoff:3.500A) Processing helix chain 't' and resid 15 through 51 removed outlier: 4.381A 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 210 Processing helix chain 't' and resid 231 through 239 removed outlier: 3.650A pdb=" N VAL t 235 " --> pdb=" O ASP t 231 " (cutoff:3.500A) Processing helix chain 't' and resid 246 through 257 Processing helix chain 't' and resid 260 through 269 removed outlier: 4.883A 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: 5.363A pdb=" N LYS u 50 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 60 Processing helix chain 'u' and resid 66 through 71 removed outlier: 3.807A pdb=" N THR u 70 " --> pdb=" O ASP u 66 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE u 71 " --> pdb=" O SER u 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 66 through 71' Processing helix chain 'u' and resid 82 through 131 removed outlier: 3.755A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY u 114 " --> pdb=" O ASN u 110 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN u 115 " --> pdb=" O ARG u 111 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LYS u 116 " --> pdb=" O MET u 112 " (cutoff:3.500A) removed outlier: 7.335A 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: 5.492A 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: 4.119A pdb=" N PHE v 128 " --> pdb=" O LEU v 124 " (cutoff:3.500A) removed outlier: 4.187A 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: 4.400A 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: 3.928A pdb=" N LEU v 178 " --> pdb=" O ASP v 174 " (cutoff:3.500A) removed outlier: 5.867A 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: 4.589A pdb=" N LEU v 285 " --> pdb=" O ASP v 281 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N GLN v 286 " --> pdb=" O LEU v 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 281 through 286' Processing helix chain 'w' and resid 35 through 40 removed outlier: 3.665A pdb=" N LEU w 39 " --> pdb=" O ASP w 35 " (cutoff:3.500A) 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: 4.407A pdb=" N LYS w 153 " --> pdb=" O GLY w 149 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU w 154 " --> pdb=" O ALA w 150 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP w 155 " --> pdb=" O ASN w 151 " (cutoff:3.500A) removed outlier: 4.029A 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 'w' and resid 169 through 174 removed outlier: 4.266A pdb=" N LEU w 173 " --> pdb=" O ASP w 170 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE w 174 " --> pdb=" O ASN w 171 " (cutoff:3.500A) 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: 5.119A 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: 3.896A pdb=" N ILE x 363 " --> pdb=" O ASN x 359 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 17 removed outlier: 3.644A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 43 removed outlier: 3.889A 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: 4.821A pdb=" N ASP y 238 " --> pdb=" O GLY y 234 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N THR y 239 " --> pdb=" O ASN y 235 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 56 removed outlier: 4.069A pdb=" N GLY z 20 " --> pdb=" O VAL z 16 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL z 21 " --> pdb=" O LYS z 17 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE z 22 " --> pdb=" O ARG z 18 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN z 23 " --> pdb=" O ARG z 19 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) removed outlier: 3.688A 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: 4.385A pdb=" N GLN 4 78 " --> pdb=" O THR 4 74 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR 4 79 " --> pdb=" O ARG 4 75 " (cutoff:3.500A) removed outlier: 5.544A 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: 3.619A pdb=" N ALA 4 201 " --> pdb=" O LEU 4 197 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU 4 202 " --> pdb=" O LEU 4 198 " (cutoff:3.500A) removed outlier: 4.083A 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: 3.591A pdb=" N LYS 4 384 " --> pdb=" O THR 4 380 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN 4 385 " --> pdb=" O LYS 4 381 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY 4 386 " --> pdb=" O ILE 4 382 " (cutoff:3.500A) Processing helix chain '4' and resid 391 through 396 removed outlier: 3.926A pdb=" N LEU 4 395 " --> pdb=" O LYS 4 391 " (cutoff:3.500A) removed outlier: 3.973A 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: 3.774A pdb=" N SER 4 418 " --> pdb=" O LYS 4 414 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU 4 425 " --> pdb=" O LEU 4 421 " (cutoff:3.500A) Processing helix chain '4' and resid 444 through 451 removed outlier: 3.638A pdb=" N ILE 4 448 " --> pdb=" O PRO 4 444 " (cutoff:3.500A) Processing helix chain '4' and resid 466 through 472 removed outlier: 4.662A pdb=" N GLU 4 472 " --> pdb=" O LEU 4 468 " (cutoff:3.500A) Processing helix chain '4' and resid 481 through 492 Processing helix chain '4' and resid 547 through 563 removed outlier: 5.192A pdb=" N LYS 4 563 " --> pdb=" O LEU 4 559 " (cutoff:3.500A) Processing helix chain '4' and resid 528 through 533 removed outlier: 3.937A 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: 3.836A pdb=" N GLN A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 100 through 103 removed outlier: 4.813A pdb=" N ASN A 100 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 111 through 114 removed outlier: 4.292A pdb=" N THR A 111 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 58 through 64 Processing sheet with id= 5, first strand: chain 'A' and resid 145 through 150 removed outlier: 4.294A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '8' and resid 11 through 16 removed outlier: 4.370A pdb=" N THR 8 59 " --> pdb=" O VAL 8 74 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.503A pdb=" N GLN B 182 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N HIS B 177 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL B 158 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N GLY B 185 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 12.296A pdb=" N SER B 156 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 53 through 60 removed outlier: 6.908A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 12.861A pdb=" N LYS B 333 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N LYS B 222 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N HIS B 273 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 284 through 288 removed outlier: 3.708A pdb=" N GLY B 288 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 5.130A 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 87 through 91 removed outlier: 7.982A pdb=" N VAL B 87 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 84 through 87 removed outlier: 4.034A pdb=" N LYS B 201 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 213 through 216 removed outlier: 4.377A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 4 through 8 removed outlier: 5.156A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 224 through 230 removed outlier: 5.524A pdb=" N PHE C 247 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 72 through 75 removed outlier: 6.730A pdb=" N ILE D 64 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 37 through 43 removed outlier: 3.967A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS E 50 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU E 64 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 133 through 138 removed outlier: 7.837A pdb=" N TYR F 133 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LYS F 82 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN F 112 " --> pdb=" O LEU F 207 " (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: 4.925A pdb=" N GLN H 51 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 17 through 20 removed outlier: 5.839A 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: 6.123A 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: 6.086A pdb=" N GLU H 143 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 5.557A 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: 5.124A 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: 7.769A pdb=" N ILE J 65 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER J 22 " --> pdb=" O GLY J 124 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLY J 124 " --> pdb=" O SER J 22 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 52 through 55 removed outlier: 4.814A pdb=" N THR J 53 " --> pdb=" O ARG J 60 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG J 60 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ARG J 55 " --> pdb=" O GLY J 58 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 89 through 92 removed outlier: 4.386A pdb=" N ASP J 170 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU J 91 " --> pdb=" O ASP J 170 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'K' and resid 97 through 101 Processing sheet with id= 29, first strand: chain 'K' and resid 122 through 126 Processing sheet with id= 30, first strand: chain 'K' and resid 242 through 248 removed outlier: 5.577A pdb=" N THR K 242 " --> pdb=" O ASN K 84 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU K 78 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE K 279 " --> pdb=" O PRO K 290 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE K 281 " --> pdb=" O VAL K 288 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL K 288 " --> pdb=" O ILE K 281 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR K 283 " --> pdb=" O SER K 286 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'L' and resid 56 through 59 Processing sheet with id= 32, first strand: chain 'M' and resid 19 through 24 removed outlier: 4.403A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS M 31 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.529A pdb=" N VAL N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY N 58 " --> pdb=" O ASP N 136 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'N' and resid 117 through 121 removed outlier: 3.699A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 36, first strand: chain 'P' and resid 16 through 20 removed outlier: 6.415A pdb=" N VAL P 149 " --> pdb=" O SER P 115 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS P 111 " --> pdb=" O LYS P 153 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'P' and resid 57 through 60 removed outlier: 5.323A pdb=" N LYS P 80 " --> pdb=" O PHE P 60 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'P' and resid 116 through 122 Processing sheet with id= 39, first strand: chain 'P' and resid 124 through 131 Processing sheet with id= 40, first strand: chain 'Q' and resid 79 through 83 Processing sheet with id= 41, first strand: chain 'R' and resid 21 through 25 removed outlier: 6.547A pdb=" N LYS R 21 " --> pdb=" O LYS R 53 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR R 49 " --> pdb=" O ASP R 25 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'S' and resid 24 through 31 removed outlier: 6.674A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'S' and resid 86 through 96 removed outlier: 3.514A pdb=" N HIS S 88 " --> pdb=" O TYR S 81 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'S' and resid 6 through 10 removed outlier: 4.682A pdb=" N GLU S 6 " --> pdb=" O ILE S 64 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'T' and resid 38 through 42 removed outlier: 4.365A pdb=" N ASP T 38 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS T 60 " --> pdb=" O ILE T 42 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'U' and resid 54 through 58 removed outlier: 5.813A pdb=" N ASN U 101 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N TRP U 92 " --> pdb=" O TYR U 108 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 21 through 24 removed outlier: 4.386A pdb=" N ALA V 21 " --> pdb=" O ILE V 36 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 56 through 60 removed outlier: 4.363A pdb=" N ASP V 56 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP V 97 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA V 82 " --> pdb=" O ASP V 97 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'V' and resid 84 through 87 removed outlier: 3.616A pdb=" N VAL V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'W' and resid 63 through 67 removed outlier: 6.893A pdb=" N VAL W 42 " --> pdb=" O SER W 218 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'W' and resid 135 through 139 removed outlier: 6.728A pdb=" N PHE W 135 " --> pdb=" O VAL W 188 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU W 139 " --> pdb=" O SER W 184 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SER W 184 " --> pdb=" O GLU W 139 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'W' and resid 173 through 176 Processing sheet with id= 53, first strand: chain 'W' and resid 38 through 42 removed outlier: 8.499A pdb=" N ARG W 38 " --> pdb=" O ASN W 223 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'X' and resid 81 through 86 removed outlier: 3.931A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'Y' and resid 72 through 75 Processing sheet with id= 56, first strand: chain 'Y' and resid 86 through 89 removed outlier: 4.275A pdb=" N ALA Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Z' and resid 9 through 14 removed outlier: 4.199A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'Z' and resid 42 through 45 Processing sheet with id= 59, first strand: chain 'a' and resid 99 through 102 Processing sheet with id= 60, first strand: chain 'b' and resid 204 through 210 removed outlier: 4.677A pdb=" N ARG b 168 " --> pdb=" O ARG b 215 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR b 221 " --> pdb=" O ILE b 172 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY b 174 " --> pdb=" O THR b 221 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU b 316 " --> pdb=" O VAL b 283 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.392A pdb=" N LYS c 22 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS c 66 " --> pdb=" O LYS c 40 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'd' and resid 48 through 51 removed outlier: 5.046A pdb=" N ASP d 48 " --> pdb=" O LEU d 89 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N THR d 9 " --> pdb=" O VAL d 109 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'e' and resid 71 through 77 Processing sheet with id= 64, first strand: chain 'f' and resid 10 through 14 removed outlier: 5.932A pdb=" N LYS f 10 " --> pdb=" O GLU f 33 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG f 82 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS f 47 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'f' and resid 8 through 14 removed outlier: 4.115A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.559A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'k' and resid 2 through 5 removed outlier: 4.511A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE k 27 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'm' and resid 291 through 294 removed outlier: 4.441A pdb=" N ASN m 292 " --> pdb=" O SER m 289 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER m 289 " --> pdb=" O ASN m 292 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS m 367 " --> pdb=" O PHE m 320 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY m 322 " --> pdb=" O CYS m 367 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE m 362 " --> pdb=" O LEU m 358 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'n' and resid 177 through 182 Processing sheet with id= 70, first strand: chain 'n' and resid 385 through 388 Processing sheet with id= 71, first strand: chain 'o' and resid 118 through 123 removed outlier: 3.819A pdb=" N GLU o 119 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'p' and resid 47 through 50 removed outlier: 6.953A pdb=" N ILE p 54 " --> pdb=" O GLY p 50 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'r' and resid 148 through 151 Processing sheet with id= 74, first strand: chain 'r' and resid 190 through 195 removed outlier: 3.858A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN r 256 " --> pdb=" O THR r 246 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TYR r 242 " --> pdb=" O LEU r 260 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR r 219 " --> pdb=" O VAL r 245 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 't' and resid 128 through 134 Processing sheet with id= 76, first strand: chain 't' and resid 193 through 198 removed outlier: 5.470A pdb=" N TYR t 193 " --> pdb=" O VAL t 147 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR t 173 " --> pdb=" O ARG t 146 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN t 172 " --> pdb=" O LEU t 273 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 't' and resid 213 through 217 Processing sheet with id= 78, first strand: chain 'u' and resid 3 through 6 removed outlier: 4.600A pdb=" N SER u 11 " --> pdb=" O CYS u 6 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'u' and resid 18 through 23 removed outlier: 4.301A pdb=" N LYS u 27 " --> pdb=" O ARG u 23 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'v' and resid 56 through 60 removed outlier: 7.395A pdb=" N SER v 92 " --> pdb=" O GLY v 35 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER v 85 " --> pdb=" O THR v 105 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ASN v 98 " --> pdb=" O VAL v 118 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU v 115 " --> pdb=" O GLY v 235 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP v 231 " --> pdb=" O ALA v 119 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASN v 198 " --> pdb=" O GLN v 187 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'v' and resid 262 through 266 removed outlier: 6.195A pdb=" N ASN v 262 " --> pdb=" O ARG v 274 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASP v 270 " --> pdb=" O ASP v 266 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'v' and resid 111 through 115 removed outlier: 8.969A pdb=" N TYR v 111 " --> pdb=" O PRO v 240 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'v' and resid 204 through 210 No H-bonds generated for sheet with id= 83 Processing sheet with id= 84, first strand: chain 'w' and resid 17 through 23 removed outlier: 5.691A pdb=" N SER w 31 " --> pdb=" O PRO w 18 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'w' and resid 69 through 72 Processing sheet with id= 86, first strand: chain 'x' and resid 48 through 53 removed outlier: 5.404A pdb=" N PHE x 79 " --> pdb=" O ILE x 97 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'x' and resid 136 through 140 removed outlier: 5.014A pdb=" N MET x 509 " --> pdb=" O GLY x 505 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY x 505 " --> pdb=" O MET x 509 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG x 500 " --> pdb=" O SER x 495 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'x' and resid 148 through 152 removed outlier: 6.343A pdb=" N ARG x 158 " --> pdb=" O ALA x 152 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER x 157 " --> pdb=" O CYS x 173 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR x 167 " --> pdb=" O ALA x 163 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE x 170 " --> pdb=" O MET x 179 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'x' and resid 191 through 195 removed outlier: 5.608A pdb=" N VAL x 200 " --> pdb=" O SER x 195 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR x 209 " --> pdb=" O SER x 205 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEU x 212 " --> pdb=" O LEU x 221 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'x' and resid 233 through 238 removed outlier: 3.825A pdb=" N SER x 234 " --> pdb=" O SER x 254 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ARG x 250 " --> pdb=" O GLU x 238 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE x 262 " --> pdb=" O GLN x 271 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'x' and resid 283 through 287 removed outlier: 4.453A pdb=" N LEU x 291 " --> pdb=" O GLY x 287 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL x 303 " --> pdb=" O ILE x 313 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG x 311 " --> pdb=" O ASP x 305 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'x' and resid 324 through 329 removed outlier: 7.004A pdb=" N MET x 373 " --> pdb=" O SER x 329 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR x 382 " --> pdb=" O SER x 378 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'x' and resid 406 through 411 removed outlier: 5.636A pdb=" N TYR x 416 " --> pdb=" O SER x 411 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER x 425 " --> pdb=" O SER x 421 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'x' and resid 448 through 453 removed outlier: 3.755A pdb=" N GLN x 449 " --> pdb=" O CYS x 462 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU x 458 " --> pdb=" O SER x 453 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ARG x 457 " --> pdb=" O VAL x 473 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR x 467 " --> pdb=" O SER x 463 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'x' and resid 167 through 170 Processing sheet with id= 96, first strand: chain 'x' and resid 259 through 262 removed outlier: 3.857A pdb=" N TYR x 272 " --> pdb=" O ILE x 262 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'x' and resid 300 through 303 Processing sheet with id= 98, first strand: chain 'y' and resid 1 through 5 Processing sheet with id= 99, first strand: chain 'y' and resid 23 through 27 Processing sheet with id=100, first strand: chain 'y' and resid 69 through 73 Processing sheet with id=101, first strand: chain 'y' and resid 114 through 117 Processing sheet with id=102, first strand: chain 'y' and resid 158 through 161 Processing sheet with id=103, first strand: chain '4' and resid 93 through 97 removed outlier: 3.873A pdb=" N ASP 4 137 " --> pdb=" O ILE 4 160 " (cutoff:3.500A) removed outlier: 13.485A pdb=" N THR 4 151 " --> pdb=" O VAL 4 508 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N VAL 4 508 " --> pdb=" O THR 4 151 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU 4 153 " --> pdb=" O THR 4 506 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR 4 506 " --> pdb=" O GLU 4 153 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG 4 502 " --> pdb=" O THR 4 157 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N VAL 4 159 " --> pdb=" O VAL 4 500 " (cutoff:3.500A) removed outlier: 13.802A pdb=" N VAL 4 500 " --> pdb=" O VAL 4 159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU 4 315 " --> pdb=" O LEU 4 509 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain '4' and resid 335 through 340 removed outlier: 4.911A pdb=" N ILE 4 437 " --> pdb=" O VAL 4 340 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain '4' and resid 568 through 572 Processing sheet with id=106, first strand: chain '4' and resid 506 through 511 removed outlier: 6.631A pdb=" N THR 4 506 " --> pdb=" O LEU 4 525 " (cutoff:3.500A) 3881 hydrogen bonds defined for protein. 11517 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2495 hydrogen bonds 4024 hydrogen bond angles 0 basepair planarities 1011 basepair parallelities 1606 stacking parallelities Total time for adding SS restraints: 257.06 Time building geometry restraints manager: 62.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 17753 1.30 - 1.44: 64645 1.44 - 1.57: 78040 1.57 - 1.70: 6642 1.70 - 1.83: 381 Bond restraints: 167461 Sorted by residual: bond pdb=" C2' A2M 11133 " pdb=" C1' A2M 11133 " ideal model delta sigma weight residual 1.305 1.574 -0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C2' A2M 1 807 " pdb=" C1' A2M 1 807 " ideal model delta sigma weight residual 1.305 1.574 -0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C2' A2M 12220 " pdb=" C1' A2M 12220 " ideal model delta sigma weight residual 1.305 1.572 -0.267 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C2' A2M 1 649 " pdb=" C1' A2M 1 649 " ideal model delta sigma weight residual 1.305 1.566 -0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C2' A2M 1 876 " pdb=" C1' A2M 1 876 " ideal model delta sigma weight residual 1.305 1.565 -0.260 2.00e-02 2.50e+03 1.68e+02 ... (remaining 167456 not shown) Histogram of bond angle deviations from ideal: 97.69 - 105.61: 17567 105.61 - 113.53: 101575 113.53 - 121.45: 81305 121.45 - 129.37: 39104 129.37 - 137.29: 2580 Bond angle restraints: 242131 Sorted by residual: angle pdb=" C1' A2M 1 817 " pdb=" N9 A2M 1 817 " pdb=" C8 A2M 1 817 " ideal model delta sigma weight residual 88.50 129.01 -40.51 3.00e+00 1.11e-01 1.82e+02 angle pdb=" C1' A2M 1 807 " pdb=" N9 A2M 1 807 " pdb=" C8 A2M 1 807 " ideal model delta sigma weight residual 88.50 128.73 -40.23 3.00e+00 1.11e-01 1.80e+02 angle pdb=" C1' A2M 11133 " pdb=" N9 A2M 11133 " pdb=" C8 A2M 11133 " ideal model delta sigma weight residual 88.50 128.06 -39.56 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C1' A2M 1 876 " pdb=" N9 A2M 1 876 " pdb=" C8 A2M 1 876 " ideal model delta sigma weight residual 88.50 127.97 -39.47 3.00e+00 1.11e-01 1.73e+02 angle pdb=" C1' A2M 11449 " pdb=" N9 A2M 11449 " pdb=" C8 A2M 11449 " ideal model delta sigma weight residual 88.50 127.89 -39.39 3.00e+00 1.11e-01 1.72e+02 ... (remaining 242126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 97289 35.97 - 71.93: 7532 71.93 - 107.90: 846 107.90 - 143.87: 19 143.87 - 179.83: 47 Dihedral angle restraints: 105733 sinusoidal: 74354 harmonic: 31379 Sorted by residual: dihedral pdb=" O4' U 12822 " pdb=" C1' U 12822 " pdb=" N1 U 12822 " pdb=" C2 U 12822 " ideal model delta sinusoidal sigma weight residual 200.00 38.20 161.80 1 1.50e+01 4.44e-03 8.32e+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 38.87 161.13 1 1.50e+01 4.44e-03 8.30e+01 dihedral pdb=" O4' C 6 59 " pdb=" C1' C 6 59 " pdb=" N1 C 6 59 " pdb=" C2 C 6 59 " ideal model delta sinusoidal sigma weight residual 200.00 39.65 160.35 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 105730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 27317 0.067 - 0.135: 2164 0.135 - 0.202: 140 0.202 - 0.270: 7 0.270 - 0.337: 7 Chirality restraints: 29635 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 -2.73 0.34 2.00e-01 2.50e+01 2.85e+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 -2.72 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C2' A2M 1 807 " pdb=" C3' A2M 1 807 " pdb=" O2' A2M 1 807 " pdb=" C1' A2M 1 807 " both_signs ideal model delta sigma weight residual False -2.39 -2.71 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 29632 not shown) Planarity restraints: 18333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12793 " 0.069 2.00e-02 2.50e+03 6.03e-01 8.17e+03 pdb=" C4' OMG 12793 " 0.439 2.00e-02 2.50e+03 pdb=" O4' OMG 12793 " 0.622 2.00e-02 2.50e+03 pdb=" C3' OMG 12793 " -0.596 2.00e-02 2.50e+03 pdb=" O3' OMG 12793 " -0.652 2.00e-02 2.50e+03 pdb=" C2' OMG 12793 " -0.171 2.00e-02 2.50e+03 pdb=" O2' OMG 12793 " 0.990 2.00e-02 2.50e+03 pdb=" C1' OMG 12793 " 0.219 2.00e-02 2.50e+03 pdb=" N9 OMG 12793 " -0.920 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 1MA 12142 " -0.917 2.00e-02 2.50e+03 5.99e-01 8.08e+03 pdb=" C4' 1MA 12142 " 0.190 2.00e-02 2.50e+03 pdb=" O4' 1MA 12142 " 0.829 2.00e-02 2.50e+03 pdb=" C3' 1MA 12142 " -0.257 2.00e-02 2.50e+03 pdb=" O3' 1MA 12142 " 0.842 2.00e-02 2.50e+03 pdb=" C2' 1MA 12142 " -0.595 2.00e-02 2.50e+03 pdb=" O2' 1MA 12142 " -0.562 2.00e-02 2.50e+03 pdb=" C1' 1MA 12142 " 0.472 2.00e-02 2.50e+03 pdb=" N9 1MA 12142 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 12959 " 0.072 2.00e-02 2.50e+03 5.81e-01 7.59e+03 pdb=" C4' OMC 12959 " 0.417 2.00e-02 2.50e+03 pdb=" O4' OMC 12959 " 0.548 2.00e-02 2.50e+03 pdb=" C3' OMC 12959 " -0.602 2.00e-02 2.50e+03 pdb=" O3' OMC 12959 " -0.633 2.00e-02 2.50e+03 pdb=" C2' OMC 12959 " -0.169 2.00e-02 2.50e+03 pdb=" O2' OMC 12959 " 0.988 2.00e-02 2.50e+03 pdb=" C1' OMC 12959 " 0.235 2.00e-02 2.50e+03 pdb=" N1 OMC 12959 " -0.856 2.00e-02 2.50e+03 ... (remaining 18330 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.57: 1378 2.57 - 3.21: 132326 3.21 - 3.86: 358183 3.86 - 4.50: 482162 4.50 - 5.14: 673068 Nonbonded interactions: 1647117 Sorted by model distance: nonbonded pdb=" O3G GTP m 501 " pdb="MG MG m 502 " model vdw 1.929 2.170 nonbonded pdb=" OP1 A 12138 " pdb="MG MG 13426 " model vdw 1.961 2.170 nonbonded pdb=" OP2 U 12141 " pdb="MG MG 13426 " model vdw 1.969 2.170 nonbonded pdb=" OP1 A 11835 " pdb="MG MG 13437 " model vdw 1.977 2.170 nonbonded pdb=" OP1 C 1 893 " pdb="MG MG 13462 " model vdw 1.980 2.170 ... (remaining 1647112 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=0.21 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 19.350 Check model and map are aligned: 1.700 Set scattering table: 1.010 Process input model: 600.740 Find NCS groups from input model: 3.920 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:10.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 641.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 0.269 167461 Z= 0.311 Angle : 0.676 40.514 242131 Z= 0.318 Chirality : 0.037 0.337 29635 Planarity : 0.018 0.603 18333 Dihedral : 20.489 179.835 85417 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.10 % Allowed : 3.52 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.08), residues: 10648 helix: 1.70 (0.08), residues: 4164 sheet: 0.29 (0.13), residues: 1575 loop : -0.27 (0.08), residues: 4909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP w 114 HIS 0.007 0.001 HIS y 118 PHE 0.034 0.002 PHE F 229 TYR 0.018 0.001 TYR C 194 ARG 0.004 0.000 ARG j 55 *********************** 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 1803 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1794 time to evaluate : 8.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 53 GLU cc_start: 0.6593 (mt-10) cc_final: 0.6355 (mt-10) REVERT: 5 67 GLU cc_start: 0.5505 (pp20) cc_final: 0.5255 (pp20) REVERT: 8 111 GLU cc_start: 0.6334 (tp30) cc_final: 0.6013 (tp30) REVERT: 9 5 ASN cc_start: 0.8735 (m-40) cc_final: 0.8506 (m-40) REVERT: 9 29 GLN cc_start: 0.7789 (tt0) cc_final: 0.7524 (tt0) REVERT: B 67 PHE cc_start: 0.8601 (m-80) cc_final: 0.8340 (m-80) REVERT: B 323 MET cc_start: 0.8428 (ttm) cc_final: 0.8224 (ttp) REVERT: C 67 THR cc_start: 0.8496 (m) cc_final: 0.8172 (m) REVERT: C 93 MET cc_start: 0.8814 (pmm) cc_final: 0.8612 (pmm) REVERT: C 99 MET cc_start: 0.8373 (ptm) cc_final: 0.7687 (ptm) REVERT: D 40 HIS cc_start: 0.8230 (m-70) cc_final: 0.7764 (m-70) REVERT: G 54 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7832 (mt-10) REVERT: G 89 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7596 (mm-30) REVERT: H 129 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7694 (mmm160) REVERT: I 1 MET cc_start: 0.3467 (tmm) cc_final: 0.3220 (tmm) REVERT: I 14 ARG cc_start: 0.7741 (ttt-90) cc_final: 0.7431 (ttt90) REVERT: K 71 GLU cc_start: 0.3316 (tt0) cc_final: 0.3055 (tm-30) REVERT: K 88 PHE cc_start: 0.6169 (m-80) cc_final: 0.5884 (m-80) REVERT: K 329 PHE cc_start: 0.6029 (t80) cc_final: 0.5731 (t80) REVERT: L 18 TRP cc_start: 0.6633 (p-90) cc_final: 0.6384 (p-90) REVERT: L 49 ARG cc_start: 0.8300 (ptt90) cc_final: 0.8037 (mtm-85) REVERT: N 181 ASN cc_start: 0.7836 (m-40) cc_final: 0.7628 (m110) REVERT: S 43 TYR cc_start: 0.7990 (t80) cc_final: 0.7470 (t80) REVERT: T 104 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6897 (tm-30) REVERT: V 97 ASP cc_start: 0.8572 (p0) cc_final: 0.8335 (p0) REVERT: W 104 PHE cc_start: 0.7757 (m-80) cc_final: 0.7520 (m-80) REVERT: W 194 LYS cc_start: 0.6159 (ttmm) cc_final: 0.5881 (mttt) REVERT: X 64 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7399 (mt-10) REVERT: b 191 ASP cc_start: 0.6504 (p0) cc_final: 0.6237 (p0) REVERT: b 370 ASP cc_start: 0.6140 (p0) cc_final: 0.5707 (p0) REVERT: c 36 GLN cc_start: 0.7814 (mt0) cc_final: 0.7581 (mt0) REVERT: d 9 THR cc_start: 0.8793 (m) cc_final: 0.8475 (m) REVERT: e 81 ASP cc_start: 0.7129 (m-30) cc_final: 0.6923 (m-30) REVERT: f 67 MET cc_start: 0.9221 (mtp) cc_final: 0.8977 (mtp) REVERT: g 102 LYS cc_start: 0.7680 (mtmt) cc_final: 0.7433 (mtmm) REVERT: n 262 TYR cc_start: 0.7019 (m-80) cc_final: 0.6815 (m-10) REVERT: o 104 GLU cc_start: 0.7173 (mp0) cc_final: 0.6800 (mp0) REVERT: o 179 TYR cc_start: 0.7492 (m-80) cc_final: 0.7013 (m-80) REVERT: p 85 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7645 (ttp80) REVERT: q 251 GLU cc_start: 0.5871 (tp30) cc_final: 0.5669 (tp30) REVERT: s 17 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7637 (mm-30) REVERT: t 40 LYS cc_start: 0.6835 (ttpp) cc_final: 0.6443 (ptmt) REVERT: t 97 LYS cc_start: 0.5269 (pttm) cc_final: 0.4950 (ptpp) REVERT: t 128 LEU cc_start: 0.4575 (pt) cc_final: 0.4281 (mp) REVERT: u 1 MET cc_start: 0.7912 (ttp) cc_final: 0.7609 (ttp) REVERT: u 24 ASN cc_start: 0.7116 (m-40) cc_final: 0.6913 (m-40) REVERT: v 13 LYS cc_start: 0.6034 (mmtt) cc_final: 0.5633 (mtpp) REVERT: v 78 PHE cc_start: 0.7430 (m-10) cc_final: 0.7096 (m-80) REVERT: v 179 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6372 (mt0) REVERT: v 216 LYS cc_start: 0.6290 (ptmm) cc_final: 0.5845 (tmmm) REVERT: x 124 ARG cc_start: 0.6150 (mmt180) cc_final: 0.5940 (mmt180) REVERT: x 373 MET cc_start: 0.7564 (mmm) cc_final: 0.7222 (mtp) REVERT: x 509 MET cc_start: 0.7830 (mmt) cc_final: 0.7457 (mmt) REVERT: y 62 MET cc_start: 0.8540 (mmm) cc_final: 0.8220 (mmm) REVERT: y 169 ASP cc_start: 0.7731 (m-30) cc_final: 0.7492 (m-30) REVERT: y 201 ASP cc_start: 0.8313 (m-30) cc_final: 0.8108 (m-30) REVERT: 4 401 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.5475 (p90) REVERT: 4 573 GLN cc_start: 0.6730 (mm-40) cc_final: 0.6453 (mm110) outliers start: 9 outliers final: 4 residues processed: 1801 average time/residue: 2.4681 time to fit residues: 6234.9437 Evaluate side-chains 1366 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1361 time to evaluate : 8.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain x residue 424 ASN Chi-restraints excluded: chain 4 residue 200 CYS Chi-restraints excluded: chain 4 residue 401 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1169 optimal weight: 8.9990 chunk 1049 optimal weight: 10.0000 chunk 582 optimal weight: 30.0000 chunk 358 optimal weight: 20.0000 chunk 708 optimal weight: 4.9990 chunk 560 optimal weight: 0.9980 chunk 1085 optimal weight: 8.9990 chunk 420 optimal weight: 9.9990 chunk 660 optimal weight: 0.9990 chunk 807 optimal weight: 3.9990 chunk 1257 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN C 160 GLN D 57 ASN G 61 GLN G 221 ASN H 157 ASN I 99 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN M 56 GLN O 50 ASN O 193 GLN Q 126 GLN Q 136 ASN R 34 GLN R 39 ASN R 68 GLN S 88 HIS S 122 HIS U 25 ASN V 24 ASN W 14 GLN Y 81 GLN Z 78 ASN b 208 HIS b 384 ASN h 68 GLN i 92 ASN k 76 ASN m 165 ASN m 342 GLN n 69 GLN n 144 ASN o 154 ASN p 32 GLN t 300 GLN v 144 GLN v 156 GLN w 201 ASN x 66 GLN z 86 HIS 4 457 ASN 4 551 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 167461 Z= 0.214 Angle : 0.673 18.493 242131 Z= 0.358 Chirality : 0.038 0.292 29635 Planarity : 0.006 0.133 18333 Dihedral : 22.288 179.800 63376 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.17 % Allowed : 9.40 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.08), residues: 10648 helix: 1.95 (0.08), residues: 4167 sheet: 0.26 (0.12), residues: 1579 loop : -0.22 (0.08), residues: 4902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP m 212 HIS 0.007 0.001 HIS P 145 PHE 0.033 0.002 PHE F 229 TYR 0.020 0.002 TYR d 12 ARG 0.006 0.001 ARG m 281 *********************** 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 1599 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1397 time to evaluate : 9.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 5 ASN cc_start: 0.8760 (m-40) cc_final: 0.8491 (m-40) REVERT: 9 29 GLN cc_start: 0.7766 (tt0) cc_final: 0.7517 (mt0) REVERT: B 67 PHE cc_start: 0.8622 (m-80) cc_final: 0.8357 (m-80) REVERT: B 248 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7534 (mttt) REVERT: B 323 MET cc_start: 0.8443 (ttm) cc_final: 0.8181 (ttp) REVERT: B 335 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8296 (tp) REVERT: C 93 MET cc_start: 0.8896 (pmm) cc_final: 0.8686 (pmm) REVERT: C 99 MET cc_start: 0.8410 (ptm) cc_final: 0.7641 (ptm) REVERT: C 338 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7694 (mptp) REVERT: D 40 HIS cc_start: 0.8266 (m-70) cc_final: 0.7782 (m-70) REVERT: F 78 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6763 (mm-30) REVERT: F 170 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: F 218 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7795 (mtm110) REVERT: F 234 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: G 89 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7626 (mm-30) REVERT: I 1 MET cc_start: 0.3585 (tmm) cc_final: 0.3242 (tmm) REVERT: I 14 ARG cc_start: 0.7768 (ttt-90) cc_final: 0.7385 (ttt90) REVERT: I 78 LYS cc_start: 0.7427 (tttp) cc_final: 0.7184 (tttt) REVERT: K 71 GLU cc_start: 0.3694 (tt0) cc_final: 0.3369 (tm-30) REVERT: K 158 LYS cc_start: 0.6767 (OUTLIER) cc_final: 0.6550 (ttmm) REVERT: L 18 TRP cc_start: 0.6690 (p-90) cc_final: 0.6436 (p-90) REVERT: N 181 ASN cc_start: 0.7757 (m-40) cc_final: 0.7543 (m110) REVERT: R 144 GLN cc_start: 0.6814 (OUTLIER) cc_final: 0.6312 (tm130) REVERT: S 43 TYR cc_start: 0.7989 (t80) cc_final: 0.7393 (t80) REVERT: S 158 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7321 (ttpp) REVERT: T 104 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6811 (tm-30) REVERT: T 131 GLN cc_start: 0.8461 (tp40) cc_final: 0.8034 (mp10) REVERT: U 70 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.6235 (tmtp) REVERT: W 104 PHE cc_start: 0.7743 (m-80) cc_final: 0.7530 (m-80) REVERT: W 194 LYS cc_start: 0.6120 (ttmm) cc_final: 0.5846 (mttt) REVERT: Y 55 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6905 (mm-30) REVERT: b 191 ASP cc_start: 0.6501 (p0) cc_final: 0.6223 (p0) REVERT: b 370 ASP cc_start: 0.6284 (p0) cc_final: 0.5831 (p0) REVERT: b 533 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6432 (pt0) REVERT: b 604 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7785 (mtp180) REVERT: c 36 GLN cc_start: 0.7927 (mt0) cc_final: 0.7621 (mt0) REVERT: d 9 THR cc_start: 0.8818 (m) cc_final: 0.8495 (m) REVERT: d 94 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: e 81 ASP cc_start: 0.7187 (m-30) cc_final: 0.6966 (m-30) REVERT: f 67 MET cc_start: 0.9229 (mtp) cc_final: 0.8979 (mtp) REVERT: i 70 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6492 (mtt180) REVERT: m 63 ASP cc_start: 0.7413 (t0) cc_final: 0.7211 (t70) REVERT: m 130 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6523 (ttt90) REVERT: n 174 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6572 (mtm180) REVERT: n 230 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6698 (m-70) REVERT: n 262 TYR cc_start: 0.7027 (m-80) cc_final: 0.6825 (m-10) REVERT: n 375 ILE cc_start: 0.7160 (mt) cc_final: 0.6842 (mt) REVERT: n 430 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: n 441 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5790 (tt) REVERT: o 104 GLU cc_start: 0.7221 (mp0) cc_final: 0.6847 (mp0) REVERT: o 179 TYR cc_start: 0.7527 (m-80) cc_final: 0.7000 (m-80) REVERT: q 265 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6718 (mp) REVERT: r 87 LEU cc_start: 0.8432 (mt) cc_final: 0.8201 (mt) REVERT: s 17 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7768 (mm-30) REVERT: t 23 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.5742 (mmp80) REVERT: t 40 LYS cc_start: 0.6917 (ttpp) cc_final: 0.6599 (ptmm) REVERT: t 130 ARG cc_start: 0.5768 (OUTLIER) cc_final: 0.5242 (mtp85) REVERT: t 293 GLU cc_start: 0.6361 (mt-10) cc_final: 0.6154 (mm-30) REVERT: u 1 MET cc_start: 0.7987 (ttp) cc_final: 0.7661 (ttp) REVERT: v 13 LYS cc_start: 0.6092 (mmtt) cc_final: 0.5677 (mtpp) REVERT: v 78 PHE cc_start: 0.7464 (m-10) cc_final: 0.6960 (m-80) REVERT: v 216 LYS cc_start: 0.6288 (ptmm) cc_final: 0.5827 (tmmm) REVERT: w 124 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6351 (mtpt) REVERT: w 199 MET cc_start: 0.6320 (mtm) cc_final: 0.6005 (ttp) REVERT: x 126 VAL cc_start: 0.6172 (OUTLIER) cc_final: 0.5915 (t) REVERT: x 373 MET cc_start: 0.7631 (mmm) cc_final: 0.7237 (mtp) REVERT: x 395 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7402 (tp) REVERT: y 62 MET cc_start: 0.8537 (mmm) cc_final: 0.8190 (mmm) REVERT: y 169 ASP cc_start: 0.7766 (m-30) cc_final: 0.7515 (m-30) REVERT: 4 401 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.5590 (p90) REVERT: 4 573 GLN cc_start: 0.6670 (mm-40) cc_final: 0.6458 (mm110) outliers start: 202 outliers final: 96 residues processed: 1496 average time/residue: 2.4069 time to fit residues: 5102.4467 Evaluate side-chains 1448 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1325 time to evaluate : 8.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain 9 residue 109 LEU Chi-restraints excluded: chain 9 residue 110 LEU Chi-restraints excluded: chain 9 residue 147 LEU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain S residue 158 LYS Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain b residue 232 MET Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain b residue 537 THR Chi-restraints excluded: chain b residue 604 ARG Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain d residue 24 SER Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain k residue 3 ARG Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain m residue 37 LYS Chi-restraints excluded: chain m residue 124 ASP Chi-restraints excluded: chain m residue 128 LYS Chi-restraints excluded: chain m residue 130 ARG Chi-restraints excluded: chain m residue 311 THR Chi-restraints excluded: chain m residue 312 ASP Chi-restraints excluded: chain n residue 91 THR Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 358 SER Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 430 GLN Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 131 SER Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 399 SER Chi-restraints excluded: chain q residue 415 LEU Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 23 ARG Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain u residue 139 VAL Chi-restraints excluded: chain v residue 124 LEU Chi-restraints excluded: chain v residue 187 GLN Chi-restraints excluded: chain v residue 222 GLU Chi-restraints excluded: chain v residue 234 ILE Chi-restraints excluded: chain v residue 253 LYS Chi-restraints excluded: chain v residue 275 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 36 LYS Chi-restraints excluded: chain w residue 85 SER Chi-restraints excluded: chain w residue 124 LYS Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 308 SER Chi-restraints excluded: chain x residue 395 ILE Chi-restraints excluded: chain x residue 424 ASN Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 331 LYS Chi-restraints excluded: chain 4 residue 401 PHE Chi-restraints excluded: chain 4 residue 465 THR Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 494 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 698 optimal weight: 9.9990 chunk 390 optimal weight: 5.9990 chunk 1046 optimal weight: 20.0000 chunk 856 optimal weight: 5.9990 chunk 346 optimal weight: 30.0000 chunk 1259 optimal weight: 1.9990 chunk 1361 optimal weight: 3.9990 chunk 1122 optimal weight: 5.9990 chunk 1249 optimal weight: 5.9990 chunk 429 optimal weight: 0.9980 chunk 1010 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 HIS D 57 ASN G 221 ASN H 157 ASN I 99 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN M 62 GLN P 10 ASN Q 126 GLN Q 136 ASN R 34 GLN R 39 ASN S 88 HIS S 122 HIS S 138 GLN U 25 ASN V 24 ASN W 14 GLN Y 81 GLN Z 78 ASN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 362 HIS b 384 ASN i 92 ASN k 76 ASN m 165 ASN m 342 GLN n 69 GLN o 154 ASN ** t 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 121 ASN w 201 ASN 4 457 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 167461 Z= 0.212 Angle : 0.665 18.660 242131 Z= 0.356 Chirality : 0.038 0.266 29635 Planarity : 0.006 0.134 18333 Dihedral : 22.255 179.746 63375 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.58 % Allowed : 10.49 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.08), residues: 10648 helix: 1.97 (0.08), residues: 4166 sheet: 0.26 (0.13), residues: 1555 loop : -0.22 (0.08), residues: 4927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP w 114 HIS 0.007 0.001 HIS P 145 PHE 0.032 0.002 PHE F 229 TYR 0.021 0.002 TYR C 194 ARG 0.007 0.001 ARG m 281 *********************** 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 1624 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1384 time to evaluate : 9.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 5 ASN cc_start: 0.8784 (m-40) cc_final: 0.8510 (m-40) REVERT: 9 26 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7897 (mtpt) REVERT: 9 29 GLN cc_start: 0.7756 (tt0) cc_final: 0.7510 (mt0) REVERT: B 67 PHE cc_start: 0.8616 (m-80) cc_final: 0.8357 (m-80) REVERT: B 248 LYS cc_start: 0.7864 (mmtt) cc_final: 0.7534 (mttt) REVERT: B 323 MET cc_start: 0.8429 (ttm) cc_final: 0.8181 (ttp) REVERT: B 335 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8291 (tp) REVERT: C 67 THR cc_start: 0.8506 (m) cc_final: 0.8186 (m) REVERT: C 93 MET cc_start: 0.8879 (pmm) cc_final: 0.8673 (pmm) REVERT: C 99 MET cc_start: 0.8475 (ptm) cc_final: 0.7683 (ptm) REVERT: C 338 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7590 (mptp) REVERT: D 40 HIS cc_start: 0.8306 (m-70) cc_final: 0.7805 (m-70) REVERT: D 254 LYS cc_start: 0.5882 (OUTLIER) cc_final: 0.5484 (mptt) REVERT: F 170 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: F 218 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7775 (mtm110) REVERT: F 234 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: G 89 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7636 (mm-30) REVERT: G 245 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7542 (ttpt) REVERT: I 1 MET cc_start: 0.3597 (tmm) cc_final: 0.3340 (tmm) REVERT: I 14 ARG cc_start: 0.7773 (ttt-90) cc_final: 0.7350 (ttt90) REVERT: I 48 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.6625 (mm110) REVERT: I 78 LYS cc_start: 0.7400 (tttp) cc_final: 0.7152 (tttt) REVERT: K 71 GLU cc_start: 0.3528 (tt0) cc_final: 0.3204 (tm-30) REVERT: K 140 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5693 (mm) REVERT: K 158 LYS cc_start: 0.6787 (OUTLIER) cc_final: 0.6559 (ttmm) REVERT: L 18 TRP cc_start: 0.6690 (p-90) cc_final: 0.6420 (p-90) REVERT: L 49 ARG cc_start: 0.8592 (ptt90) cc_final: 0.8284 (mtm-85) REVERT: N 181 ASN cc_start: 0.7725 (m-40) cc_final: 0.7518 (m110) REVERT: R 144 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6385 (tm130) REVERT: S 43 TYR cc_start: 0.7937 (t80) cc_final: 0.7328 (t80) REVERT: T 104 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6720 (tm-30) REVERT: T 131 GLN cc_start: 0.8469 (tp40) cc_final: 0.8048 (mp10) REVERT: U 70 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.6225 (tmtp) REVERT: V 110 LYS cc_start: 0.8528 (tttp) cc_final: 0.8208 (tptt) REVERT: W 194 LYS cc_start: 0.6027 (ttmm) cc_final: 0.5815 (mttt) REVERT: Y 55 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6879 (mm-30) REVERT: b 191 ASP cc_start: 0.6509 (p0) cc_final: 0.6220 (p0) REVERT: b 370 ASP cc_start: 0.6354 (p0) cc_final: 0.5897 (p0) REVERT: b 396 ARG cc_start: 0.6665 (mtm110) cc_final: 0.6296 (mtm110) REVERT: b 533 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6495 (pt0) REVERT: b 551 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6384 (ttp80) REVERT: b 604 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7831 (mtp180) REVERT: c 36 GLN cc_start: 0.7912 (mt0) cc_final: 0.7605 (mt0) REVERT: d 9 THR cc_start: 0.8793 (m) cc_final: 0.8496 (m) REVERT: f 67 MET cc_start: 0.9228 (mtp) cc_final: 0.8992 (mtp) REVERT: h 64 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: i 70 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6502 (mtt180) REVERT: m 130 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6656 (ttt90) REVERT: n 138 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7499 (tpp) REVERT: n 174 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6582 (mtm180) REVERT: n 230 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.6750 (m-70) REVERT: n 262 TYR cc_start: 0.7117 (m-80) cc_final: 0.6889 (m-10) REVERT: n 375 ILE cc_start: 0.7145 (mt) cc_final: 0.6855 (mt) REVERT: n 430 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: n 441 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5804 (tt) REVERT: o 104 GLU cc_start: 0.7223 (mp0) cc_final: 0.6862 (mp0) REVERT: o 200 MET cc_start: 0.3058 (ppp) cc_final: 0.2540 (ptp) REVERT: p 36 ARG cc_start: 0.7908 (ttm170) cc_final: 0.7702 (mtt-85) REVERT: q 210 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6748 (mm-30) REVERT: q 255 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6656 (mp) REVERT: q 259 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6630 (mttt) REVERT: q 265 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6643 (mp) REVERT: s 4 ARG cc_start: 0.8060 (mmt90) cc_final: 0.7796 (mmt90) REVERT: s 17 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7751 (mm-30) REVERT: t 23 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.5800 (mmp80) REVERT: t 40 LYS cc_start: 0.6925 (ttpp) cc_final: 0.6589 (ptmm) REVERT: t 130 ARG cc_start: 0.5743 (OUTLIER) cc_final: 0.5081 (mtp85) REVERT: u 1 MET cc_start: 0.7958 (ttp) cc_final: 0.7618 (ttp) REVERT: u 117 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7162 (tp30) REVERT: u 118 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7339 (mptp) REVERT: v 13 LYS cc_start: 0.6143 (mmtt) cc_final: 0.5687 (mtpp) REVERT: v 72 MET cc_start: 0.5384 (OUTLIER) cc_final: 0.4772 (mmt) REVERT: v 78 PHE cc_start: 0.7544 (m-10) cc_final: 0.6999 (m-80) REVERT: v 216 LYS cc_start: 0.6289 (ptmm) cc_final: 0.5832 (tmmm) REVERT: w 21 TYR cc_start: 0.7762 (m-80) cc_final: 0.7380 (m-80) REVERT: w 124 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6366 (mtpt) REVERT: x 126 VAL cc_start: 0.6164 (OUTLIER) cc_final: 0.5922 (t) REVERT: x 395 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7474 (tp) REVERT: y 62 MET cc_start: 0.8530 (mmm) cc_final: 0.8197 (mmm) REVERT: 4 158 MET cc_start: 0.7431 (ptm) cc_final: 0.7066 (ptm) REVERT: 4 401 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.5612 (p90) REVERT: 4 573 GLN cc_start: 0.6633 (mm-40) cc_final: 0.6413 (mm110) outliers start: 240 outliers final: 113 residues processed: 1513 average time/residue: 2.4558 time to fit residues: 5252.8547 Evaluate side-chains 1482 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1332 time to evaluate : 8.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 5 residue 78 MET Chi-restraints excluded: chain 9 residue 26 LYS Chi-restraints excluded: chain 9 residue 50 ILE Chi-restraints excluded: chain 9 residue 147 LEU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 245 LYS Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain b residue 232 MET Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain b residue 537 THR Chi-restraints excluded: chain b residue 551 ARG Chi-restraints excluded: chain b residue 604 ARG Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain d residue 24 SER Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain h residue 64 GLU Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain m residue 37 LYS Chi-restraints excluded: chain m residue 124 ASP Chi-restraints excluded: chain m residue 128 LYS Chi-restraints excluded: chain m residue 130 ARG Chi-restraints excluded: chain m residue 311 THR Chi-restraints excluded: chain m residue 312 ASP Chi-restraints excluded: chain n residue 91 THR Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 358 SER Chi-restraints excluded: chain n residue 430 GLN Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 131 SER Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 255 LEU Chi-restraints excluded: chain q residue 259 LYS Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 399 SER Chi-restraints excluded: chain q residue 415 LEU Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 23 ARG Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain u residue 118 LYS Chi-restraints excluded: chain v residue 72 MET Chi-restraints excluded: chain v residue 124 LEU Chi-restraints excluded: chain v residue 187 GLN Chi-restraints excluded: chain v residue 222 GLU Chi-restraints excluded: chain v residue 234 ILE Chi-restraints excluded: chain v residue 253 LYS Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 36 LYS Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 72 THR Chi-restraints excluded: chain w residue 77 VAL Chi-restraints excluded: chain w residue 124 LYS Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 178 THR Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 308 SER Chi-restraints excluded: chain x residue 395 ILE Chi-restraints excluded: chain x residue 424 ASN Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 331 LYS Chi-restraints excluded: chain 4 residue 401 PHE Chi-restraints excluded: chain 4 residue 465 THR Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 494 GLU Chi-restraints excluded: chain 4 residue 516 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1244 optimal weight: 20.0000 chunk 947 optimal weight: 7.9990 chunk 653 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 601 optimal weight: 0.4980 chunk 846 optimal weight: 0.9990 chunk 1264 optimal weight: 9.9990 chunk 1338 optimal weight: 9.9990 chunk 660 optimal weight: 2.9990 chunk 1198 optimal weight: 8.9990 chunk 360 optimal weight: 40.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 HIS G 221 ASN H 157 ASN H 163 GLN I 99 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN M 62 GLN P 10 ASN Q 126 GLN Q 136 ASN R 34 GLN R 39 ASN S 88 HIS S 122 HIS S 138 GLN U 25 ASN V 24 ASN W 14 GLN Y 81 GLN Z 78 ASN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 384 ASN i 92 ASN k 76 ASN m 165 ASN m 342 GLN o 154 ASN v 121 ASN w 201 ASN x 17 GLN x 208 ASN 4 457 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 167461 Z= 0.234 Angle : 0.692 18.728 242131 Z= 0.369 Chirality : 0.039 0.273 29635 Planarity : 0.006 0.135 18333 Dihedral : 22.275 179.602 63375 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.88 % Allowed : 11.18 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.08), residues: 10648 helix: 1.90 (0.08), residues: 4174 sheet: 0.25 (0.13), residues: 1531 loop : -0.23 (0.08), residues: 4943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP w 114 HIS 0.007 0.001 HIS P 145 PHE 0.033 0.002 PHE F 229 TYR 0.022 0.002 TYR I 85 ARG 0.009 0.001 ARG m 281 *********************** 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 1641 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1373 time to evaluate : 9.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 5 ASN cc_start: 0.8835 (m-40) cc_final: 0.8538 (m-40) REVERT: 9 26 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7909 (mtpt) REVERT: 9 29 GLN cc_start: 0.7770 (tt0) cc_final: 0.7517 (mt0) REVERT: B 67 PHE cc_start: 0.8592 (m-80) cc_final: 0.8344 (m-80) REVERT: B 248 LYS cc_start: 0.7885 (mmtt) cc_final: 0.7536 (mttt) REVERT: B 323 MET cc_start: 0.8435 (ttm) cc_final: 0.8204 (ttp) REVERT: B 335 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8314 (tp) REVERT: C 67 THR cc_start: 0.8524 (m) cc_final: 0.8206 (m) REVERT: C 93 MET cc_start: 0.8891 (pmm) cc_final: 0.8667 (pmm) REVERT: C 99 MET cc_start: 0.8532 (ptm) cc_final: 0.7685 (ptm) REVERT: C 338 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7659 (mptp) REVERT: D 40 HIS cc_start: 0.8284 (m-70) cc_final: 0.7755 (m-70) REVERT: D 254 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5522 (mptt) REVERT: F 170 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: F 218 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7772 (mtm180) REVERT: F 234 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: G 89 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7640 (mm-30) REVERT: I 1 MET cc_start: 0.3605 (tmm) cc_final: 0.3292 (tmm) REVERT: I 14 ARG cc_start: 0.7764 (ttt-90) cc_final: 0.7306 (ttt90) REVERT: I 48 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6544 (mm110) REVERT: I 78 LYS cc_start: 0.7379 (tttp) cc_final: 0.7127 (tttt) REVERT: K 140 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5677 (mm) REVERT: K 158 LYS cc_start: 0.6775 (OUTLIER) cc_final: 0.6504 (ttmm) REVERT: L 18 TRP cc_start: 0.6708 (p-90) cc_final: 0.6428 (p-90) REVERT: L 49 ARG cc_start: 0.8628 (ptt90) cc_final: 0.8347 (mtm-85) REVERT: P 126 ARG cc_start: 0.7717 (mtt-85) cc_final: 0.7478 (mtt180) REVERT: P 152 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: R 144 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6512 (tm130) REVERT: S 43 TYR cc_start: 0.7962 (t80) cc_final: 0.7335 (t80) REVERT: T 104 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6789 (tm-30) REVERT: T 131 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8056 (mp10) REVERT: U 70 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.6250 (tmtp) REVERT: W 38 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5318 (tpt-90) REVERT: W 194 LYS cc_start: 0.6079 (ttmm) cc_final: 0.5820 (mttt) REVERT: Y 55 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6869 (mm-30) REVERT: b 191 ASP cc_start: 0.6512 (p0) cc_final: 0.6250 (p0) REVERT: b 370 ASP cc_start: 0.6496 (p0) cc_final: 0.6032 (p0) REVERT: b 533 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6499 (pt0) REVERT: b 551 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6356 (ttp80) REVERT: b 604 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7832 (mtp180) REVERT: b 610 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7353 (ptm160) REVERT: b 643 LYS cc_start: 0.7383 (tptp) cc_final: 0.7059 (tptm) REVERT: c 36 GLN cc_start: 0.7911 (mt0) cc_final: 0.7622 (mt0) REVERT: d 9 THR cc_start: 0.8806 (m) cc_final: 0.8475 (m) REVERT: d 94 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: f 67 MET cc_start: 0.9224 (mtp) cc_final: 0.8980 (mtp) REVERT: i 70 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.6469 (mtt180) REVERT: m 130 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6641 (ttt90) REVERT: n 13 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7654 (ttp80) REVERT: n 138 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7497 (ttp) REVERT: n 174 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6566 (mtm180) REVERT: n 230 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.6765 (m-70) REVERT: n 262 TYR cc_start: 0.7130 (m-80) cc_final: 0.6885 (m-10) REVERT: n 375 ILE cc_start: 0.7146 (mt) cc_final: 0.6827 (mt) REVERT: n 430 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: n 441 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5837 (tt) REVERT: o 104 GLU cc_start: 0.7185 (mp0) cc_final: 0.6843 (mp0) REVERT: q 210 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6714 (mm-30) REVERT: q 259 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6664 (mttt) REVERT: q 265 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6686 (mp) REVERT: s 4 ARG cc_start: 0.8059 (mmt90) cc_final: 0.7713 (mmt90) REVERT: s 17 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7796 (mm-30) REVERT: t 23 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.5836 (mmp80) REVERT: t 40 LYS cc_start: 0.6913 (ttpp) cc_final: 0.6570 (ptmm) REVERT: t 130 ARG cc_start: 0.5822 (OUTLIER) cc_final: 0.5139 (mtp85) REVERT: t 217 LYS cc_start: 0.5630 (tttt) cc_final: 0.5413 (tttp) REVERT: u 1 MET cc_start: 0.7948 (ttp) cc_final: 0.7601 (ttp) REVERT: u 98 GLU cc_start: 0.6836 (tt0) cc_final: 0.6610 (tt0) REVERT: u 118 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7346 (mptp) REVERT: v 13 LYS cc_start: 0.6127 (mmtt) cc_final: 0.5666 (mtpp) REVERT: v 72 MET cc_start: 0.5389 (OUTLIER) cc_final: 0.4966 (mtt) REVERT: v 78 PHE cc_start: 0.7482 (m-10) cc_final: 0.7024 (m-80) REVERT: v 216 LYS cc_start: 0.6269 (ptmm) cc_final: 0.5780 (tmmm) REVERT: v 222 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.6206 (tp30) REVERT: w 21 TYR cc_start: 0.7790 (m-80) cc_final: 0.7359 (m-80) REVERT: w 124 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6368 (mtpt) REVERT: x 126 VAL cc_start: 0.6190 (OUTLIER) cc_final: 0.5960 (t) REVERT: y 62 MET cc_start: 0.8520 (mmm) cc_final: 0.8213 (mmm) REVERT: 4 246 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7076 (ttm170) REVERT: 4 401 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.5640 (p90) REVERT: 4 573 GLN cc_start: 0.6631 (mm-40) cc_final: 0.6393 (mm110) outliers start: 268 outliers final: 130 residues processed: 1529 average time/residue: 2.5073 time to fit residues: 5470.5808 Evaluate side-chains 1500 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1330 time to evaluate : 9.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 5 residue 78 MET Chi-restraints excluded: chain 9 residue 26 LYS Chi-restraints excluded: chain 9 residue 147 LEU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 208 GLU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 449 ILE Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain b residue 537 THR Chi-restraints excluded: chain b residue 551 ARG Chi-restraints excluded: chain b residue 604 ARG Chi-restraints excluded: chain b residue 610 ARG Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain d residue 24 SER Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain m residue 37 LYS Chi-restraints excluded: chain m residue 128 LYS Chi-restraints excluded: chain m residue 130 ARG Chi-restraints excluded: chain m residue 311 THR Chi-restraints excluded: chain n residue 13 ARG Chi-restraints excluded: chain n residue 91 THR Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 358 SER Chi-restraints excluded: chain n residue 430 GLN Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 131 SER Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 259 LYS Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 399 SER Chi-restraints excluded: chain q residue 415 LEU Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 23 ARG Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 118 LYS Chi-restraints excluded: chain u residue 139 VAL Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain v residue 72 MET Chi-restraints excluded: chain v residue 187 GLN Chi-restraints excluded: chain v residue 222 GLU Chi-restraints excluded: chain v residue 234 ILE Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 36 LYS Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 77 VAL Chi-restraints excluded: chain w residue 124 LYS Chi-restraints excluded: chain w residue 164 ASP Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain x residue 32 VAL Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 265 THR Chi-restraints excluded: chain x residue 308 SER Chi-restraints excluded: chain x residue 393 LYS Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 424 ASN Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 331 LYS Chi-restraints excluded: chain 4 residue 401 PHE Chi-restraints excluded: chain 4 residue 465 THR Chi-restraints excluded: chain 4 residue 466 LEU Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 494 GLU Chi-restraints excluded: chain 4 residue 516 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1114 optimal weight: 30.0000 chunk 759 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 996 optimal weight: 8.9990 chunk 552 optimal weight: 10.0000 chunk 1142 optimal weight: 9.9990 chunk 925 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 683 optimal weight: 0.9980 chunk 1201 optimal weight: 9.9990 chunk 337 optimal weight: 40.0000 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN G 221 ASN H 157 ASN H 163 GLN I 99 ASN I 106 GLN J 68 HIS ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN M 62 GLN P 10 ASN Q 126 GLN Q 136 ASN R 39 ASN S 88 HIS S 122 HIS S 138 GLN T 54 HIS U 25 ASN V 24 ASN W 14 GLN Y 81 GLN Z 78 ASN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 152 GLN b 384 ASN i 92 ASN k 76 ASN m 165 ASN m 342 GLN o 154 ASN p 32 GLN t 303 ASN v 121 ASN w 201 ASN x 208 ASN x 314 ASN z 86 HIS 4 457 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 167461 Z= 0.249 Angle : 0.704 19.006 242131 Z= 0.374 Chirality : 0.040 0.288 29635 Planarity : 0.006 0.136 18333 Dihedral : 22.288 179.437 63375 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.13 % Allowed : 11.71 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.08), residues: 10648 helix: 1.85 (0.08), residues: 4171 sheet: 0.18 (0.13), residues: 1544 loop : -0.25 (0.08), residues: 4933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP w 114 HIS 0.007 0.001 HIS P 145 PHE 0.033 0.002 PHE F 229 TYR 0.023 0.002 TYR I 85 ARG 0.008 0.001 ARG m 281 *********************** 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 1651 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1360 time to evaluate : 9.070 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 5 ASN cc_start: 0.8776 (m-40) cc_final: 0.8476 (m-40) REVERT: 9 26 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7904 (mtpt) REVERT: 9 29 GLN cc_start: 0.7770 (tt0) cc_final: 0.7541 (mt0) REVERT: B 67 PHE cc_start: 0.8598 (m-80) cc_final: 0.8316 (m-80) REVERT: B 248 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7510 (mttt) REVERT: B 323 MET cc_start: 0.8428 (ttm) cc_final: 0.8200 (ttp) REVERT: C 67 THR cc_start: 0.8529 (m) cc_final: 0.8214 (m) REVERT: C 93 MET cc_start: 0.8896 (pmm) cc_final: 0.8693 (pmm) REVERT: C 99 MET cc_start: 0.8537 (ptm) cc_final: 0.7678 (ptm) REVERT: C 338 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7651 (mptp) REVERT: D 40 HIS cc_start: 0.8271 (m-70) cc_final: 0.7714 (m-70) REVERT: D 254 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5536 (mptt) REVERT: F 170 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: F 218 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7775 (mtm110) REVERT: F 234 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: G 89 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7646 (mm-30) REVERT: I 1 MET cc_start: 0.3739 (tmm) cc_final: 0.3364 (tmm) REVERT: I 14 ARG cc_start: 0.7767 (ttt-90) cc_final: 0.7306 (ttt90) REVERT: I 78 LYS cc_start: 0.7389 (tttp) cc_final: 0.7132 (tttt) REVERT: K 140 LEU cc_start: 0.6027 (OUTLIER) cc_final: 0.5691 (mm) REVERT: K 158 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6517 (ttmm) REVERT: L 18 TRP cc_start: 0.6723 (p-90) cc_final: 0.6435 (p-90) REVERT: L 49 ARG cc_start: 0.8612 (ptt90) cc_final: 0.8322 (mtm-85) REVERT: P 131 ARG cc_start: 0.8211 (mmt180) cc_final: 0.7956 (mmt180) REVERT: P 152 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: Q 3 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8158 (mt) REVERT: R 144 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6559 (tm130) REVERT: S 43 TYR cc_start: 0.7960 (t80) cc_final: 0.7384 (t80) REVERT: T 104 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6907 (tm-30) REVERT: T 131 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8072 (mp10) REVERT: U 70 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.6252 (tmtp) REVERT: W 38 ARG cc_start: 0.6152 (OUTLIER) cc_final: 0.5530 (tpt-90) REVERT: W 194 LYS cc_start: 0.6085 (ttmm) cc_final: 0.5845 (mttt) REVERT: X 70 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: Y 55 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6859 (mm-30) REVERT: b 370 ASP cc_start: 0.6614 (p0) cc_final: 0.6131 (p0) REVERT: b 396 ARG cc_start: 0.6623 (mtm110) cc_final: 0.6280 (mtm110) REVERT: b 551 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6360 (ttp80) REVERT: b 610 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7334 (ptm160) REVERT: c 36 GLN cc_start: 0.7908 (mt0) cc_final: 0.7634 (mt0) REVERT: d 9 THR cc_start: 0.8815 (m) cc_final: 0.8491 (m) REVERT: d 94 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: f 67 MET cc_start: 0.9225 (mtp) cc_final: 0.8983 (mtp) REVERT: i 70 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6463 (mtt180) REVERT: k 5 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7948 (pp) REVERT: m 63 ASP cc_start: 0.7470 (t0) cc_final: 0.7240 (t70) REVERT: m 130 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6632 (ttt90) REVERT: n 13 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7718 (ttp80) REVERT: n 138 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7509 (ttp) REVERT: n 174 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6581 (mtm180) REVERT: n 230 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.6711 (m-70) REVERT: n 262 TYR cc_start: 0.7107 (m-80) cc_final: 0.6856 (m-10) REVERT: n 375 ILE cc_start: 0.7212 (mt) cc_final: 0.7002 (mt) REVERT: n 430 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: n 441 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5880 (tt) REVERT: o 104 GLU cc_start: 0.7181 (mp0) cc_final: 0.6857 (mp0) REVERT: q 259 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6690 (mttt) REVERT: q 263 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6765 (mtm-85) REVERT: q 265 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6722 (mp) REVERT: r 23 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7544 (mtt180) REVERT: r 41 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7555 (mptt) REVERT: s 4 ARG cc_start: 0.7995 (mmt90) cc_final: 0.7706 (mmt90) REVERT: s 17 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7799 (mm-30) REVERT: t 23 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.5836 (mmp80) REVERT: t 33 ARG cc_start: 0.6359 (mtm110) cc_final: 0.6048 (mtm180) REVERT: t 40 LYS cc_start: 0.6915 (ttpp) cc_final: 0.6568 (ptmm) REVERT: t 130 ARG cc_start: 0.5934 (OUTLIER) cc_final: 0.5114 (mtp85) REVERT: t 217 LYS cc_start: 0.5639 (tttt) cc_final: 0.5420 (tttp) REVERT: u 1 MET cc_start: 0.7946 (ttp) cc_final: 0.7501 (ttp) REVERT: u 98 GLU cc_start: 0.6843 (tt0) cc_final: 0.6597 (tt0) REVERT: u 117 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7172 (tp30) REVERT: u 118 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7348 (mptp) REVERT: v 13 LYS cc_start: 0.6241 (mmtt) cc_final: 0.5712 (mtpp) REVERT: v 29 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7324 (mt0) REVERT: v 72 MET cc_start: 0.5404 (OUTLIER) cc_final: 0.4827 (mmt) REVERT: v 78 PHE cc_start: 0.7546 (m-80) cc_final: 0.7108 (m-80) REVERT: v 90 MET cc_start: 0.5858 (mpp) cc_final: 0.5580 (mtm) REVERT: v 216 LYS cc_start: 0.6242 (ptmm) cc_final: 0.5744 (tmmm) REVERT: v 222 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.6238 (tp30) REVERT: v 258 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.5974 (tppt) REVERT: w 21 TYR cc_start: 0.7798 (m-80) cc_final: 0.7367 (m-80) REVERT: w 38 ASP cc_start: 0.3461 (OUTLIER) cc_final: 0.2706 (p0) REVERT: w 124 LYS cc_start: 0.6719 (OUTLIER) cc_final: 0.6361 (mtpt) REVERT: w 196 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6971 (mtm110) REVERT: x 126 VAL cc_start: 0.6230 (OUTLIER) cc_final: 0.6005 (t) REVERT: y 62 MET cc_start: 0.8540 (mmm) cc_final: 0.8245 (mmm) REVERT: 4 29 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6634 (mtt180) REVERT: 4 246 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7028 (ttm170) REVERT: 4 573 GLN cc_start: 0.6590 (mm-40) cc_final: 0.6335 (mm110) outliers start: 291 outliers final: 157 residues processed: 1532 average time/residue: 2.4401 time to fit residues: 5294.8610 Evaluate side-chains 1527 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1324 time to evaluate : 9.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 5 residue 78 MET Chi-restraints excluded: chain 8 residue 138 SER Chi-restraints excluded: chain 9 residue 26 LYS Chi-restraints excluded: chain 9 residue 50 ILE Chi-restraints excluded: chain 9 residue 147 LEU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 182 ILE Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain b residue 4 SER Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 331 VAL Chi-restraints excluded: chain b residue 449 ILE Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain b residue 537 THR Chi-restraints excluded: chain b residue 551 ARG Chi-restraints excluded: chain b residue 610 ARG Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain d residue 24 SER Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain m residue 37 LYS Chi-restraints excluded: chain m residue 128 LYS Chi-restraints excluded: chain m residue 130 ARG Chi-restraints excluded: chain m residue 311 THR Chi-restraints excluded: chain n residue 13 ARG Chi-restraints excluded: chain n residue 91 THR Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 358 SER Chi-restraints excluded: chain n residue 430 GLN Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain n residue 442 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 131 SER Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 259 LYS Chi-restraints excluded: chain q residue 263 ARG Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 399 SER Chi-restraints excluded: chain q residue 415 LEU Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain r residue 23 ARG Chi-restraints excluded: chain r residue 41 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 23 ARG Chi-restraints excluded: chain t residue 85 LYS Chi-restraints excluded: chain t residue 93 ILE Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain t residue 303 ASN Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain u residue 118 LYS Chi-restraints excluded: chain u residue 139 VAL Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 72 MET Chi-restraints excluded: chain v residue 187 GLN Chi-restraints excluded: chain v residue 222 GLU Chi-restraints excluded: chain v residue 234 ILE Chi-restraints excluded: chain v residue 258 LYS Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 38 ASP Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 72 THR Chi-restraints excluded: chain w residue 77 VAL Chi-restraints excluded: chain w residue 85 SER Chi-restraints excluded: chain w residue 124 LYS Chi-restraints excluded: chain w residue 164 ASP Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 32 VAL Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 265 THR Chi-restraints excluded: chain x residue 308 SER Chi-restraints excluded: chain x residue 393 LYS Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 424 ASN Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain 4 residue 29 ARG Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 331 LYS Chi-restraints excluded: chain 4 residue 401 PHE Chi-restraints excluded: chain 4 residue 465 THR Chi-restraints excluded: chain 4 residue 466 LEU Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 494 GLU Chi-restraints excluded: chain 4 residue 514 VAL Chi-restraints excluded: chain 4 residue 516 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 450 optimal weight: 2.9990 chunk 1205 optimal weight: 7.9990 chunk 264 optimal weight: 10.0000 chunk 786 optimal weight: 9.9990 chunk 330 optimal weight: 10.0000 chunk 1340 optimal weight: 20.0000 chunk 1112 optimal weight: 6.9990 chunk 620 optimal weight: 4.9990 chunk 111 optimal weight: 30.0000 chunk 443 optimal weight: 0.0060 chunk 703 optimal weight: 9.9990 overall best weight: 4.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 221 ASN H 157 ASN H 163 GLN I 99 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN O 122 GLN P 10 ASN Q 126 GLN Q 136 ASN R 34 GLN S 88 HIS S 122 HIS S 138 GLN S 142 GLN U 25 ASN V 24 ASN W 14 GLN X 85 GLN Y 81 GLN Z 78 ASN Z 106 GLN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 384 ASN i 92 ASN k 76 ASN m 165 ASN m 342 GLN n 69 GLN o 154 ASN v 121 ASN ** w 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 314 ASN x 387 ASN 4 457 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 167461 Z= 0.247 Angle : 0.703 18.920 242131 Z= 0.374 Chirality : 0.040 0.306 29635 Planarity : 0.006 0.136 18333 Dihedral : 22.289 179.383 63375 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.92 % Allowed : 12.28 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.08), residues: 10648 helix: 1.82 (0.08), residues: 4184 sheet: 0.17 (0.13), residues: 1544 loop : -0.26 (0.08), residues: 4920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP w 114 HIS 0.007 0.001 HIS P 145 PHE 0.033 0.002 PHE F 229 TYR 0.023 0.002 TYR I 85 ARG 0.008 0.001 ARG m 281 *********************** 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 1625 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1353 time to evaluate : 9.219 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 5 ASN cc_start: 0.8828 (m-40) cc_final: 0.8523 (m-40) REVERT: 9 26 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7909 (mtpt) REVERT: 9 29 GLN cc_start: 0.7781 (tt0) cc_final: 0.7554 (mt0) REVERT: B 67 PHE cc_start: 0.8600 (m-80) cc_final: 0.8317 (m-80) REVERT: B 248 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7536 (mttt) REVERT: B 323 MET cc_start: 0.8430 (ttm) cc_final: 0.8205 (ttp) REVERT: B 335 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8317 (tp) REVERT: C 67 THR cc_start: 0.8533 (m) cc_final: 0.8216 (m) REVERT: C 99 MET cc_start: 0.8544 (ptm) cc_final: 0.7663 (ptm) REVERT: C 337 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6678 (mt-10) REVERT: C 338 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7668 (mptp) REVERT: D 40 HIS cc_start: 0.8272 (m-70) cc_final: 0.7719 (m-70) REVERT: D 254 LYS cc_start: 0.6019 (OUTLIER) cc_final: 0.5529 (mptt) REVERT: F 170 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: F 218 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7777 (mtm180) REVERT: F 234 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: G 89 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7653 (mm-30) REVERT: G 245 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7576 (ttpt) REVERT: I 14 ARG cc_start: 0.7775 (ttt-90) cc_final: 0.7300 (ttt90) REVERT: I 78 LYS cc_start: 0.7388 (tttp) cc_final: 0.7126 (tttt) REVERT: K 140 LEU cc_start: 0.6032 (OUTLIER) cc_final: 0.5687 (mm) REVERT: K 158 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6521 (ttmm) REVERT: L 18 TRP cc_start: 0.6719 (p-90) cc_final: 0.6432 (p-90) REVERT: L 49 ARG cc_start: 0.8615 (ptt90) cc_final: 0.8327 (mtm-85) REVERT: P 152 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: P 167 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7678 (ptp-170) REVERT: Q 3 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8191 (mt) REVERT: R 144 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6544 (tm130) REVERT: S 43 TYR cc_start: 0.7960 (t80) cc_final: 0.7384 (t80) REVERT: T 104 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6952 (tm-30) REVERT: T 131 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: U 70 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.6254 (tmtp) REVERT: W 38 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.5524 (tpt-90) REVERT: W 143 TYR cc_start: 0.8045 (m-80) cc_final: 0.7839 (m-80) REVERT: W 194 LYS cc_start: 0.6103 (ttmm) cc_final: 0.5858 (mttt) REVERT: W 235 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5575 (mmm) REVERT: X 70 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: Y 55 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6853 (mm-30) REVERT: b 370 ASP cc_start: 0.6701 (p0) cc_final: 0.6224 (p0) REVERT: b 396 ARG cc_start: 0.6556 (mtm110) cc_final: 0.6184 (mtm110) REVERT: b 551 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6386 (ttp80) REVERT: b 588 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.6919 (mtp180) REVERT: b 610 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7306 (ptm160) REVERT: c 36 GLN cc_start: 0.7934 (mt0) cc_final: 0.7580 (mt0) REVERT: d 9 THR cc_start: 0.8805 (m) cc_final: 0.8479 (m) REVERT: d 94 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: f 67 MET cc_start: 0.9224 (mtp) cc_final: 0.8986 (mtp) REVERT: i 70 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.6462 (mtt180) REVERT: k 5 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7935 (pp) REVERT: m 130 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6580 (ttt90) REVERT: n 13 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7716 (ttp80) REVERT: n 138 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7514 (ttp) REVERT: n 174 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6570 (mtm180) REVERT: n 230 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.6783 (m-70) REVERT: n 262 TYR cc_start: 0.7052 (m-80) cc_final: 0.6802 (m-10) REVERT: n 375 ILE cc_start: 0.7219 (mt) cc_final: 0.7012 (mt) REVERT: n 441 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5886 (tt) REVERT: o 102 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.5819 (m-80) REVERT: o 104 GLU cc_start: 0.7307 (mp0) cc_final: 0.6918 (mp0) REVERT: p 24 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7301 (mtm-85) REVERT: p 36 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.7669 (mtt-85) REVERT: q 259 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6738 (mttt) REVERT: q 263 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6765 (mtm-85) REVERT: q 265 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6722 (mp) REVERT: r 41 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7552 (mptt) REVERT: s 4 ARG cc_start: 0.7994 (mmt90) cc_final: 0.7732 (mmt90) REVERT: s 17 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7805 (mm-30) REVERT: t 23 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.5811 (mmp80) REVERT: t 33 ARG cc_start: 0.6365 (mtm110) cc_final: 0.6053 (mtm180) REVERT: t 40 LYS cc_start: 0.6904 (ttpp) cc_final: 0.6551 (ptmm) REVERT: t 130 ARG cc_start: 0.5937 (OUTLIER) cc_final: 0.5236 (mtp85) REVERT: t 217 LYS cc_start: 0.5642 (tttt) cc_final: 0.5418 (tttp) REVERT: u 1 MET cc_start: 0.7949 (ttp) cc_final: 0.7491 (ttp) REVERT: u 98 GLU cc_start: 0.6839 (tt0) cc_final: 0.6591 (tt0) REVERT: u 117 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7175 (tp30) REVERT: u 118 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7353 (mptp) REVERT: v 13 LYS cc_start: 0.6243 (mmtt) cc_final: 0.5714 (mtpp) REVERT: v 78 PHE cc_start: 0.7539 (m-80) cc_final: 0.7109 (m-80) REVERT: v 216 LYS cc_start: 0.6209 (ptmm) cc_final: 0.5707 (tmmm) REVERT: v 222 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6231 (tp30) REVERT: v 258 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.6047 (tppt) REVERT: w 21 TYR cc_start: 0.7807 (m-80) cc_final: 0.7357 (m-80) REVERT: w 124 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6365 (mtpt) REVERT: w 196 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6979 (mtm110) REVERT: x 126 VAL cc_start: 0.6125 (OUTLIER) cc_final: 0.5920 (t) REVERT: x 395 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7530 (tp) REVERT: x 424 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.7691 (m-40) REVERT: y 62 MET cc_start: 0.8541 (mmm) cc_final: 0.8253 (mmm) REVERT: 4 246 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7046 (ttm170) REVERT: 4 573 GLN cc_start: 0.6454 (mm-40) cc_final: 0.6192 (mm110) outliers start: 272 outliers final: 159 residues processed: 1512 average time/residue: 2.3907 time to fit residues: 5123.4149 Evaluate side-chains 1534 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1324 time to evaluate : 8.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 5 residue 78 MET Chi-restraints excluded: chain 8 residue 138 SER Chi-restraints excluded: chain 9 residue 26 LYS Chi-restraints excluded: chain 9 residue 147 LEU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 245 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 167 ARG Chi-restraints excluded: chain P residue 182 ILE Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 235 MET Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 4 SER Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 449 ILE Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain b residue 537 THR Chi-restraints excluded: chain b residue 551 ARG Chi-restraints excluded: chain b residue 588 ARG Chi-restraints excluded: chain b residue 610 ARG Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain d residue 24 SER Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain m residue 37 LYS Chi-restraints excluded: chain m residue 128 LYS Chi-restraints excluded: chain m residue 130 ARG Chi-restraints excluded: chain m residue 311 THR Chi-restraints excluded: chain n residue 13 ARG Chi-restraints excluded: chain n residue 91 THR Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 358 SER Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain n residue 442 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 131 SER Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 259 LYS Chi-restraints excluded: chain q residue 263 ARG Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 399 SER Chi-restraints excluded: chain q residue 415 LEU Chi-restraints excluded: chain q residue 446 THR Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain r residue 41 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 23 ARG Chi-restraints excluded: chain t residue 85 LYS Chi-restraints excluded: chain t residue 93 ILE Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain u residue 118 LYS Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 187 GLN Chi-restraints excluded: chain v residue 222 GLU Chi-restraints excluded: chain v residue 234 ILE Chi-restraints excluded: chain v residue 258 LYS Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 36 LYS Chi-restraints excluded: chain w residue 49 LYS Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 77 VAL Chi-restraints excluded: chain w residue 124 LYS Chi-restraints excluded: chain w residue 163 ASP Chi-restraints excluded: chain w residue 164 ASP Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 32 VAL Chi-restraints excluded: chain x residue 126 VAL Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 308 SER Chi-restraints excluded: chain x residue 393 LYS Chi-restraints excluded: chain x residue 395 ILE Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 424 ASN Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 331 LYS Chi-restraints excluded: chain 4 residue 401 PHE Chi-restraints excluded: chain 4 residue 465 THR Chi-restraints excluded: chain 4 residue 466 LEU Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 494 GLU Chi-restraints excluded: chain 4 residue 514 VAL Chi-restraints excluded: chain 4 residue 516 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1291 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 763 optimal weight: 5.9990 chunk 978 optimal weight: 7.9990 chunk 758 optimal weight: 4.9990 chunk 1128 optimal weight: 9.9990 chunk 748 optimal weight: 0.0030 chunk 1334 optimal weight: 6.9990 chunk 835 optimal weight: 5.9990 chunk 813 optimal weight: 10.0000 chunk 616 optimal weight: 7.9990 overall best weight: 4.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 221 ASN H 157 ASN H 163 GLN I 99 ASN I 106 GLN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN P 10 ASN Q 126 GLN Q 136 ASN R 34 GLN S 88 HIS S 122 HIS S 138 GLN S 142 GLN U 25 ASN V 24 ASN W 14 GLN Y 81 GLN Z 78 ASN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 384 ASN h 62 GLN i 92 ASN k 76 ASN m 165 ASN m 342 GLN o 154 ASN v 121 ASN w 8 ASN x 314 ASN z 86 HIS 4 255 ASN 4 457 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 167461 Z= 0.256 Angle : 0.713 19.060 242131 Z= 0.379 Chirality : 0.040 0.367 29635 Planarity : 0.006 0.137 18333 Dihedral : 22.296 179.325 63375 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.09 % Allowed : 12.35 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.08), residues: 10648 helix: 1.79 (0.08), residues: 4183 sheet: 0.14 (0.12), residues: 1544 loop : -0.27 (0.08), residues: 4921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP w 114 HIS 0.008 0.001 HIS C 311 PHE 0.033 0.002 PHE F 229 TYR 0.023 0.002 TYR I 85 ARG 0.009 0.001 ARG m 281 *********************** 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 1637 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1349 time to evaluate : 8.413 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 5 ASN cc_start: 0.8819 (m-40) cc_final: 0.8517 (m-40) REVERT: 9 26 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7895 (mtpt) REVERT: 9 29 GLN cc_start: 0.7782 (tt0) cc_final: 0.7518 (mt0) REVERT: B 67 PHE cc_start: 0.8603 (m-80) cc_final: 0.8320 (m-80) REVERT: B 248 LYS cc_start: 0.7878 (mmtt) cc_final: 0.7508 (mttt) REVERT: B 323 MET cc_start: 0.8438 (ttm) cc_final: 0.8222 (ttp) REVERT: B 335 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8320 (tp) REVERT: C 67 THR cc_start: 0.8551 (m) cc_final: 0.8239 (m) REVERT: C 99 MET cc_start: 0.8558 (ptm) cc_final: 0.7663 (ptm) REVERT: C 338 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7671 (mptp) REVERT: D 40 HIS cc_start: 0.8268 (m-70) cc_final: 0.7767 (m-70) REVERT: D 254 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.5500 (mptt) REVERT: F 170 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: F 218 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7779 (mtm180) REVERT: F 234 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: G 89 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7659 (mm-30) REVERT: G 245 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7577 (ttpt) REVERT: I 16 ARG cc_start: 0.7968 (ttt90) cc_final: 0.7767 (ttt90) REVERT: I 78 LYS cc_start: 0.7386 (tttp) cc_final: 0.7124 (tttt) REVERT: K 140 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5705 (mm) REVERT: K 158 LYS cc_start: 0.6794 (OUTLIER) cc_final: 0.6498 (ttmm) REVERT: L 18 TRP cc_start: 0.6718 (p-90) cc_final: 0.6426 (p-90) REVERT: L 49 ARG cc_start: 0.8593 (ptt90) cc_final: 0.8310 (mtm-85) REVERT: P 152 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7222 (mt-10) REVERT: P 167 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7714 (ptp-170) REVERT: Q 3 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8210 (mt) REVERT: R 144 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6619 (tm130) REVERT: S 43 TYR cc_start: 0.7958 (t80) cc_final: 0.7384 (t80) REVERT: T 104 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6975 (tm-30) REVERT: T 131 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: U 70 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6263 (tmtp) REVERT: W 38 ARG cc_start: 0.6149 (OUTLIER) cc_final: 0.5526 (tpt-90) REVERT: W 194 LYS cc_start: 0.6110 (ttmm) cc_final: 0.5853 (mttt) REVERT: W 235 MET cc_start: 0.6098 (OUTLIER) cc_final: 0.5643 (mmm) REVERT: X 70 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: X 85 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: Y 55 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6844 (mm-30) REVERT: b 370 ASP cc_start: 0.6689 (p0) cc_final: 0.6205 (p0) REVERT: b 396 ARG cc_start: 0.6582 (mtm110) cc_final: 0.6195 (mtm110) REVERT: b 551 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6388 (ttp80) REVERT: b 588 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.6928 (mtp180) REVERT: b 610 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7380 (ptm160) REVERT: c 36 GLN cc_start: 0.7939 (mt0) cc_final: 0.7601 (mt0) REVERT: d 9 THR cc_start: 0.8822 (m) cc_final: 0.8501 (m) REVERT: d 94 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: f 67 MET cc_start: 0.9225 (mtp) cc_final: 0.8985 (mtp) REVERT: i 70 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.6475 (mtt180) REVERT: k 5 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7939 (pp) REVERT: m 130 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6568 (ttt90) REVERT: m 184 MET cc_start: 0.2597 (OUTLIER) cc_final: 0.2203 (pmm) REVERT: n 13 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7714 (ttp80) REVERT: n 138 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7509 (ttp) REVERT: n 174 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6610 (mtm180) REVERT: n 230 HIS cc_start: 0.7431 (OUTLIER) cc_final: 0.6681 (m-70) REVERT: n 262 TYR cc_start: 0.7064 (m-80) cc_final: 0.6805 (m-10) REVERT: n 375 ILE cc_start: 0.7177 (mt) cc_final: 0.6971 (mt) REVERT: n 441 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5895 (tt) REVERT: o 102 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.5628 (m-10) REVERT: o 104 GLU cc_start: 0.7335 (mp0) cc_final: 0.6956 (mp0) REVERT: p 24 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7310 (mtm-85) REVERT: p 36 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7678 (mtt-85) REVERT: q 259 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6740 (mttt) REVERT: q 263 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6771 (mtm-85) REVERT: q 265 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6730 (mp) REVERT: r 41 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7562 (mptt) REVERT: s 17 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7808 (mm-30) REVERT: t 23 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.5820 (mmp80) REVERT: t 33 ARG cc_start: 0.6423 (mtm110) cc_final: 0.6111 (mtm180) REVERT: t 40 LYS cc_start: 0.6902 (ttpp) cc_final: 0.6554 (ptmm) REVERT: t 98 ASP cc_start: 0.5129 (OUTLIER) cc_final: 0.4747 (m-30) REVERT: t 130 ARG cc_start: 0.5909 (OUTLIER) cc_final: 0.5234 (mtp85) REVERT: u 1 MET cc_start: 0.7944 (ttp) cc_final: 0.7481 (ttp) REVERT: u 98 GLU cc_start: 0.6772 (tt0) cc_final: 0.6515 (tt0) REVERT: u 117 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7177 (tp30) REVERT: u 118 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7354 (mptp) REVERT: v 13 LYS cc_start: 0.6248 (mmtt) cc_final: 0.5712 (mtpp) REVERT: v 78 PHE cc_start: 0.7526 (m-80) cc_final: 0.7084 (m-80) REVERT: v 216 LYS cc_start: 0.6218 (ptmm) cc_final: 0.5709 (tmmm) REVERT: v 222 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6258 (tp30) REVERT: v 258 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.6058 (tppt) REVERT: v 260 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7096 (tttt) REVERT: w 21 TYR cc_start: 0.7843 (m-80) cc_final: 0.7367 (m-80) REVERT: w 124 LYS cc_start: 0.6726 (OUTLIER) cc_final: 0.6366 (mtpt) REVERT: w 196 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6983 (mtm110) REVERT: y 62 MET cc_start: 0.8544 (mmm) cc_final: 0.8257 (mmm) REVERT: 4 25 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7553 (mp) REVERT: 4 29 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6594 (mtt180) REVERT: 4 246 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7052 (ttm170) REVERT: 4 573 GLN cc_start: 0.6429 (mm-40) cc_final: 0.6160 (mm110) outliers start: 288 outliers final: 174 residues processed: 1521 average time/residue: 2.3946 time to fit residues: 5146.5875 Evaluate side-chains 1551 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1324 time to evaluate : 8.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 5 residue 78 MET Chi-restraints excluded: chain 8 residue 138 SER Chi-restraints excluded: chain 9 residue 26 LYS Chi-restraints excluded: chain 9 residue 147 LEU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 208 GLU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 245 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 167 ARG Chi-restraints excluded: chain P residue 182 ILE Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 235 MET Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 85 GLN Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 4 SER Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 449 ILE Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain b residue 537 THR Chi-restraints excluded: chain b residue 551 ARG Chi-restraints excluded: chain b residue 588 ARG Chi-restraints excluded: chain b residue 610 ARG Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain d residue 24 SER Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain g residue 87 GLU Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 65 LEU Chi-restraints excluded: chain m residue 37 LYS Chi-restraints excluded: chain m residue 128 LYS Chi-restraints excluded: chain m residue 130 ARG Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 184 MET Chi-restraints excluded: chain m residue 311 THR Chi-restraints excluded: chain n residue 13 ARG Chi-restraints excluded: chain n residue 91 THR Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 138 MET Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 358 SER Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain n residue 442 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 131 SER Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain o residue 180 LYS Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 259 LYS Chi-restraints excluded: chain q residue 263 ARG Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 399 SER Chi-restraints excluded: chain q residue 415 LEU Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain r residue 41 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 23 ARG Chi-restraints excluded: chain t residue 85 LYS Chi-restraints excluded: chain t residue 93 ILE Chi-restraints excluded: chain t residue 98 ASP Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain u residue 24 ASN Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain u residue 118 LYS Chi-restraints excluded: chain u residue 139 VAL Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 187 GLN Chi-restraints excluded: chain v residue 222 GLU Chi-restraints excluded: chain v residue 234 ILE Chi-restraints excluded: chain v residue 258 LYS Chi-restraints excluded: chain v residue 260 LYS Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 36 LYS Chi-restraints excluded: chain w residue 49 LYS Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 72 THR Chi-restraints excluded: chain w residue 77 VAL Chi-restraints excluded: chain w residue 124 LYS Chi-restraints excluded: chain w residue 164 ASP Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 32 VAL Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 308 SER Chi-restraints excluded: chain x residue 393 LYS Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 29 ARG Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 331 LYS Chi-restraints excluded: chain 4 residue 401 PHE Chi-restraints excluded: chain 4 residue 465 THR Chi-restraints excluded: chain 4 residue 466 LEU Chi-restraints excluded: chain 4 residue 467 THR Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 494 GLU Chi-restraints excluded: chain 4 residue 514 VAL Chi-restraints excluded: chain 4 residue 516 THR Chi-restraints excluded: chain 4 residue 522 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 825 optimal weight: 9.9990 chunk 533 optimal weight: 1.9990 chunk 797 optimal weight: 9.9990 chunk 402 optimal weight: 4.9990 chunk 262 optimal weight: 20.0000 chunk 258 optimal weight: 40.0000 chunk 848 optimal weight: 0.8980 chunk 909 optimal weight: 3.9990 chunk 659 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 1049 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 221 ASN G 243 GLN H 157 ASN H 163 GLN I 99 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN P 10 ASN Q 126 GLN Q 136 ASN R 34 GLN S 88 HIS S 122 HIS S 138 GLN S 142 GLN U 25 ASN V 24 ASN W 14 GLN Y 81 GLN Z 78 ASN b 152 GLN b 384 ASN i 92 ASN k 76 ASN m 165 ASN m 342 GLN o 154 ASN ** t 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 121 ASN x 314 ASN 4 255 ASN 4 457 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1116 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= 0.174 Angle : 0.641 17.853 242131 Z= 0.347 Chirality : 0.037 0.266 29635 Planarity : 0.006 0.130 18333 Dihedral : 22.217 178.890 63373 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.49 % Allowed : 13.12 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.08), residues: 10648 helix: 2.01 (0.08), residues: 4174 sheet: 0.19 (0.13), residues: 1537 loop : -0.21 (0.08), residues: 4937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP w 114 HIS 0.006 0.001 HIS C 311 PHE 0.027 0.001 PHE F 229 TYR 0.020 0.002 TYR C 194 ARG 0.008 0.000 ARG m 281 *********************** 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 1585 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1353 time to evaluate : 8.110 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: 8 87 GLU cc_start: 0.5441 (mt-10) cc_final: 0.4482 (mm-30) REVERT: 9 5 ASN cc_start: 0.8782 (m-40) cc_final: 0.8503 (m-40) REVERT: 9 29 GLN cc_start: 0.7751 (tt0) cc_final: 0.7516 (mt0) REVERT: B 67 PHE cc_start: 0.8581 (m-80) cc_final: 0.8328 (m-80) REVERT: B 248 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7528 (mttt) REVERT: B 323 MET cc_start: 0.8423 (ttm) cc_final: 0.8173 (ttp) REVERT: B 335 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8275 (tp) REVERT: C 99 MET cc_start: 0.8530 (ptm) cc_final: 0.7618 (ptm) REVERT: C 338 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7606 (mptp) REVERT: D 40 HIS cc_start: 0.8267 (m-70) cc_final: 0.7730 (m-70) REVERT: D 254 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5518 (mptt) REVERT: F 170 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7230 (tt0) REVERT: F 218 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7775 (mtm110) REVERT: F 234 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: G 89 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7631 (mm-30) REVERT: G 146 LYS cc_start: 0.8226 (mttp) cc_final: 0.8021 (mttm) REVERT: K 140 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5696 (mm) REVERT: K 158 LYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6476 (ttmm) REVERT: L 18 TRP cc_start: 0.6704 (p-90) cc_final: 0.6431 (p-90) REVERT: L 49 ARG cc_start: 0.8560 (ptt90) cc_final: 0.8258 (mtm-85) REVERT: O 155 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7622 (ttpt) REVERT: P 152 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7143 (tt0) REVERT: P 167 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7679 (ptp-170) REVERT: Q 3 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8201 (mt) REVERT: R 144 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6521 (tm130) REVERT: S 43 TYR cc_start: 0.7949 (t80) cc_final: 0.7313 (t80) REVERT: T 104 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6862 (tm-30) REVERT: T 131 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: U 70 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.6215 (tmtp) REVERT: W 38 ARG cc_start: 0.6071 (OUTLIER) cc_final: 0.5453 (tpt-90) REVERT: W 194 LYS cc_start: 0.6085 (ttmm) cc_final: 0.5812 (mttt) REVERT: Y 55 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6830 (mm-30) REVERT: b 370 ASP cc_start: 0.6633 (p0) cc_final: 0.6161 (p0) REVERT: b 588 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.6872 (mtp180) REVERT: b 610 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7316 (ptm160) REVERT: b 643 LYS cc_start: 0.7383 (tptp) cc_final: 0.7049 (tptm) REVERT: c 36 GLN cc_start: 0.7887 (mt0) cc_final: 0.7543 (mt0) REVERT: d 9 THR cc_start: 0.8783 (m) cc_final: 0.8449 (m) REVERT: d 94 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: f 67 MET cc_start: 0.9212 (mtp) cc_final: 0.8999 (mtp) REVERT: i 70 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6474 (mtt180) REVERT: k 5 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7967 (pp) REVERT: m 130 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6548 (ttt90) REVERT: n 174 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6576 (mtm180) REVERT: n 230 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.6739 (m-70) REVERT: n 262 TYR cc_start: 0.7088 (m-80) cc_final: 0.6832 (m-10) REVERT: n 375 ILE cc_start: 0.7150 (mt) cc_final: 0.6848 (mt) REVERT: n 441 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6002 (tt) REVERT: o 104 GLU cc_start: 0.7201 (mp0) cc_final: 0.6857 (mp0) REVERT: q 259 LYS cc_start: 0.7096 (mtmm) cc_final: 0.6681 (mttt) REVERT: q 265 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6647 (mp) REVERT: r 41 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7591 (mptt) REVERT: s 17 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7777 (mm-30) REVERT: t 23 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.5764 (mmp80) REVERT: t 33 ARG cc_start: 0.6434 (mtm110) cc_final: 0.6129 (mtm180) REVERT: t 40 LYS cc_start: 0.6856 (ttpp) cc_final: 0.6508 (ptmm) REVERT: t 130 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5230 (mtp85) REVERT: u 1 MET cc_start: 0.7947 (ttp) cc_final: 0.7572 (ttp) REVERT: u 117 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7149 (tp30) REVERT: v 13 LYS cc_start: 0.6116 (mmtt) cc_final: 0.5617 (mtpp) REVERT: v 29 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7276 (mt0) REVERT: v 78 PHE cc_start: 0.7541 (m-80) cc_final: 0.7112 (m-80) REVERT: v 216 LYS cc_start: 0.6230 (ptmm) cc_final: 0.5720 (tmmm) REVERT: v 258 LYS cc_start: 0.6572 (OUTLIER) cc_final: 0.6110 (tppt) REVERT: w 21 TYR cc_start: 0.7833 (m-80) cc_final: 0.7366 (m-80) REVERT: w 38 ASP cc_start: 0.3455 (OUTLIER) cc_final: 0.2621 (p0) REVERT: w 124 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.6361 (mtpt) REVERT: w 196 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7017 (mtm110) REVERT: x 373 MET cc_start: 0.7593 (mmm) cc_final: 0.7225 (mtp) REVERT: x 424 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.7651 (m-40) REVERT: y 62 MET cc_start: 0.8523 (mmm) cc_final: 0.8232 (mmm) REVERT: 4 29 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6541 (mtt180) REVERT: 4 246 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7002 (ttm170) REVERT: 4 573 GLN cc_start: 0.6278 (mm-40) cc_final: 0.6043 (mm110) outliers start: 232 outliers final: 149 residues processed: 1494 average time/residue: 2.2672 time to fit residues: 4790.8218 Evaluate side-chains 1519 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1332 time to evaluate : 8.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 5 residue 78 MET Chi-restraints excluded: chain 9 residue 147 LEU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 155 LYS Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 167 ARG Chi-restraints excluded: chain P residue 182 ILE Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 93 LYS Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain b residue 449 ILE Chi-restraints excluded: chain b residue 537 THR Chi-restraints excluded: chain b residue 588 ARG Chi-restraints excluded: chain b residue 610 ARG Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain d residue 24 SER Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 65 LEU Chi-restraints excluded: chain m residue 37 LYS Chi-restraints excluded: chain m residue 116 SER Chi-restraints excluded: chain m residue 128 LYS Chi-restraints excluded: chain m residue 130 ARG Chi-restraints excluded: chain n residue 91 THR Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 358 SER Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain n residue 442 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 131 SER Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 399 SER Chi-restraints excluded: chain q residue 415 LEU Chi-restraints excluded: chain q residue 436 ARG Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain r residue 41 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 23 ARG Chi-restraints excluded: chain t residue 85 LYS Chi-restraints excluded: chain t residue 93 ILE Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 187 GLN Chi-restraints excluded: chain v residue 234 ILE Chi-restraints excluded: chain v residue 258 LYS Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 36 LYS Chi-restraints excluded: chain w residue 38 ASP Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 72 THR Chi-restraints excluded: chain w residue 124 LYS Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 32 VAL Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 308 SER Chi-restraints excluded: chain x residue 313 ILE Chi-restraints excluded: chain x residue 393 LYS Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 424 ASN Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain 4 residue 29 ARG Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 331 LYS Chi-restraints excluded: chain 4 residue 401 PHE Chi-restraints excluded: chain 4 residue 465 THR Chi-restraints excluded: chain 4 residue 467 THR Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 494 GLU Chi-restraints excluded: chain 4 residue 514 VAL Chi-restraints excluded: chain 4 residue 516 THR Chi-restraints excluded: chain 4 residue 522 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1214 optimal weight: 5.9990 chunk 1278 optimal weight: 9.9990 chunk 1166 optimal weight: 2.9990 chunk 1243 optimal weight: 1.9990 chunk 748 optimal weight: 0.2980 chunk 541 optimal weight: 20.0000 chunk 976 optimal weight: 5.9990 chunk 381 optimal weight: 6.9990 chunk 1124 optimal weight: 2.9990 chunk 1176 optimal weight: 20.0000 chunk 1239 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 221 ASN H 157 ASN H 163 GLN I 99 ASN I 106 GLN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN P 10 ASN Q 126 GLN Q 136 ASN R 34 GLN S 88 HIS S 122 HIS S 138 GLN S 142 GLN U 25 ASN V 24 ASN W 14 GLN Y 81 GLN Z 78 ASN Z 106 GLN b 384 ASN i 92 ASN k 76 ASN m 90 GLN m 165 ASN m 342 GLN o 154 ASN t 291 GLN ** t 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 121 ASN 4 33 GLN 4 255 ASN 4 457 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1110 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= 0.176 Angle : 0.639 18.081 242131 Z= 0.346 Chirality : 0.037 0.270 29635 Planarity : 0.006 0.130 18333 Dihedral : 22.183 179.201 63373 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.55 % Allowed : 13.26 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.08), residues: 10648 helix: 2.04 (0.08), residues: 4172 sheet: 0.20 (0.13), residues: 1533 loop : -0.20 (0.08), residues: 4943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP w 114 HIS 0.006 0.001 HIS C 311 PHE 0.027 0.001 PHE F 229 TYR 0.020 0.002 TYR C 194 ARG 0.009 0.000 ARG b 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21296 Ramachandran restraints generated. 10648 Oldfield, 0 Emsley, 10648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1346 time to evaluate : 8.479 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 5 ASN cc_start: 0.8784 (m-40) cc_final: 0.8508 (m-40) REVERT: 9 29 GLN cc_start: 0.7747 (tt0) cc_final: 0.7511 (mt0) REVERT: B 67 PHE cc_start: 0.8592 (m-80) cc_final: 0.8341 (m-80) REVERT: B 248 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7475 (mttt) REVERT: B 335 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8250 (tp) REVERT: C 99 MET cc_start: 0.8523 (ptm) cc_final: 0.7621 (ptm) REVERT: C 338 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7598 (mptp) REVERT: D 40 HIS cc_start: 0.8255 (m-70) cc_final: 0.7734 (m-70) REVERT: D 254 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.5496 (mptt) REVERT: F 39 GLU cc_start: 0.6320 (mm-30) cc_final: 0.6097 (mm-30) REVERT: F 170 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: F 218 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7793 (mtm180) REVERT: F 234 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: G 89 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7618 (mm-30) REVERT: G 146 LYS cc_start: 0.8188 (mttp) cc_final: 0.7985 (mttm) REVERT: I 14 ARG cc_start: 0.7763 (ttt-90) cc_final: 0.7354 (ttt90) REVERT: K 78 LEU cc_start: 0.6391 (tp) cc_final: 0.6140 (tp) REVERT: K 140 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5729 (mm) REVERT: K 158 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6464 (ttmm) REVERT: L 18 TRP cc_start: 0.6703 (p-90) cc_final: 0.6430 (p-90) REVERT: L 49 ARG cc_start: 0.8579 (ptt90) cc_final: 0.8274 (mtm-85) REVERT: N 109 ARG cc_start: 0.8088 (tpt-90) cc_final: 0.7874 (tpt-90) REVERT: O 155 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7614 (ttpt) REVERT: P 152 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: P 167 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7525 (ptp-110) REVERT: Q 3 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8190 (mt) REVERT: R 144 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6401 (tm130) REVERT: S 43 TYR cc_start: 0.7949 (t80) cc_final: 0.7315 (t80) REVERT: T 104 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6891 (tm-30) REVERT: T 131 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8047 (mp10) REVERT: U 70 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.6225 (tmtp) REVERT: W 38 ARG cc_start: 0.6071 (OUTLIER) cc_final: 0.5450 (tpt-90) REVERT: W 194 LYS cc_start: 0.6089 (ttmm) cc_final: 0.5849 (mttt) REVERT: Y 55 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6815 (mm-30) REVERT: b 370 ASP cc_start: 0.6598 (p0) cc_final: 0.6132 (p0) REVERT: b 396 ARG cc_start: 0.6620 (mtm110) cc_final: 0.6323 (mtm110) REVERT: b 533 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6464 (pt0) REVERT: b 588 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.6891 (mtp180) REVERT: b 610 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7340 (ptm160) REVERT: b 643 LYS cc_start: 0.7390 (tptp) cc_final: 0.7116 (tptm) REVERT: c 36 GLN cc_start: 0.7885 (mt0) cc_final: 0.7536 (mt0) REVERT: d 9 THR cc_start: 0.8784 (m) cc_final: 0.8450 (m) REVERT: d 94 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: f 67 MET cc_start: 0.9211 (mtp) cc_final: 0.9001 (mtp) REVERT: i 70 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6473 (mtt180) REVERT: k 5 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7963 (pp) REVERT: m 130 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6572 (ttt90) REVERT: n 174 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6587 (mtm180) REVERT: n 230 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6715 (m-70) REVERT: n 262 TYR cc_start: 0.7104 (m-80) cc_final: 0.6849 (m-10) REVERT: n 375 ILE cc_start: 0.7143 (mt) cc_final: 0.6842 (mt) REVERT: n 441 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.6038 (tt) REVERT: o 104 GLU cc_start: 0.7200 (mp0) cc_final: 0.6853 (mp0) REVERT: q 259 LYS cc_start: 0.7111 (mtmm) cc_final: 0.6696 (mttt) REVERT: q 265 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6645 (mp) REVERT: s 17 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7775 (mm-30) REVERT: t 23 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.5728 (mmp80) REVERT: t 33 ARG cc_start: 0.6398 (mtm110) cc_final: 0.6091 (mtm180) REVERT: t 40 LYS cc_start: 0.6908 (ttpp) cc_final: 0.6562 (ptmm) REVERT: t 130 ARG cc_start: 0.5833 (OUTLIER) cc_final: 0.5301 (mtp85) REVERT: t 217 LYS cc_start: 0.5644 (tttt) cc_final: 0.5433 (tttp) REVERT: u 1 MET cc_start: 0.7944 (ttp) cc_final: 0.7548 (ttp) REVERT: u 117 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7156 (tp30) REVERT: v 13 LYS cc_start: 0.6115 (mmtt) cc_final: 0.5540 (mtpp) REVERT: v 29 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7270 (mt0) REVERT: v 78 PHE cc_start: 0.7544 (m-80) cc_final: 0.7097 (m-80) REVERT: v 216 LYS cc_start: 0.6248 (ptmm) cc_final: 0.5735 (tmmm) REVERT: v 258 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.6040 (mppt) REVERT: v 260 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7045 (tttt) REVERT: w 21 TYR cc_start: 0.7802 (m-80) cc_final: 0.7415 (m-80) REVERT: w 38 ASP cc_start: 0.3480 (OUTLIER) cc_final: 0.2647 (p0) REVERT: w 124 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6369 (mtpt) REVERT: w 196 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6996 (mtm110) REVERT: x 373 MET cc_start: 0.7599 (mmm) cc_final: 0.7235 (mtp) REVERT: x 424 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.7647 (m-40) REVERT: y 62 MET cc_start: 0.8521 (mmm) cc_final: 0.8229 (mmm) REVERT: 4 25 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7563 (mp) REVERT: 4 29 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6603 (mtt180) REVERT: 4 246 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.6995 (ttm170) REVERT: 4 573 GLN cc_start: 0.6157 (mm-40) cc_final: 0.5920 (mm110) outliers start: 237 outliers final: 157 residues processed: 1491 average time/residue: 2.2606 time to fit residues: 4782.4473 Evaluate side-chains 1521 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1324 time to evaluate : 7.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 5 residue 78 MET Chi-restraints excluded: chain 9 residue 110 LEU Chi-restraints excluded: chain 9 residue 147 LEU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 155 LYS Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 167 ARG Chi-restraints excluded: chain P residue 182 ILE Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 4 SER Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 449 ILE Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain b residue 537 THR Chi-restraints excluded: chain b residue 588 ARG Chi-restraints excluded: chain b residue 610 ARG Chi-restraints excluded: chain b residue 639 ARG Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain d residue 24 SER Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 65 LEU Chi-restraints excluded: chain m residue 37 LYS Chi-restraints excluded: chain m residue 116 SER Chi-restraints excluded: chain m residue 128 LYS Chi-restraints excluded: chain m residue 130 ARG Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain n residue 91 THR Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 358 SER Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 131 SER Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 399 SER Chi-restraints excluded: chain q residue 415 LEU Chi-restraints excluded: chain q residue 436 ARG Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 23 ARG Chi-restraints excluded: chain t residue 85 LYS Chi-restraints excluded: chain t residue 93 ILE Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 171 THR Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 187 GLN Chi-restraints excluded: chain v residue 234 ILE Chi-restraints excluded: chain v residue 258 LYS Chi-restraints excluded: chain v residue 260 LYS Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 36 LYS Chi-restraints excluded: chain w residue 38 ASP Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 72 THR Chi-restraints excluded: chain w residue 124 LYS Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 32 VAL Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 308 SER Chi-restraints excluded: chain x residue 313 ILE Chi-restraints excluded: chain x residue 393 LYS Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 424 ASN Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 126 GLU Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain 4 residue 25 LEU Chi-restraints excluded: chain 4 residue 29 ARG Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 331 LYS Chi-restraints excluded: chain 4 residue 401 PHE Chi-restraints excluded: chain 4 residue 465 THR Chi-restraints excluded: chain 4 residue 467 THR Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 494 GLU Chi-restraints excluded: chain 4 residue 514 VAL Chi-restraints excluded: chain 4 residue 516 THR Chi-restraints excluded: chain 4 residue 522 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 816 optimal weight: 5.9990 chunk 1315 optimal weight: 9.9990 chunk 802 optimal weight: 5.9990 chunk 624 optimal weight: 0.4980 chunk 914 optimal weight: 0.9990 chunk 1379 optimal weight: 30.0000 chunk 1269 optimal weight: 8.9990 chunk 1098 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 848 optimal weight: 20.0000 chunk 673 optimal weight: 3.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 221 ASN H 157 ASN H 163 GLN I 99 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN O 182 ASN P 10 ASN Q 126 GLN Q 136 ASN R 34 GLN S 88 HIS S 122 HIS S 138 GLN S 142 GLN U 25 ASN V 24 ASN W 14 GLN Y 81 GLN Z 78 ASN Z 106 GLN b 384 ASN i 92 ASN k 76 ASN m 90 GLN m 165 ASN m 342 GLN o 154 ASN v 121 ASN 4 255 ASN 4 457 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 167461 Z= 0.202 Angle : 0.663 18.473 242131 Z= 0.356 Chirality : 0.038 0.290 29635 Planarity : 0.006 0.132 18333 Dihedral : 22.198 179.366 63373 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.37 % Allowed : 13.68 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.08), residues: 10648 helix: 1.98 (0.08), residues: 4168 sheet: 0.19 (0.13), residues: 1542 loop : -0.21 (0.08), residues: 4938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP w 114 HIS 0.007 0.001 HIS C 311 PHE 0.030 0.002 PHE F 229 TYR 0.021 0.002 TYR C 194 ARG 0.008 0.000 ARG m 281 ********************** 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 1551 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1330 time to evaluate : 8.482 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 5 ASN cc_start: 0.8791 (m-40) cc_final: 0.8515 (m-40) REVERT: 9 29 GLN cc_start: 0.7752 (tt0) cc_final: 0.7519 (mt0) REVERT: B 67 PHE cc_start: 0.8594 (m-80) cc_final: 0.8319 (m-80) REVERT: B 248 LYS cc_start: 0.7833 (mmtt) cc_final: 0.7502 (mttt) REVERT: B 335 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8276 (tp) REVERT: C 99 MET cc_start: 0.8540 (ptm) cc_final: 0.7634 (ptm) REVERT: C 338 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7590 (mptp) REVERT: D 40 HIS cc_start: 0.8264 (m-70) cc_final: 0.7737 (m-70) REVERT: D 254 LYS cc_start: 0.6086 (OUTLIER) cc_final: 0.5561 (mptt) REVERT: F 170 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: F 218 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7798 (mtm180) REVERT: F 234 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: G 89 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7648 (mm-30) REVERT: I 14 ARG cc_start: 0.7767 (ttt-90) cc_final: 0.7335 (ttt90) REVERT: K 140 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5740 (mm) REVERT: K 158 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6468 (ttmm) REVERT: L 18 TRP cc_start: 0.6710 (p-90) cc_final: 0.6436 (p-90) REVERT: L 49 ARG cc_start: 0.8614 (ptt90) cc_final: 0.8297 (mtm-85) REVERT: N 109 ARG cc_start: 0.8118 (tpt-90) cc_final: 0.7902 (tpt-90) REVERT: O 155 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7628 (ttpt) REVERT: P 152 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7146 (tt0) REVERT: P 167 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7535 (ptp-110) REVERT: Q 3 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8199 (mt) REVERT: R 144 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6393 (tm130) REVERT: S 43 TYR cc_start: 0.7949 (t80) cc_final: 0.7376 (t80) REVERT: T 104 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6899 (tm-30) REVERT: T 131 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: U 70 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.6239 (tmtp) REVERT: W 38 ARG cc_start: 0.6077 (OUTLIER) cc_final: 0.5456 (tpt-90) REVERT: W 194 LYS cc_start: 0.6100 (ttmm) cc_final: 0.5813 (mttt) REVERT: Y 55 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6820 (mm-30) REVERT: b 370 ASP cc_start: 0.6695 (p0) cc_final: 0.6236 (p0) REVERT: b 396 ARG cc_start: 0.6605 (mtm110) cc_final: 0.6275 (mtm110) REVERT: b 533 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6441 (pt0) REVERT: b 588 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.6893 (mtp180) REVERT: b 610 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7342 (ptm160) REVERT: b 643 LYS cc_start: 0.7393 (tptp) cc_final: 0.7112 (tptm) REVERT: c 36 GLN cc_start: 0.7928 (mt0) cc_final: 0.7562 (mt0) REVERT: d 9 THR cc_start: 0.8808 (m) cc_final: 0.8484 (m) REVERT: d 94 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: f 67 MET cc_start: 0.9216 (mtp) cc_final: 0.8995 (mtp) REVERT: i 70 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.6513 (mtt180) REVERT: k 5 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7961 (pp) REVERT: m 130 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6572 (ttt90) REVERT: m 184 MET cc_start: 0.2451 (pmm) cc_final: 0.1865 (ptp) REVERT: n 174 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6575 (mtm180) REVERT: n 230 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6719 (m-70) REVERT: n 262 TYR cc_start: 0.7091 (m-80) cc_final: 0.6835 (m-10) REVERT: n 375 ILE cc_start: 0.7157 (mt) cc_final: 0.6946 (mt) REVERT: n 441 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6016 (tt) REVERT: o 104 GLU cc_start: 0.7202 (mp0) cc_final: 0.6862 (mp0) REVERT: q 259 LYS cc_start: 0.7112 (mtmm) cc_final: 0.6712 (mttt) REVERT: q 263 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6746 (mtm-85) REVERT: q 265 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6666 (mp) REVERT: r 41 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7545 (mptt) REVERT: s 17 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7782 (mm-30) REVERT: t 23 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.5756 (mmp80) REVERT: t 40 LYS cc_start: 0.6881 (ttpp) cc_final: 0.6529 (ptmm) REVERT: t 130 ARG cc_start: 0.5837 (OUTLIER) cc_final: 0.5347 (mtp85) REVERT: t 217 LYS cc_start: 0.5650 (tttt) cc_final: 0.5437 (tttp) REVERT: u 1 MET cc_start: 0.7946 (ttp) cc_final: 0.7586 (ttp) REVERT: u 117 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7163 (tp30) REVERT: v 13 LYS cc_start: 0.6116 (mmtt) cc_final: 0.5543 (mtpp) REVERT: v 29 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7272 (mt0) REVERT: v 78 PHE cc_start: 0.7533 (m-80) cc_final: 0.7091 (m-80) REVERT: v 216 LYS cc_start: 0.6246 (ptmm) cc_final: 0.5749 (tmmm) REVERT: v 258 LYS cc_start: 0.6378 (OUTLIER) cc_final: 0.6015 (mppt) REVERT: v 260 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7091 (tttt) REVERT: v 281 ASP cc_start: 0.8015 (t0) cc_final: 0.7776 (t0) REVERT: w 21 TYR cc_start: 0.7828 (m-80) cc_final: 0.7446 (m-80) REVERT: w 38 ASP cc_start: 0.3509 (OUTLIER) cc_final: 0.2676 (p0) REVERT: w 124 LYS cc_start: 0.6729 (OUTLIER) cc_final: 0.6375 (mtpt) REVERT: w 196 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.7010 (mtm110) REVERT: x 373 MET cc_start: 0.7602 (mmm) cc_final: 0.7308 (mtp) REVERT: x 424 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.7699 (m-40) REVERT: y 62 MET cc_start: 0.8531 (mmm) cc_final: 0.8232 (mmm) REVERT: 4 29 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6606 (mtt180) REVERT: 4 246 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7022 (ttm170) REVERT: 4 573 GLN cc_start: 0.6143 (mm-40) cc_final: 0.5873 (mm110) outliers start: 221 outliers final: 156 residues processed: 1470 average time/residue: 2.2443 time to fit residues: 4690.1279 Evaluate side-chains 1519 residues out of total 9306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1322 time to evaluate : 8.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain 5 residue 78 MET Chi-restraints excluded: chain 9 residue 110 LEU Chi-restraints excluded: chain 9 residue 147 LEU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 218 ARG Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 158 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 297 VAL Chi-restraints excluded: chain K residue 331 LYS Chi-restraints excluded: chain K residue 334 MET Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 155 LYS Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain P residue 167 ARG Chi-restraints excluded: chain P residue 182 ILE Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 93 LYS Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 4 SER Chi-restraints excluded: chain b residue 25 THR Chi-restraints excluded: chain b residue 449 ILE Chi-restraints excluded: chain b residue 533 GLU Chi-restraints excluded: chain b residue 537 THR Chi-restraints excluded: chain b residue 588 ARG Chi-restraints excluded: chain b residue 610 ARG Chi-restraints excluded: chain b residue 639 ARG Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain d residue 24 SER Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain k residue 5 ILE Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 65 LEU Chi-restraints excluded: chain m residue 37 LYS Chi-restraints excluded: chain m residue 116 SER Chi-restraints excluded: chain m residue 128 LYS Chi-restraints excluded: chain m residue 130 ARG Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 311 THR Chi-restraints excluded: chain n residue 91 THR Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 124 SER Chi-restraints excluded: chain n residue 174 ARG Chi-restraints excluded: chain n residue 176 VAL Chi-restraints excluded: chain n residue 230 HIS Chi-restraints excluded: chain n residue 358 SER Chi-restraints excluded: chain n residue 441 LEU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 131 SER Chi-restraints excluded: chain o residue 174 GLU Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 214 VAL Chi-restraints excluded: chain q residue 263 ARG Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 399 SER Chi-restraints excluded: chain q residue 415 LEU Chi-restraints excluded: chain q residue 436 ARG Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain r residue 41 LYS Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain t residue 23 ARG Chi-restraints excluded: chain t residue 85 LYS Chi-restraints excluded: chain t residue 93 ILE Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 171 THR Chi-restraints excluded: chain t residue 183 VAL Chi-restraints excluded: chain t residue 237 GLU Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 105 THR Chi-restraints excluded: chain v residue 187 GLN Chi-restraints excluded: chain v residue 234 ILE Chi-restraints excluded: chain v residue 258 LYS Chi-restraints excluded: chain v residue 260 LYS Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain w residue 36 LYS Chi-restraints excluded: chain w residue 38 ASP Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 124 LYS Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 196 ARG Chi-restraints excluded: chain x residue 32 VAL Chi-restraints excluded: chain x residue 139 ILE Chi-restraints excluded: chain x residue 308 SER Chi-restraints excluded: chain x residue 393 LYS Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 424 ASN Chi-restraints excluded: chain y residue 28 VAL Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain 4 residue 29 ARG Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 110 ASP Chi-restraints excluded: chain 4 residue 124 THR Chi-restraints excluded: chain 4 residue 246 ARG Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 331 LYS Chi-restraints excluded: chain 4 residue 401 PHE Chi-restraints excluded: chain 4 residue 465 THR Chi-restraints excluded: chain 4 residue 467 THR Chi-restraints excluded: chain 4 residue 492 THR Chi-restraints excluded: chain 4 residue 494 GLU Chi-restraints excluded: chain 4 residue 514 VAL Chi-restraints excluded: chain 4 residue 516 THR Chi-restraints excluded: chain 4 residue 522 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 872 optimal weight: 7.9990 chunk 1170 optimal weight: 20.0000 chunk 336 optimal weight: 40.0000 chunk 1013 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 1100 optimal weight: 10.0000 chunk 460 optimal weight: 1.9990 chunk 1130 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN C 175 HIS D 57 ASN G 221 ASN H 157 ASN H 163 GLN I 99 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN O 182 ASN P 10 ASN Q 126 GLN Q 136 ASN R 34 GLN S 88 HIS S 122 HIS S 138 GLN S 142 GLN U 25 ASN V 24 ASN W 14 GLN Y 81 GLN Z 78 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 384 ASN i 92 ASN k 76 ASN m 90 GLN m 165 ASN m 342 GLN o 154 ASN p 32 GLN t 291 GLN v 121 ASN ** w 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 457 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.167098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3360 r_free = 0.3360 target = 0.125039 restraints weight = 137216.747| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 0.94 r_work: 0.3023 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 167461 Z= 0.396 Angle : 0.854 20.762 242131 Z= 0.440 Chirality : 0.047 0.403 29635 Planarity : 0.007 0.145 18333 Dihedral : 22.405 179.772 63373 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.55 % Allowed : 13.64 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.08), residues: 10648 helix: 1.50 (0.08), residues: 4174 sheet: 0.05 (0.12), residues: 1543 loop : -0.37 (0.08), residues: 4931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP x 231 HIS 0.010 0.002 HIS P 145 PHE 0.039 0.003 PHE F 229 TYR 0.031 0.003 TYR A 133 ARG 0.011 0.001 ARG l 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 67552.43 seconds wall clock time: 1164 minutes 21.25 seconds (69861.25 seconds total)