Starting phenix.real_space_refine on Thu Feb 22 11:42:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6em1_3893/02_2024/6em1_3893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6em1_3893/02_2024/6em1_3893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6em1_3893/02_2024/6em1_3893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6em1_3893/02_2024/6em1_3893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6em1_3893/02_2024/6em1_3893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6em1_3893/02_2024/6em1_3893.pdb" } resolution = 3.6 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2008 5.49 5 S 142 5.16 5 C 55494 2.51 5 N 18143 2.21 5 O 24191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "x ARG 51": "NH1" <-> "NH2" Residue "x ARG 64": "NH1" <-> "NH2" Residue "x ARG 272": "NH1" <-> "NH2" Residue "x TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "3 ARG 123": "NH1" <-> "NH2" Residue "4 PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 60": "NH1" <-> "NH2" Residue "4 PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 223": "OD1" <-> "OD2" Residue "4 TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 252": "NH1" <-> "NH2" Residue "5 PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 300": "NH1" <-> "NH2" Residue "5 ARG 382": "NH1" <-> "NH2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "b ARG 24": "NH1" <-> "NH2" Residue "b ARG 27": "NH1" <-> "NH2" Residue "b ARG 34": "NH1" <-> "NH2" Residue "b ARG 43": "NH1" <-> "NH2" Residue "b ARG 79": "NH1" <-> "NH2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 135": "NH1" <-> "NH2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 154": "NH1" <-> "NH2" Residue "b ARG 302": "NH1" <-> "NH2" Residue "b ARG 332": "NH1" <-> "NH2" Residue "J ARG 258": "NH1" <-> "NH2" Residue "r ARG 9": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "u ARG 2": "NH1" <-> "NH2" Residue "u ARG 23": "NH1" <-> "NH2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u ARG 43": "NH1" <-> "NH2" Residue "u ARG 44": "NH1" <-> "NH2" Residue "u ARG 56": "NH1" <-> "NH2" Residue "u ARG 75": "NH1" <-> "NH2" Residue "u ARG 80": "NH1" <-> "NH2" Residue "u ARG 83": "NH1" <-> "NH2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u ARG 111": "NH1" <-> "NH2" Residue "u ARG 113": "NH1" <-> "NH2" Residue "v ARG 7": "NH1" <-> "NH2" Residue "W ARG 31": "NH1" <-> "NH2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 81": "NH1" <-> "NH2" Residue "W ARG 166": "NH1" <-> "NH2" Residue "W ARG 198": "NH1" <-> "NH2" Residue "y ARG 85": "NH1" <-> "NH2" Residue "y ARG 100": "NH1" <-> "NH2" Residue "z ARG 6": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H ARG 166": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "P TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "K ARG 34": "NH1" <-> "NH2" Residue "K ARG 170": "NH1" <-> "NH2" Residue "K ARG 240": "NH1" <-> "NH2" Residue "K ARG 277": "NH1" <-> "NH2" Residue "K ARG 285": "NH1" <-> "NH2" Residue "m ARG 362": "NH1" <-> "NH2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o ARG 121": "NH1" <-> "NH2" Residue "o PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 207": "NH1" <-> "NH2" Residue "n ARG 18": "NH1" <-> "NH2" Residue "n ARG 34": "NH1" <-> "NH2" Residue "n ARG 88": "NH1" <-> "NH2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 104": "NH1" <-> "NH2" Residue "n ARG 109": "NH1" <-> "NH2" Residue "n ARG 174": "NH1" <-> "NH2" Residue "n TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 369": "NH1" <-> "NH2" Residue "n ARG 414": "NH1" <-> "NH2" Residue "n ARG 424": "NH1" <-> "NH2" Residue "t ARG 74": "NH1" <-> "NH2" Residue "t ARG 77": "NH1" <-> "NH2" Residue "t PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 130": "NH1" <-> "NH2" Residue "t ARG 146": "NH1" <-> "NH2" Residue "t ARG 148": "NH1" <-> "NH2" Residue "t ARG 205": "NH1" <-> "NH2" Residue "t ARG 211": "NH1" <-> "NH2" Residue "t ARG 213": "NH1" <-> "NH2" Residue "t ARG 275": "NH1" <-> "NH2" Residue "t ARG 299": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 99980 Number of models: 1 Model: "" Number of chains: 45 Chain: "x" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2268 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 12, 'TRANS': 254} Chain breaks: 2 Chain: "F" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1936 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "3" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1434 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 5, 'TRANS': 167} Chain: "4" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1853 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 3 Chain: "5" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3055 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 372} Chain breaks: 3 Chain: "A" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1211 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 10, 'TRANS': 134} Chain breaks: 2 Chain: "b" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3410 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 20, 'TRANS': 400} Chain breaks: 3 Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 549 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "r" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 628 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "s" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 224 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "u" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 976 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "v" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1087 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain breaks: 2 Chain: "W" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1870 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "y" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 444 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "B" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2646 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2611 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 326} Chain: "e" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1009 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "E" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1205 Classifications: {'peptide': 151} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143} Chain breaks: 1 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: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1231 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 8, 'TRANS': 150} Chain breaks: 1 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: "H" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1510 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "i" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 594 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "j" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 566 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'TRANS': 69} Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 864 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1041 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "N" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1513 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} 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: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1062 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain breaks: 1 Chain: "Q" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1009 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "S" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1432 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "V" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 936 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "Y" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "1" Number of atoms: 38221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1785, 38221 Classifications: {'RNA': 1785} Modifications used: {'rna2p_pur': 183, 'rna2p_pyr': 122, 'rna3p_pur': 816, 'rna3p_pyr': 664} Link IDs: {'rna2p': 305, 'rna3p': 1479} Chain breaks: 12 Chain: "2" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 14, 'rna3p_pur': 61, 'rna3p_pyr': 66} Link IDs: {'rna2p': 30, 'rna3p': 127} Chain breaks: 6 Chain: "6" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1370 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 20, 'rna3p_pur': 21, 'rna3p_pyr': 16} Link IDs: {'rna2p': 27, 'rna3p': 37} Chain breaks: 1 Chain: "K" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2073 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "m" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1362 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 17, 'TRANS': 143} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1590 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 9, 'TRANS': 184} 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: "n" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Chain: "t" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1935 Classifications: {'peptide': 244} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 234} Chain breaks: 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: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16649 SG CYS u 9 171.889 57.042 205.116 1.00221.58 S ATOM 16834 SG CYS u 32 169.526 58.134 207.535 1.00299.18 S ATOM 16866 SG CYS u 36 168.450 56.825 203.872 1.00197.00 S ATOM 35308 SG CYS j 19 110.585 101.946 134.325 1.00109.48 S ATOM 35333 SG CYS j 22 110.012 104.578 137.086 1.00 87.45 S ATOM 35433 SG CYS j 34 108.834 101.124 137.532 1.00 98.44 S ATOM 35451 SG CYS j 37 107.354 103.379 135.144 1.00 75.92 S Residues with excluded nonbonded symmetry interactions: 202 residue: pdb=" N ASP 4 57 " occ=0.52 ... (6 atoms not shown) pdb=" OD2 ASP 4 57 " occ=0.52 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 ... (remaining 190 not shown) Time building chain proxies: 40.68, per 1000 atoms: 0.41 Number of scatterers: 99980 At special positions: 0 Unit cell: (215.716, 228.724, 328.452, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 142 16.00 P 2008 15.00 O 24191 8.00 N 18143 7.00 C 55494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 3 28 " - pdb=" SG CYS 3 38 " distance=2.72 Simple disulfide: pdb=" SG CYS 3 28 " - pdb=" SG CYS 3 43 " distance=2.61 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 Atom "ATOM 80398 O5' G 13199 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 37.86 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb=" ZN u 201 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 36 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 32 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 9 " Number of angles added : 6 13872 Ramachandran restraints generated. 6936 Oldfield, 0 Emsley, 6936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13416 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 75 sheets defined 39.7% alpha, 13.9% beta 600 base pairs and 1018 stacking pairs defined. Time for finding SS restraints: 31.43 Creating SS restraints... Processing helix chain 'x' and resid 12 through 19 Processing helix chain 'x' and resid 21 through 44 removed outlier: 4.356A pdb=" N ASN x 27 " --> pdb=" O LYS x 23 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS x 28 " --> pdb=" O HIS x 24 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU x 40 " --> pdb=" O LYS x 36 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU x 43 " --> pdb=" O LYS x 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 45 through 50 removed outlier: 3.638A pdb=" N GLN x 50 " --> pdb=" O GLU x 46 " (cutoff:3.500A) Processing helix chain 'x' and resid 50 through 55 removed outlier: 3.735A pdb=" N GLU x 54 " --> pdb=" O GLN x 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 79 through 86 removed outlier: 3.995A pdb=" N ARG x 83 " --> pdb=" O ASP x 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN x 86 " --> pdb=" O MET x 82 " (cutoff:3.500A) Processing helix chain 'x' and resid 104 through 118 removed outlier: 3.703A pdb=" N TYR x 108 " --> pdb=" O LYS x 104 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE x 113 " --> pdb=" O GLU x 109 " (cutoff:3.500A) Processing helix chain 'x' and resid 132 through 142 Processing helix chain 'x' and resid 206 through 218 removed outlier: 3.703A pdb=" N VAL x 210 " --> pdb=" O LEU x 206 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG x 212 " --> pdb=" O GLN x 208 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER x 216 " --> pdb=" O ARG x 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 72 removed outlier: 3.612A pdb=" N SER F 16 " --> pdb=" O GLN F 12 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS F 70 " --> pdb=" O LYS F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.764A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 130 removed outlier: 3.506A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS F 128 " --> pdb=" O LEU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 133 No H-bonds generated for 'chain 'F' and resid 131 through 133' Processing helix chain 'F' and resid 140 through 152 removed outlier: 3.912A pdb=" N ILE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 Processing helix chain 'F' and resid 174 through 177 removed outlier: 3.657A pdb=" N GLY F 177 " --> pdb=" O GLY F 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 174 through 177' Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 222 through 226 Processing helix chain 'F' and resid 235 through 244 removed outlier: 3.545A pdb=" N SER F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 12 removed outlier: 3.915A pdb=" N GLN 3 8 " --> pdb=" O GLU 3 4 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL 3 9 " --> pdb=" O ILE 3 5 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN 3 12 " --> pdb=" O GLN 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 67 through 72 removed outlier: 3.642A pdb=" N ALA 3 70 " --> pdb=" O PRO 3 67 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N HIS 3 71 " --> pdb=" O GLU 3 68 " (cutoff:3.500A) Processing helix chain '3' and resid 85 through 98 removed outlier: 3.620A pdb=" N GLN 3 91 " --> pdb=" O THR 3 87 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS 3 96 " --> pdb=" O GLN 3 92 " (cutoff:3.500A) Processing helix chain '3' and resid 101 through 117 removed outlier: 4.439A pdb=" N LYS 3 109 " --> pdb=" O ARG 3 105 " (cutoff:3.500A) Processing helix chain '3' and resid 121 through 126 Processing helix chain '3' and resid 140 through 145 Processing helix chain '3' and resid 146 through 157 removed outlier: 3.760A pdb=" N ARG 3 150 " --> pdb=" O GLN 3 146 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS 3 151 " --> pdb=" O ASN 3 147 " (cutoff:3.500A) Processing helix chain '3' and resid 157 through 168 removed outlier: 3.613A pdb=" N ALA 3 161 " --> pdb=" O LYS 3 157 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 11 Processing helix chain '4' and resid 14 through 32 removed outlier: 3.775A pdb=" N ARG 4 18 " --> pdb=" O ASN 4 14 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN 4 20 " --> pdb=" O LYS 4 16 " (cutoff:3.500A) Processing helix chain '4' and resid 38 through 55 removed outlier: 3.627A pdb=" N TYR 4 51 " --> pdb=" O LYS 4 47 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA 4 52 " --> pdb=" O GLY 4 48 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET 4 53 " --> pdb=" O LEU 4 49 " (cutoff:3.500A) Processing helix chain '4' and resid 61 through 71 removed outlier: 4.485A pdb=" N ASN 4 67 " --> pdb=" O GLN 4 63 " (cutoff:3.500A) Processing helix chain '4' and resid 71 through 76 Processing helix chain '4' and resid 91 through 109 removed outlier: 3.530A pdb=" N LYS 4 97 " --> pdb=" O LYS 4 93 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG 4 100 " --> pdb=" O ILE 4 96 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE 4 102 " --> pdb=" O PHE 4 98 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS 4 107 " --> pdb=" O TRP 4 103 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 135 removed outlier: 3.600A pdb=" N TYR 4 121 " --> pdb=" O ARG 4 117 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU 4 129 " --> pdb=" O ILE 4 125 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU 4 133 " --> pdb=" O LEU 4 129 " (cutoff:3.500A) Processing helix chain '4' and resid 142 through 150 removed outlier: 4.084A pdb=" N ASP 4 147 " --> pdb=" O LYS 4 143 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU 4 148 " --> pdb=" O LYS 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 182 removed outlier: 3.882A pdb=" N ILE 4 171 " --> pdb=" O THR 4 167 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU 4 178 " --> pdb=" O VAL 4 174 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP 4 179 " --> pdb=" O ASP 4 175 " (cutoff:3.500A) Processing helix chain '4' and resid 218 through 218 No H-bonds generated for 'chain '4' and resid 218 through 218' Processing helix chain '4' and resid 221 through 226 removed outlier: 4.241A pdb=" N ALA 4 226 " --> pdb=" O GLN 4 222 " (cutoff:3.500A) Processing helix chain '4' and resid 231 through 242 removed outlier: 3.680A pdb=" N LYS 4 239 " --> pdb=" O ARG 4 235 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU 4 240 " --> pdb=" O GLU 4 236 " (cutoff:3.500A) Processing helix chain '5' and resid 119 through 127 removed outlier: 4.029A pdb=" N LEU 5 123 " --> pdb=" O ASP 5 119 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU 5 126 " --> pdb=" O LYS 5 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.929A pdb=" N LEU A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.795A pdb=" N ALA A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.538A pdb=" N PHE A 143 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 159 removed outlier: 4.634A pdb=" N ILE A 152 " --> pdb=" O HIS A 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 14 through 28 removed outlier: 3.650A pdb=" N VAL b 21 " --> pdb=" O LEU b 17 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN b 23 " --> pdb=" O ASP b 19 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN b 26 " --> pdb=" O LEU b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 66 removed outlier: 3.544A pdb=" N TYR b 52 " --> pdb=" O ARG b 48 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL b 58 " --> pdb=" O GLY b 54 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE b 64 " --> pdb=" O LYS b 60 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS b 66 " --> pdb=" O GLU b 62 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 84 removed outlier: 3.796A pdb=" N ASP b 80 " --> pdb=" O PRO b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 117 removed outlier: 4.206A pdb=" N ILE b 98 " --> pdb=" O SER b 94 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER b 99 " --> pdb=" O LEU b 95 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER b 103 " --> pdb=" O SER b 99 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU b 106 " --> pdb=" O LYS b 102 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG b 114 " --> pdb=" O ARG b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 142 removed outlier: 3.550A pdb=" N LYS b 129 " --> pdb=" O CYS b 125 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE b 139 " --> pdb=" O ARG b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 160 removed outlier: 3.956A pdb=" N TYR b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 removed outlier: 4.336A pdb=" N CYS b 186 " --> pdb=" O SER b 182 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE b 187 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR b 188 " --> pdb=" O LEU b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.777A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE b 243 " --> pdb=" O SER b 239 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA b 244 " --> pdb=" O ILE b 240 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS b 245 " --> pdb=" O TYR b 241 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU b 246 " --> pdb=" O ALA b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 274 removed outlier: 3.646A pdb=" N GLN b 267 " --> pdb=" O THR b 263 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS b 269 " --> pdb=" O GLU b 265 " (cutoff:3.500A) Processing helix chain 'b' and resid 274 through 279 removed outlier: 4.308A pdb=" N PHE b 278 " --> pdb=" O ILE b 274 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA b 279 " --> pdb=" O LYS b 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 274 through 279' Processing helix chain 'b' and resid 280 through 282 No H-bonds generated for 'chain 'b' and resid 280 through 282' Processing helix chain 'b' and resid 308 through 312 removed outlier: 3.714A pdb=" N GLU b 311 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 342 removed outlier: 4.276A pdb=" N VAL b 328 " --> pdb=" O LEU b 324 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL b 331 " --> pdb=" O ASN b 327 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG b 332 " --> pdb=" O VAL b 328 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU b 337 " --> pdb=" O ASN b 333 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU b 340 " --> pdb=" O CYS b 336 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA b 341 " --> pdb=" O GLU b 337 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER b 342 " --> pdb=" O LYS b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 removed outlier: 3.976A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU b 385 " --> pdb=" O SER b 381 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 407 removed outlier: 3.621A pdb=" N ALA b 404 " --> pdb=" O ARG b 400 " (cutoff:3.500A) Processing helix chain 'b' and resid 424 through 429 removed outlier: 3.943A pdb=" N TRP b 427 " --> pdb=" O ASP b 424 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS b 428 " --> pdb=" O ASP b 425 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN b 429 " --> pdb=" O GLU b 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 424 through 429' Processing helix chain 'b' and resid 442 through 444 No H-bonds generated for 'chain 'b' and resid 442 through 444' Processing helix chain 'b' and resid 448 through 465 removed outlier: 3.621A pdb=" N LYS b 452 " --> pdb=" O GLU b 448 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU b 459 " --> pdb=" O ALA b 455 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU b 461 " --> pdb=" O GLU b 457 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS b 462 " --> pdb=" O GLU b 458 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN b 465 " --> pdb=" O GLU b 461 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 208 removed outlier: 3.699A pdb=" N HIS J 203 " --> pdb=" O LYS J 199 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU J 206 " --> pdb=" O LYS J 202 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG J 207 " --> pdb=" O HIS J 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 221 removed outlier: 3.685A pdb=" N HIS J 220 " --> pdb=" O SER J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 259 removed outlier: 3.967A pdb=" N LEU J 244 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE J 246 " --> pdb=" O ARG J 242 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA J 253 " --> pdb=" O GLN J 249 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL J 254 " --> pdb=" O SER J 250 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU J 255 " --> pdb=" O LEU J 251 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL J 256 " --> pdb=" O ASP J 252 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP J 259 " --> pdb=" O LEU J 255 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 removed outlier: 3.614A pdb=" N HIS r 10 " --> pdb=" O TYR r 6 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 41 removed outlier: 4.506A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER r 36 " --> pdb=" O SER r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 43 through 70 removed outlier: 3.734A pdb=" N GLY r 47 " --> pdb=" O THR r 43 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS r 52 " --> pdb=" O LYS r 48 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA r 56 " --> pdb=" O LYS r 52 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS r 68 " --> pdb=" O LYS r 64 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 17 Processing helix chain 's' and resid 19 through 32 removed outlier: 4.141A pdb=" N ALA s 25 " --> pdb=" O LYS s 21 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU s 30 " --> pdb=" O HIS s 26 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS s 31 " --> pdb=" O ARG s 27 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS s 32 " --> pdb=" O LYS s 28 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 removed outlier: 3.796A pdb=" N GLN u 42 " --> pdb=" O LYS u 38 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 57 removed outlier: 4.128A pdb=" N ARG u 56 " --> pdb=" O THR u 52 " (cutoff:3.500A) Processing helix chain 'u' and resid 88 through 113 removed outlier: 3.643A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU u 98 " --> pdb=" O ALA u 94 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU u 104 " --> pdb=" O ARG u 100 " (cutoff:3.500A) Processing helix chain 'v' and resid 4 through 12 removed outlier: 3.517A pdb=" N LYS v 8 " --> pdb=" O VAL v 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET v 9 " --> pdb=" O ARG v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 39 removed outlier: 3.745A pdb=" N ALA v 38 " --> pdb=" O PRO v 34 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN v 39 " --> pdb=" O ILE v 35 " (cutoff:3.500A) Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 158 through 163 Processing helix chain 'v' and resid 164 through 166 No H-bonds generated for 'chain 'v' and resid 164 through 166' Processing helix chain 'v' and resid 178 through 193 removed outlier: 3.562A pdb=" N GLU v 183 " --> pdb=" O GLU v 179 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS v 191 " --> pdb=" O LYS v 187 " (cutoff:3.500A) Processing helix chain 'v' and resid 195 through 201 Processing helix chain 'v' and resid 211 through 226 removed outlier: 3.534A pdb=" N ARG v 225 " --> pdb=" O ARG v 221 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.918A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG W 25 " --> pdb=" O GLU W 21 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG W 31 " --> pdb=" O PHE W 27 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 60 removed outlier: 4.060A pdb=" N TRP W 60 " --> pdb=" O ILE W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 removed outlier: 3.945A pdb=" N LEU W 77 " --> pdb=" O LEU W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 89 through 96 removed outlier: 4.033A pdb=" N SER W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS W 96 " --> pdb=" O LEU W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 removed outlier: 3.642A pdb=" N VAL W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR W 115 " --> pdb=" O THR W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 161 through 168 removed outlier: 3.538A pdb=" N ASN W 167 " --> pdb=" O PRO W 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 196 through 206 removed outlier: 4.011A pdb=" N LEU W 203 " --> pdb=" O GLN W 199 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 42 removed outlier: 3.941A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) Processing helix chain 'y' and resid 59 through 63 removed outlier: 3.808A pdb=" N THR y 63 " --> pdb=" O GLY y 60 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 88 removed outlier: 3.686A pdb=" N ARG y 85 " --> pdb=" O LEU y 81 " (cutoff:3.500A) Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 133 removed outlier: 3.911A pdb=" N GLU y 126 " --> pdb=" O ASP y 122 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP y 131 " --> pdb=" O GLU y 127 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 175 removed outlier: 3.674A pdb=" N LEU y 173 " --> pdb=" O ASP y 169 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER y 175 " --> pdb=" O GLU y 171 " (cutoff:3.500A) Processing helix chain 'y' and resid 211 through 222 removed outlier: 3.619A pdb=" N VAL y 217 " --> pdb=" O PRO y 213 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 17 removed outlier: 3.805A pdb=" N LEU z 11 " --> pdb=" O ALA z 7 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN z 12 " --> pdb=" O SER z 8 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER z 15 " --> pdb=" O LEU z 11 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL z 16 " --> pdb=" O ASN z 12 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS z 17 " --> pdb=" O ALA z 13 " (cutoff:3.500A) Processing helix chain 'z' and resid 18 through 22 removed outlier: 5.833A pdb=" N VAL z 21 " --> pdb=" O ARG z 18 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE z 22 " --> pdb=" O ARG z 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 18 through 22' Processing helix chain 'z' and resid 23 through 34 removed outlier: 3.773A pdb=" N ASP z 27 " --> pdb=" O GLN z 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN z 31 " --> pdb=" O ASP z 27 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG z 32 " --> pdb=" O ALA z 28 " (cutoff:3.500A) Processing helix chain 'z' and resid 35 through 56 removed outlier: 3.541A pdb=" N LEU z 41 " --> pdb=" O LEU z 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU z 53 " --> pdb=" O LEU z 49 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN z 55 " --> pdb=" O LYS z 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 117 removed outlier: 3.525A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.830A pdb=" N GLU B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'C' and resid 31 through 44 removed outlier: 4.564A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.585A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 138 Processing helix chain 'C' and resid 154 through 157 Processing helix chain 'C' and resid 161 through 173 removed outlier: 3.710A pdb=" N ALA C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 184 removed outlier: 3.563A pdb=" N LEU C 179 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 195 removed outlier: 3.616A pdb=" N ARG C 195 " --> pdb=" O GLY C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.343A pdb=" N ASN C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.510A pdb=" N LEU C 238 " --> pdb=" O ASN C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.989A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 322 through 327 removed outlier: 3.596A pdb=" N ARG C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 337 removed outlier: 3.544A pdb=" N GLU C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 45 Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 83 removed outlier: 3.638A pdb=" N GLU e 83 " --> pdb=" O VAL e 79 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 88 removed outlier: 4.306A pdb=" N MET e 87 " --> pdb=" O THR e 84 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 4.449A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG e 111 " --> pdb=" O VAL e 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.663A pdb=" N ALA E 107 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 152 removed outlier: 3.616A pdb=" N GLU E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR E 152 " --> pdb=" O GLU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.534A pdb=" N SER E 160 " --> pdb=" O LYS E 156 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 43 removed outlier: 3.654A pdb=" N ALA f 41 " --> pdb=" O THR f 37 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 101 through 117 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 160 through 165 removed outlier: 4.770A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 173 Processing helix chain 'G' and resid 182 through 189 removed outlier: 3.987A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'h' and resid 5 through 11 removed outlier: 3.993A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 34 removed outlier: 3.659A pdb=" N GLU h 27 " --> pdb=" O ASP h 23 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 70 removed outlier: 4.012A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG h 63 " --> pdb=" O ASN h 59 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU h 69 " --> pdb=" O ALA h 65 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 90 Processing helix chain 'h' and resid 93 through 99 removed outlier: 3.729A pdb=" N SER h 98 " --> pdb=" O LYS h 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.600A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N MET H 78 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL H 82 " --> pdb=" O MET H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'H' and resid 150 through 164 removed outlier: 3.545A pdb=" N VAL H 154 " --> pdb=" O SER H 150 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 49 removed outlier: 3.729A pdb=" N GLY i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 63 removed outlier: 4.101A pdb=" N ASP i 59 " --> pdb=" O ARG i 55 " (cutoff:3.500A) Processing helix chain 'i' and resid 64 through 77 removed outlier: 4.244A pdb=" N ARG i 68 " --> pdb=" O SER i 64 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS i 71 " --> pdb=" O LYS i 67 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL i 72 " --> pdb=" O ARG i 68 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 99 removed outlier: 3.586A pdb=" N ASN i 92 " --> pdb=" O GLU i 88 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG i 98 " --> pdb=" O ILE i 94 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG i 99 " --> pdb=" O ALA i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 55 removed outlier: 3.775A pdb=" N ARG j 55 " --> pdb=" O ALA j 51 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 68 No H-bonds generated for 'chain 'j' and resid 66 through 68' Processing helix chain 'j' and resid 69 through 75 Processing helix chain 'L' and resid 27 through 46 removed outlier: 3.693A pdb=" N ASN L 37 " --> pdb=" O VAL L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 92 Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 95 removed outlier: 3.662A pdb=" N LYS M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 111 removed outlier: 3.618A pdb=" N ARG M 109 " --> pdb=" O GLN M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 135 removed outlier: 3.625A pdb=" N TYR M 129 " --> pdb=" O LYS M 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.621A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.668A pdb=" N LEU N 22 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG N 24 " --> pdb=" O ARG N 20 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL N 25 " --> pdb=" O PHE N 21 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 50 Processing helix chain 'N' and resid 97 through 110 removed outlier: 3.940A pdb=" N THR N 101 " --> pdb=" O SER N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 145 removed outlier: 3.918A pdb=" N ASP N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix removed outlier: 3.643A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.635A pdb=" N GLY N 163 " --> pdb=" O GLU N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 172 Processing helix chain 'N' and resid 188 through 195 Processing helix chain 'O' and resid 15 through 29 removed outlier: 4.244A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU O 27 " --> pdb=" O VAL O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 51 removed outlier: 4.408A pdb=" N ASN O 50 " --> pdb=" O GLU O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 60 Processing helix chain 'O' and resid 65 through 69 Processing helix chain 'O' and resid 75 through 84 Processing helix chain 'O' and resid 138 through 144 Processing helix chain 'O' and resid 149 through 159 Processing helix chain 'O' and resid 160 through 185 removed outlier: 4.114A pdb=" N GLU O 166 " --> pdb=" O VAL O 162 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR O 167 " --> pdb=" O SER O 163 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL O 178 " --> pdb=" O PHE O 174 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA O 183 " --> pdb=" O ALA O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 198 Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.504A pdb=" N THR P 29 " --> pdb=" O SER P 25 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 76 Processing helix chain 'P' and resid 84 through 105 removed outlier: 3.924A pdb=" N VAL P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 41 removed outlier: 3.879A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG Q 38 " --> pdb=" O THR Q 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP Q 41 " --> pdb=" O ALA Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 54 removed outlier: 4.114A pdb=" N LYS Q 50 " --> pdb=" O LYS Q 46 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 71 removed outlier: 3.503A pdb=" N ALA Q 70 " --> pdb=" O ARG Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 116 Processing helix chain 'Q' and resid 124 through 131 Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.618A pdb=" N TYR S 43 " --> pdb=" O SER S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 113 Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'V' and resid 119 through 124 removed outlier: 3.537A pdb=" N ASP V 124 " --> pdb=" O LYS V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 128 through 132 Processing helix chain 'Y' and resid 11 through 20 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 3.759A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 43 Processing helix chain 'Y' and resid 75 through 78 Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'K' and resid 33 through 49 removed outlier: 3.697A pdb=" N VAL K 37 " --> pdb=" O PRO K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 77 Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 130 through 135 Processing helix chain 'K' and resid 136 through 145 removed outlier: 3.957A pdb=" N LEU K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 175 Processing helix chain 'K' and resid 184 through 188 removed outlier: 4.550A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 188' Processing helix chain 'K' and resid 189 through 194 removed outlier: 3.793A pdb=" N LEU K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 232 removed outlier: 3.822A pdb=" N LEU K 222 " --> pdb=" O SER K 218 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN K 225 " --> pdb=" O THR K 221 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 274 removed outlier: 3.825A pdb=" N ASP K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS K 272 " --> pdb=" O GLU K 268 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA K 273 " --> pdb=" O GLN K 269 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR K 274 " --> pdb=" O LEU K 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 301 removed outlier: 3.548A pdb=" N GLU K 300 " --> pdb=" O VAL K 297 " (cutoff:3.500A) Processing helix chain 'm' and resid 262 through 266 Processing helix chain 'm' and resid 269 through 285 removed outlier: 4.061A pdb=" N ARG m 281 " --> pdb=" O MET m 277 " (cutoff:3.500A) Processing helix chain 'm' and resid 290 through 300 removed outlier: 3.962A pdb=" N LYS m 295 " --> pdb=" O PRO m 291 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU m 296 " --> pdb=" O LYS m 292 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS m 298 " --> pdb=" O LEU m 294 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS m 300 " --> pdb=" O GLU m 296 " (cutoff:3.500A) Processing helix chain 'm' and resid 349 through 357 removed outlier: 3.749A pdb=" N GLU m 355 " --> pdb=" O LYS m 351 " (cutoff:3.500A) Processing helix chain 'm' and resid 383 through 396 removed outlier: 3.708A pdb=" N TYR m 395 " --> pdb=" O SER m 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 287 removed outlier: 4.394A pdb=" N LEU D 278 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS D 285 " --> pdb=" O PHE D 281 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 312 removed outlier: 4.507A pdb=" N GLU D 307 " --> pdb=" O LYS D 303 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 337 removed outlier: 3.688A pdb=" N PHE D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU D 334 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 378 removed outlier: 4.319A pdb=" N HIS D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 434 removed outlier: 3.815A pdb=" N LYS D 434 " --> pdb=" O GLU D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 456 removed outlier: 3.899A pdb=" N SER D 449 " --> pdb=" O ASP D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 475 removed outlier: 3.594A pdb=" N ALA D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 475 " --> pdb=" O ALA D 471 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 111 Processing helix chain 'o' and resid 141 through 153 Processing helix chain 'o' and resid 192 through 212 removed outlier: 3.755A pdb=" N LEU o 211 " --> pdb=" O ARG o 207 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA o 212 " --> pdb=" O ILE o 208 " (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 64 through 72 Processing helix chain 'n' and resid 74 through 97 removed outlier: 3.726A pdb=" N ALA n 78 " --> pdb=" O GLU n 74 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA n 93 " --> pdb=" O LYS n 89 " (cutoff:3.500A) Processing helix chain 'n' and resid 99 through 108 Processing helix chain 'n' and resid 115 through 120 removed outlier: 3.886A pdb=" N LYS n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU n 120 " --> pdb=" O HIS n 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 115 through 120' Processing helix chain 'n' and resid 124 through 144 removed outlier: 4.345A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN n 137 " --> pdb=" O ASP n 133 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET n 138 " --> pdb=" O ASP n 134 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU n 139 " --> pdb=" O ALA n 135 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN n 144 " --> pdb=" O PHE n 140 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 173 removed outlier: 3.508A pdb=" N ILE n 156 " --> pdb=" O SER n 152 " (cutoff:3.500A) Processing helix chain 'n' and resid 216 through 241 removed outlier: 3.682A pdb=" N THR n 220 " --> pdb=" O ARG n 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR n 227 " --> pdb=" O GLU n 223 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 254 Processing helix chain 'n' and resid 354 through 359 Processing helix chain 'n' and resid 376 through 384 Processing helix chain 'n' and resid 391 through 394 Processing helix chain 'n' and resid 428 through 430 No H-bonds generated for 'chain 'n' and resid 428 through 430' Processing helix chain 'n' and resid 431 through 439 removed outlier: 4.386A pdb=" N ASN n 437 " --> pdb=" O PHE n 433 " (cutoff:3.500A) Processing helix chain 'n' and resid 443 through 447 removed outlier: 4.009A pdb=" N LYS n 446 " --> pdb=" O PRO n 443 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 87 removed outlier: 3.983A pdb=" N THR t 65 " --> pdb=" O ILE t 61 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG t 70 " --> pdb=" O LEU t 66 " (cutoff:3.500A) Processing helix chain 't' and resid 156 through 166 removed outlier: 3.747A pdb=" N ILE t 162 " --> pdb=" O LYS t 158 " (cutoff:3.500A) Processing helix chain 't' and resid 182 through 191 removed outlier: 4.246A pdb=" N LEU t 186 " --> pdb=" O ASN t 182 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS t 188 " --> pdb=" O TYR t 184 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL t 189 " --> pdb=" O PRO t 185 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE t 190 " --> pdb=" O LEU t 186 " (cutoff:3.500A) Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 232 through 239 Processing helix chain 't' and resid 246 through 256 Processing helix chain 't' and resid 260 through 265 Processing helix chain 't' and resid 281 through 299 removed outlier: 3.657A pdb=" N ARG t 285 " --> pdb=" O GLY t 281 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU t 286 " --> pdb=" O SER t 282 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER t 296 " --> pdb=" O ARG t 292 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG t 297 " --> pdb=" O GLU t 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'x' and resid 120 through 123 removed outlier: 6.528A pdb=" N ILE x 95 " --> pdb=" O THR x 122 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP x 146 " --> pdb=" O LYS x 94 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY x 159 " --> pdb=" O ASN x 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 196 through 198 removed outlier: 3.900A pdb=" N ARG x 253 " --> pdb=" O LYS x 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 83 through 87 Processing sheet with id=AA4, first strand: chain 'F' and resid 135 through 136 Processing sheet with id=AA5, first strand: chain 'F' and resid 153 through 155 Processing sheet with id=AA6, first strand: chain '3' and resid 50 through 55 Processing sheet with id=AA7, first strand: chain '3' and resid 135 through 136 Processing sheet with id=AA8, first strand: chain '5' and resid 34 through 38 removed outlier: 6.770A pdb=" N ARG 5 2 " --> pdb=" O LEU 5 410 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE 5 406 " --> pdb=" O SER 5 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 51 through 52 removed outlier: 6.159A pdb=" N VAL 5 67 " --> pdb=" O SER 5 113 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER 5 113 " --> pdb=" O VAL 5 67 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU 5 69 " --> pdb=" O THR 5 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 140 through 145 removed outlier: 6.668A pdb=" N ALA 5 158 " --> pdb=" O VAL 5 141 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU 5 143 " --> pdb=" O VAL 5 156 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL 5 156 " --> pdb=" O LEU 5 143 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N THR 5 154 " --> pdb=" O PRO 5 145 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU 5 163 " --> pdb=" O THR 5 159 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA 5 179 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS 5 168 " --> pdb=" O LYS 5 177 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS 5 177 " --> pdb=" O LYS 5 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '5' and resid 189 through 192 removed outlier: 4.805A pdb=" N GLY 5 209 " --> pdb=" O LEU 5 213 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU 5 213 " --> pdb=" O GLY 5 209 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP 5 230 " --> pdb=" O LEU 5 216 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU 5 218 " --> pdb=" O GLN 5 228 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLN 5 228 " --> pdb=" O GLU 5 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '5' and resid 248 through 251 removed outlier: 4.667A pdb=" N HIS 5 278 " --> pdb=" O THR 5 274 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA 5 292 " --> pdb=" O LYS 5 281 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '5' and resid 303 through 308 removed outlier: 5.288A pdb=" N GLN 5 305 " --> pdb=" O THR 5 336 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR 5 336 " --> pdb=" O GLN 5 305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '5' and resid 369 through 370 removed outlier: 6.420A pdb=" N VAL 5 384 " --> pdb=" O LYS 5 397 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS 5 397 " --> pdb=" O VAL 5 384 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE 5 386 " --> pdb=" O LEU 5 395 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS 5 393 " --> pdb=" O ASP 5 388 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 35 through 37 removed outlier: 4.214A pdb=" N TYR A 98 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 137 through 138 removed outlier: 5.867A pdb=" N LEU A 137 " --> pdb=" O VAL J 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 176 through 177 removed outlier: 3.605A pdb=" N VAL A 176 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR A 191 " --> pdb=" O VAL A 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 180 through 182 removed outlier: 4.258A pdb=" N SER A 180 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 182 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 185 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 168 through 172 removed outlier: 4.174A pdb=" N ARG b 168 " --> pdb=" O ARG b 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 251 through 255 removed outlier: 6.356A pdb=" N TYR b 252 " --> pdb=" O VAL b 286 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN b 288 " --> pdb=" O TYR b 252 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N MET b 254 " --> pdb=" O ASN b 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'b' and resid 435 through 436 removed outlier: 3.806A pdb=" N LYS b 439 " --> pdb=" O LEU b 436 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'u' and resid 4 through 5 removed outlier: 3.732A pdb=" N TYR u 4 " --> pdb=" O CYS u 13 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'u' and resid 28 through 30 removed outlier: 3.634A pdb=" N TYR V 94 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL u 22 " --> pdb=" O TYR V 94 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU V 93 " --> pdb=" O TRP V 85 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 64 through 66 removed outlier: 3.552A pdb=" N VAL W 42 " --> pdb=" O ALA W 219 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS W 44 " --> pdb=" O VAL W 217 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL W 217 " --> pdb=" O HIS W 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 120 through 123 Processing sheet with id=AC8, first strand: chain 'W' and resid 174 through 176 Processing sheet with id=AC9, first strand: chain 'y' and resid 2 through 4 Processing sheet with id=AD1, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.859A pdb=" N CYS y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'y' and resid 64 through 65 removed outlier: 6.438A pdb=" N LEU y 70 " --> pdb=" O GLN y 95 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'y' and resid 109 through 110 Processing sheet with id=AD4, first strand: chain 'y' and resid 152 through 154 removed outlier: 6.563A pdb=" N GLY y 159 " --> pdb=" O VAL y 182 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 355 through 359 removed outlier: 4.859A pdb=" N SER B 355 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP B 59 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILE B 359 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 217 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B 278 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ALA B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR B 276 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 57 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU B 74 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.213A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 157 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 162 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.213A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 15 through 21 removed outlier: 6.009A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 8 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL C 151 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C 150 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 62 through 64 Processing sheet with id=AE1, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AE2, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.390A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'E' and resid 77 through 80 removed outlier: 6.506A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'f' and resid 8 through 16 removed outlier: 6.540A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 177 through 180 removed outlier: 6.233A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'h' and resid 115 through 118 removed outlier: 4.734A pdb=" N LYS h 115 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE8, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE9, first strand: chain 'H' and resid 33 through 37 Processing sheet with id=AF1, first strand: chain 'H' and resid 133 through 136 removed outlier: 3.560A pdb=" N LYS H 87 " --> pdb=" O GLY H 185 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG H 91 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL H 181 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL H 93 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE H 179 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 102 through 104 removed outlier: 3.501A pdb=" N ASN H 102 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'j' and resid 16 through 17 removed outlier: 3.558A pdb=" N THR j 33 " --> pdb=" O HIS j 28 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 23 through 24 removed outlier: 7.121A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'L' and resid 58 through 59 Processing sheet with id=AF6, first strand: chain 'M' and resid 32 through 34 removed outlier: 5.758A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 37 through 38 removed outlier: 5.315A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.400A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.400A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN N 122 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.527A pdb=" N LEU P 148 " --> pdb=" O ALA P 17 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL P 149 " --> pdb=" O SER P 115 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.527A pdb=" N LEU P 148 " --> pdb=" O ALA P 17 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Q' and resid 62 through 63 removed outlier: 4.484A pdb=" N VAL Q 101 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL Q 83 " --> pdb=" O VAL Q 101 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA Q 103 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY Q 85 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Q' and resid 62 through 63 removed outlier: 3.760A pdb=" N LEU Q 138 " --> pdb=" O THR Q 80 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 27 through 31 removed outlier: 7.325A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 88 through 96 removed outlier: 7.050A pdb=" N ASN S 74 " --> pdb=" O GLU S 128 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU S 128 " --> pdb=" O ASN S 74 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY S 76 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL S 126 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'V' and resid 22 through 24 removed outlier: 7.146A pdb=" N ASN V 33 " --> pdb=" O LYS V 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS V 63 " --> pdb=" O ASN V 33 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET V 74 " --> pdb=" O ALA V 60 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'V' and resid 114 through 118 removed outlier: 6.025A pdb=" N SER V 133 " --> pdb=" O ILE V 114 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N GLY V 116 " --> pdb=" O SER V 133 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL V 135 " --> pdb=" O GLY V 116 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AH1, first strand: chain 'Y' and resid 94 through 99 removed outlier: 3.509A pdb=" N ILE Y 97 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL Y 85 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N LEU Y 99 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N ASP Y 83 " --> pdb=" O LEU Y 99 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA Y 79 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL Y 73 " --> pdb=" O ALA Y 79 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLN Y 81 " --> pdb=" O SER Y 71 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP Y 83 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS Y 69 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL Y 85 " --> pdb=" O GLU Y 67 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N GLU Y 67 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 243 through 250 removed outlier: 3.554A pdb=" N LEU K 248 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN K 79 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 98 through 101 Processing sheet with id=AH4, first strand: chain 'K' and resid 151 through 155 removed outlier: 6.779A pdb=" N VAL K 123 " --> pdb=" O GLU K 153 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE K 155 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU K 125 " --> pdb=" O ILE K 155 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE K 180 " --> pdb=" O ILE K 207 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE K 209 " --> pdb=" O ILE K 180 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA K 182 " --> pdb=" O ILE K 209 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 212 through 213 Processing sheet with id=AH6, first strand: chain 'D' and resid 317 through 318 removed outlier: 6.317A pdb=" N LEU D 317 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N THR D 346 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 292 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N CYS D 345 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL D 294 " --> pdb=" O CYS D 345 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 391 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 363 " --> pdb=" O LEU D 391 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'o' and resid 117 through 124 removed outlier: 3.547A pdb=" N GLU o 119 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS o 160 " --> pdb=" O LEU o 157 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU o 157 " --> pdb=" O HIS o 160 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR o 155 " --> pdb=" O LEU o 162 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'n' and resid 178 through 181 removed outlier: 3.706A pdb=" N LYS n 178 " --> pdb=" O GLN n 189 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'n' and resid 386 through 389 Processing sheet with id=AI1, first strand: chain 't' and resid 129 through 130 removed outlier: 3.628A pdb=" N ILE t 129 " --> pdb=" O THR t 104 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR t 104 " --> pdb=" O ILE t 129 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 't' and resid 129 through 130 removed outlier: 3.628A pdb=" N ILE t 129 " --> pdb=" O THR t 104 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR t 104 " --> pdb=" O ILE t 129 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE t 99 " --> pdb=" O VAL t 309 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLU t 311 " --> pdb=" O PHE t 99 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU t 101 " --> pdb=" O GLU t 311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 't' and resid 174 through 179 1977 hydrogen bonds defined for protein. 5649 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1475 hydrogen bonds 2384 hydrogen bond angles 0 basepair planarities 600 basepair parallelities 1018 stacking parallelities Total time for adding SS restraints: 75.06 Time building geometry restraints manager: 40.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.52: 77271 1.52 - 1.83: 28847 1.83 - 2.13: 6 2.13 - 2.44: 0 2.44 - 2.75: 1 Bond restraints: 106125 Sorted by residual: bond pdb=" C GLU x 285 " pdb=" N MET x 286 " ideal model delta sigma weight residual 1.332 2.748 -1.415 1.40e-02 5.10e+03 1.02e+04 bond pdb=" C LEU Y 126 " pdb=" O LEU Y 126 " ideal model delta sigma weight residual 1.231 1.443 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" CZ ARG N 105 " pdb=" NH1 ARG N 105 " ideal model delta sigma weight residual 1.323 1.418 -0.095 1.40e-02 5.10e+03 4.58e+01 bond pdb=" NE ARG N 105 " pdb=" CZ ARG N 105 " ideal model delta sigma weight residual 1.326 1.391 -0.065 1.10e-02 8.26e+03 3.49e+01 bond pdb=" O5' A 11159 " pdb=" C5' A 11159 " ideal model delta sigma weight residual 1.424 1.512 -0.088 1.50e-02 4.44e+03 3.47e+01 ... (remaining 106120 not shown) Histogram of bond angle deviations from ideal: 95.58 - 103.63: 6789 103.63 - 111.68: 49969 111.68 - 119.72: 48198 119.72 - 127.77: 44452 127.77 - 135.81: 3530 Bond angle restraints: 152938 Sorted by residual: angle pdb=" O GLU x 285 " pdb=" C GLU x 285 " pdb=" N MET x 286 " ideal model delta sigma weight residual 122.09 103.98 18.11 1.23e+00 6.61e-01 2.17e+02 angle pdb=" O3' A 1 649 " pdb=" C3' A 1 649 " pdb=" C2' A 1 649 " ideal model delta sigma weight residual 113.70 129.27 -15.57 1.50e+00 4.44e-01 1.08e+02 angle pdb=" C4' U 11347 " pdb=" C3' U 11347 " pdb=" O3' U 11347 " ideal model delta sigma weight residual 113.00 128.28 -15.28 1.50e+00 4.44e-01 1.04e+02 angle pdb=" O3' C 1 480 " pdb=" C3' C 1 480 " pdb=" C2' C 1 480 " ideal model delta sigma weight residual 109.50 124.50 -15.00 1.50e+00 4.44e-01 1.00e+02 angle pdb=" CA GLU x 285 " pdb=" C GLU x 285 " pdb=" N MET x 286 " ideal model delta sigma weight residual 118.04 105.04 13.00 1.32e+00 5.74e-01 9.71e+01 ... (remaining 152933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 60337 35.86 - 71.73: 5920 71.73 - 107.59: 581 107.59 - 143.46: 10 143.46 - 179.32: 64 Dihedral angle restraints: 66912 sinusoidal: 46242 harmonic: 20670 Sorted by residual: dihedral pdb=" CA VAL 4 225 " pdb=" C VAL 4 225 " pdb=" N ALA 4 226 " pdb=" CA ALA 4 226 " ideal model delta harmonic sigma weight residual 180.00 90.00 90.00 0 5.00e+00 4.00e-02 3.24e+02 dihedral pdb=" CA GLU x 285 " pdb=" C GLU x 285 " pdb=" N MET x 286 " pdb=" CA MET x 286 " ideal model delta harmonic sigma weight residual 180.00 102.34 77.66 0 5.00e+00 4.00e-02 2.41e+02 dihedral pdb=" O4' U 13214 " pdb=" C1' U 13214 " pdb=" N1 U 13214 " pdb=" C2 U 13214 " ideal model delta sinusoidal sigma weight residual 200.00 22.80 177.20 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 66909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 17559 0.208 - 0.417: 1080 0.417 - 0.625: 36 0.625 - 0.834: 14 0.834 - 1.042: 2 Chirality restraints: 18691 Sorted by residual: chirality pdb=" C3' A 1 649 " pdb=" C4' A 1 649 " pdb=" O3' A 1 649 " pdb=" C2' A 1 649 " both_signs ideal model delta sigma weight residual False -2.48 -1.44 -1.04 2.00e-01 2.50e+01 2.71e+01 chirality pdb=" C3' U 11347 " pdb=" C4' U 11347 " pdb=" O3' U 11347 " pdb=" C2' U 11347 " both_signs ideal model delta sigma weight residual False -2.48 -1.55 -0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" C3' C 1 480 " pdb=" C4' C 1 480 " pdb=" O3' C 1 480 " pdb=" C2' C 1 480 " both_signs ideal model delta sigma weight residual False -2.74 -1.99 -0.76 2.00e-01 2.50e+01 1.44e+01 ... (remaining 18688 not shown) Planarity restraints: 11918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU x 285 " 0.134 2.00e-02 2.50e+03 2.10e-01 4.40e+02 pdb=" C GLU x 285 " -0.355 2.00e-02 2.50e+03 pdb=" O GLU x 285 " 0.173 2.00e-02 2.50e+03 pdb=" N MET x 286 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU 4 136 " -0.038 2.00e-02 2.50e+03 8.01e-02 6.42e+01 pdb=" C LEU 4 136 " 0.138 2.00e-02 2.50e+03 pdb=" O LEU 4 136 " -0.054 2.00e-02 2.50e+03 pdb=" N GLN 4 137 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 11389 " 0.069 2.00e-02 2.50e+03 2.94e-02 2.60e+01 pdb=" N9 G 11389 " -0.069 2.00e-02 2.50e+03 pdb=" C8 G 11389 " -0.015 2.00e-02 2.50e+03 pdb=" N7 G 11389 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G 11389 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G 11389 " 0.012 2.00e-02 2.50e+03 pdb=" O6 G 11389 " 0.016 2.00e-02 2.50e+03 pdb=" N1 G 11389 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G 11389 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G 11389 " -0.010 2.00e-02 2.50e+03 pdb=" N3 G 11389 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G 11389 " -0.007 2.00e-02 2.50e+03 ... (remaining 11915 not shown) Histogram of nonbonded interaction distances: 0.99 - 1.77: 44 1.77 - 2.55: 663 2.55 - 3.34: 109814 3.34 - 4.12: 294218 4.12 - 4.90: 448124 Warning: very small nonbonded interaction distances. Nonbonded interactions: 852863 Sorted by model distance: nonbonded pdb=" NH2 ARG G 84 " pdb=" NH1 ARG t 57 " model vdw 0.990 3.200 nonbonded pdb=" NE1 TRP 4 54 " pdb=" NE ARG 4 117 " model vdw 0.996 3.200 nonbonded pdb=" NH1 ARG G 84 " pdb=" NH2 ARG t 57 " model vdw 1.135 3.200 nonbonded pdb=" C5' U 2 127 " pdb=" OH TYR n 64 " model vdw 1.281 3.440 nonbonded pdb=" O LEU O 52 " pdb=" N TYR O 54 " model vdw 1.331 2.520 ... (remaining 852858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 7.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 19.640 Check model and map are aligned: 1.090 Set scattering table: 0.670 Process input model: 274.380 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 308.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.009 1.415 106125 Z= 0.573 Angle : 1.366 20.715 152938 Z= 0.878 Chirality : 0.106 1.042 18691 Planarity : 0.006 0.210 11918 Dihedral : 23.182 179.321 53490 Min Nonbonded Distance : 0.990 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 3.11 % Allowed : 9.40 % Favored : 87.49 % Rotamer: Outliers : 9.41 % Allowed : 13.59 % Favored : 77.00 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.15 (0.08), residues: 6936 helix: -3.24 (0.07), residues: 2562 sheet: -2.02 (0.15), residues: 914 loop : -2.51 (0.09), residues: 3460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP j 49 HIS 0.015 0.002 HIS e 88 PHE 0.044 0.003 PHE x 263 TYR 0.030 0.003 TYR v 50 ARG 0.016 0.001 ARG Y 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13872 Ramachandran restraints generated. 6936 Oldfield, 0 Emsley, 6936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13872 Ramachandran restraints generated. 6936 Oldfield, 0 Emsley, 6936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2342 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 581 poor density : 1761 time to evaluate : 6.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 14 LYS cc_start: 0.7677 (ttmm) cc_final: 0.7467 (ttpt) REVERT: x 15 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8139 (ttp-110) REVERT: x 17 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7924 (tm-30) REVERT: x 33 MET cc_start: 0.9183 (mmm) cc_final: 0.8755 (tmm) REVERT: x 40 GLU cc_start: 0.8194 (pp20) cc_final: 0.7459 (tp30) REVERT: x 50 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8235 (tp40) REVERT: x 80 ASP cc_start: 0.8373 (t0) cc_final: 0.8130 (t0) REVERT: x 83 ARG cc_start: 0.8766 (ttt180) cc_final: 0.8503 (tpt170) REVERT: x 88 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7669 (m-40) REVERT: x 105 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8295 (mttm) REVERT: x 109 GLU cc_start: 0.9615 (tp30) cc_final: 0.9378 (mm-30) REVERT: x 127 LYS cc_start: 0.8795 (mttt) cc_final: 0.8540 (pttt) REVERT: x 130 TYR cc_start: 0.8078 (m-80) cc_final: 0.7782 (m-10) REVERT: x 133 LYS cc_start: 0.8496 (tmtp) cc_final: 0.8038 (tttp) REVERT: x 223 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6769 (p0) REVERT: x 235 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: x 237 ASP cc_start: 0.9075 (t0) cc_final: 0.8720 (t0) REVERT: x 247 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8174 (m) REVERT: x 253 ARG cc_start: 0.8624 (ttt-90) cc_final: 0.8162 (tmm160) REVERT: x 274 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7776 (mp) REVERT: x 281 GLU cc_start: 0.9151 (tt0) cc_final: 0.8518 (tm-30) REVERT: x 286 MET cc_start: 0.8560 (mpp) cc_final: 0.8236 (mpp) REVERT: F 8 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9202 (p) REVERT: F 10 GLU cc_start: 0.9459 (mp0) cc_final: 0.8944 (mm-30) REVERT: F 19 GLN cc_start: 0.9193 (mt0) cc_final: 0.8981 (pt0) REVERT: F 21 LYS cc_start: 0.8837 (mttt) cc_final: 0.8308 (tptt) REVERT: F 39 GLU cc_start: 0.9278 (tt0) cc_final: 0.9077 (tm-30) REVERT: F 76 TYR cc_start: 0.8706 (t80) cc_final: 0.8225 (t80) REVERT: F 119 VAL cc_start: 0.9313 (OUTLIER) cc_final: 0.8932 (p) REVERT: F 121 LYS cc_start: 0.9377 (tptt) cc_final: 0.8762 (mptt) REVERT: F 125 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9140 (mt-10) REVERT: F 182 ASP cc_start: 0.9206 (m-30) cc_final: 0.8887 (t0) REVERT: 3 32 TYR cc_start: 0.8976 (m-80) cc_final: 0.8655 (m-10) REVERT: 3 56 ASP cc_start: 0.8858 (m-30) cc_final: 0.8575 (m-30) REVERT: 3 59 LYS cc_start: 0.8188 (mttt) cc_final: 0.7877 (mptt) REVERT: 3 91 GLN cc_start: 0.9578 (tt0) cc_final: 0.9231 (tm-30) REVERT: 3 92 GLN cc_start: 0.9485 (tp-100) cc_final: 0.9222 (tt0) REVERT: 3 95 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8949 (tt0) REVERT: 3 144 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7970 (mtm180) REVERT: 3 149 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8549 (tt0) REVERT: 3 150 ARG cc_start: 0.8883 (mtt180) cc_final: 0.8307 (tpt-90) REVERT: 3 160 LYS cc_start: 0.8950 (mttt) cc_final: 0.8586 (tppt) REVERT: 3 163 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9038 (tm-30) REVERT: 3 167 MET cc_start: 0.9473 (mmm) cc_final: 0.9233 (mmm) REVERT: 4 8 LYS cc_start: 0.9230 (pttt) cc_final: 0.8824 (mmmt) REVERT: 4 38 LYS cc_start: 0.8699 (mttm) cc_final: 0.8458 (mmmt) REVERT: 4 39 GLN cc_start: 0.8093 (mt0) cc_final: 0.7825 (tp40) REVERT: 4 43 ASN cc_start: 0.9087 (t0) cc_final: 0.8664 (m-40) REVERT: 4 50 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7807 (t80) REVERT: 4 75 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8064 (tp) REVERT: 4 99 SER cc_start: 0.9282 (OUTLIER) cc_final: 0.8975 (t) REVERT: 4 140 ASN cc_start: 0.7996 (p0) cc_final: 0.7643 (p0) REVERT: 4 153 VAL cc_start: 0.7027 (t) cc_final: 0.6816 (t) REVERT: 4 179 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8641 (t0) REVERT: 4 183 ARG cc_start: 0.8945 (ttm-80) cc_final: 0.8602 (mtp85) REVERT: 4 234 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8811 (tp) REVERT: 4 240 GLU cc_start: 0.9361 (tt0) cc_final: 0.9140 (mm-30) REVERT: 5 1 MET cc_start: 0.7920 (ptp) cc_final: 0.7040 (mtm) REVERT: 5 71 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8872 (tppt) REVERT: 5 75 HIS cc_start: 0.7230 (p90) cc_final: 0.7015 (p90) REVERT: 5 112 SER cc_start: 0.8287 (t) cc_final: 0.8046 (p) REVERT: 5 169 LYS cc_start: 0.8791 (tttt) cc_final: 0.8505 (tmtt) REVERT: 5 174 LYS cc_start: 0.9335 (mmmm) cc_final: 0.9105 (tptt) REVERT: 5 184 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8794 (mtmm) REVERT: 5 204 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8464 (mm) REVERT: 5 211 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8576 (tm-30) REVERT: 5 219 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8360 (tp) REVERT: 5 225 SER cc_start: 0.8497 (t) cc_final: 0.8086 (p) REVERT: 5 301 GLU cc_start: 0.9192 (tp30) cc_final: 0.8858 (tp30) REVERT: 5 306 MET cc_start: 0.9146 (ttt) cc_final: 0.8690 (ttt) REVERT: 5 337 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8579 (p0) REVERT: 5 409 MET cc_start: 0.8674 (ttm) cc_final: 0.7775 (ttm) REVERT: 5 412 ASP cc_start: 0.8155 (p0) cc_final: 0.7694 (p0) REVERT: A 58 HIS cc_start: 0.1593 (p-80) cc_final: 0.1153 (p90) REVERT: A 79 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8813 (mt-10) REVERT: A 92 ARG cc_start: 0.4675 (mtp85) cc_final: 0.4249 (mmt180) REVERT: A 141 GLN cc_start: 0.7426 (tp40) cc_final: 0.7216 (pp30) REVERT: A 142 ARG cc_start: 0.7019 (mtp180) cc_final: 0.6798 (mtp85) REVERT: A 177 MET cc_start: 0.8528 (mmm) cc_final: 0.8160 (mmm) REVERT: b 35 PRO cc_start: 0.5460 (Cg_endo) cc_final: 0.5044 (Cg_exo) REVERT: b 48 ARG cc_start: 0.8260 (tmt-80) cc_final: 0.7742 (ttm110) REVERT: b 63 ASP cc_start: 0.9264 (m-30) cc_final: 0.8937 (m-30) REVERT: b 103 SER cc_start: 0.8894 (m) cc_final: 0.8686 (p) REVERT: b 114 ARG cc_start: 0.8252 (ttp-170) cc_final: 0.7694 (tmt170) REVERT: b 116 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6412 (tt) REVERT: b 171 LEU cc_start: 0.6696 (mm) cc_final: 0.6379 (mp) REVERT: b 189 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7520 (pttp) REVERT: b 232 MET cc_start: 0.6039 (mtm) cc_final: 0.5180 (mmt) REVERT: b 234 ASN cc_start: 0.8637 (m110) cc_final: 0.8357 (m-40) REVERT: b 237 MET cc_start: 0.6029 (tpp) cc_final: 0.5091 (mmp) REVERT: b 265 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8190 (pp20) REVERT: b 305 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5391 (mp) REVERT: b 394 ASN cc_start: 0.7985 (m-40) cc_final: 0.7764 (m-40) REVERT: b 397 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8445 (mtpp) REVERT: b 436 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6475 (mt) REVERT: J 222 SER cc_start: 0.7324 (t) cc_final: 0.7066 (m) REVERT: J 243 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6659 (mp0) REVERT: r 3 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7663 (tp40) REVERT: r 9 ARG cc_start: 0.9405 (mtm-85) cc_final: 0.8581 (mtt180) REVERT: r 16 LYS cc_start: 0.8238 (mttt) cc_final: 0.7986 (mmmt) REVERT: r 19 ASP cc_start: 0.8763 (m-30) cc_final: 0.8113 (p0) REVERT: r 20 HIS cc_start: 0.8936 (t-90) cc_final: 0.8601 (t-90) REVERT: r 22 GLU cc_start: 0.7858 (mp0) cc_final: 0.7502 (mp0) REVERT: r 23 ARG cc_start: 0.7558 (mmp-170) cc_final: 0.6910 (mtt-85) REVERT: r 61 MET cc_start: 0.8797 (mmm) cc_final: 0.8451 (tpp) REVERT: r 64 LYS cc_start: 0.8929 (mttp) cc_final: 0.8585 (ttpt) REVERT: r 65 ILE cc_start: 0.8423 (mt) cc_final: 0.8024 (pt) REVERT: r 72 LYS cc_start: 0.6633 (OUTLIER) cc_final: 0.6382 (mmmt) REVERT: s 16 LYS cc_start: 0.7217 (ttpt) cc_final: 0.6773 (ttmt) REVERT: u 20 MET cc_start: 0.7106 (ttp) cc_final: 0.6397 (tpp) REVERT: u 43 ARG cc_start: 0.8503 (mtp180) cc_final: 0.7577 (mmm160) REVERT: u 45 ASN cc_start: 0.8248 (t0) cc_final: 0.7919 (t0) REVERT: u 47 ARG cc_start: 0.9020 (ttm110) cc_final: 0.8747 (mmt-90) REVERT: u 63 LEU cc_start: 0.5907 (pt) cc_final: 0.5031 (pp) REVERT: u 98 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7736 (mt-10) REVERT: u 110 ASN cc_start: 0.8201 (m-40) cc_final: 0.7361 (m-40) REVERT: v 27 LYS cc_start: 0.8460 (mttt) cc_final: 0.8177 (ttpp) REVERT: v 29 ASN cc_start: 0.8588 (m-40) cc_final: 0.7995 (t0) REVERT: v 39 ASN cc_start: 0.9086 (m-40) cc_final: 0.8865 (m110) REVERT: v 41 ASP cc_start: 0.8726 (t70) cc_final: 0.8341 (t70) REVERT: v 164 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: v 186 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8759 (pt0) REVERT: v 195 ASP cc_start: 0.8975 (m-30) cc_final: 0.8732 (t0) REVERT: W 6 ARG cc_start: 0.7510 (ttt90) cc_final: 0.7274 (ptm-80) REVERT: W 12 LEU cc_start: 0.8275 (mt) cc_final: 0.7900 (mt) REVERT: W 16 ASP cc_start: 0.7482 (m-30) cc_final: 0.6658 (p0) REVERT: W 40 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8437 (m) REVERT: W 66 ILE cc_start: 0.8899 (mm) cc_final: 0.8508 (mp) REVERT: W 67 MET cc_start: 0.8037 (mtp) cc_final: 0.7227 (mmm) REVERT: W 87 GLU cc_start: 0.9073 (mp0) cc_final: 0.8807 (tp30) REVERT: W 88 ASN cc_start: 0.7476 (m110) cc_final: 0.7208 (t0) REVERT: W 128 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7769 (m-40) REVERT: W 141 ILE cc_start: 0.8426 (mp) cc_final: 0.8216 (tt) REVERT: W 143 TYR cc_start: 0.8497 (m-80) cc_final: 0.8225 (m-10) REVERT: W 154 ASP cc_start: 0.5511 (t0) cc_final: 0.5146 (t70) REVERT: W 157 MET cc_start: 0.8643 (mtp) cc_final: 0.8257 (mtp) REVERT: W 168 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8382 (mttt) REVERT: W 174 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7850 (pttt) REVERT: y 1 MET cc_start: 0.2722 (mmt) cc_final: 0.2168 (mtp) REVERT: y 7 PHE cc_start: 0.8691 (t80) cc_final: 0.8387 (t80) REVERT: y 11 ASN cc_start: 0.8477 (m110) cc_final: 0.8164 (p0) REVERT: y 34 PHE cc_start: 0.7845 (t80) cc_final: 0.7559 (t80) REVERT: y 50 HIS cc_start: 0.7060 (m-70) cc_final: 0.6634 (m-70) REVERT: y 67 ARG cc_start: 0.5792 (ptt180) cc_final: 0.5355 (ptt-90) REVERT: y 118 HIS cc_start: 0.7594 (t-90) cc_final: 0.7213 (t70) REVERT: y 122 ASP cc_start: 0.8568 (p0) cc_final: 0.7914 (t70) REVERT: y 123 ARG cc_start: 0.8510 (ttt180) cc_final: 0.8308 (mmm160) REVERT: y 127 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8357 (mm-30) REVERT: y 154 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8608 (tt) REVERT: y 197 MET cc_start: 0.8260 (ppp) cc_final: 0.7900 (ppp) REVERT: z 6 ARG cc_start: 0.6667 (mtm110) cc_final: 0.6079 (tpt90) REVERT: z 37 LEU cc_start: 0.7555 (tp) cc_final: 0.7307 (tp) REVERT: B 17 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8296 (mm) REVERT: B 53 MET cc_start: 0.8014 (tpp) cc_final: 0.7349 (mmm) REVERT: B 61 ASP cc_start: 0.7095 (m-30) cc_final: 0.6865 (p0) REVERT: B 62 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7410 (ttm-80) REVERT: B 66 LYS cc_start: 0.8067 (mtpp) cc_final: 0.7537 (mptt) REVERT: B 74 GLU cc_start: 0.8547 (pt0) cc_final: 0.7777 (tp30) REVERT: B 93 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8940 (p) REVERT: B 114 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8826 (p) REVERT: B 214 MET cc_start: 0.8371 (mmt) cc_final: 0.8164 (mmt) REVERT: B 306 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7646 (p) REVERT: B 316 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8168 (mp0) REVERT: B 333 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8171 (mtmm) REVERT: B 344 THR cc_start: 0.8551 (m) cc_final: 0.8177 (t) REVERT: B 369 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.7595 (ttm-80) REVERT: C 14 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8062 (mp0) REVERT: C 73 ARG cc_start: 0.8727 (mtt180) cc_final: 0.8141 (ptt90) REVERT: C 99 MET cc_start: 0.9211 (ptm) cc_final: 0.8912 (ptt) REVERT: C 164 GLU cc_start: 0.9405 (tt0) cc_final: 0.9068 (tp30) REVERT: C 220 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.8781 (ptp90) REVERT: C 285 ASP cc_start: 0.8323 (t0) cc_final: 0.7915 (t0) REVERT: C 294 GLU cc_start: 0.9239 (tp30) cc_final: 0.9017 (tm-30) REVERT: C 326 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8679 (ttp-170) REVERT: e 24 ARG cc_start: 0.8503 (tpp80) cc_final: 0.7852 (mmm160) REVERT: e 27 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8771 (ptt90) REVERT: e 34 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9004 (ttpt) REVERT: e 52 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: e 83 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8651 (tt0) REVERT: e 90 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8579 (mtpp) REVERT: e 100 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9210 (mm) REVERT: e 105 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.9005 (mtt90) REVERT: e 113 LYS cc_start: 0.8681 (ttmm) cc_final: 0.8432 (tptt) REVERT: E 22 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8439 (mtt180) REVERT: E 29 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8726 (pttm) REVERT: E 92 SER cc_start: 0.9030 (t) cc_final: 0.8801 (t) REVERT: E 99 GLU cc_start: 0.9475 (mt-10) cc_final: 0.8957 (tp30) REVERT: E 142 ASP cc_start: 0.8670 (m-30) cc_final: 0.8464 (t0) REVERT: E 169 ASP cc_start: 0.8337 (m-30) cc_final: 0.8020 (m-30) REVERT: f 22 VAL cc_start: 0.9077 (t) cc_final: 0.8736 (p) REVERT: f 33 GLU cc_start: 0.9024 (tt0) cc_final: 0.8779 (tm-30) REVERT: f 49 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9188 (mt) REVERT: f 97 SER cc_start: 0.9090 (OUTLIER) cc_final: 0.8863 (p) REVERT: G 74 THR cc_start: 0.9394 (t) cc_final: 0.9074 (t) REVERT: G 77 GLN cc_start: 0.9255 (pt0) cc_final: 0.8993 (pt0) REVERT: G 79 GLN cc_start: 0.9013 (pt0) cc_final: 0.8540 (mp10) REVERT: G 100 GLU cc_start: 0.9060 (tt0) cc_final: 0.8078 (mt-10) REVERT: G 142 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9332 (mp) REVERT: G 162 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9171 (tp) REVERT: G 217 THR cc_start: 0.9651 (m) cc_final: 0.9442 (p) REVERT: G 218 ILE cc_start: 0.9391 (mt) cc_final: 0.9024 (mt) REVERT: G 225 LYS cc_start: 0.8809 (mtpt) cc_final: 0.8419 (tptp) REVERT: G 231 LYS cc_start: 0.8092 (mtmm) cc_final: 0.7680 (mmmt) REVERT: h 20 GLN cc_start: 0.9363 (tp40) cc_final: 0.8757 (tp40) REVERT: h 34 GLN cc_start: 0.7911 (mt0) cc_final: 0.7496 (mm-40) REVERT: h 43 LYS cc_start: 0.9376 (tttt) cc_final: 0.8980 (tptt) REVERT: h 44 ILE cc_start: 0.9374 (tt) cc_final: 0.9147 (pt) REVERT: h 60 GLU cc_start: 0.9364 (tt0) cc_final: 0.9146 (tm-30) REVERT: h 61 GLN cc_start: 0.9279 (mt0) cc_final: 0.8901 (mt0) REVERT: h 94 LYS cc_start: 0.8774 (ttpp) cc_final: 0.8539 (ptmt) REVERT: h 102 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8461 (tm-30) REVERT: H 7 GLU cc_start: 0.9174 (pt0) cc_final: 0.8963 (pt0) REVERT: H 23 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7971 (mpp80) REVERT: H 62 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7211 (ttm-80) REVERT: H 90 MET cc_start: 0.9247 (mtp) cc_final: 0.8897 (mtp) REVERT: H 153 ASP cc_start: 0.9466 (m-30) cc_final: 0.8943 (t0) REVERT: H 160 ASP cc_start: 0.9021 (m-30) cc_final: 0.8740 (p0) REVERT: H 162 GLN cc_start: 0.9028 (tt0) cc_final: 0.8550 (tm-30) REVERT: i 50 LEU cc_start: 0.9385 (mt) cc_final: 0.9141 (mt) REVERT: i 86 LYS cc_start: 0.8840 (tppt) cc_final: 0.8637 (mmtm) REVERT: j 30 GLN cc_start: 0.8604 (mt0) cc_final: 0.8191 (tp40) REVERT: j 31 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8568 (mtpt) REVERT: j 55 ARG cc_start: 0.9036 (mtm180) cc_final: 0.8803 (ttm110) REVERT: j 65 ARG cc_start: 0.9024 (mtm-85) cc_final: 0.8778 (mtp180) REVERT: j 67 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9297 (tp) REVERT: j 75 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8802 (tttp) REVERT: L 42 ARG cc_start: 0.8690 (ttt90) cc_final: 0.8490 (ttt90) REVERT: L 67 ARG cc_start: 0.9419 (ptm-80) cc_final: 0.8650 (mtm180) REVERT: L 102 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8177 (mt0) REVERT: L 104 ARG cc_start: 0.8654 (ttt-90) cc_final: 0.8049 (mtm180) REVERT: M 62 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8903 (mm110) REVERT: M 126 GLN cc_start: 0.9194 (mt0) cc_final: 0.8933 (mm-40) REVERT: N 6 TYR cc_start: 0.9094 (m-80) cc_final: 0.8892 (m-80) REVERT: N 10 LEU cc_start: 0.9216 (tt) cc_final: 0.8952 (tt) REVERT: N 19 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9141 (mp) REVERT: N 28 TRP cc_start: 0.9185 (t60) cc_final: 0.8805 (t60) REVERT: N 29 GLU cc_start: 0.9642 (OUTLIER) cc_final: 0.9381 (tm-30) REVERT: N 105 ARG cc_start: 0.9083 (mtt180) cc_final: 0.8677 (tpp80) REVERT: N 119 TYR cc_start: 0.9448 (p90) cc_final: 0.9018 (p90) REVERT: N 126 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.9030 (p) REVERT: N 144 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8366 (mmt90) REVERT: N 174 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8559 (mm) REVERT: N 196 THR cc_start: 0.7921 (m) cc_final: 0.7662 (p) REVERT: O 41 LEU cc_start: 0.9559 (tp) cc_final: 0.9249 (tp) REVERT: O 42 ASN cc_start: 0.9310 (OUTLIER) cc_final: 0.8962 (m110) REVERT: O 48 PHE cc_start: 0.9534 (OUTLIER) cc_final: 0.9314 (t80) REVERT: O 53 LYS cc_start: 0.9228 (mttt) cc_final: 0.8893 (mmtm) REVERT: O 66 LYS cc_start: 0.8857 (mttp) cc_final: 0.8457 (mtmt) REVERT: O 68 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7486 (ttt90) REVERT: O 157 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8806 (tp30) REVERT: P 23 ARG cc_start: 0.8947 (mtp180) cc_final: 0.8479 (mtm180) REVERT: P 30 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8199 (tmt170) REVERT: P 36 ILE cc_start: 0.9624 (tt) cc_final: 0.9328 (tp) REVERT: P 41 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8865 (tm) REVERT: P 62 ARG cc_start: 0.8483 (ttm170) cc_final: 0.7371 (ttm110) REVERT: P 69 ARG cc_start: 0.8682 (mtp180) cc_final: 0.7612 (ptp-170) REVERT: P 87 SER cc_start: 0.9314 (OUTLIER) cc_final: 0.9029 (p) REVERT: P 89 LYS cc_start: 0.9404 (ttpp) cc_final: 0.9113 (tppt) REVERT: P 120 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8654 (p0) REVERT: P 152 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8402 (tt0) REVERT: P 153 LYS cc_start: 0.8618 (tptt) cc_final: 0.7855 (ttpp) REVERT: P 155 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8308 (mp0) REVERT: Q 24 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.8931 (p) REVERT: S 23 LYS cc_start: 0.8115 (mttt) cc_final: 0.7406 (tmtt) REVERT: S 27 MET cc_start: 0.8631 (ptm) cc_final: 0.8290 (ptt) REVERT: S 66 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8741 (tm-30) REVERT: S 70 THR cc_start: 0.8650 (p) cc_final: 0.8370 (t) REVERT: S 80 ARG cc_start: 0.8275 (ttt180) cc_final: 0.8027 (ttm-80) REVERT: S 125 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8617 (tptm) REVERT: S 148 LEU cc_start: 0.8854 (tp) cc_final: 0.8579 (tp) REVERT: V 24 ASN cc_start: 0.8452 (m-40) cc_final: 0.8223 (m110) REVERT: V 34 LEU cc_start: 0.7084 (mt) cc_final: 0.6683 (mp) REVERT: V 54 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6474 (mt) REVERT: V 81 GLN cc_start: 0.5246 (tt0) cc_final: 0.4133 (tt0) REVERT: V 86 ARG cc_start: 0.6790 (tmm-80) cc_final: 0.5963 (mmt-90) REVERT: V 93 LEU cc_start: 0.7897 (pt) cc_final: 0.7522 (tp) REVERT: V 102 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7437 (mp) REVERT: V 109 MET cc_start: 0.7907 (mmm) cc_final: 0.6899 (mmm) REVERT: V 110 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7666 (mmtt) REVERT: Y 54 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8351 (p0) REVERT: Y 55 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8525 (mm-30) REVERT: Y 66 GLN cc_start: 0.9197 (mt0) cc_final: 0.8950 (mt0) REVERT: Y 67 GLU cc_start: 0.9089 (pt0) cc_final: 0.8868 (pp20) REVERT: Y 69 LYS cc_start: 0.9162 (tttt) cc_final: 0.8831 (ttmm) REVERT: Y 87 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7314 (ptmm) REVERT: Y 88 GLU cc_start: 0.9363 (mp0) cc_final: 0.8882 (mm-30) REVERT: Y 105 VAL cc_start: 0.9488 (OUTLIER) cc_final: 0.9268 (m) REVERT: K 34 ARG cc_start: 0.8196 (mtp-110) cc_final: 0.7464 (ppt170) REVERT: K 112 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7075 (mm-30) REVERT: K 154 ILE cc_start: 0.7538 (pt) cc_final: 0.6971 (pt) REVERT: m 277 MET cc_start: 0.6102 (mmm) cc_final: 0.5426 (mmm) REVERT: D 277 PHE cc_start: 0.8762 (t80) cc_final: 0.8537 (t80) REVERT: D 342 ILE cc_start: 0.8642 (tt) cc_final: 0.8411 (mm) REVERT: D 360 TRP cc_start: 0.7361 (m100) cc_final: 0.6666 (m100) REVERT: D 415 TYR cc_start: 0.6855 (m-80) cc_final: 0.6340 (m-80) REVERT: D 422 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6423 (pp) REVERT: D 437 TYR cc_start: 0.7764 (t80) cc_final: 0.7013 (t80) REVERT: D 448 ARG cc_start: 0.5118 (tmt90) cc_final: 0.4465 (tpt170) REVERT: D 454 TYR cc_start: 0.6290 (t80) cc_final: 0.6059 (t80) REVERT: o 139 PHE cc_start: 0.6193 (m-10) cc_final: 0.5844 (m-80) REVERT: o 141 ASN cc_start: 0.6977 (t0) cc_final: 0.6242 (t0) REVERT: o 194 LYS cc_start: 0.8652 (mttt) cc_final: 0.8174 (mmmm) REVERT: n 149 ASN cc_start: 0.7025 (p0) cc_final: 0.6795 (p0) REVERT: n 220 THR cc_start: 0.6731 (p) cc_final: 0.6032 (p) REVERT: t 88 ASN cc_start: 0.8021 (m-40) cc_final: 0.7744 (t0) outliers start: 581 outliers final: 157 residues processed: 2200 average time/residue: 1.0019 time to fit residues: 3626.1450 Evaluate side-chains 1261 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1031 time to evaluate : 6.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 15 ARG Chi-restraints excluded: chain x residue 50 GLN Chi-restraints excluded: chain x residue 87 SER Chi-restraints excluded: chain x residue 88 ASN Chi-restraints excluded: chain x residue 101 VAL Chi-restraints excluded: chain x residue 104 LYS Chi-restraints excluded: chain x residue 125 LYS Chi-restraints excluded: chain x residue 132 LEU Chi-restraints excluded: chain x residue 149 ILE Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 165 LEU Chi-restraints excluded: chain x residue 176 SER Chi-restraints excluded: chain x residue 209 THR Chi-restraints excluded: chain x residue 223 ASP Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 235 GLN Chi-restraints excluded: chain x residue 239 ILE Chi-restraints excluded: chain x residue 247 VAL Chi-restraints excluded: chain x residue 263 PHE Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain x residue 274 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain 3 residue 28 CYS Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 106 HIS Chi-restraints excluded: chain 3 residue 144 ARG Chi-restraints excluded: chain 4 residue 19 VAL Chi-restraints excluded: chain 4 residue 20 ASN Chi-restraints excluded: chain 4 residue 30 THR Chi-restraints excluded: chain 4 residue 50 TYR Chi-restraints excluded: chain 4 residue 75 LEU Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 99 SER Chi-restraints excluded: chain 4 residue 111 PHE Chi-restraints excluded: chain 4 residue 123 LEU Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 179 ASP Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 190 LEU Chi-restraints excluded: chain 5 residue 204 ILE Chi-restraints excluded: chain 5 residue 219 ILE Chi-restraints excluded: chain 5 residue 251 LEU Chi-restraints excluded: chain 5 residue 280 THR Chi-restraints excluded: chain 5 residue 337 ASP Chi-restraints excluded: chain 5 residue 340 LYS Chi-restraints excluded: chain 5 residue 351 MET Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 189 LYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 277 LEU Chi-restraints excluded: chain b residue 305 LEU Chi-restraints excluded: chain b residue 436 LEU Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain r residue 3 GLN Chi-restraints excluded: chain r residue 72 LYS Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain v residue 164 GLU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain W residue 174 LYS Chi-restraints excluded: chain y residue 154 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain e residue 27 ARG Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 52 GLN Chi-restraints excluded: chain e residue 82 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 100 ILE Chi-restraints excluded: chain e residue 105 ARG Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain h residue 119 LYS Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 49 ARG Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 144 ARG Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 156 LEU Chi-restraints excluded: chain O residue 157 GLU Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 189 ASP Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 30 ARG Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain t residue 141 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 750 optimal weight: 30.0000 chunk 673 optimal weight: 5.9990 chunk 373 optimal weight: 0.8980 chunk 230 optimal weight: 0.0470 chunk 454 optimal weight: 6.9990 chunk 359 optimal weight: 6.9990 chunk 696 optimal weight: 30.0000 chunk 269 optimal weight: 5.9990 chunk 423 optimal weight: 6.9990 chunk 518 optimal weight: 0.9990 chunk 807 optimal weight: 5.9990 overall best weight: 2.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 88 ASN x 90 ASN ** x 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 102 ASN x 164 HIS x 187 HIS x 228 GLN ** x 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 257 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN F 186 HIS ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 23 ASN ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 41 GLN 4 14 ASN 4 63 GLN 5 34 HIS 5 63 ASN 5 191 GLN 5 237 ASN 5 269 GLN 5 285 GLN 5 286 HIS 5 299 ASN 5 305 GLN ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 ASN b 26 GLN b 70 ASN b 89 ASN b 90 HIS b 208 HIS b 217 GLN b 238 GLN ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN r 10 HIS ** r 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 7 HIS u 101 GLN v 10 ASN ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 33 ASN v 206 ASN W 22 ASN W 167 ASN W 205 GLN ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 232 ASN y 11 ASN y 33 ASN y 86 ASN y 157 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN C 58 HIS C 87 GLN C 114 ASN C 260 GLN ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN e 52 GLN E 167 ASN f 42 GLN G 95 ASN G 137 ASN h 59 ASN h 68 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 162 GLN H 163 GLN L 37 ASN L 114 GLN L 120 GLN M 126 GLN ** N 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN N 178 HIS O 42 ASN O 50 ASN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 GLN P 121 GLN Q 73 GLN Q 126 GLN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 49 HIS S 62 ASN S 74 ASN S 142 GLN K 42 ASN K 262 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 428 GLN D 441 GLN n 150 GLN n 164 ASN n 191 ASN n 437 ASN ** t 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 154 ASN t 238 GLN ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 89 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 106125 Z= 0.255 Angle : 0.755 22.680 152938 Z= 0.386 Chirality : 0.043 0.328 18691 Planarity : 0.006 0.068 11918 Dihedral : 23.360 179.924 39329 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.41 % Favored : 93.02 % Rotamer: Outliers : 6.71 % Allowed : 19.70 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.77 (0.09), residues: 6938 helix: -1.63 (0.09), residues: 2642 sheet: -1.56 (0.15), residues: 998 loop : -2.04 (0.10), residues: 3298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 360 HIS 0.012 0.001 HIS x 31 PHE 0.033 0.002 PHE W 116 TYR 0.042 0.002 TYR 4 76 ARG 0.015 0.001 ARG x 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1532 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 414 poor density : 1118 time to evaluate : 6.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 15 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7972 (ttp80) REVERT: x 17 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7924 (tm-30) REVERT: x 33 MET cc_start: 0.8983 (mmm) cc_final: 0.8647 (tmm) REVERT: x 40 GLU cc_start: 0.8063 (pp20) cc_final: 0.7390 (tp30) REVERT: x 50 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8377 (tp40) REVERT: x 80 ASP cc_start: 0.8189 (t0) cc_final: 0.7977 (t0) REVERT: x 105 LYS cc_start: 0.8647 (mtmt) cc_final: 0.8354 (mttm) REVERT: x 203 GLN cc_start: 0.5498 (tm-30) cc_final: 0.5213 (tm-30) REVERT: x 235 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8382 (tp40) REVERT: x 281 GLU cc_start: 0.9349 (tt0) cc_final: 0.8497 (tm-30) REVERT: x 283 LYS cc_start: 0.9116 (mttt) cc_final: 0.8686 (mtpt) REVERT: x 285 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8553 (pt0) REVERT: x 286 MET cc_start: 0.7916 (mpp) cc_final: 0.7367 (mpp) REVERT: F 10 GLU cc_start: 0.9248 (mp0) cc_final: 0.8844 (mm-30) REVERT: F 19 GLN cc_start: 0.9007 (mt0) cc_final: 0.8654 (pp30) REVERT: F 21 LYS cc_start: 0.8761 (mttt) cc_final: 0.8349 (tptt) REVERT: F 76 TYR cc_start: 0.8537 (t80) cc_final: 0.8207 (t80) REVERT: F 121 LYS cc_start: 0.9339 (tttt) cc_final: 0.8980 (mptt) REVERT: 3 32 TYR cc_start: 0.8654 (m-80) cc_final: 0.8390 (m-10) REVERT: 3 143 ARG cc_start: 0.7490 (mmt90) cc_final: 0.7177 (mmt90) REVERT: 3 149 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8249 (tt0) REVERT: 3 150 ARG cc_start: 0.8639 (mtt180) cc_final: 0.8124 (tpt-90) REVERT: 3 160 LYS cc_start: 0.8897 (mttt) cc_final: 0.8457 (tppt) REVERT: 3 167 MET cc_start: 0.9433 (mmm) cc_final: 0.8941 (mmm) REVERT: 4 8 LYS cc_start: 0.9258 (pttt) cc_final: 0.8756 (mmtt) REVERT: 4 38 LYS cc_start: 0.8557 (mttm) cc_final: 0.8258 (mtmm) REVERT: 4 75 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7827 (tp) REVERT: 4 153 VAL cc_start: 0.6843 (t) cc_final: 0.6492 (t) REVERT: 4 164 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8155 (mmtt) REVERT: 4 179 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8817 (t0) REVERT: 4 234 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8679 (tp) REVERT: 5 1 MET cc_start: 0.8017 (ptp) cc_final: 0.6879 (mtm) REVERT: 5 71 LYS cc_start: 0.9043 (ttmt) cc_final: 0.8760 (tppt) REVERT: 5 112 SER cc_start: 0.8197 (t) cc_final: 0.7987 (p) REVERT: 5 204 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8381 (mm) REVERT: 5 211 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8592 (tm-30) REVERT: 5 225 SER cc_start: 0.8498 (t) cc_final: 0.8260 (p) REVERT: 5 242 MET cc_start: 0.9152 (mmm) cc_final: 0.8887 (mpp) REVERT: 5 260 LYS cc_start: 0.8320 (mttp) cc_final: 0.8002 (ptmm) REVERT: 5 301 GLU cc_start: 0.9202 (tp30) cc_final: 0.8622 (tp30) REVERT: 5 366 TYR cc_start: 0.8634 (t80) cc_final: 0.8264 (t80) REVERT: 5 412 ASP cc_start: 0.8029 (p0) cc_final: 0.7450 (p0) REVERT: A 33 THR cc_start: 0.7483 (p) cc_final: 0.6950 (t) REVERT: A 42 ASN cc_start: 0.3274 (p0) cc_final: 0.2989 (p0) REVERT: A 79 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8925 (mt-10) REVERT: A 140 ASP cc_start: 0.6369 (p0) cc_final: 0.6106 (p0) REVERT: A 141 GLN cc_start: 0.7436 (tp40) cc_final: 0.7225 (pp30) REVERT: A 142 ARG cc_start: 0.6968 (mtp180) cc_final: 0.6639 (mtp85) REVERT: A 179 PHE cc_start: 0.7681 (m-80) cc_final: 0.7296 (t80) REVERT: b 26 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: b 47 MET cc_start: 0.8233 (mtt) cc_final: 0.8032 (mmm) REVERT: b 48 ARG cc_start: 0.8290 (tmt-80) cc_final: 0.7742 (ttm110) REVERT: b 63 ASP cc_start: 0.9093 (m-30) cc_final: 0.8859 (m-30) REVERT: b 114 ARG cc_start: 0.8151 (ttp-170) cc_final: 0.7591 (tmt170) REVERT: b 116 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6119 (tt) REVERT: b 189 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7586 (pttt) REVERT: b 232 MET cc_start: 0.5676 (mtm) cc_final: 0.5132 (mmt) REVERT: b 234 ASN cc_start: 0.8672 (m110) cc_final: 0.8433 (m-40) REVERT: b 305 LEU cc_start: 0.5675 (mt) cc_final: 0.5407 (mt) REVERT: b 397 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8463 (mtpp) REVERT: J 248 LYS cc_start: 0.6431 (pptt) cc_final: 0.6193 (pptt) REVERT: r 9 ARG cc_start: 0.9295 (mtm-85) cc_final: 0.8841 (mtm-85) REVERT: r 12 LYS cc_start: 0.8710 (mttt) cc_final: 0.8456 (mmmt) REVERT: r 16 LYS cc_start: 0.8307 (mttt) cc_final: 0.8058 (mmmt) REVERT: r 19 ASP cc_start: 0.8688 (m-30) cc_final: 0.7766 (p0) REVERT: r 23 ARG cc_start: 0.7410 (mmp-170) cc_final: 0.7032 (mtt-85) REVERT: r 24 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8594 (tptt) REVERT: r 28 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8662 (mp0) REVERT: r 41 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7883 (ttpp) REVERT: r 65 ILE cc_start: 0.8342 (mt) cc_final: 0.8065 (pt) REVERT: s 16 LYS cc_start: 0.6912 (ttpt) cc_final: 0.6680 (ttmt) REVERT: u 43 ARG cc_start: 0.8626 (mtp180) cc_final: 0.7875 (mmm160) REVERT: u 45 ASN cc_start: 0.8231 (t0) cc_final: 0.7983 (t0) REVERT: u 93 MET cc_start: 0.5660 (mpp) cc_final: 0.5400 (mpp) REVERT: v 27 LYS cc_start: 0.8135 (mttt) cc_final: 0.7852 (ttpp) REVERT: v 28 ILE cc_start: 0.8439 (pt) cc_final: 0.8148 (tt) REVERT: v 29 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.7877 (t0) REVERT: v 41 ASP cc_start: 0.8746 (t70) cc_final: 0.8175 (t70) REVERT: v 164 GLU cc_start: 0.8020 (pt0) cc_final: 0.7614 (tm-30) REVERT: v 212 GLU cc_start: 0.9560 (mp0) cc_final: 0.9144 (tt0) REVERT: W 6 ARG cc_start: 0.7749 (ttt90) cc_final: 0.7401 (ptm-80) REVERT: W 66 ILE cc_start: 0.8908 (mm) cc_final: 0.8588 (mp) REVERT: W 67 MET cc_start: 0.8035 (mtp) cc_final: 0.7166 (mmm) REVERT: W 87 GLU cc_start: 0.9169 (mp0) cc_final: 0.8880 (tp30) REVERT: W 88 ASN cc_start: 0.7637 (m110) cc_final: 0.7094 (t0) REVERT: W 110 ASN cc_start: 0.9385 (m-40) cc_final: 0.9042 (p0) REVERT: W 141 ILE cc_start: 0.8373 (mp) cc_final: 0.8003 (tt) REVERT: W 157 MET cc_start: 0.8651 (mtp) cc_final: 0.8221 (mtp) REVERT: W 168 LYS cc_start: 0.8603 (ttpt) cc_final: 0.8250 (mttt) REVERT: y 1 MET cc_start: 0.3104 (mmt) cc_final: 0.2633 (mtp) REVERT: y 7 PHE cc_start: 0.8582 (t80) cc_final: 0.8317 (t80) REVERT: y 34 PHE cc_start: 0.7804 (t80) cc_final: 0.7548 (t80) REVERT: y 118 HIS cc_start: 0.7765 (t-90) cc_final: 0.7189 (t70) REVERT: y 122 ASP cc_start: 0.8451 (p0) cc_final: 0.7997 (p0) REVERT: y 127 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8400 (mm-30) REVERT: y 154 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8460 (tt) REVERT: y 215 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8446 (mt) REVERT: z 6 ARG cc_start: 0.6873 (mtm110) cc_final: 0.5714 (tpt90) REVERT: B 17 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8274 (mm) REVERT: B 53 MET cc_start: 0.7867 (tpp) cc_final: 0.6795 (mmm) REVERT: B 66 LYS cc_start: 0.7981 (mtpp) cc_final: 0.7643 (mptt) REVERT: B 74 GLU cc_start: 0.8605 (pt0) cc_final: 0.7618 (tp30) REVERT: B 114 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8802 (p) REVERT: B 316 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8163 (mp0) REVERT: B 369 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7893 (ttm-80) REVERT: C 73 ARG cc_start: 0.8648 (mtt180) cc_final: 0.8159 (ptt90) REVERT: C 85 SER cc_start: 0.8153 (p) cc_final: 0.7949 (t) REVERT: C 99 MET cc_start: 0.9062 (ptm) cc_final: 0.8857 (ptt) REVERT: C 118 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8873 (tttt) REVERT: C 164 GLU cc_start: 0.9295 (tt0) cc_final: 0.8977 (tp30) REVERT: C 288 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6897 (mmm160) REVERT: C 326 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8407 (ttm110) REVERT: e 81 ASP cc_start: 0.8885 (m-30) cc_final: 0.8410 (t0) REVERT: e 83 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8498 (tt0) REVERT: E 29 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8739 (pttt) REVERT: E 102 ASN cc_start: 0.9252 (p0) cc_final: 0.9035 (p0) REVERT: E 169 ASP cc_start: 0.8326 (m-30) cc_final: 0.7971 (m-30) REVERT: f 22 VAL cc_start: 0.8896 (t) cc_final: 0.8645 (p) REVERT: f 33 GLU cc_start: 0.9057 (tt0) cc_final: 0.8845 (tm-30) REVERT: f 49 ILE cc_start: 0.9470 (mt) cc_final: 0.9150 (mt) REVERT: f 65 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8411 (mtt180) REVERT: G 79 GLN cc_start: 0.9021 (pt0) cc_final: 0.8601 (mp10) REVERT: G 225 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8423 (tptp) REVERT: h 43 LYS cc_start: 0.9368 (tttt) cc_final: 0.8957 (tptt) REVERT: h 60 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.9067 (tm-30) REVERT: h 61 GLN cc_start: 0.8966 (mt0) cc_final: 0.8621 (mt0) REVERT: H 19 SER cc_start: 0.8041 (m) cc_final: 0.7535 (t) REVERT: H 62 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7172 (ttm-80) REVERT: H 78 MET cc_start: 0.8634 (ttm) cc_final: 0.8360 (ttt) REVERT: H 116 ASN cc_start: 0.9267 (t0) cc_final: 0.8745 (t0) REVERT: H 153 ASP cc_start: 0.9442 (m-30) cc_final: 0.8982 (t0) REVERT: H 156 GLN cc_start: 0.8841 (tp40) cc_final: 0.8533 (tp40) REVERT: H 157 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8966 (m-40) REVERT: H 162 GLN cc_start: 0.8933 (tt0) cc_final: 0.8545 (tm-30) REVERT: H 179 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8678 (tp) REVERT: i 86 LYS cc_start: 0.8662 (tppt) cc_final: 0.8453 (mmtm) REVERT: j 30 GLN cc_start: 0.8427 (mt0) cc_final: 0.8051 (tp40) REVERT: j 31 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8505 (mtpt) REVERT: L 34 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8808 (p) REVERT: L 42 ARG cc_start: 0.8488 (ttt90) cc_final: 0.8267 (ttt90) REVERT: L 46 ILE cc_start: 0.8873 (mm) cc_final: 0.8511 (mt) REVERT: L 49 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8598 (mtm110) REVERT: L 67 ARG cc_start: 0.9472 (ptm-80) cc_final: 0.8748 (mtm180) REVERT: L 104 ARG cc_start: 0.8577 (ttt-90) cc_final: 0.7854 (mtm180) REVERT: M 62 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8975 (mm110) REVERT: M 99 TRP cc_start: 0.8401 (t-100) cc_final: 0.8112 (t60) REVERT: N 6 TYR cc_start: 0.8781 (m-80) cc_final: 0.8475 (m-80) REVERT: N 15 GLN cc_start: 0.8599 (mt0) cc_final: 0.7900 (tt0) REVERT: N 28 TRP cc_start: 0.8961 (t60) cc_final: 0.8719 (t60) REVERT: N 119 TYR cc_start: 0.9392 (p90) cc_final: 0.8871 (p90) REVERT: N 131 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8596 (mm-30) REVERT: N 174 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8406 (mm) REVERT: N 196 THR cc_start: 0.7940 (m) cc_final: 0.7735 (p) REVERT: N 201 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.9054 (mtp85) REVERT: O 12 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7370 (tptm) REVERT: O 53 LYS cc_start: 0.8796 (mttt) cc_final: 0.8567 (tttt) REVERT: O 57 PHE cc_start: 0.8843 (t80) cc_final: 0.8601 (t80) REVERT: O 66 LYS cc_start: 0.8986 (mttp) cc_final: 0.8739 (mtmt) REVERT: O 68 ARG cc_start: 0.7590 (ttp80) cc_final: 0.6659 (ttt90) REVERT: O 90 HIS cc_start: 0.9058 (OUTLIER) cc_final: 0.7079 (p-80) REVERT: O 124 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8885 (mt) REVERT: O 150 GLU cc_start: 0.8173 (tp30) cc_final: 0.7722 (tt0) REVERT: P 23 ARG cc_start: 0.9077 (mtp180) cc_final: 0.8671 (mtm180) REVERT: P 30 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8455 (tmt170) REVERT: P 53 ASP cc_start: 0.9539 (m-30) cc_final: 0.9285 (t0) REVERT: P 69 ARG cc_start: 0.8657 (mtp180) cc_final: 0.8453 (ptp-170) REVERT: P 94 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8635 (mp) REVERT: P 120 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8480 (p0) REVERT: P 154 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8184 (mm-30) REVERT: P 155 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8099 (mp0) REVERT: P 157 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7319 (t) REVERT: Q 23 ASN cc_start: 0.8929 (t0) cc_final: 0.8522 (t0) REVERT: S 34 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8374 (mp0) REVERT: S 80 ARG cc_start: 0.8125 (ttt180) cc_final: 0.7918 (ttm-80) REVERT: V 40 LYS cc_start: 0.6645 (mtpp) cc_final: 0.6422 (mtmm) REVERT: V 85 TRP cc_start: 0.7355 (p90) cc_final: 0.5812 (p90) REVERT: V 86 ARG cc_start: 0.6735 (tmm-80) cc_final: 0.6058 (mmt-90) REVERT: V 102 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7479 (mp) REVERT: V 109 MET cc_start: 0.7566 (mmm) cc_final: 0.6907 (mmm) REVERT: V 126 TRP cc_start: 0.7952 (m100) cc_final: 0.7567 (m100) REVERT: Y 55 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8432 (mm-30) REVERT: Y 66 GLN cc_start: 0.9094 (mt0) cc_final: 0.8864 (mt0) REVERT: Y 67 GLU cc_start: 0.9133 (pt0) cc_final: 0.8691 (pp20) REVERT: Y 87 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7490 (ptmm) REVERT: Y 108 LYS cc_start: 0.8740 (tptt) cc_final: 0.8511 (tmtt) REVERT: K 34 ARG cc_start: 0.8268 (mtp-110) cc_final: 0.7389 (ppt170) REVERT: K 121 PHE cc_start: 0.6204 (OUTLIER) cc_final: 0.4889 (t80) REVERT: K 179 LEU cc_start: 0.7873 (mm) cc_final: 0.7428 (mm) REVERT: K 181 LEU cc_start: 0.7836 (tp) cc_final: 0.7494 (tp) REVERT: K 275 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6772 (pp30) REVERT: D 276 ARG cc_start: 0.7719 (mmm160) cc_final: 0.6604 (mmt180) REVERT: D 307 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8429 (mm-30) REVERT: D 340 ARG cc_start: 0.7786 (ptm160) cc_final: 0.7474 (ttt-90) REVERT: D 463 TYR cc_start: 0.5634 (m-80) cc_final: 0.5207 (m-80) REVERT: o 194 LYS cc_start: 0.8651 (mttt) cc_final: 0.8403 (mmmm) REVERT: n 69 GLN cc_start: 0.7285 (mt0) cc_final: 0.6676 (tp-100) REVERT: n 104 ARG cc_start: 0.8079 (ptm-80) cc_final: 0.7720 (ptm160) REVERT: n 106 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8656 (mm-30) REVERT: n 236 LEU cc_start: 0.6095 (mt) cc_final: 0.5854 (mt) REVERT: t 297 ARG cc_start: 0.6896 (mtm110) cc_final: 0.6557 (tpt90) REVERT: t 312 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.7900 (p) outliers start: 414 outliers final: 188 residues processed: 1445 average time/residue: 0.9413 time to fit residues: 2285.3023 Evaluate side-chains 1125 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 896 time to evaluate : 6.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 15 ARG Chi-restraints excluded: chain x residue 18 ILE Chi-restraints excluded: chain x residue 50 GLN Chi-restraints excluded: chain x residue 95 ILE Chi-restraints excluded: chain x residue 101 VAL Chi-restraints excluded: chain x residue 104 LYS Chi-restraints excluded: chain x residue 121 VAL Chi-restraints excluded: chain x residue 125 LYS Chi-restraints excluded: chain x residue 132 LEU Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 165 LEU Chi-restraints excluded: chain x residue 191 THR Chi-restraints excluded: chain x residue 204 THR Chi-restraints excluded: chain x residue 209 THR Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 234 ASN Chi-restraints excluded: chain x residue 235 GLN Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain 3 residue 3 ASP Chi-restraints excluded: chain 3 residue 28 CYS Chi-restraints excluded: chain 3 residue 47 ASN Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 72 THR Chi-restraints excluded: chain 3 residue 76 LEU Chi-restraints excluded: chain 3 residue 106 HIS Chi-restraints excluded: chain 3 residue 137 VAL Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 75 LEU Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 107 CYS Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 179 ASP Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 5 residue 64 SER Chi-restraints excluded: chain 5 residue 110 ILE Chi-restraints excluded: chain 5 residue 136 LEU Chi-restraints excluded: chain 5 residue 156 VAL Chi-restraints excluded: chain 5 residue 204 ILE Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 5 residue 280 THR Chi-restraints excluded: chain 5 residue 286 HIS Chi-restraints excluded: chain 5 residue 351 MET Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 26 GLN Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 189 LYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 277 LEU Chi-restraints excluded: chain b residue 317 ILE Chi-restraints excluded: chain b residue 444 PHE Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain u residue 55 PHE Chi-restraints excluded: chain u residue 88 THR Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 124 TYR Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 154 LEU Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 211 THR Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 65 ARG Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 179 ILE Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain i residue 28 TYR Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain N residue 201 ARG Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 30 ARG Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain K residue 275 GLN Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 338 TYR Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 333 PHE Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain o residue 107 LEU Chi-restraints excluded: chain n residue 94 LEU Chi-restraints excluded: chain n residue 116 HIS Chi-restraints excluded: chain n residue 137 ASN Chi-restraints excluded: chain n residue 152 SER Chi-restraints excluded: chain n residue 164 ASN Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain t residue 101 LEU Chi-restraints excluded: chain t residue 104 THR Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 134 THR Chi-restraints excluded: chain t residue 157 ASN Chi-restraints excluded: chain t residue 172 ASN Chi-restraints excluded: chain t residue 180 THR Chi-restraints excluded: chain t residue 312 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 448 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 671 optimal weight: 8.9990 chunk 549 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 808 optimal weight: 9.9990 chunk 873 optimal weight: 1.9990 chunk 720 optimal weight: 10.0000 chunk 802 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 648 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 23 ASN ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 ASN ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 GLN ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 164 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN C 115 HIS C 291 ASN E 138 GLN G 192 GLN ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN H 64 HIS ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN L 105 ASN ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN M 41 GLN N 23 GLN ** N 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 GLN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN K 284 ASN K 295 GLN D 436 ASN o 100 HIS o 204 HIS n 108 ASN n 164 ASN ** t 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 106125 Z= 0.345 Angle : 0.732 17.279 152938 Z= 0.375 Chirality : 0.042 0.269 18691 Planarity : 0.006 0.117 11918 Dihedral : 23.238 179.721 39071 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.94 % Favored : 91.63 % Rotamer: Outliers : 6.69 % Allowed : 21.28 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.22 (0.09), residues: 6938 helix: -0.95 (0.09), residues: 2656 sheet: -1.48 (0.15), residues: 1011 loop : -1.85 (0.10), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP m 246 HIS 0.035 0.002 HIS 5 286 PHE 0.030 0.002 PHE b 123 TYR 0.028 0.002 TYR 4 121 ARG 0.018 0.001 ARG N 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 413 poor density : 931 time to evaluate : 6.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 15 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8167 (ttp-110) REVERT: x 17 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7873 (tm-30) REVERT: x 33 MET cc_start: 0.8978 (mmm) cc_final: 0.8681 (tmm) REVERT: x 40 GLU cc_start: 0.8051 (pp20) cc_final: 0.7414 (tp30) REVERT: x 50 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8515 (tp40) REVERT: x 80 ASP cc_start: 0.7887 (t0) cc_final: 0.7640 (t0) REVERT: x 281 GLU cc_start: 0.9346 (tt0) cc_final: 0.8781 (tp30) REVERT: x 285 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8784 (mp0) REVERT: F 19 GLN cc_start: 0.9073 (mt0) cc_final: 0.8722 (pp30) REVERT: F 21 LYS cc_start: 0.8737 (mttt) cc_final: 0.8386 (tptt) REVERT: F 76 TYR cc_start: 0.8624 (t80) cc_final: 0.8375 (t80) REVERT: F 121 LYS cc_start: 0.9299 (tttt) cc_final: 0.8883 (mptt) REVERT: 3 129 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7130 (tm-30) REVERT: 3 131 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8337 (mm-30) REVERT: 3 143 ARG cc_start: 0.7587 (mmt90) cc_final: 0.7329 (mmt90) REVERT: 3 160 LYS cc_start: 0.8836 (mttt) cc_final: 0.8526 (tppt) REVERT: 3 167 MET cc_start: 0.9352 (mmm) cc_final: 0.8989 (mmm) REVERT: 4 8 LYS cc_start: 0.9320 (pttt) cc_final: 0.8847 (mmtt) REVERT: 4 38 LYS cc_start: 0.8526 (mttm) cc_final: 0.8293 (mtmm) REVERT: 4 75 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7734 (tp) REVERT: 4 91 ASN cc_start: 0.8627 (m-40) cc_final: 0.7955 (p0) REVERT: 4 111 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8223 (t80) REVERT: 4 153 VAL cc_start: 0.6831 (t) cc_final: 0.6620 (t) REVERT: 4 164 LYS cc_start: 0.8532 (mtpp) cc_final: 0.8126 (mmtt) REVERT: 5 1 MET cc_start: 0.8290 (ptp) cc_final: 0.6910 (mtm) REVERT: 5 204 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8311 (mm) REVERT: 5 220 ASP cc_start: 0.8616 (t70) cc_final: 0.8097 (p0) REVERT: 5 242 MET cc_start: 0.9099 (mmm) cc_final: 0.8899 (mpp) REVERT: 5 260 LYS cc_start: 0.8427 (mttp) cc_final: 0.8079 (ptmm) REVERT: 5 301 GLU cc_start: 0.9147 (tp30) cc_final: 0.8676 (tp30) REVERT: 5 412 ASP cc_start: 0.7953 (p0) cc_final: 0.7395 (p0) REVERT: A 30 LYS cc_start: 0.1346 (tmtt) cc_final: 0.1065 (tmtt) REVERT: A 42 ASN cc_start: 0.3090 (p0) cc_final: 0.2398 (p0) REVERT: A 79 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8920 (mt-10) REVERT: A 81 TYR cc_start: 0.8485 (m-80) cc_final: 0.8122 (m-80) REVERT: A 142 ARG cc_start: 0.7149 (mtp180) cc_final: 0.6819 (mtp85) REVERT: b 48 ARG cc_start: 0.8138 (tmt-80) cc_final: 0.7591 (ttm110) REVERT: b 116 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6081 (tt) REVERT: b 189 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7618 (pttp) REVERT: b 232 MET cc_start: 0.5992 (mtm) cc_final: 0.4434 (mmt) REVERT: b 234 ASN cc_start: 0.8639 (m110) cc_final: 0.8285 (m-40) REVERT: b 237 MET cc_start: 0.5975 (mmt) cc_final: 0.5579 (mmm) REVERT: b 397 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8473 (mtpp) REVERT: r 3 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7723 (mm110) REVERT: r 9 ARG cc_start: 0.9385 (mtm-85) cc_final: 0.8906 (mtm-85) REVERT: r 12 LYS cc_start: 0.8710 (mttt) cc_final: 0.8433 (mmmt) REVERT: r 16 LYS cc_start: 0.8399 (mttt) cc_final: 0.8163 (mmmt) REVERT: r 24 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8671 (tptt) REVERT: r 28 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8701 (mp0) REVERT: s 16 LYS cc_start: 0.6749 (ttpt) cc_final: 0.6426 (ttmt) REVERT: s 17 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7953 (mm-30) REVERT: u 43 ARG cc_start: 0.8653 (mtp180) cc_final: 0.7894 (tpt90) REVERT: u 45 ASN cc_start: 0.8110 (t0) cc_final: 0.7873 (t0) REVERT: u 93 MET cc_start: 0.5836 (mpp) cc_final: 0.5369 (mpp) REVERT: u 104 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: v 27 LYS cc_start: 0.8186 (mttt) cc_final: 0.7857 (ttpp) REVERT: v 28 ILE cc_start: 0.8523 (pt) cc_final: 0.8287 (tt) REVERT: v 29 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8006 (t0) REVERT: v 41 ASP cc_start: 0.8701 (t70) cc_final: 0.8204 (t70) REVERT: v 164 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: v 195 ASP cc_start: 0.8702 (m-30) cc_final: 0.8253 (t70) REVERT: W 5 LYS cc_start: 0.8920 (pttm) cc_final: 0.8668 (ptmm) REVERT: W 6 ARG cc_start: 0.7886 (ttt90) cc_final: 0.7662 (tmm-80) REVERT: W 66 ILE cc_start: 0.8932 (mm) cc_final: 0.8614 (mp) REVERT: W 67 MET cc_start: 0.8058 (mtp) cc_final: 0.7382 (mmm) REVERT: W 87 GLU cc_start: 0.9208 (mp0) cc_final: 0.8938 (tp30) REVERT: W 88 ASN cc_start: 0.7641 (m110) cc_final: 0.7143 (t0) REVERT: W 110 ASN cc_start: 0.9383 (m-40) cc_final: 0.9075 (p0) REVERT: W 116 PHE cc_start: 0.7667 (m-10) cc_final: 0.7430 (m-10) REVERT: W 157 MET cc_start: 0.8823 (mtp) cc_final: 0.8431 (mtp) REVERT: y 1 MET cc_start: 0.3275 (mmt) cc_final: 0.2678 (mtp) REVERT: y 34 PHE cc_start: 0.7822 (t80) cc_final: 0.7573 (t80) REVERT: y 62 MET cc_start: 0.7810 (tpp) cc_final: 0.7593 (tpp) REVERT: y 90 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8327 (p0) REVERT: y 100 ARG cc_start: 0.8148 (tmt90) cc_final: 0.7606 (mmp-170) REVERT: y 127 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8238 (mm-30) REVERT: y 215 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8456 (mt) REVERT: z 6 ARG cc_start: 0.7400 (mtm110) cc_final: 0.6081 (tpt90) REVERT: B 17 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8237 (mm) REVERT: B 53 MET cc_start: 0.7807 (tpp) cc_final: 0.7415 (mmm) REVERT: B 66 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7727 (mptt) REVERT: B 74 GLU cc_start: 0.8527 (pt0) cc_final: 0.7535 (tp30) REVERT: B 114 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8915 (p) REVERT: B 316 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8102 (mp0) REVERT: B 369 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7663 (ttm-80) REVERT: B 380 MET cc_start: 0.6410 (tpp) cc_final: 0.6156 (tpp) REVERT: C 73 ARG cc_start: 0.8748 (mtt180) cc_final: 0.8191 (ptt-90) REVERT: C 115 HIS cc_start: 0.9311 (OUTLIER) cc_final: 0.8655 (t70) REVERT: C 164 GLU cc_start: 0.9388 (tt0) cc_final: 0.9078 (tp30) REVERT: e 23 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8905 (p0) REVERT: e 27 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8477 (ptt180) REVERT: e 81 ASP cc_start: 0.8833 (m-30) cc_final: 0.8539 (t0) REVERT: e 83 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8454 (tt0) REVERT: E 9 TRP cc_start: 0.8517 (OUTLIER) cc_final: 0.7981 (m-90) REVERT: E 29 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8736 (pttt) REVERT: E 169 ASP cc_start: 0.8263 (m-30) cc_final: 0.7891 (m-30) REVERT: f 22 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8742 (p) REVERT: f 33 GLU cc_start: 0.9150 (tt0) cc_final: 0.8911 (tm-30) REVERT: f 65 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8493 (mtt-85) REVERT: h 43 LYS cc_start: 0.9291 (tttt) cc_final: 0.8842 (tptp) REVERT: h 60 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8947 (tm-30) REVERT: H 7 GLU cc_start: 0.9107 (tt0) cc_final: 0.8720 (tt0) REVERT: H 10 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8172 (tp) REVERT: H 19 SER cc_start: 0.8195 (m) cc_final: 0.7614 (t) REVERT: H 78 MET cc_start: 0.8545 (ttm) cc_final: 0.8248 (ttt) REVERT: H 153 ASP cc_start: 0.9508 (m-30) cc_final: 0.9152 (t0) REVERT: H 160 ASP cc_start: 0.9064 (m-30) cc_final: 0.8808 (t0) REVERT: H 162 GLN cc_start: 0.8819 (tt0) cc_final: 0.8371 (tm-30) REVERT: H 179 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8564 (tp) REVERT: i 47 ILE cc_start: 0.9076 (mt) cc_final: 0.8800 (mm) REVERT: j 30 GLN cc_start: 0.8463 (mt0) cc_final: 0.8217 (tt0) REVERT: j 31 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8499 (mtpt) REVERT: j 75 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8904 (tttp) REVERT: L 46 ILE cc_start: 0.8992 (mm) cc_final: 0.8655 (mm) REVERT: L 49 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8524 (mtm110) REVERT: L 67 ARG cc_start: 0.9504 (ptm-80) cc_final: 0.8841 (mtm180) REVERT: L 102 GLN cc_start: 0.8614 (mm-40) cc_final: 0.7940 (mt0) REVERT: L 104 ARG cc_start: 0.8604 (ttt-90) cc_final: 0.7856 (mtm180) REVERT: M 4 ASP cc_start: 0.5609 (OUTLIER) cc_final: 0.3905 (p0) REVERT: M 27 GLN cc_start: 0.8465 (tt0) cc_final: 0.8133 (tm-30) REVERT: M 37 GLU cc_start: 0.9069 (tt0) cc_final: 0.8537 (tp30) REVERT: M 38 ILE cc_start: 0.9617 (mp) cc_final: 0.9312 (mt) REVERT: M 47 ASP cc_start: 0.8813 (t70) cc_final: 0.8309 (t70) REVERT: M 62 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8738 (mp10) REVERT: N 4 TYR cc_start: 0.9022 (m-10) cc_final: 0.8352 (m-10) REVERT: N 6 TYR cc_start: 0.8786 (m-80) cc_final: 0.8410 (m-80) REVERT: N 15 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: N 17 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8563 (p0) REVERT: N 28 TRP cc_start: 0.9055 (t60) cc_final: 0.8775 (t60) REVERT: N 43 THR cc_start: 0.8771 (p) cc_final: 0.8542 (p) REVERT: N 119 TYR cc_start: 0.9408 (p90) cc_final: 0.8996 (p90) REVERT: N 196 THR cc_start: 0.7955 (m) cc_final: 0.7696 (p) REVERT: N 201 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8634 (mtp180) REVERT: O 28 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9229 (mt) REVERT: O 53 LYS cc_start: 0.9054 (mttt) cc_final: 0.8594 (mmtm) REVERT: O 65 ASN cc_start: 0.7820 (t0) cc_final: 0.7479 (t0) REVERT: O 66 LYS cc_start: 0.8966 (mttp) cc_final: 0.8662 (mtmt) REVERT: O 190 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8608 (p) REVERT: P 23 ARG cc_start: 0.9085 (mtp180) cc_final: 0.8619 (mtm180) REVERT: P 30 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8315 (tmt170) REVERT: P 120 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8540 (p0) REVERT: P 152 GLU cc_start: 0.8293 (tt0) cc_final: 0.7177 (mm-30) REVERT: P 154 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7952 (mp0) REVERT: P 155 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8046 (mm-30) REVERT: Q 23 ASN cc_start: 0.8992 (t0) cc_final: 0.8570 (t0) REVERT: S 61 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.9234 (mt) REVERT: S 118 PHE cc_start: 0.8493 (t80) cc_final: 0.8281 (t80) REVERT: V 40 LYS cc_start: 0.6921 (mtpp) cc_final: 0.6606 (mtmm) REVERT: V 57 MET cc_start: 0.7854 (mtp) cc_final: 0.7649 (mtp) REVERT: V 102 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7495 (tp) REVERT: V 109 MET cc_start: 0.7567 (mmm) cc_final: 0.7108 (mmm) REVERT: Y 11 ASP cc_start: 0.8280 (t0) cc_final: 0.8043 (t0) REVERT: Y 54 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8190 (m-30) REVERT: Y 55 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8530 (tp30) REVERT: Y 66 GLN cc_start: 0.9095 (mt0) cc_final: 0.8832 (mt0) REVERT: Y 67 GLU cc_start: 0.8981 (pt0) cc_final: 0.8574 (pp20) REVERT: K 34 ARG cc_start: 0.8314 (mtp-110) cc_final: 0.7497 (ppt170) REVERT: K 42 ASN cc_start: 0.7939 (m-40) cc_final: 0.7715 (m-40) REVERT: K 121 PHE cc_start: 0.6228 (OUTLIER) cc_final: 0.4325 (t80) REVERT: K 179 LEU cc_start: 0.7803 (mm) cc_final: 0.7219 (mm) REVERT: K 181 LEU cc_start: 0.7751 (tp) cc_final: 0.7512 (tp) REVERT: K 231 MET cc_start: 0.7631 (mpp) cc_final: 0.7329 (mmm) REVERT: m 271 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7995 (p0) REVERT: D 274 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.7996 (p0) REVERT: D 275 LYS cc_start: 0.8706 (mmtp) cc_final: 0.8400 (mmtp) REVERT: D 280 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8648 (mt) REVERT: D 340 ARG cc_start: 0.7750 (ptm160) cc_final: 0.7314 (ttt-90) REVERT: D 345 CYS cc_start: 0.6798 (t) cc_final: 0.6267 (t) REVERT: D 463 TYR cc_start: 0.5881 (m-80) cc_final: 0.5660 (m-80) REVERT: o 154 ASN cc_start: 0.7176 (m-40) cc_final: 0.6718 (m-40) REVERT: o 194 LYS cc_start: 0.8656 (mttt) cc_final: 0.8422 (mmmm) REVERT: n 69 GLN cc_start: 0.7427 (mt0) cc_final: 0.6776 (tp-100) REVERT: n 198 ARG cc_start: 0.3205 (OUTLIER) cc_final: 0.2939 (mtm180) REVERT: t 297 ARG cc_start: 0.7271 (mtm110) cc_final: 0.6662 (tpt90) outliers start: 413 outliers final: 230 residues processed: 1252 average time/residue: 1.0042 time to fit residues: 2155.3159 Evaluate side-chains 1094 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 819 time to evaluate : 6.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 15 ARG Chi-restraints excluded: chain x residue 50 GLN Chi-restraints excluded: chain x residue 95 ILE Chi-restraints excluded: chain x residue 101 VAL Chi-restraints excluded: chain x residue 104 LYS Chi-restraints excluded: chain x residue 121 VAL Chi-restraints excluded: chain x residue 125 LYS Chi-restraints excluded: chain x residue 132 LEU Chi-restraints excluded: chain x residue 148 VAL Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 165 LEU Chi-restraints excluded: chain x residue 191 THR Chi-restraints excluded: chain x residue 209 THR Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 234 ASN Chi-restraints excluded: chain x residue 239 ILE Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain 3 residue 28 CYS Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 66 THR Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 72 THR Chi-restraints excluded: chain 3 residue 76 LEU Chi-restraints excluded: chain 3 residue 106 HIS Chi-restraints excluded: chain 3 residue 131 GLU Chi-restraints excluded: chain 3 residue 137 VAL Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 4 residue 20 ASN Chi-restraints excluded: chain 4 residue 75 LEU Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 107 CYS Chi-restraints excluded: chain 4 residue 111 PHE Chi-restraints excluded: chain 4 residue 118 LEU Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 171 ILE Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 5 residue 64 SER Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 110 ILE Chi-restraints excluded: chain 5 residue 204 ILE Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 5 residue 280 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 175 TYR Chi-restraints excluded: chain b residue 189 LYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 277 LEU Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain J residue 222 SER Chi-restraints excluded: chain r residue 3 GLN Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 59 VAL Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain u residue 55 PHE Chi-restraints excluded: chain u residue 88 THR Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 156 THR Chi-restraints excluded: chain v residue 164 GLU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 124 TYR Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 148 VAL Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 211 THR Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 27 ARG Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 35 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 65 ARG Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 179 ILE Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain i residue 29 LYS Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 59 THR Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 201 ARG Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 30 ARG Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 154 HIS Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 257 THR Chi-restraints excluded: chain m residue 271 ASN Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 333 PHE Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain o residue 209 LYS Chi-restraints excluded: chain n residue 31 ASP Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain n residue 83 HIS Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 116 HIS Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 137 ASN Chi-restraints excluded: chain n residue 152 SER Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 198 ARG Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 243 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 407 VAL Chi-restraints excluded: chain t residue 104 THR Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 134 THR Chi-restraints excluded: chain t residue 172 ASN Chi-restraints excluded: chain t residue 177 VAL Chi-restraints excluded: chain t residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 799 optimal weight: 20.0000 chunk 608 optimal weight: 10.0000 chunk 419 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 385 optimal weight: 6.9990 chunk 543 optimal weight: 30.0000 chunk 811 optimal weight: 4.9990 chunk 859 optimal weight: 30.0000 chunk 424 optimal weight: 0.8980 chunk 769 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 208 GLN x 262 GLN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 23 ASN ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 41 GLN 3 146 GLN ** 4 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 ASN A 45 HIS ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 HIS N 122 ASN N 182 ASN ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 GLN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 26 GLN D 337 ASN D 375 HIS o 100 HIS ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 150 GLN ** t 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 106125 Z= 0.312 Angle : 0.682 17.514 152938 Z= 0.349 Chirality : 0.040 0.266 18691 Planarity : 0.005 0.106 11918 Dihedral : 23.231 179.972 39019 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.35 % Favored : 92.26 % Rotamer: Outliers : 6.30 % Allowed : 22.42 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.90 (0.10), residues: 6938 helix: -0.56 (0.10), residues: 2652 sheet: -1.41 (0.15), residues: 994 loop : -1.76 (0.10), residues: 3292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP n 166 HIS 0.019 0.001 HIS C 115 PHE 0.047 0.002 PHE b 123 TYR 0.031 0.002 TYR 4 76 ARG 0.017 0.001 ARG N 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 389 poor density : 863 time to evaluate : 6.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 15 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8110 (ttp-110) REVERT: x 17 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7927 (tm-30) REVERT: x 33 MET cc_start: 0.8983 (mmm) cc_final: 0.8653 (tmm) REVERT: x 40 GLU cc_start: 0.7939 (pp20) cc_final: 0.7328 (tp30) REVERT: x 80 ASP cc_start: 0.7784 (t0) cc_final: 0.7488 (t0) REVERT: x 206 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9007 (tt) REVERT: x 281 GLU cc_start: 0.9303 (tt0) cc_final: 0.8761 (tp30) REVERT: x 285 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8764 (mp0) REVERT: x 286 MET cc_start: 0.8224 (mpp) cc_final: 0.7843 (mpp) REVERT: F 19 GLN cc_start: 0.9043 (mt0) cc_final: 0.8726 (pp30) REVERT: F 21 LYS cc_start: 0.8719 (mttt) cc_final: 0.8364 (tptt) REVERT: F 121 LYS cc_start: 0.9268 (tttt) cc_final: 0.8855 (mptt) REVERT: 3 131 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8450 (mm-30) REVERT: 3 150 ARG cc_start: 0.8606 (mtt180) cc_final: 0.8173 (tpt-90) REVERT: 3 160 LYS cc_start: 0.8815 (mttt) cc_final: 0.8529 (tppt) REVERT: 3 167 MET cc_start: 0.9336 (mmm) cc_final: 0.9011 (mmm) REVERT: 4 8 LYS cc_start: 0.9324 (pttt) cc_final: 0.8859 (mmtt) REVERT: 4 38 LYS cc_start: 0.8474 (mttm) cc_final: 0.8243 (mtmm) REVERT: 4 111 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8290 (t80) REVERT: 4 164 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8134 (mmtt) REVERT: 4 247 ARG cc_start: 0.8409 (mtm180) cc_final: 0.8185 (tpm170) REVERT: 5 1 MET cc_start: 0.8301 (ptp) cc_final: 0.7026 (mtm) REVERT: 5 57 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8558 (mm-30) REVERT: 5 105 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8056 (pt) REVERT: 5 112 SER cc_start: 0.8350 (t) cc_final: 0.8110 (p) REVERT: 5 204 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8181 (mm) REVERT: 5 211 GLU cc_start: 0.9243 (tp30) cc_final: 0.8629 (tm-30) REVERT: 5 220 ASP cc_start: 0.8616 (t70) cc_final: 0.8096 (p0) REVERT: 5 260 LYS cc_start: 0.8360 (mttp) cc_final: 0.8019 (ptmm) REVERT: 5 301 GLU cc_start: 0.9151 (tp30) cc_final: 0.8825 (tp30) REVERT: 5 366 TYR cc_start: 0.8794 (t80) cc_final: 0.8489 (t80) REVERT: 5 412 ASP cc_start: 0.7948 (p0) cc_final: 0.7443 (p0) REVERT: A 30 LYS cc_start: 0.1608 (tmtt) cc_final: 0.1376 (tmtt) REVERT: A 42 ASN cc_start: 0.3132 (p0) cc_final: 0.2739 (p0) REVERT: A 79 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8937 (mt-10) REVERT: A 81 TYR cc_start: 0.8585 (m-80) cc_final: 0.8141 (m-80) REVERT: b 48 ARG cc_start: 0.8138 (tmt-80) cc_final: 0.7640 (ttm110) REVERT: b 189 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7599 (pttp) REVERT: b 232 MET cc_start: 0.5855 (mtm) cc_final: 0.4652 (mmt) REVERT: b 234 ASN cc_start: 0.8689 (m110) cc_final: 0.8447 (m-40) REVERT: b 237 MET cc_start: 0.5702 (mmt) cc_final: 0.5356 (mmt) REVERT: r 3 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7448 (tp40) REVERT: r 9 ARG cc_start: 0.9362 (mtm-85) cc_final: 0.8893 (mtm-85) REVERT: r 12 LYS cc_start: 0.8776 (mttt) cc_final: 0.8498 (mmmt) REVERT: r 16 LYS cc_start: 0.8440 (mttt) cc_final: 0.8228 (mmmt) REVERT: r 24 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8615 (tptt) REVERT: r 28 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8623 (mp0) REVERT: s 16 LYS cc_start: 0.6792 (ttpt) cc_final: 0.6409 (ttmt) REVERT: s 17 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7911 (mm-30) REVERT: u 1 MET cc_start: 0.4926 (ttt) cc_final: 0.4040 (tpt) REVERT: u 43 ARG cc_start: 0.8673 (mtp180) cc_final: 0.7877 (tpt90) REVERT: u 45 ASN cc_start: 0.8097 (t0) cc_final: 0.7849 (t0) REVERT: u 57 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7867 (mmmt) REVERT: v 27 LYS cc_start: 0.8158 (mttt) cc_final: 0.7848 (ttpp) REVERT: v 29 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.7957 (t0) REVERT: v 41 ASP cc_start: 0.8740 (t70) cc_final: 0.8305 (t0) REVERT: v 190 LYS cc_start: 0.8982 (mtmt) cc_final: 0.8653 (mmtm) REVERT: v 195 ASP cc_start: 0.8567 (m-30) cc_final: 0.8242 (t70) REVERT: W 5 LYS cc_start: 0.8971 (pttm) cc_final: 0.8594 (ptmm) REVERT: W 6 ARG cc_start: 0.7981 (ttt90) cc_final: 0.7609 (tmm-80) REVERT: W 66 ILE cc_start: 0.9006 (mm) cc_final: 0.8692 (mp) REVERT: W 67 MET cc_start: 0.7878 (mtp) cc_final: 0.7244 (mmm) REVERT: W 87 GLU cc_start: 0.9208 (mp0) cc_final: 0.8953 (tp30) REVERT: W 88 ASN cc_start: 0.7720 (m110) cc_final: 0.7186 (t0) REVERT: W 110 ASN cc_start: 0.9415 (m-40) cc_final: 0.9077 (p0) REVERT: W 157 MET cc_start: 0.8824 (mtp) cc_final: 0.8432 (mtp) REVERT: y 1 MET cc_start: 0.3557 (mmt) cc_final: 0.2929 (mtp) REVERT: y 100 ARG cc_start: 0.8032 (tmt90) cc_final: 0.7343 (mmp-170) REVERT: y 127 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8236 (mm-30) REVERT: y 202 TYR cc_start: 0.5632 (p90) cc_final: 0.5284 (p90) REVERT: y 215 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8476 (mt) REVERT: z 6 ARG cc_start: 0.7369 (mtm110) cc_final: 0.6082 (tpt90) REVERT: B 17 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8227 (mm) REVERT: B 53 MET cc_start: 0.7594 (tpp) cc_final: 0.7148 (mmm) REVERT: B 66 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7810 (mptt) REVERT: B 74 GLU cc_start: 0.8492 (pt0) cc_final: 0.7537 (tp30) REVERT: B 114 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8884 (p) REVERT: B 316 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8139 (mp0) REVERT: B 369 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7949 (ttm-80) REVERT: B 380 MET cc_start: 0.6570 (tpp) cc_final: 0.6146 (tpp) REVERT: C 73 ARG cc_start: 0.8763 (mtt180) cc_final: 0.8182 (ptt-90) REVERT: C 164 GLU cc_start: 0.9366 (tt0) cc_final: 0.9033 (tp30) REVERT: C 220 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8780 (ptp90) REVERT: C 294 GLU cc_start: 0.8961 (tp30) cc_final: 0.8559 (tm-30) REVERT: e 23 ASP cc_start: 0.9125 (OUTLIER) cc_final: 0.8746 (p0) REVERT: e 24 ARG cc_start: 0.8494 (tpp80) cc_final: 0.7784 (mmm160) REVERT: e 27 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8408 (ptt180) REVERT: e 81 ASP cc_start: 0.8854 (m-30) cc_final: 0.8549 (t0) REVERT: E 169 ASP cc_start: 0.8311 (m-30) cc_final: 0.7945 (m-30) REVERT: f 33 GLU cc_start: 0.9152 (tt0) cc_final: 0.8911 (tm-30) REVERT: G 173 MET cc_start: 0.9250 (mmm) cc_final: 0.8885 (mmm) REVERT: G 228 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6785 (pp20) REVERT: h 45 LYS cc_start: 0.8527 (tttt) cc_final: 0.8302 (ptpt) REVERT: h 60 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8958 (tm-30) REVERT: H 153 ASP cc_start: 0.9476 (m-30) cc_final: 0.9219 (t0) REVERT: H 162 GLN cc_start: 0.8911 (tt0) cc_final: 0.8554 (tm-30) REVERT: j 15 SER cc_start: 0.7720 (OUTLIER) cc_final: 0.7500 (t) REVERT: j 30 GLN cc_start: 0.8438 (mt0) cc_final: 0.8169 (tt0) REVERT: j 31 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8473 (mtpt) REVERT: j 75 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8917 (tttp) REVERT: L 49 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8637 (mtp-110) REVERT: L 67 ARG cc_start: 0.9521 (ptm-80) cc_final: 0.8919 (mtm180) REVERT: L 102 GLN cc_start: 0.8660 (mm-40) cc_final: 0.7980 (mt0) REVERT: L 104 ARG cc_start: 0.8651 (ttt-90) cc_final: 0.7879 (mtm180) REVERT: M 37 GLU cc_start: 0.9094 (tt0) cc_final: 0.8566 (tp30) REVERT: M 38 ILE cc_start: 0.9584 (mp) cc_final: 0.9294 (mt) REVERT: M 56 GLN cc_start: 0.8885 (pt0) cc_final: 0.8323 (pm20) REVERT: M 62 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8733 (mp10) REVERT: N 15 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: N 17 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8508 (p0) REVERT: N 28 TRP cc_start: 0.9043 (t60) cc_final: 0.8749 (t60) REVERT: N 119 TYR cc_start: 0.9364 (p90) cc_final: 0.9016 (p90) REVERT: N 131 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8661 (mm-30) REVERT: N 196 THR cc_start: 0.7948 (m) cc_final: 0.7691 (p) REVERT: O 53 LYS cc_start: 0.9017 (mttt) cc_final: 0.8686 (mmtt) REVERT: O 65 ASN cc_start: 0.8223 (t0) cc_final: 0.7788 (t0) REVERT: O 66 LYS cc_start: 0.9004 (mttp) cc_final: 0.8585 (mtmt) REVERT: P 23 ARG cc_start: 0.9113 (mtp180) cc_final: 0.8622 (mtm180) REVERT: P 52 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8486 (mm) REVERT: P 120 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8561 (p0) REVERT: P 152 GLU cc_start: 0.8429 (tt0) cc_final: 0.7665 (tp30) REVERT: P 154 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7770 (mp0) REVERT: P 155 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8020 (mp0) REVERT: Q 23 ASN cc_start: 0.8967 (t0) cc_final: 0.8516 (t0) REVERT: S 25 PHE cc_start: 0.7942 (m-80) cc_final: 0.7698 (m-80) REVERT: V 40 LYS cc_start: 0.6742 (mtpp) cc_final: 0.6439 (mtmm) REVERT: V 102 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7800 (mp) REVERT: V 109 MET cc_start: 0.7720 (mmm) cc_final: 0.7248 (mmm) REVERT: V 112 SER cc_start: 0.8079 (p) cc_final: 0.7807 (p) REVERT: Y 11 ASP cc_start: 0.8262 (t0) cc_final: 0.8029 (t0) REVERT: Y 54 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8335 (m-30) REVERT: Y 55 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8593 (tp30) REVERT: Y 66 GLN cc_start: 0.9096 (mt0) cc_final: 0.8828 (mt0) REVERT: Y 67 GLU cc_start: 0.8969 (pt0) cc_final: 0.8552 (pp20) REVERT: K 121 PHE cc_start: 0.6168 (OUTLIER) cc_final: 0.4101 (t80) REVERT: K 179 LEU cc_start: 0.7798 (mm) cc_final: 0.7266 (mm) REVERT: m 271 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8117 (p0) REVERT: m 277 MET cc_start: 0.7367 (mmm) cc_final: 0.7056 (mmm) REVERT: D 343 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7092 (tt) REVERT: o 194 LYS cc_start: 0.8643 (mttt) cc_final: 0.8419 (mmmm) REVERT: n 69 GLN cc_start: 0.7380 (mt0) cc_final: 0.6925 (tp-100) REVERT: n 260 SER cc_start: 0.8087 (OUTLIER) cc_final: 0.7765 (m) REVERT: n 445 ASN cc_start: 0.6702 (m-40) cc_final: 0.5922 (p0) REVERT: t 297 ARG cc_start: 0.7446 (mtm110) cc_final: 0.6786 (tpt90) outliers start: 389 outliers final: 253 residues processed: 1155 average time/residue: 0.9338 time to fit residues: 1847.6316 Evaluate side-chains 1089 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 802 time to evaluate : 6.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 15 ARG Chi-restraints excluded: chain x residue 95 ILE Chi-restraints excluded: chain x residue 101 VAL Chi-restraints excluded: chain x residue 104 LYS Chi-restraints excluded: chain x residue 121 VAL Chi-restraints excluded: chain x residue 125 LYS Chi-restraints excluded: chain x residue 132 LEU Chi-restraints excluded: chain x residue 148 VAL Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 165 LEU Chi-restraints excluded: chain x residue 191 THR Chi-restraints excluded: chain x residue 204 THR Chi-restraints excluded: chain x residue 206 LEU Chi-restraints excluded: chain x residue 209 THR Chi-restraints excluded: chain x residue 215 GLN Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 234 ASN Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain 3 residue 23 ASN Chi-restraints excluded: chain 3 residue 28 CYS Chi-restraints excluded: chain 3 residue 52 THR Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 72 THR Chi-restraints excluded: chain 3 residue 76 LEU Chi-restraints excluded: chain 3 residue 129 GLU Chi-restraints excluded: chain 3 residue 131 GLU Chi-restraints excluded: chain 3 residue 137 VAL Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 20 ASN Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 107 CYS Chi-restraints excluded: chain 4 residue 111 PHE Chi-restraints excluded: chain 4 residue 150 ILE Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 64 SER Chi-restraints excluded: chain 5 residue 105 ILE Chi-restraints excluded: chain 5 residue 164 LEU Chi-restraints excluded: chain 5 residue 204 ILE Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 5 residue 280 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 189 LYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 277 LEU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 317 ILE Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 222 SER Chi-restraints excluded: chain r residue 3 GLN Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 59 VAL Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain u residue 55 PHE Chi-restraints excluded: chain u residue 57 LYS Chi-restraints excluded: chain u residue 88 THR Chi-restraints excluded: chain v residue 10 ASN Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 156 THR Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 124 TYR Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain y residue 125 THR Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 148 VAL Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 167 VAL Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 211 THR Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 27 ARG Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 35 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 59 THR Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 154 HIS Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 256 LEU Chi-restraints excluded: chain m residue 257 THR Chi-restraints excluded: chain m residue 271 ASN Chi-restraints excluded: chain m residue 283 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 333 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 360 TRP Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain o residue 93 ILE Chi-restraints excluded: chain o residue 137 LEU Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain o residue 160 HIS Chi-restraints excluded: chain o residue 209 LYS Chi-restraints excluded: chain n residue 31 ASP Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 116 HIS Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 137 ASN Chi-restraints excluded: chain n residue 152 SER Chi-restraints excluded: chain n residue 164 ASN Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 243 ILE Chi-restraints excluded: chain n residue 260 SER Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 407 VAL Chi-restraints excluded: chain n residue 412 VAL Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 134 THR Chi-restraints excluded: chain t residue 177 VAL Chi-restraints excluded: chain t residue 180 THR Chi-restraints excluded: chain t residue 302 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 715 optimal weight: 10.0000 chunk 487 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 639 optimal weight: 10.0000 chunk 354 optimal weight: 9.9990 chunk 733 optimal weight: 50.0000 chunk 593 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 438 optimal weight: 3.9990 chunk 771 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 262 GLN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 73 HIS 5 152 ASN 5 299 ASN ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 208 HIS ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN N 122 ASN ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS Y 26 GLN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 GLN ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 ASN ** t 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 106125 Z= 0.246 Angle : 0.644 17.452 152938 Z= 0.329 Chirality : 0.039 0.278 18691 Planarity : 0.005 0.068 11918 Dihedral : 23.192 179.730 38992 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.34 % Favored : 92.27 % Rotamer: Outliers : 6.04 % Allowed : 23.34 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.68 (0.10), residues: 6938 helix: -0.33 (0.10), residues: 2655 sheet: -1.30 (0.16), residues: 1001 loop : -1.66 (0.10), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP n 166 HIS 0.011 0.001 HIS J 215 PHE 0.047 0.002 PHE b 123 TYR 0.034 0.002 TYR 4 76 ARG 0.011 0.000 ARG S 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 373 poor density : 867 time to evaluate : 6.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 33 MET cc_start: 0.8983 (mmm) cc_final: 0.8625 (tmm) REVERT: x 40 GLU cc_start: 0.7908 (pp20) cc_final: 0.7227 (tp30) REVERT: x 80 ASP cc_start: 0.7753 (t0) cc_final: 0.7444 (t0) REVERT: x 206 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8965 (tt) REVERT: x 281 GLU cc_start: 0.9302 (tt0) cc_final: 0.8745 (tp30) REVERT: x 285 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8720 (mp0) REVERT: x 286 MET cc_start: 0.8280 (mpp) cc_final: 0.7878 (mpp) REVERT: F 19 GLN cc_start: 0.9004 (mt0) cc_final: 0.8704 (pp30) REVERT: F 21 LYS cc_start: 0.8726 (mttt) cc_final: 0.8373 (tptt) REVERT: F 121 LYS cc_start: 0.9261 (tttt) cc_final: 0.8831 (mptt) REVERT: 3 4 GLU cc_start: 0.9464 (tp30) cc_final: 0.9245 (tp30) REVERT: 3 95 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8791 (tt0) REVERT: 3 131 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8466 (mm-30) REVERT: 3 143 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7228 (tpt-90) REVERT: 3 150 ARG cc_start: 0.8615 (mtt180) cc_final: 0.8176 (tpt-90) REVERT: 3 160 LYS cc_start: 0.8805 (mttt) cc_final: 0.8523 (tppt) REVERT: 3 167 MET cc_start: 0.9312 (mmm) cc_final: 0.9015 (mmm) REVERT: 4 8 LYS cc_start: 0.9297 (pttt) cc_final: 0.8824 (mmtt) REVERT: 4 38 LYS cc_start: 0.8459 (mttm) cc_final: 0.8245 (mtmm) REVERT: 4 111 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8311 (t80) REVERT: 4 164 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8111 (mmtt) REVERT: 4 247 ARG cc_start: 0.8473 (mtm180) cc_final: 0.8245 (tpm170) REVERT: 5 1 MET cc_start: 0.8333 (ptp) cc_final: 0.7126 (mtm) REVERT: 5 105 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8043 (pt) REVERT: 5 112 SER cc_start: 0.8500 (t) cc_final: 0.8253 (p) REVERT: 5 204 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8153 (mm) REVERT: 5 211 GLU cc_start: 0.9231 (tp30) cc_final: 0.8601 (tm-30) REVERT: 5 220 ASP cc_start: 0.8627 (t70) cc_final: 0.8207 (p0) REVERT: 5 301 GLU cc_start: 0.9159 (tp30) cc_final: 0.8878 (tp30) REVERT: 5 366 TYR cc_start: 0.8802 (t80) cc_final: 0.8447 (t80) REVERT: 5 412 ASP cc_start: 0.8002 (p0) cc_final: 0.7508 (p0) REVERT: A 79 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8943 (mt-10) REVERT: A 81 TYR cc_start: 0.8562 (m-80) cc_final: 0.8180 (m-80) REVERT: A 177 MET cc_start: 0.7604 (tpt) cc_final: 0.7133 (tmm) REVERT: b 48 ARG cc_start: 0.8025 (tmt-80) cc_final: 0.7581 (ttm110) REVERT: b 147 LEU cc_start: 0.9034 (mm) cc_final: 0.8761 (mt) REVERT: b 189 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7586 (pttt) REVERT: b 232 MET cc_start: 0.5555 (mtm) cc_final: 0.4372 (mmt) REVERT: b 234 ASN cc_start: 0.8736 (m110) cc_final: 0.8513 (m-40) REVERT: b 237 MET cc_start: 0.5666 (mmt) cc_final: 0.5434 (mmt) REVERT: b 274 ILE cc_start: 0.8091 (mm) cc_final: 0.7858 (tt) REVERT: r 3 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7690 (mm110) REVERT: r 9 ARG cc_start: 0.9332 (mtm-85) cc_final: 0.8847 (mtm-85) REVERT: r 12 LYS cc_start: 0.8762 (mttt) cc_final: 0.8406 (mmmt) REVERT: r 16 LYS cc_start: 0.8445 (mttt) cc_final: 0.8232 (mmmt) REVERT: r 17 ARG cc_start: 0.9302 (ttp80) cc_final: 0.8877 (tpp80) REVERT: r 24 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8641 (tptt) REVERT: r 28 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8668 (mp0) REVERT: s 16 LYS cc_start: 0.6706 (ttpt) cc_final: 0.6344 (ttmt) REVERT: s 17 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7941 (mm-30) REVERT: u 28 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7837 (pt0) REVERT: u 43 ARG cc_start: 0.8685 (mtp180) cc_final: 0.7858 (tpt90) REVERT: u 52 THR cc_start: 0.7437 (t) cc_final: 0.7214 (t) REVERT: u 93 MET cc_start: 0.5973 (mpp) cc_final: 0.5757 (mpp) REVERT: v 27 LYS cc_start: 0.8135 (mttt) cc_final: 0.7826 (ttpp) REVERT: v 29 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.7898 (t0) REVERT: v 41 ASP cc_start: 0.8763 (t70) cc_final: 0.8333 (t0) REVERT: v 190 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8641 (mmtm) REVERT: W 5 LYS cc_start: 0.8987 (pttm) cc_final: 0.8643 (ptmm) REVERT: W 66 ILE cc_start: 0.8994 (mm) cc_final: 0.8669 (mp) REVERT: W 67 MET cc_start: 0.7879 (mtp) cc_final: 0.7246 (mmm) REVERT: W 87 GLU cc_start: 0.9175 (mp0) cc_final: 0.8913 (tp30) REVERT: W 88 ASN cc_start: 0.7624 (m110) cc_final: 0.7073 (t0) REVERT: W 110 ASN cc_start: 0.9389 (m-40) cc_final: 0.9087 (p0) REVERT: W 157 MET cc_start: 0.8831 (mtp) cc_final: 0.8431 (mtp) REVERT: y 1 MET cc_start: 0.3813 (mmt) cc_final: 0.3053 (mtp) REVERT: y 100 ARG cc_start: 0.7966 (tmt90) cc_final: 0.7351 (mmp-170) REVERT: y 127 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8194 (mm-30) REVERT: y 154 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8469 (tt) REVERT: y 215 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8482 (mt) REVERT: z 6 ARG cc_start: 0.7020 (mtm110) cc_final: 0.5744 (tpt90) REVERT: B 17 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8202 (mm) REVERT: B 53 MET cc_start: 0.7521 (tpp) cc_final: 0.7050 (mmm) REVERT: B 66 LYS cc_start: 0.8267 (mtpp) cc_final: 0.7808 (mptt) REVERT: B 74 GLU cc_start: 0.8417 (pt0) cc_final: 0.7454 (tp30) REVERT: B 114 VAL cc_start: 0.9184 (OUTLIER) cc_final: 0.8913 (p) REVERT: B 277 SER cc_start: 0.8148 (m) cc_final: 0.7801 (p) REVERT: B 316 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8123 (mp0) REVERT: B 369 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7929 (ttm-80) REVERT: B 380 MET cc_start: 0.6681 (tpp) cc_final: 0.6315 (tpp) REVERT: C 73 ARG cc_start: 0.8764 (mtt180) cc_final: 0.8144 (ptt-90) REVERT: C 164 GLU cc_start: 0.9359 (tt0) cc_final: 0.9016 (tp30) REVERT: C 220 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8731 (ptp90) REVERT: C 294 GLU cc_start: 0.8933 (tp30) cc_final: 0.8541 (tm-30) REVERT: e 23 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8614 (p0) REVERT: e 24 ARG cc_start: 0.8510 (tpp80) cc_final: 0.7808 (mmm160) REVERT: e 27 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8415 (ptt180) REVERT: e 34 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8654 (ttpt) REVERT: e 81 ASP cc_start: 0.8852 (m-30) cc_final: 0.8554 (t0) REVERT: E 169 ASP cc_start: 0.8285 (m-30) cc_final: 0.7962 (m-30) REVERT: f 33 GLU cc_start: 0.9149 (tt0) cc_final: 0.8845 (tm-30) REVERT: G 112 GLU cc_start: 0.9429 (mm-30) cc_final: 0.9222 (tp30) REVERT: G 173 MET cc_start: 0.9316 (mmm) cc_final: 0.8784 (mmm) REVERT: G 228 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6828 (pp20) REVERT: h 45 LYS cc_start: 0.8530 (tttt) cc_final: 0.8317 (ptpt) REVERT: h 60 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8960 (tm-30) REVERT: h 94 LYS cc_start: 0.8579 (ttpp) cc_final: 0.8333 (ptmm) REVERT: H 54 LYS cc_start: 0.9035 (mmtm) cc_final: 0.8757 (mmtm) REVERT: H 116 ASN cc_start: 0.9228 (t0) cc_final: 0.8740 (t0) REVERT: H 135 GLU cc_start: 0.8278 (mp0) cc_final: 0.8001 (mp0) REVERT: H 153 ASP cc_start: 0.9488 (m-30) cc_final: 0.9236 (t0) REVERT: H 162 GLN cc_start: 0.8755 (tt0) cc_final: 0.8505 (tm-30) REVERT: j 15 SER cc_start: 0.7710 (OUTLIER) cc_final: 0.7490 (t) REVERT: j 30 GLN cc_start: 0.8445 (mt0) cc_final: 0.8140 (tt0) REVERT: j 31 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8453 (mtpt) REVERT: j 75 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8903 (tttp) REVERT: L 49 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8540 (mtp-110) REVERT: L 67 ARG cc_start: 0.9522 (ptm-80) cc_final: 0.8906 (mtm180) REVERT: L 102 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8097 (mt0) REVERT: L 104 ARG cc_start: 0.8618 (ttt-90) cc_final: 0.7897 (mtm180) REVERT: M 47 ASP cc_start: 0.8752 (t70) cc_final: 0.8315 (t70) REVERT: M 56 GLN cc_start: 0.8868 (pt0) cc_final: 0.8321 (pm20) REVERT: M 62 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8761 (mp10) REVERT: N 15 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: N 17 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8515 (p0) REVERT: N 28 TRP cc_start: 0.9031 (t60) cc_final: 0.8742 (t60) REVERT: N 119 TYR cc_start: 0.9344 (p90) cc_final: 0.8914 (p90) REVERT: N 131 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8595 (mm-30) REVERT: N 201 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.8687 (mtp180) REVERT: O 53 LYS cc_start: 0.9014 (mttt) cc_final: 0.8557 (mmtm) REVERT: O 65 ASN cc_start: 0.8123 (t0) cc_final: 0.7728 (t0) REVERT: O 66 LYS cc_start: 0.8954 (mttp) cc_final: 0.8671 (mtmt) REVERT: P 23 ARG cc_start: 0.9116 (mtp180) cc_final: 0.8608 (mtm180) REVERT: P 52 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8502 (mm) REVERT: P 88 VAL cc_start: 0.9356 (t) cc_final: 0.9115 (p) REVERT: P 145 HIS cc_start: 0.9110 (OUTLIER) cc_final: 0.8435 (m-70) REVERT: P 152 GLU cc_start: 0.8443 (tt0) cc_final: 0.7710 (tp30) REVERT: P 154 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7741 (mp0) REVERT: P 155 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8015 (mp0) REVERT: Q 23 ASN cc_start: 0.8924 (t0) cc_final: 0.8459 (t0) REVERT: S 25 PHE cc_start: 0.7861 (m-80) cc_final: 0.7637 (m-80) REVERT: V 40 LYS cc_start: 0.6608 (mtpp) cc_final: 0.6313 (mtmm) REVERT: V 102 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7685 (mp) REVERT: V 109 MET cc_start: 0.7694 (mmm) cc_final: 0.7360 (mmm) REVERT: V 112 SER cc_start: 0.8086 (p) cc_final: 0.7808 (p) REVERT: V 126 TRP cc_start: 0.7929 (m100) cc_final: 0.7652 (m100) REVERT: Y 11 ASP cc_start: 0.8249 (t0) cc_final: 0.8016 (t0) REVERT: Y 54 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8389 (m-30) REVERT: Y 55 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8597 (tp30) REVERT: Y 66 GLN cc_start: 0.9108 (mt0) cc_final: 0.8840 (mt0) REVERT: Y 67 GLU cc_start: 0.9016 (pt0) cc_final: 0.8608 (pp20) REVERT: K 34 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.7597 (ppt170) REVERT: K 80 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6796 (pp) REVERT: K 81 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6922 (mt) REVERT: K 121 PHE cc_start: 0.6172 (OUTLIER) cc_final: 0.4169 (t80) REVERT: K 129 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: K 179 LEU cc_start: 0.7735 (mm) cc_final: 0.7211 (mm) REVERT: K 181 LEU cc_start: 0.8000 (tp) cc_final: 0.7625 (tp) REVERT: K 201 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7839 (tttm) REVERT: K 293 TYR cc_start: 0.6876 (t80) cc_final: 0.6644 (t80) REVERT: D 277 PHE cc_start: 0.8445 (t80) cc_final: 0.7642 (t80) REVERT: D 343 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7010 (tt) REVERT: o 194 LYS cc_start: 0.8661 (mttt) cc_final: 0.8414 (mmmm) REVERT: n 69 GLN cc_start: 0.7453 (mt0) cc_final: 0.7227 (tp-100) REVERT: n 260 SER cc_start: 0.8013 (OUTLIER) cc_final: 0.7675 (m) REVERT: n 445 ASN cc_start: 0.6622 (m-40) cc_final: 0.5999 (p0) REVERT: t 157 ASN cc_start: 0.4409 (OUTLIER) cc_final: 0.3400 (p0) REVERT: t 160 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6489 (t80) REVERT: t 297 ARG cc_start: 0.7570 (mtm110) cc_final: 0.6835 (tpt170) outliers start: 373 outliers final: 251 residues processed: 1151 average time/residue: 0.9426 time to fit residues: 1869.6831 Evaluate side-chains 1092 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 801 time to evaluate : 6.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 18 ILE Chi-restraints excluded: chain x residue 95 ILE Chi-restraints excluded: chain x residue 104 LYS Chi-restraints excluded: chain x residue 121 VAL Chi-restraints excluded: chain x residue 125 LYS Chi-restraints excluded: chain x residue 132 LEU Chi-restraints excluded: chain x residue 148 VAL Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 165 LEU Chi-restraints excluded: chain x residue 204 THR Chi-restraints excluded: chain x residue 206 LEU Chi-restraints excluded: chain x residue 209 THR Chi-restraints excluded: chain x residue 215 GLN Chi-restraints excluded: chain x residue 234 ASN Chi-restraints excluded: chain x residue 239 ILE Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain 3 residue 28 CYS Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 52 THR Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 72 THR Chi-restraints excluded: chain 3 residue 76 LEU Chi-restraints excluded: chain 3 residue 129 GLU Chi-restraints excluded: chain 3 residue 131 GLU Chi-restraints excluded: chain 3 residue 137 VAL Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 20 ASN Chi-restraints excluded: chain 4 residue 58 ARG Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 107 CYS Chi-restraints excluded: chain 4 residue 111 PHE Chi-restraints excluded: chain 4 residue 150 ILE Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 171 ILE Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 5 residue 64 SER Chi-restraints excluded: chain 5 residue 105 ILE Chi-restraints excluded: chain 5 residue 204 ILE Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 5 residue 280 THR Chi-restraints excluded: chain 5 residue 303 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 189 LYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 277 LEU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 317 ILE Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 222 SER Chi-restraints excluded: chain r residue 3 GLN Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain s residue 8 SER Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain u residue 55 PHE Chi-restraints excluded: chain u residue 88 THR Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 156 THR Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 124 TYR Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain y residue 22 THR Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 148 VAL Chi-restraints excluded: chain y residue 154 LEU Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 211 THR Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain e residue 11 LYS Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 27 ARG Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 35 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 59 THR Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain N residue 201 ARG Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain O residue 153 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 145 HIS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 201 LYS Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 257 THR Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain D residue 283 PHE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain o residue 90 SER Chi-restraints excluded: chain o residue 93 ILE Chi-restraints excluded: chain o residue 137 LEU Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain o residue 160 HIS Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 209 LYS Chi-restraints excluded: chain n residue 31 ASP Chi-restraints excluded: chain n residue 83 HIS Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 116 HIS Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 152 SER Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 243 ILE Chi-restraints excluded: chain n residue 260 SER Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 407 VAL Chi-restraints excluded: chain n residue 412 VAL Chi-restraints excluded: chain t residue 104 THR Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 134 THR Chi-restraints excluded: chain t residue 157 ASN Chi-restraints excluded: chain t residue 160 PHE Chi-restraints excluded: chain t residue 172 ASN Chi-restraints excluded: chain t residue 177 VAL Chi-restraints excluded: chain t residue 180 THR Chi-restraints excluded: chain t residue 302 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 289 optimal weight: 7.9990 chunk 773 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 504 optimal weight: 9.9990 chunk 212 optimal weight: 0.5980 chunk 860 optimal weight: 30.0000 chunk 714 optimal weight: 10.0000 chunk 398 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 284 optimal weight: 0.9980 chunk 451 optimal weight: 6.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 262 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 63 ASN 5 299 ASN ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 GLN ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 6 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 GLN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS Y 26 GLN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 ASN n 164 ASN n 189 GLN ** t 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 106125 Z= 0.275 Angle : 0.656 17.635 152938 Z= 0.334 Chirality : 0.039 0.271 18691 Planarity : 0.005 0.061 11918 Dihedral : 23.182 179.757 38976 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.62 % Favored : 92.00 % Rotamer: Outliers : 6.54 % Allowed : 23.45 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.54 (0.10), residues: 6938 helix: -0.19 (0.10), residues: 2646 sheet: -1.20 (0.16), residues: 992 loop : -1.62 (0.11), residues: 3300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP n 166 HIS 0.008 0.001 HIS K 212 PHE 0.060 0.002 PHE b 123 TYR 0.057 0.002 TYR 4 76 ARG 0.014 0.001 ARG n 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 404 poor density : 823 time to evaluate : 6.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 33 MET cc_start: 0.9003 (mmm) cc_final: 0.8615 (tmm) REVERT: x 80 ASP cc_start: 0.7678 (t0) cc_final: 0.7340 (t0) REVERT: x 206 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8935 (tt) REVERT: x 281 GLU cc_start: 0.9287 (tt0) cc_final: 0.8743 (tp30) REVERT: x 285 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8806 (mp0) REVERT: x 286 MET cc_start: 0.8308 (mpp) cc_final: 0.7949 (mpp) REVERT: x 291 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7246 (mptt) REVERT: F 19 GLN cc_start: 0.8945 (mt0) cc_final: 0.8659 (pp30) REVERT: F 21 LYS cc_start: 0.8713 (mttt) cc_final: 0.8386 (tptt) REVERT: F 121 LYS cc_start: 0.9238 (tttt) cc_final: 0.8825 (mttp) REVERT: F 158 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8078 (mmtm) REVERT: 3 91 GLN cc_start: 0.9633 (mt0) cc_final: 0.9432 (mm110) REVERT: 3 131 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8541 (mm-30) REVERT: 3 143 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7310 (tpt-90) REVERT: 3 150 ARG cc_start: 0.8620 (mtt180) cc_final: 0.8192 (tpt-90) REVERT: 3 160 LYS cc_start: 0.8813 (mttt) cc_final: 0.8540 (tppt) REVERT: 3 167 MET cc_start: 0.9291 (mmm) cc_final: 0.9007 (mmm) REVERT: 4 8 LYS cc_start: 0.9299 (pttt) cc_final: 0.8840 (mmtt) REVERT: 4 38 LYS cc_start: 0.8419 (mttm) cc_final: 0.8185 (mtmm) REVERT: 4 111 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8383 (t80) REVERT: 4 164 LYS cc_start: 0.8543 (mtpp) cc_final: 0.8151 (mmtt) REVERT: 5 1 MET cc_start: 0.8292 (ptp) cc_final: 0.7044 (mtm) REVERT: 5 57 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8535 (mm-30) REVERT: 5 112 SER cc_start: 0.8472 (t) cc_final: 0.8226 (p) REVERT: 5 204 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8119 (mm) REVERT: 5 220 ASP cc_start: 0.8622 (t70) cc_final: 0.8183 (p0) REVERT: 5 301 GLU cc_start: 0.9175 (tp30) cc_final: 0.8895 (tp30) REVERT: 5 412 ASP cc_start: 0.7976 (p0) cc_final: 0.7490 (p0) REVERT: A 79 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8912 (mt-10) REVERT: A 81 TYR cc_start: 0.8578 (m-80) cc_final: 0.8234 (m-80) REVERT: A 181 ILE cc_start: 0.5823 (tt) cc_final: 0.5613 (tt) REVERT: b 48 ARG cc_start: 0.8101 (tmt-80) cc_final: 0.7631 (ttm110) REVERT: b 189 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7588 (pttt) REVERT: b 232 MET cc_start: 0.5615 (mtm) cc_final: 0.4514 (mmt) REVERT: b 274 ILE cc_start: 0.8186 (mm) cc_final: 0.7961 (tt) REVERT: r 3 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7357 (mm110) REVERT: r 5 ASP cc_start: 0.7973 (t0) cc_final: 0.7454 (t0) REVERT: r 9 ARG cc_start: 0.9348 (mtm-85) cc_final: 0.8724 (mtm-85) REVERT: r 12 LYS cc_start: 0.8724 (mttt) cc_final: 0.8443 (mmmt) REVERT: r 17 ARG cc_start: 0.9256 (ttp80) cc_final: 0.8781 (tpp80) REVERT: r 24 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8648 (tptt) REVERT: r 28 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8659 (mp0) REVERT: s 16 LYS cc_start: 0.6678 (ttpt) cc_final: 0.6382 (ttmt) REVERT: u 1 MET cc_start: 0.4897 (ttt) cc_final: 0.3824 (tpt) REVERT: u 20 MET cc_start: 0.5786 (mtp) cc_final: 0.5174 (mtp) REVERT: u 28 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7799 (pp20) REVERT: u 43 ARG cc_start: 0.8672 (mtp180) cc_final: 0.7955 (tpt90) REVERT: u 52 THR cc_start: 0.7364 (t) cc_final: 0.7097 (t) REVERT: u 93 MET cc_start: 0.5677 (mpp) cc_final: 0.5465 (mpp) REVERT: v 27 LYS cc_start: 0.8167 (mttt) cc_final: 0.7839 (ttpp) REVERT: v 29 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8030 (t0) REVERT: v 41 ASP cc_start: 0.8822 (t70) cc_final: 0.8410 (t0) REVERT: v 195 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7866 (t0) REVERT: W 5 LYS cc_start: 0.9001 (pttm) cc_final: 0.8706 (ptmm) REVERT: W 66 ILE cc_start: 0.8969 (mm) cc_final: 0.8604 (mp) REVERT: W 67 MET cc_start: 0.7883 (mtp) cc_final: 0.7270 (mmm) REVERT: W 87 GLU cc_start: 0.9170 (mp0) cc_final: 0.8886 (tp30) REVERT: W 88 ASN cc_start: 0.7634 (m110) cc_final: 0.7009 (t0) REVERT: W 110 ASN cc_start: 0.9396 (m-40) cc_final: 0.9108 (p0) REVERT: y 127 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8305 (mm-30) REVERT: y 154 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8502 (tt) REVERT: y 215 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8498 (mt) REVERT: B 17 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8113 (mm) REVERT: B 53 MET cc_start: 0.7571 (tpp) cc_final: 0.7110 (mmm) REVERT: B 66 LYS cc_start: 0.8318 (mtpp) cc_final: 0.7827 (mptt) REVERT: B 74 GLU cc_start: 0.8403 (pt0) cc_final: 0.7459 (tp30) REVERT: B 277 SER cc_start: 0.8193 (m) cc_final: 0.7828 (p) REVERT: B 333 LYS cc_start: 0.8256 (mtmm) cc_final: 0.8034 (mtmt) REVERT: B 369 ARG cc_start: 0.8214 (mtm-85) cc_final: 0.8013 (ttm-80) REVERT: B 380 MET cc_start: 0.6674 (tpp) cc_final: 0.6335 (tpp) REVERT: C 73 ARG cc_start: 0.8740 (mtt180) cc_final: 0.8144 (ptt-90) REVERT: C 164 GLU cc_start: 0.9376 (tt0) cc_final: 0.9052 (tp30) REVERT: C 220 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8748 (ptp90) REVERT: C 294 GLU cc_start: 0.8938 (tp30) cc_final: 0.8558 (tm-30) REVERT: e 23 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8657 (p0) REVERT: e 24 ARG cc_start: 0.8480 (tpp80) cc_final: 0.7754 (mmm160) REVERT: e 27 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8441 (ptt180) REVERT: e 34 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8614 (ttpt) REVERT: e 81 ASP cc_start: 0.8876 (m-30) cc_final: 0.8567 (t0) REVERT: E 102 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8835 (p0) REVERT: E 143 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8766 (mmtm) REVERT: E 169 ASP cc_start: 0.8271 (m-30) cc_final: 0.7948 (m-30) REVERT: f 33 GLU cc_start: 0.9179 (tt0) cc_final: 0.8905 (tm-30) REVERT: G 173 MET cc_start: 0.9330 (mmm) cc_final: 0.8746 (mmm) REVERT: G 228 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6778 (pp20) REVERT: h 45 LYS cc_start: 0.8540 (tttt) cc_final: 0.8322 (ptpt) REVERT: h 60 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8984 (tm-30) REVERT: h 94 LYS cc_start: 0.8589 (ttpp) cc_final: 0.8306 (ptmm) REVERT: H 116 ASN cc_start: 0.9221 (t0) cc_final: 0.8743 (t0) REVERT: H 153 ASP cc_start: 0.9477 (m-30) cc_final: 0.9274 (t0) REVERT: H 162 GLN cc_start: 0.8761 (tt0) cc_final: 0.8487 (tm-30) REVERT: j 15 SER cc_start: 0.7808 (OUTLIER) cc_final: 0.7564 (t) REVERT: j 30 GLN cc_start: 0.8438 (mt0) cc_final: 0.8134 (tt0) REVERT: j 31 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8484 (mtpt) REVERT: j 75 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8886 (tttp) REVERT: L 49 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8427 (mtp-110) REVERT: L 67 ARG cc_start: 0.9527 (ptm-80) cc_final: 0.8894 (mtm180) REVERT: L 102 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8157 (mt0) REVERT: L 104 ARG cc_start: 0.8391 (ttt-90) cc_final: 0.7821 (mtm180) REVERT: M 56 GLN cc_start: 0.8853 (pt0) cc_final: 0.8330 (pm20) REVERT: M 62 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8735 (mp10) REVERT: N 15 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: N 119 TYR cc_start: 0.9330 (p90) cc_final: 0.9002 (p90) REVERT: N 126 THR cc_start: 0.9166 (m) cc_final: 0.8915 (p) REVERT: N 131 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8686 (mm-30) REVERT: N 201 ARG cc_start: 0.9256 (OUTLIER) cc_final: 0.8618 (mtp180) REVERT: O 53 LYS cc_start: 0.9035 (mttt) cc_final: 0.8429 (mmtm) REVERT: O 65 ASN cc_start: 0.8058 (t0) cc_final: 0.7653 (t0) REVERT: O 66 LYS cc_start: 0.8864 (mttp) cc_final: 0.8587 (mtmt) REVERT: O 90 HIS cc_start: 0.8853 (OUTLIER) cc_final: 0.8081 (p90) REVERT: O 122 GLN cc_start: 0.7893 (pt0) cc_final: 0.7436 (tt0) REVERT: P 23 ARG cc_start: 0.9113 (mtp180) cc_final: 0.8589 (mtm180) REVERT: P 30 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8234 (tmt170) REVERT: P 34 GLN cc_start: 0.8779 (tp-100) cc_final: 0.8047 (tt0) REVERT: P 52 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8432 (mm) REVERT: P 88 VAL cc_start: 0.9270 (t) cc_final: 0.9020 (p) REVERT: P 120 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8473 (p0) REVERT: P 145 HIS cc_start: 0.9059 (OUTLIER) cc_final: 0.8469 (m-70) REVERT: P 152 GLU cc_start: 0.8481 (tt0) cc_final: 0.7763 (tp30) REVERT: P 154 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7682 (mp0) REVERT: P 155 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8027 (mp0) REVERT: S 25 PHE cc_start: 0.7705 (m-80) cc_final: 0.7503 (m-80) REVERT: V 40 LYS cc_start: 0.6669 (mtpp) cc_final: 0.6323 (mtmm) REVERT: V 102 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7664 (mp) REVERT: V 109 MET cc_start: 0.7608 (mmm) cc_final: 0.7022 (mmm) REVERT: V 112 SER cc_start: 0.8023 (p) cc_final: 0.7742 (p) REVERT: V 126 TRP cc_start: 0.7880 (m100) cc_final: 0.7632 (m100) REVERT: Y 54 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8406 (m-30) REVERT: Y 66 GLN cc_start: 0.9126 (mt0) cc_final: 0.8869 (mt0) REVERT: Y 67 GLU cc_start: 0.8991 (pt0) cc_final: 0.8624 (pp20) REVERT: K 76 LYS cc_start: 0.7975 (ptmt) cc_final: 0.7377 (mmmt) REVERT: K 80 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6827 (pp) REVERT: K 81 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6934 (mt) REVERT: K 121 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.4189 (t80) REVERT: K 129 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: K 179 LEU cc_start: 0.7577 (mm) cc_final: 0.7247 (mm) REVERT: K 293 TYR cc_start: 0.6625 (t80) cc_final: 0.6010 (t80) REVERT: m 277 MET cc_start: 0.6707 (mmm) cc_final: 0.6395 (mmm) REVERT: D 340 ARG cc_start: 0.7667 (ptm160) cc_final: 0.7337 (ttt-90) REVERT: o 97 ARG cc_start: 0.7392 (ttm170) cc_final: 0.7191 (ttm110) REVERT: o 194 LYS cc_start: 0.8623 (mttt) cc_final: 0.8386 (mmmm) REVERT: o 200 MET cc_start: 0.4756 (ttp) cc_final: 0.3887 (ppp) REVERT: n 69 GLN cc_start: 0.7735 (mt0) cc_final: 0.7344 (tp-100) REVERT: n 260 SER cc_start: 0.7958 (OUTLIER) cc_final: 0.7618 (m) REVERT: n 445 ASN cc_start: 0.6802 (m-40) cc_final: 0.6197 (p0) REVERT: t 160 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6641 (t80) REVERT: t 300 GLN cc_start: 0.7487 (pp30) cc_final: 0.7214 (pp30) outliers start: 404 outliers final: 286 residues processed: 1128 average time/residue: 0.9320 time to fit residues: 1804.5372 Evaluate side-chains 1112 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 784 time to evaluate : 6.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 95 ILE Chi-restraints excluded: chain x residue 104 LYS Chi-restraints excluded: chain x residue 121 VAL Chi-restraints excluded: chain x residue 125 LYS Chi-restraints excluded: chain x residue 132 LEU Chi-restraints excluded: chain x residue 148 VAL Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 165 LEU Chi-restraints excluded: chain x residue 204 THR Chi-restraints excluded: chain x residue 206 LEU Chi-restraints excluded: chain x residue 209 THR Chi-restraints excluded: chain x residue 215 GLN Chi-restraints excluded: chain x residue 234 ASN Chi-restraints excluded: chain x residue 239 ILE Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain x residue 291 LYS Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain 3 residue 3 ASP Chi-restraints excluded: chain 3 residue 28 CYS Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 52 THR Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 72 THR Chi-restraints excluded: chain 3 residue 76 LEU Chi-restraints excluded: chain 3 residue 129 GLU Chi-restraints excluded: chain 3 residue 131 GLU Chi-restraints excluded: chain 3 residue 137 VAL Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 105 VAL Chi-restraints excluded: chain 4 residue 107 CYS Chi-restraints excluded: chain 4 residue 111 PHE Chi-restraints excluded: chain 4 residue 150 ILE Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 169 ILE Chi-restraints excluded: chain 4 residue 171 ILE Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 5 residue 64 SER Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 5 residue 152 ASN Chi-restraints excluded: chain 5 residue 204 ILE Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 5 residue 280 THR Chi-restraints excluded: chain 5 residue 294 ILE Chi-restraints excluded: chain 5 residue 303 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 189 LYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 269 LYS Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 277 LEU Chi-restraints excluded: chain b residue 287 ILE Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain J residue 206 GLU Chi-restraints excluded: chain J residue 222 SER Chi-restraints excluded: chain r residue 3 GLN Chi-restraints excluded: chain r residue 11 ILE Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 59 VAL Chi-restraints excluded: chain s residue 8 SER Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain u residue 55 PHE Chi-restraints excluded: chain u residue 88 THR Chi-restraints excluded: chain v residue 10 ASN Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 156 THR Chi-restraints excluded: chain v residue 195 ASP Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 109 VAL Chi-restraints excluded: chain W residue 124 TYR Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain y residue 6 GLN Chi-restraints excluded: chain y residue 22 THR Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 154 LEU Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 211 THR Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain z residue 34 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain e residue 11 LYS Chi-restraints excluded: chain e residue 15 LYS Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 27 ARG Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 35 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 59 THR Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain N residue 201 ARG Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain O residue 153 VAL Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 30 ARG Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 96 GLN Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 145 HIS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 154 HIS Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 256 LEU Chi-restraints excluded: chain m residue 257 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 360 TRP Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain o residue 90 SER Chi-restraints excluded: chain o residue 93 ILE Chi-restraints excluded: chain o residue 137 LEU Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain o residue 160 HIS Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 209 LYS Chi-restraints excluded: chain n residue 31 ASP Chi-restraints excluded: chain n residue 83 HIS Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 116 HIS Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 152 SER Chi-restraints excluded: chain n residue 164 ASN Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 243 ILE Chi-restraints excluded: chain n residue 260 SER Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 407 VAL Chi-restraints excluded: chain n residue 412 VAL Chi-restraints excluded: chain n residue 416 VAL Chi-restraints excluded: chain t residue 104 THR Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 134 THR Chi-restraints excluded: chain t residue 160 PHE Chi-restraints excluded: chain t residue 172 ASN Chi-restraints excluded: chain t residue 177 VAL Chi-restraints excluded: chain t residue 180 THR Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 302 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 829 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 490 optimal weight: 1.9990 chunk 628 optimal weight: 7.9990 chunk 486 optimal weight: 6.9990 chunk 724 optimal weight: 10.0000 chunk 480 optimal weight: 0.7980 chunk 856 optimal weight: 30.0000 chunk 536 optimal weight: 30.0000 chunk 522 optimal weight: 2.9990 chunk 395 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 262 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 HIS ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 GLN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS V 81 GLN Y 26 GLN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 154 ASN ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 ASN n 164 ASN n 189 GLN ** t 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 106125 Z= 0.234 Angle : 0.632 17.359 152938 Z= 0.323 Chirality : 0.038 0.323 18691 Planarity : 0.005 0.061 11918 Dihedral : 23.169 179.961 38970 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.08 % Favored : 92.56 % Rotamer: Outliers : 5.81 % Allowed : 24.47 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.47 (0.10), residues: 6938 helix: -0.09 (0.10), residues: 2652 sheet: -1.24 (0.16), residues: 1010 loop : -1.59 (0.11), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP K 253 HIS 0.034 0.001 HIS O 90 PHE 0.053 0.002 PHE m 247 TYR 0.046 0.002 TYR 4 76 ARG 0.011 0.000 ARG K 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 359 poor density : 828 time to evaluate : 6.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 33 MET cc_start: 0.9019 (mmm) cc_final: 0.8601 (tmm) REVERT: x 80 ASP cc_start: 0.7619 (t0) cc_final: 0.7296 (t0) REVERT: x 206 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8944 (tt) REVERT: x 281 GLU cc_start: 0.9267 (tt0) cc_final: 0.8787 (tp30) REVERT: x 285 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8793 (mp0) REVERT: x 286 MET cc_start: 0.8321 (mpp) cc_final: 0.7990 (mpp) REVERT: x 291 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7217 (mptt) REVERT: F 19 GLN cc_start: 0.8922 (mt0) cc_final: 0.8655 (pp30) REVERT: F 21 LYS cc_start: 0.8732 (mttt) cc_final: 0.8443 (tptt) REVERT: F 121 LYS cc_start: 0.9229 (tttt) cc_final: 0.8788 (mttp) REVERT: F 158 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8094 (mmtm) REVERT: F 225 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8668 (pt0) REVERT: 3 4 GLU cc_start: 0.9423 (tp30) cc_final: 0.9173 (tp30) REVERT: 3 95 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8780 (tt0) REVERT: 3 130 GLU cc_start: 0.8285 (pm20) cc_final: 0.7857 (mt-10) REVERT: 3 131 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8523 (mm-30) REVERT: 3 143 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7072 (tpt-90) REVERT: 3 150 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8206 (tpt-90) REVERT: 3 160 LYS cc_start: 0.8813 (mttt) cc_final: 0.8559 (tppt) REVERT: 3 167 MET cc_start: 0.9271 (mmm) cc_final: 0.8993 (mmm) REVERT: 4 8 LYS cc_start: 0.9266 (pttt) cc_final: 0.8815 (mmtt) REVERT: 4 38 LYS cc_start: 0.8412 (mttm) cc_final: 0.8186 (mtmm) REVERT: 4 164 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8126 (mmtt) REVERT: 4 182 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8609 (mt-10) REVERT: 5 1 MET cc_start: 0.8248 (ptp) cc_final: 0.7028 (mtm) REVERT: 5 112 SER cc_start: 0.8456 (t) cc_final: 0.8209 (p) REVERT: 5 204 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8008 (mm) REVERT: 5 220 ASP cc_start: 0.8638 (t70) cc_final: 0.8209 (p0) REVERT: 5 301 GLU cc_start: 0.9172 (tp30) cc_final: 0.8885 (tp30) REVERT: 5 366 TYR cc_start: 0.8779 (t80) cc_final: 0.8461 (t80) REVERT: 5 412 ASP cc_start: 0.7991 (p0) cc_final: 0.7546 (p0) REVERT: A 46 ARG cc_start: 0.8414 (mtt180) cc_final: 0.8149 (mtt180) REVERT: A 79 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8905 (mt-10) REVERT: A 81 TYR cc_start: 0.8595 (m-80) cc_final: 0.8219 (m-80) REVERT: A 172 PHE cc_start: 0.3184 (OUTLIER) cc_final: 0.2628 (t80) REVERT: A 181 ILE cc_start: 0.5967 (tt) cc_final: 0.5728 (tt) REVERT: b 48 ARG cc_start: 0.8088 (tmt-80) cc_final: 0.7609 (ttm110) REVERT: b 189 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7604 (pttt) REVERT: b 232 MET cc_start: 0.5993 (mtm) cc_final: 0.4637 (mmp) REVERT: b 237 MET cc_start: 0.5541 (mmt) cc_final: 0.5332 (mmt) REVERT: r 3 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7535 (mm110) REVERT: r 5 ASP cc_start: 0.7972 (t0) cc_final: 0.7526 (t0) REVERT: r 9 ARG cc_start: 0.9316 (mtm-85) cc_final: 0.8880 (mtm-85) REVERT: r 12 LYS cc_start: 0.8690 (mttt) cc_final: 0.8399 (mmmt) REVERT: r 17 ARG cc_start: 0.9217 (ttp80) cc_final: 0.8788 (tpp80) REVERT: r 24 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8628 (tptt) REVERT: r 28 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8647 (mp0) REVERT: s 17 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7965 (mm-30) REVERT: u 1 MET cc_start: 0.4468 (ttt) cc_final: 0.3619 (tpt) REVERT: u 5 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7820 (mm110) REVERT: u 28 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7837 (pp20) REVERT: u 43 ARG cc_start: 0.8692 (mtp180) cc_final: 0.8003 (tpt90) REVERT: u 52 THR cc_start: 0.7323 (t) cc_final: 0.7071 (t) REVERT: u 93 MET cc_start: 0.5654 (mpp) cc_final: 0.5429 (mpp) REVERT: v 27 LYS cc_start: 0.8149 (mttt) cc_final: 0.7824 (ttpp) REVERT: v 29 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8036 (t0) REVERT: v 41 ASP cc_start: 0.8820 (t70) cc_final: 0.8410 (t0) REVERT: v 190 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8658 (mmtm) REVERT: W 5 LYS cc_start: 0.8971 (pttm) cc_final: 0.8605 (ptmm) REVERT: W 66 ILE cc_start: 0.8928 (mm) cc_final: 0.8540 (mp) REVERT: W 67 MET cc_start: 0.7887 (mtp) cc_final: 0.7283 (mmm) REVERT: W 87 GLU cc_start: 0.9129 (mp0) cc_final: 0.8808 (tt0) REVERT: W 88 ASN cc_start: 0.7544 (m110) cc_final: 0.6665 (t0) REVERT: W 110 ASN cc_start: 0.9404 (m-40) cc_final: 0.9117 (p0) REVERT: W 157 MET cc_start: 0.8984 (ttm) cc_final: 0.8070 (mtp) REVERT: y 50 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7507 (m-70) REVERT: y 127 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8313 (mm-30) REVERT: y 154 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8531 (tt) REVERT: y 215 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8508 (mt) REVERT: B 17 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8094 (mm) REVERT: B 53 MET cc_start: 0.7482 (tpp) cc_final: 0.7008 (mmm) REVERT: B 66 LYS cc_start: 0.8342 (mtpp) cc_final: 0.7849 (mptt) REVERT: B 74 GLU cc_start: 0.8363 (pt0) cc_final: 0.7463 (tp30) REVERT: B 213 GLU cc_start: 0.8569 (tt0) cc_final: 0.8053 (tp30) REVERT: B 277 SER cc_start: 0.7997 (m) cc_final: 0.7684 (p) REVERT: B 333 LYS cc_start: 0.8249 (mtmm) cc_final: 0.8027 (mtmt) REVERT: B 380 MET cc_start: 0.6724 (tpp) cc_final: 0.6479 (tpp) REVERT: C 73 ARG cc_start: 0.8725 (mtt180) cc_final: 0.8122 (ptt-90) REVERT: C 164 GLU cc_start: 0.9328 (tt0) cc_final: 0.9001 (tp30) REVERT: C 220 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8744 (ptp90) REVERT: C 294 GLU cc_start: 0.8927 (tp30) cc_final: 0.8576 (tm-30) REVERT: e 23 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8618 (p0) REVERT: e 24 ARG cc_start: 0.8409 (tpp80) cc_final: 0.7649 (mmm160) REVERT: e 34 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8646 (ttpt) REVERT: e 81 ASP cc_start: 0.8890 (m-30) cc_final: 0.8596 (t0) REVERT: f 33 GLU cc_start: 0.9163 (tt0) cc_final: 0.8895 (tm-30) REVERT: G 170 CYS cc_start: 0.9386 (m) cc_final: 0.9153 (m) REVERT: G 173 MET cc_start: 0.9344 (mmm) cc_final: 0.8664 (mmm) REVERT: G 185 ARG cc_start: 0.8786 (ttt90) cc_final: 0.8373 (ttt90) REVERT: G 228 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6781 (pp20) REVERT: h 45 LYS cc_start: 0.8541 (tttt) cc_final: 0.8320 (ptpt) REVERT: h 60 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.9014 (tm-30) REVERT: h 94 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8305 (ptmm) REVERT: H 116 ASN cc_start: 0.9187 (t0) cc_final: 0.8680 (t0) REVERT: H 162 GLN cc_start: 0.8777 (tt0) cc_final: 0.8493 (tm-30) REVERT: j 15 SER cc_start: 0.7817 (OUTLIER) cc_final: 0.7560 (t) REVERT: j 30 GLN cc_start: 0.8399 (mt0) cc_final: 0.8103 (tt0) REVERT: j 31 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8455 (mtpt) REVERT: j 75 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8896 (tttp) REVERT: L 49 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8412 (mtp-110) REVERT: L 54 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9188 (tp) REVERT: L 67 ARG cc_start: 0.9526 (ptm-80) cc_final: 0.8869 (mtm180) REVERT: L 102 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8167 (mt0) REVERT: L 104 ARG cc_start: 0.8405 (ttt-90) cc_final: 0.7830 (mtm180) REVERT: M 47 ASP cc_start: 0.8733 (t70) cc_final: 0.8248 (t70) REVERT: M 56 GLN cc_start: 0.8841 (pt0) cc_final: 0.8300 (pm20) REVERT: M 62 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8781 (mp10) REVERT: N 15 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: N 119 TYR cc_start: 0.9326 (p90) cc_final: 0.8967 (p90) REVERT: N 126 THR cc_start: 0.9161 (m) cc_final: 0.8934 (p) REVERT: O 53 LYS cc_start: 0.9020 (mttt) cc_final: 0.8400 (mmtm) REVERT: O 65 ASN cc_start: 0.8058 (t0) cc_final: 0.7646 (t0) REVERT: O 66 LYS cc_start: 0.8870 (mttp) cc_final: 0.8556 (mtmt) REVERT: O 90 HIS cc_start: 0.8928 (OUTLIER) cc_final: 0.7298 (p-80) REVERT: O 122 GLN cc_start: 0.7758 (pt0) cc_final: 0.7254 (tt0) REVERT: P 23 ARG cc_start: 0.9112 (mtp180) cc_final: 0.8570 (mtm180) REVERT: P 52 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8445 (mm) REVERT: P 55 GLN cc_start: 0.8674 (mp10) cc_final: 0.8254 (mp10) REVERT: P 88 VAL cc_start: 0.9253 (t) cc_final: 0.9015 (p) REVERT: P 120 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8486 (p0) REVERT: P 145 HIS cc_start: 0.9006 (OUTLIER) cc_final: 0.8422 (m-70) REVERT: P 152 GLU cc_start: 0.8482 (tt0) cc_final: 0.7753 (tp30) REVERT: P 154 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7658 (mp0) REVERT: P 155 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8029 (mp0) REVERT: V 40 LYS cc_start: 0.6445 (mtpp) cc_final: 0.6208 (mtmm) REVERT: V 102 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7945 (mp) REVERT: V 109 MET cc_start: 0.7594 (mmm) cc_final: 0.6939 (mmt) REVERT: V 112 SER cc_start: 0.7946 (p) cc_final: 0.7656 (p) REVERT: V 126 TRP cc_start: 0.7828 (m100) cc_final: 0.7570 (m100) REVERT: Y 54 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8410 (m-30) REVERT: Y 66 GLN cc_start: 0.9154 (mt0) cc_final: 0.8902 (mt0) REVERT: Y 67 GLU cc_start: 0.8996 (pt0) cc_final: 0.8595 (pp20) REVERT: K 76 LYS cc_start: 0.8029 (ptmt) cc_final: 0.7422 (mmmt) REVERT: K 80 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6809 (pp) REVERT: K 81 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7221 (mt) REVERT: K 121 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.4007 (t80) REVERT: K 179 LEU cc_start: 0.7554 (mm) cc_final: 0.7227 (mm) REVERT: K 293 TYR cc_start: 0.6516 (t80) cc_final: 0.5983 (t80) REVERT: m 277 MET cc_start: 0.6712 (mmm) cc_final: 0.6392 (mmm) REVERT: D 277 PHE cc_start: 0.7983 (t80) cc_final: 0.7644 (t80) REVERT: o 194 LYS cc_start: 0.8594 (mttt) cc_final: 0.8362 (mmmm) REVERT: o 200 MET cc_start: 0.4700 (ttp) cc_final: 0.3943 (ppp) REVERT: n 69 GLN cc_start: 0.7769 (mt0) cc_final: 0.7448 (tp-100) REVERT: n 260 SER cc_start: 0.7948 (OUTLIER) cc_final: 0.7588 (m) REVERT: n 445 ASN cc_start: 0.6799 (m-40) cc_final: 0.6330 (p0) REVERT: t 157 ASN cc_start: 0.4471 (OUTLIER) cc_final: 0.3566 (p0) REVERT: t 160 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6753 (t80) outliers start: 359 outliers final: 271 residues processed: 1103 average time/residue: 0.9061 time to fit residues: 1721.4637 Evaluate side-chains 1086 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 776 time to evaluate : 6.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 95 ILE Chi-restraints excluded: chain x residue 104 LYS Chi-restraints excluded: chain x residue 121 VAL Chi-restraints excluded: chain x residue 125 LYS Chi-restraints excluded: chain x residue 132 LEU Chi-restraints excluded: chain x residue 148 VAL Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 165 LEU Chi-restraints excluded: chain x residue 206 LEU Chi-restraints excluded: chain x residue 215 GLN Chi-restraints excluded: chain x residue 234 ASN Chi-restraints excluded: chain x residue 239 ILE Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 263 PHE Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain x residue 291 LYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain 3 residue 3 ASP Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 28 CYS Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 52 THR Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 72 THR Chi-restraints excluded: chain 3 residue 76 LEU Chi-restraints excluded: chain 3 residue 92 GLN Chi-restraints excluded: chain 3 residue 129 GLU Chi-restraints excluded: chain 3 residue 131 GLU Chi-restraints excluded: chain 3 residue 137 VAL Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 105 VAL Chi-restraints excluded: chain 4 residue 107 CYS Chi-restraints excluded: chain 4 residue 138 SER Chi-restraints excluded: chain 4 residue 150 ILE Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 5 residue 64 SER Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 5 residue 204 ILE Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 5 residue 280 THR Chi-restraints excluded: chain 5 residue 303 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 122 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 189 LYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 269 LYS Chi-restraints excluded: chain b residue 277 LEU Chi-restraints excluded: chain b residue 287 ILE Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain J residue 222 SER Chi-restraints excluded: chain r residue 3 GLN Chi-restraints excluded: chain r residue 11 ILE Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 59 VAL Chi-restraints excluded: chain s residue 8 SER Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain u residue 5 GLN Chi-restraints excluded: chain u residue 55 PHE Chi-restraints excluded: chain u residue 88 THR Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 156 THR Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 124 TYR Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain y residue 22 THR Chi-restraints excluded: chain y residue 50 HIS Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 154 LEU Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 167 VAL Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 208 LEU Chi-restraints excluded: chain y residue 211 THR Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain z residue 34 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain e residue 11 LYS Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 35 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 59 THR Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 96 GLN Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 145 HIS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 154 HIS Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 256 LEU Chi-restraints excluded: chain m residue 257 THR Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 93 ILE Chi-restraints excluded: chain o residue 137 LEU Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain o residue 160 HIS Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 209 LYS Chi-restraints excluded: chain n residue 83 HIS Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 116 HIS Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 148 THR Chi-restraints excluded: chain n residue 152 SER Chi-restraints excluded: chain n residue 164 ASN Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 243 ILE Chi-restraints excluded: chain n residue 260 SER Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 407 VAL Chi-restraints excluded: chain n residue 412 VAL Chi-restraints excluded: chain n residue 416 VAL Chi-restraints excluded: chain t residue 104 THR Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 134 THR Chi-restraints excluded: chain t residue 157 ASN Chi-restraints excluded: chain t residue 160 PHE Chi-restraints excluded: chain t residue 172 ASN Chi-restraints excluded: chain t residue 177 VAL Chi-restraints excluded: chain t residue 180 THR Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 302 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 530 optimal weight: 5.9990 chunk 342 optimal weight: 8.9990 chunk 511 optimal weight: 2.9990 chunk 258 optimal weight: 0.0070 chunk 168 optimal weight: 30.0000 chunk 166 optimal weight: 20.0000 chunk 544 optimal weight: 9.9990 chunk 583 optimal weight: 10.0000 chunk 423 optimal weight: 0.0980 chunk 79 optimal weight: 0.9980 chunk 673 optimal weight: 10.0000 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 HIS ** b 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN W 223 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 HIS ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS Y 26 GLN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 ASN n 164 ASN ** t 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 106125 Z= 0.183 Angle : 0.608 17.323 152938 Z= 0.311 Chirality : 0.037 0.274 18691 Planarity : 0.004 0.060 11918 Dihedral : 23.117 179.915 38952 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.76 % Favored : 92.94 % Rotamer: Outliers : 5.15 % Allowed : 25.28 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.32 (0.10), residues: 6938 helix: 0.06 (0.10), residues: 2650 sheet: -1.16 (0.16), residues: 998 loop : -1.52 (0.11), residues: 3290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP n 166 HIS 0.007 0.001 HIS K 212 PHE 0.043 0.002 PHE b 123 TYR 0.042 0.002 TYR 4 76 ARG 0.014 0.000 ARG o 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 838 time to evaluate : 6.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 33 MET cc_start: 0.9000 (mmm) cc_final: 0.8544 (tmm) REVERT: x 80 ASP cc_start: 0.7593 (t0) cc_final: 0.7273 (t0) REVERT: x 223 ASP cc_start: 0.7630 (p0) cc_final: 0.6814 (p0) REVERT: x 281 GLU cc_start: 0.9227 (tt0) cc_final: 0.8867 (tp30) REVERT: x 283 LYS cc_start: 0.9150 (mttt) cc_final: 0.8927 (pttp) REVERT: x 286 MET cc_start: 0.8133 (mpp) cc_final: 0.7557 (mpp) REVERT: x 291 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7106 (mptt) REVERT: F 19 GLN cc_start: 0.8875 (mt0) cc_final: 0.8548 (pp30) REVERT: F 21 LYS cc_start: 0.8723 (mttt) cc_final: 0.8449 (tptt) REVERT: F 121 LYS cc_start: 0.9214 (tttt) cc_final: 0.8807 (mttp) REVERT: F 158 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8052 (mmtm) REVERT: F 225 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8648 (pt0) REVERT: 3 4 GLU cc_start: 0.9426 (tp30) cc_final: 0.9178 (tp30) REVERT: 3 131 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8534 (mm-30) REVERT: 3 143 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7052 (tpt-90) REVERT: 3 150 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8194 (tpt-90) REVERT: 3 167 MET cc_start: 0.9231 (mmm) cc_final: 0.8896 (mmm) REVERT: 3 168 ASP cc_start: 0.9004 (m-30) cc_final: 0.8450 (t0) REVERT: 4 8 LYS cc_start: 0.9268 (pttt) cc_final: 0.8805 (mmtt) REVERT: 4 38 LYS cc_start: 0.8378 (mttm) cc_final: 0.8152 (mtmm) REVERT: 4 111 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8307 (t80) REVERT: 4 164 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8121 (mmtt) REVERT: 4 178 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8700 (tt) REVERT: 4 182 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8637 (mt-10) REVERT: 5 1 MET cc_start: 0.8213 (ptp) cc_final: 0.7028 (mtm) REVERT: 5 112 SER cc_start: 0.8456 (t) cc_final: 0.8215 (p) REVERT: 5 204 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7888 (mm) REVERT: 5 220 ASP cc_start: 0.8547 (t70) cc_final: 0.8134 (p0) REVERT: 5 366 TYR cc_start: 0.8685 (t80) cc_final: 0.8414 (t80) REVERT: 5 412 ASP cc_start: 0.7981 (p0) cc_final: 0.7551 (p0) REVERT: A 46 ARG cc_start: 0.8497 (mtt180) cc_final: 0.8269 (mtt180) REVERT: A 79 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8834 (mt-10) REVERT: A 156 LEU cc_start: 0.5766 (tp) cc_final: 0.5286 (pp) REVERT: A 172 PHE cc_start: 0.3473 (OUTLIER) cc_final: 0.2830 (t80) REVERT: b 5 TRP cc_start: 0.7097 (OUTLIER) cc_final: 0.6831 (m-90) REVERT: b 48 ARG cc_start: 0.8081 (tmt-80) cc_final: 0.7602 (ttm110) REVERT: b 189 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7617 (pttt) REVERT: b 232 MET cc_start: 0.6081 (mtm) cc_final: 0.4373 (mmt) REVERT: r 9 ARG cc_start: 0.9287 (mtm-85) cc_final: 0.8872 (mtm-85) REVERT: r 12 LYS cc_start: 0.8690 (mttt) cc_final: 0.8421 (mmmt) REVERT: r 24 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8617 (tptt) REVERT: r 28 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8625 (mp0) REVERT: u 1 MET cc_start: 0.4228 (ttt) cc_final: 0.3566 (tpt) REVERT: u 5 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7813 (mm110) REVERT: u 20 MET cc_start: 0.5940 (OUTLIER) cc_final: 0.5189 (mtp) REVERT: u 28 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7766 (pp20) REVERT: u 43 ARG cc_start: 0.8691 (mtp180) cc_final: 0.7973 (tpt90) REVERT: u 52 THR cc_start: 0.7319 (t) cc_final: 0.7066 (t) REVERT: u 93 MET cc_start: 0.5808 (mpp) cc_final: 0.5466 (mpp) REVERT: v 27 LYS cc_start: 0.8106 (mttt) cc_final: 0.7777 (ttpp) REVERT: v 29 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.7925 (t0) REVERT: v 41 ASP cc_start: 0.8859 (t70) cc_final: 0.8435 (t0) REVERT: W 5 LYS cc_start: 0.8963 (pttm) cc_final: 0.8609 (ptmm) REVERT: W 66 ILE cc_start: 0.8842 (mm) cc_final: 0.8436 (mp) REVERT: W 67 MET cc_start: 0.7915 (mtp) cc_final: 0.7324 (mmm) REVERT: W 87 GLU cc_start: 0.9129 (mp0) cc_final: 0.8811 (tt0) REVERT: W 88 ASN cc_start: 0.7482 (m110) cc_final: 0.6612 (t0) REVERT: W 110 ASN cc_start: 0.9400 (m-40) cc_final: 0.9106 (p0) REVERT: W 157 MET cc_start: 0.8916 (ttm) cc_final: 0.8056 (mtp) REVERT: y 50 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7489 (m-70) REVERT: y 127 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8316 (mm-30) REVERT: y 215 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8504 (mt) REVERT: B 53 MET cc_start: 0.7424 (tpp) cc_final: 0.6956 (mmm) REVERT: B 66 LYS cc_start: 0.8345 (mtpp) cc_final: 0.7835 (mptt) REVERT: B 74 GLU cc_start: 0.8285 (pt0) cc_final: 0.7329 (tp30) REVERT: B 277 SER cc_start: 0.8044 (m) cc_final: 0.7767 (p) REVERT: B 333 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7944 (mtmm) REVERT: B 369 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7516 (ttm-80) REVERT: B 380 MET cc_start: 0.6738 (tpp) cc_final: 0.6494 (tpp) REVERT: C 73 ARG cc_start: 0.8711 (mtt180) cc_final: 0.8124 (ptt-90) REVERT: C 164 GLU cc_start: 0.9320 (tt0) cc_final: 0.8990 (tp30) REVERT: C 177 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: C 220 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8988 (ptp90) REVERT: C 294 GLU cc_start: 0.8891 (tp30) cc_final: 0.8568 (tm-30) REVERT: e 15 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8933 (mtmt) REVERT: e 23 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8619 (p0) REVERT: e 24 ARG cc_start: 0.8418 (tpp80) cc_final: 0.7737 (tpt170) REVERT: e 27 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8359 (ptt180) REVERT: e 34 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8657 (ttpt) REVERT: e 81 ASP cc_start: 0.8872 (m-30) cc_final: 0.8585 (t0) REVERT: E 143 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8726 (mmtm) REVERT: E 169 ASP cc_start: 0.8131 (m-30) cc_final: 0.7792 (m-30) REVERT: f 33 GLU cc_start: 0.9130 (tt0) cc_final: 0.8784 (tm-30) REVERT: f 49 ILE cc_start: 0.9433 (mt) cc_final: 0.9109 (mt) REVERT: G 170 CYS cc_start: 0.9386 (m) cc_final: 0.9134 (m) REVERT: G 173 MET cc_start: 0.9362 (mmm) cc_final: 0.8639 (mmm) REVERT: G 228 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6766 (pp20) REVERT: h 45 LYS cc_start: 0.8557 (tttt) cc_final: 0.8342 (ptpt) REVERT: h 60 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.9021 (tm-30) REVERT: h 68 GLN cc_start: 0.9087 (mt0) cc_final: 0.8865 (mp10) REVERT: H 19 SER cc_start: 0.8194 (m) cc_final: 0.7487 (t) REVERT: H 116 ASN cc_start: 0.9137 (t0) cc_final: 0.8627 (t0) REVERT: H 162 GLN cc_start: 0.8779 (tt0) cc_final: 0.8522 (tm-30) REVERT: j 30 GLN cc_start: 0.8376 (mt0) cc_final: 0.8058 (tt0) REVERT: j 31 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8467 (mtpt) REVERT: j 75 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8881 (tttp) REVERT: L 49 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8372 (mtp-110) REVERT: L 67 ARG cc_start: 0.9527 (ptm-80) cc_final: 0.8883 (mtm180) REVERT: L 102 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: L 104 ARG cc_start: 0.8345 (ttt-90) cc_final: 0.7765 (mtm180) REVERT: M 47 ASP cc_start: 0.8842 (t70) cc_final: 0.8414 (t70) REVERT: M 56 GLN cc_start: 0.8822 (pt0) cc_final: 0.8313 (pm20) REVERT: M 62 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8764 (mp10) REVERT: N 7 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9016 (mp) REVERT: N 15 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: N 119 TYR cc_start: 0.9366 (p90) cc_final: 0.8961 (p90) REVERT: N 126 THR cc_start: 0.9116 (m) cc_final: 0.8892 (p) REVERT: N 143 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8536 (mtt180) REVERT: O 53 LYS cc_start: 0.9014 (mttt) cc_final: 0.8359 (mmtm) REVERT: O 122 GLN cc_start: 0.7723 (pt0) cc_final: 0.7219 (tt0) REVERT: P 23 ARG cc_start: 0.9111 (mtp180) cc_final: 0.8573 (mtm180) REVERT: P 52 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8570 (mm) REVERT: P 55 GLN cc_start: 0.8584 (mp10) cc_final: 0.8188 (mp10) REVERT: P 88 VAL cc_start: 0.9209 (t) cc_final: 0.8944 (p) REVERT: P 120 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8429 (p0) REVERT: P 145 HIS cc_start: 0.9002 (OUTLIER) cc_final: 0.8413 (m-70) REVERT: P 152 GLU cc_start: 0.8455 (tt0) cc_final: 0.7759 (tp30) REVERT: P 154 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8101 (mp0) REVERT: Q 21 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8582 (p) REVERT: V 40 LYS cc_start: 0.6382 (mtpp) cc_final: 0.6134 (mtmm) REVERT: V 102 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7776 (mp) REVERT: V 109 MET cc_start: 0.7588 (mmm) cc_final: 0.6985 (mmt) REVERT: V 112 SER cc_start: 0.7918 (p) cc_final: 0.7623 (p) REVERT: V 126 TRP cc_start: 0.7796 (m100) cc_final: 0.7557 (m100) REVERT: Y 54 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8446 (m-30) REVERT: Y 66 GLN cc_start: 0.9181 (mt0) cc_final: 0.8928 (mt0) REVERT: Y 67 GLU cc_start: 0.9016 (pt0) cc_final: 0.8621 (pp20) REVERT: K 76 LYS cc_start: 0.7857 (ptmt) cc_final: 0.7487 (mmtp) REVERT: K 80 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6837 (pp) REVERT: K 81 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7256 (mt) REVERT: K 110 TRP cc_start: 0.8015 (m100) cc_final: 0.7276 (m100) REVERT: K 121 PHE cc_start: 0.5989 (OUTLIER) cc_final: 0.3928 (t80) REVERT: K 179 LEU cc_start: 0.7495 (mm) cc_final: 0.7201 (mm) REVERT: K 293 TYR cc_start: 0.6551 (t80) cc_final: 0.6035 (t80) REVERT: m 277 MET cc_start: 0.6633 (mmm) cc_final: 0.6369 (mmm) REVERT: D 477 TYR cc_start: 0.8065 (m-80) cc_final: 0.7829 (m-10) REVERT: o 194 LYS cc_start: 0.8658 (mttt) cc_final: 0.8420 (mmmm) REVERT: o 200 MET cc_start: 0.4572 (ttp) cc_final: 0.3830 (ppp) REVERT: n 69 GLN cc_start: 0.7807 (mt0) cc_final: 0.7525 (tp-100) REVERT: n 106 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8619 (mm-30) REVERT: n 445 ASN cc_start: 0.6608 (m-40) cc_final: 0.6112 (p0) REVERT: t 160 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6754 (t80) REVERT: t 291 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8275 (pt0) outliers start: 318 outliers final: 236 residues processed: 1078 average time/residue: 0.9233 time to fit residues: 1713.1206 Evaluate side-chains 1068 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 790 time to evaluate : 6.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 95 ILE Chi-restraints excluded: chain x residue 104 LYS Chi-restraints excluded: chain x residue 121 VAL Chi-restraints excluded: chain x residue 125 LYS Chi-restraints excluded: chain x residue 132 LEU Chi-restraints excluded: chain x residue 148 VAL Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 165 LEU Chi-restraints excluded: chain x residue 234 ASN Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 263 PHE Chi-restraints excluded: chain x residue 270 LEU Chi-restraints excluded: chain x residue 291 LYS Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain 3 residue 3 ASP Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 12 GLN Chi-restraints excluded: chain 3 residue 28 CYS Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 52 THR Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 72 THR Chi-restraints excluded: chain 3 residue 76 LEU Chi-restraints excluded: chain 3 residue 129 GLU Chi-restraints excluded: chain 3 residue 137 VAL Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 105 VAL Chi-restraints excluded: chain 4 residue 107 CYS Chi-restraints excluded: chain 4 residue 111 PHE Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 5 residue 64 SER Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 5 residue 204 ILE Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 240 LEU Chi-restraints excluded: chain 5 residue 280 THR Chi-restraints excluded: chain 5 residue 303 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain b residue 5 TRP Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 122 LEU Chi-restraints excluded: chain b residue 189 LYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 269 LYS Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 277 LEU Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain J residue 222 SER Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 59 VAL Chi-restraints excluded: chain s residue 7 GLN Chi-restraints excluded: chain s residue 8 SER Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain u residue 5 GLN Chi-restraints excluded: chain u residue 20 MET Chi-restraints excluded: chain u residue 55 PHE Chi-restraints excluded: chain u residue 88 THR Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 156 THR Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 124 TYR Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain y residue 50 HIS Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 211 THR Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain z residue 34 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain e residue 11 LYS Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 27 ARG Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 35 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 104 GLN Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 59 THR Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 143 ARG Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 145 HIS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 154 HIS Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 104 HIS Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 256 LEU Chi-restraints excluded: chain m residue 257 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 137 LEU Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 209 LYS Chi-restraints excluded: chain n residue 83 HIS Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 148 THR Chi-restraints excluded: chain n residue 152 SER Chi-restraints excluded: chain n residue 164 ASN Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 243 ILE Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 407 VAL Chi-restraints excluded: chain n residue 412 VAL Chi-restraints excluded: chain n residue 416 VAL Chi-restraints excluded: chain t residue 104 THR Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 134 THR Chi-restraints excluded: chain t residue 160 PHE Chi-restraints excluded: chain t residue 172 ASN Chi-restraints excluded: chain t residue 177 VAL Chi-restraints excluded: chain t residue 180 THR Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 286 LEU Chi-restraints excluded: chain t residue 291 GLN Chi-restraints excluded: chain t residue 302 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 779 optimal weight: 8.9990 chunk 820 optimal weight: 5.9990 chunk 748 optimal weight: 10.0000 chunk 798 optimal weight: 7.9990 chunk 480 optimal weight: 0.6980 chunk 347 optimal weight: 0.0870 chunk 626 optimal weight: 10.0000 chunk 245 optimal weight: 20.0000 chunk 721 optimal weight: 10.0000 chunk 755 optimal weight: 20.0000 chunk 795 optimal weight: 8.9990 overall best weight: 4.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 286 HIS 5 299 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 3 GLN ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS Y 26 GLN K 84 ASN ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 ASN n 164 ASN ** t 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 106125 Z= 0.324 Angle : 0.686 17.058 152938 Z= 0.348 Chirality : 0.040 0.273 18691 Planarity : 0.005 0.070 11918 Dihedral : 23.164 179.701 38949 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.16 % Favored : 91.55 % Rotamer: Outliers : 5.67 % Allowed : 25.09 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.10), residues: 6938 helix: -0.06 (0.10), residues: 2652 sheet: -1.22 (0.16), residues: 991 loop : -1.62 (0.11), residues: 3295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 253 HIS 0.009 0.001 HIS K 212 PHE 0.052 0.002 PHE b 123 TYR 0.040 0.002 TYR 4 76 ARG 0.013 0.001 ARG o 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 785 time to evaluate : 6.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 33 MET cc_start: 0.8975 (mmm) cc_final: 0.8492 (tmm) REVERT: x 80 ASP cc_start: 0.7598 (t0) cc_final: 0.7283 (t0) REVERT: x 223 ASP cc_start: 0.7784 (p0) cc_final: 0.7125 (p0) REVERT: x 252 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8679 (tm-30) REVERT: x 281 GLU cc_start: 0.9254 (tt0) cc_final: 0.8803 (tp30) REVERT: x 285 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8844 (mp0) REVERT: x 286 MET cc_start: 0.8207 (mpp) cc_final: 0.7824 (mpp) REVERT: x 291 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7312 (mptt) REVERT: F 19 GLN cc_start: 0.8963 (mt0) cc_final: 0.8646 (pp30) REVERT: F 21 LYS cc_start: 0.8740 (mttt) cc_final: 0.8463 (tptt) REVERT: F 121 LYS cc_start: 0.9175 (tttt) cc_final: 0.8738 (mttp) REVERT: F 225 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8583 (pt0) REVERT: 3 4 GLU cc_start: 0.9432 (tp30) cc_final: 0.9174 (tp30) REVERT: 3 130 GLU cc_start: 0.8430 (pt0) cc_final: 0.8106 (mt-10) REVERT: 3 131 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8586 (mm-30) REVERT: 3 143 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7438 (tpt-90) REVERT: 3 150 ARG cc_start: 0.8618 (mtt180) cc_final: 0.8204 (tpt-90) REVERT: 3 167 MET cc_start: 0.9211 (mmm) cc_final: 0.8949 (mmm) REVERT: 4 8 LYS cc_start: 0.9301 (pttt) cc_final: 0.8856 (mmtt) REVERT: 4 38 LYS cc_start: 0.8469 (mttm) cc_final: 0.8230 (mtmm) REVERT: 4 75 LEU cc_start: 0.7643 (tp) cc_final: 0.7439 (tp) REVERT: 4 111 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8308 (t80) REVERT: 4 164 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8184 (mmtt) REVERT: 4 178 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8709 (tt) REVERT: 5 1 MET cc_start: 0.8305 (ptp) cc_final: 0.7116 (mtm) REVERT: 5 112 SER cc_start: 0.8444 (t) cc_final: 0.8239 (p) REVERT: 5 204 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7931 (mm) REVERT: 5 220 ASP cc_start: 0.8708 (t70) cc_final: 0.8303 (p0) REVERT: 5 412 ASP cc_start: 0.7836 (p0) cc_final: 0.7389 (p0) REVERT: A 79 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8870 (mt-10) REVERT: A 156 LEU cc_start: 0.5752 (tp) cc_final: 0.5323 (pp) REVERT: A 172 PHE cc_start: 0.3376 (OUTLIER) cc_final: 0.2699 (t80) REVERT: b 5 TRP cc_start: 0.6857 (OUTLIER) cc_final: 0.6486 (m-90) REVERT: b 48 ARG cc_start: 0.8010 (tmt-80) cc_final: 0.7530 (ttm110) REVERT: b 189 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7594 (pttp) REVERT: b 232 MET cc_start: 0.5799 (mtm) cc_final: 0.3665 (mmt) REVERT: r 5 ASP cc_start: 0.7925 (t0) cc_final: 0.7244 (t0) REVERT: r 9 ARG cc_start: 0.9297 (mtm-85) cc_final: 0.8674 (mtm-85) REVERT: r 12 LYS cc_start: 0.8799 (mttt) cc_final: 0.8542 (mmmt) REVERT: r 24 LYS cc_start: 0.8974 (ttmt) cc_final: 0.8613 (tptt) REVERT: r 28 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8648 (mp0) REVERT: u 5 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7470 (mm110) REVERT: u 20 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.5042 (mtp) REVERT: u 28 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7811 (pp20) REVERT: u 43 ARG cc_start: 0.8702 (mtp180) cc_final: 0.8011 (tpt90) REVERT: u 52 THR cc_start: 0.7305 (t) cc_final: 0.7095 (t) REVERT: u 93 MET cc_start: 0.5587 (mpp) cc_final: 0.5356 (mpp) REVERT: v 27 LYS cc_start: 0.8205 (mttt) cc_final: 0.7895 (ttpp) REVERT: v 29 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8148 (t0) REVERT: v 41 ASP cc_start: 0.8831 (t70) cc_final: 0.8264 (t0) REVERT: v 195 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7729 (t0) REVERT: W 5 LYS cc_start: 0.8995 (pttm) cc_final: 0.8616 (ptmm) REVERT: W 66 ILE cc_start: 0.8871 (mm) cc_final: 0.8446 (mp) REVERT: W 67 MET cc_start: 0.7874 (mtp) cc_final: 0.7267 (mmm) REVERT: W 87 GLU cc_start: 0.9166 (mp0) cc_final: 0.8846 (tt0) REVERT: W 88 ASN cc_start: 0.7569 (m110) cc_final: 0.6704 (t0) REVERT: W 110 ASN cc_start: 0.9414 (m-40) cc_final: 0.9112 (p0) REVERT: W 157 MET cc_start: 0.8945 (ttm) cc_final: 0.8065 (mtp) REVERT: y 50 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.7692 (m-70) REVERT: y 127 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8284 (mm-30) REVERT: y 215 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8505 (mt) REVERT: B 53 MET cc_start: 0.7423 (tpp) cc_final: 0.6998 (mmm) REVERT: B 66 LYS cc_start: 0.8399 (mtpp) cc_final: 0.7887 (mppt) REVERT: B 74 GLU cc_start: 0.8380 (pt0) cc_final: 0.7498 (tp30) REVERT: B 277 SER cc_start: 0.8092 (m) cc_final: 0.7802 (p) REVERT: B 323 MET cc_start: 0.9191 (mmm) cc_final: 0.8841 (tpp) REVERT: B 380 MET cc_start: 0.6855 (tpp) cc_final: 0.6621 (tpp) REVERT: C 73 ARG cc_start: 0.8786 (mtt180) cc_final: 0.8170 (ptt-90) REVERT: C 115 HIS cc_start: 0.9314 (OUTLIER) cc_final: 0.8746 (t70) REVERT: C 164 GLU cc_start: 0.9354 (tt0) cc_final: 0.9057 (tp30) REVERT: C 220 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.8839 (ptp90) REVERT: C 294 GLU cc_start: 0.8947 (tp30) cc_final: 0.8594 (tm-30) REVERT: e 23 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8700 (p0) REVERT: e 24 ARG cc_start: 0.8401 (tpp80) cc_final: 0.7749 (tpt170) REVERT: e 27 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8414 (ptt180) REVERT: e 34 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8621 (ttpt) REVERT: e 81 ASP cc_start: 0.8928 (m-30) cc_final: 0.8654 (t0) REVERT: E 142 ASP cc_start: 0.8778 (t0) cc_final: 0.8523 (t0) REVERT: E 143 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8723 (mmtm) REVERT: f 33 GLU cc_start: 0.9067 (tt0) cc_final: 0.8844 (tm-30) REVERT: G 100 GLU cc_start: 0.9284 (mt-10) cc_final: 0.9046 (mt-10) REVERT: G 170 CYS cc_start: 0.9412 (m) cc_final: 0.9152 (m) REVERT: G 173 MET cc_start: 0.9398 (mmm) cc_final: 0.8699 (mmm) REVERT: G 228 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6863 (pp20) REVERT: h 45 LYS cc_start: 0.8530 (tttt) cc_final: 0.8323 (ptpt) REVERT: h 60 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8967 (tm-30) REVERT: H 1 MET cc_start: 0.7582 (ppp) cc_final: 0.6994 (ppp) REVERT: H 116 ASN cc_start: 0.9203 (t0) cc_final: 0.8703 (t0) REVERT: H 162 GLN cc_start: 0.8820 (tt0) cc_final: 0.8551 (tm-30) REVERT: i 38 LYS cc_start: 0.9093 (mttm) cc_final: 0.8831 (mttp) REVERT: j 15 SER cc_start: 0.7853 (OUTLIER) cc_final: 0.7595 (t) REVERT: j 30 GLN cc_start: 0.8457 (mt0) cc_final: 0.8113 (tt0) REVERT: j 31 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8490 (mtpt) REVERT: j 75 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8925 (tttp) REVERT: L 49 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8496 (mtp-110) REVERT: L 67 ARG cc_start: 0.9521 (ptm-80) cc_final: 0.8883 (mtm180) REVERT: L 102 GLN cc_start: 0.8776 (mm-40) cc_final: 0.7532 (pt0) REVERT: L 104 ARG cc_start: 0.8300 (ttt-90) cc_final: 0.7679 (mtm180) REVERT: M 56 GLN cc_start: 0.8782 (pt0) cc_final: 0.8299 (pm20) REVERT: M 62 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8755 (mp10) REVERT: N 7 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9102 (mp) REVERT: N 119 TYR cc_start: 0.9369 (p90) cc_final: 0.9106 (p90) REVERT: N 126 THR cc_start: 0.9159 (m) cc_final: 0.8906 (p) REVERT: N 143 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8546 (mtt180) REVERT: N 201 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8607 (mtp180) REVERT: O 53 LYS cc_start: 0.9063 (mttt) cc_final: 0.8710 (tmtt) REVERT: O 60 LYS cc_start: 0.6530 (mttt) cc_final: 0.5481 (mmtt) REVERT: O 65 ASN cc_start: 0.7960 (t0) cc_final: 0.7599 (t0) REVERT: P 23 ARG cc_start: 0.9059 (mtp180) cc_final: 0.8490 (mtm180) REVERT: P 30 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8260 (tmt170) REVERT: P 34 GLN cc_start: 0.8842 (tp-100) cc_final: 0.8078 (tt0) REVERT: P 52 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8364 (mm) REVERT: P 55 GLN cc_start: 0.8632 (mp10) cc_final: 0.8243 (mp10) REVERT: P 120 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8457 (p0) REVERT: P 145 HIS cc_start: 0.9072 (OUTLIER) cc_final: 0.8443 (m-70) REVERT: P 152 GLU cc_start: 0.8501 (tt0) cc_final: 0.7801 (tp30) REVERT: P 154 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7728 (mp0) REVERT: P 155 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8043 (mp0) REVERT: V 40 LYS cc_start: 0.6391 (mtpp) cc_final: 0.6135 (mtmm) REVERT: V 102 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7925 (mp) REVERT: V 109 MET cc_start: 0.7663 (mmm) cc_final: 0.6859 (mmm) REVERT: V 112 SER cc_start: 0.7841 (p) cc_final: 0.7525 (p) REVERT: V 126 TRP cc_start: 0.7798 (m100) cc_final: 0.7588 (m100) REVERT: Y 54 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8530 (m-30) REVERT: Y 66 GLN cc_start: 0.9166 (mt0) cc_final: 0.8917 (mt0) REVERT: Y 67 GLU cc_start: 0.8968 (pt0) cc_final: 0.8552 (pp20) REVERT: K 76 LYS cc_start: 0.7924 (ptmt) cc_final: 0.7549 (mmtp) REVERT: K 80 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6800 (pp) REVERT: K 81 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7253 (mt) REVERT: K 121 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.4013 (t80) REVERT: K 179 LEU cc_start: 0.7603 (mm) cc_final: 0.7194 (mm) REVERT: K 293 TYR cc_start: 0.6344 (t80) cc_final: 0.5841 (t80) REVERT: D 275 LYS cc_start: 0.8883 (mmtp) cc_final: 0.8552 (mmtp) REVERT: o 175 LYS cc_start: 0.5956 (OUTLIER) cc_final: 0.5711 (mtpp) REVERT: o 194 LYS cc_start: 0.8587 (mttt) cc_final: 0.8374 (mmmm) REVERT: o 200 MET cc_start: 0.4583 (ttp) cc_final: 0.3823 (ppp) REVERT: n 69 GLN cc_start: 0.7950 (mt0) cc_final: 0.7596 (tp-100) REVERT: n 106 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8607 (mm-30) REVERT: n 445 ASN cc_start: 0.6444 (m-40) cc_final: 0.6171 (p0) REVERT: t 157 ASN cc_start: 0.4898 (OUTLIER) cc_final: 0.4132 (p0) REVERT: t 160 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6803 (t80) outliers start: 350 outliers final: 272 residues processed: 1058 average time/residue: 1.0153 time to fit residues: 1869.2378 Evaluate side-chains 1069 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 754 time to evaluate : 6.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 95 ILE Chi-restraints excluded: chain x residue 104 LYS Chi-restraints excluded: chain x residue 121 VAL Chi-restraints excluded: chain x residue 125 LYS Chi-restraints excluded: chain x residue 132 LEU Chi-restraints excluded: chain x residue 148 VAL Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 165 LEU Chi-restraints excluded: chain x residue 215 GLN Chi-restraints excluded: chain x residue 234 ASN Chi-restraints excluded: chain x residue 239 ILE Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 291 LYS Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 28 CYS Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 52 THR Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 72 THR Chi-restraints excluded: chain 3 residue 76 LEU Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain 3 residue 129 GLU Chi-restraints excluded: chain 3 residue 131 GLU Chi-restraints excluded: chain 3 residue 137 VAL Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 105 VAL Chi-restraints excluded: chain 4 residue 107 CYS Chi-restraints excluded: chain 4 residue 111 PHE Chi-restraints excluded: chain 4 residue 138 SER Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 171 ILE Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 5 residue 64 SER Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 5 residue 176 ILE Chi-restraints excluded: chain 5 residue 204 ILE Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 280 THR Chi-restraints excluded: chain 5 residue 286 HIS Chi-restraints excluded: chain 5 residue 294 ILE Chi-restraints excluded: chain 5 residue 303 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain b residue 5 TRP Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 122 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 189 LYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 277 LEU Chi-restraints excluded: chain b residue 287 ILE Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain J residue 222 SER Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain r residue 11 ILE Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 59 VAL Chi-restraints excluded: chain s residue 7 GLN Chi-restraints excluded: chain s residue 8 SER Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain u residue 5 GLN Chi-restraints excluded: chain u residue 20 MET Chi-restraints excluded: chain u residue 55 PHE Chi-restraints excluded: chain u residue 88 THR Chi-restraints excluded: chain v residue 4 VAL Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 35 ILE Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 156 THR Chi-restraints excluded: chain v residue 195 ASP Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 124 TYR Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain y residue 50 HIS Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 148 VAL Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 167 VAL Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 211 THR Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain z residue 34 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 11 LYS Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 27 ARG Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 83 GLU Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 35 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 59 THR Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 143 ARG Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain N residue 201 ARG Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 144 SER Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 30 ARG Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 145 HIS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain S residue 154 HIS Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 104 HIS Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 256 LEU Chi-restraints excluded: chain m residue 257 THR Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain o residue 90 SER Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 137 LEU Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 175 LYS Chi-restraints excluded: chain o residue 209 LYS Chi-restraints excluded: chain n residue 83 HIS Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 116 HIS Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 148 THR Chi-restraints excluded: chain n residue 152 SER Chi-restraints excluded: chain n residue 164 ASN Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 243 ILE Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 407 VAL Chi-restraints excluded: chain n residue 412 VAL Chi-restraints excluded: chain n residue 416 VAL Chi-restraints excluded: chain t residue 104 THR Chi-restraints excluded: chain t residue 134 THR Chi-restraints excluded: chain t residue 145 VAL Chi-restraints excluded: chain t residue 157 ASN Chi-restraints excluded: chain t residue 160 PHE Chi-restraints excluded: chain t residue 172 ASN Chi-restraints excluded: chain t residue 177 VAL Chi-restraints excluded: chain t residue 180 THR Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 286 LEU Chi-restraints excluded: chain t residue 302 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 524 optimal weight: 0.0070 chunk 844 optimal weight: 5.9990 chunk 515 optimal weight: 5.9990 chunk 400 optimal weight: 4.9990 chunk 586 optimal weight: 10.0000 chunk 885 optimal weight: 10.0000 chunk 815 optimal weight: 0.9980 chunk 705 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 544 optimal weight: 10.0000 chunk 432 optimal weight: 5.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 44 ASN ** x 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 ASN A 45 HIS ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 HIS ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS Y 26 GLN ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 164 ASN ** t 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 106125 Z= 0.247 Angle : 0.650 17.258 152938 Z= 0.331 Chirality : 0.039 0.318 18691 Planarity : 0.005 0.081 11918 Dihedral : 23.172 179.978 38947 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.19 % Favored : 92.53 % Rotamer: Outliers : 5.07 % Allowed : 25.87 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.10), residues: 6938 helix: 0.00 (0.10), residues: 2648 sheet: -1.20 (0.16), residues: 964 loop : -1.57 (0.10), residues: 3326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP m 246 HIS 0.033 0.001 HIS A 94 PHE 0.048 0.002 PHE b 123 TYR 0.038 0.002 TYR 4 76 ARG 0.015 0.001 ARG S 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 784 time to evaluate : 6.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 33 MET cc_start: 0.8937 (mmm) cc_final: 0.8519 (tmm) REVERT: x 80 ASP cc_start: 0.7597 (t0) cc_final: 0.7297 (t0) REVERT: x 223 ASP cc_start: 0.7915 (p0) cc_final: 0.7575 (p0) REVERT: x 252 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8652 (tm-30) REVERT: x 281 GLU cc_start: 0.9267 (tt0) cc_final: 0.8895 (tp30) REVERT: x 283 LYS cc_start: 0.9147 (mttt) cc_final: 0.8940 (pttp) REVERT: x 286 MET cc_start: 0.8294 (mpp) cc_final: 0.7815 (mpp) REVERT: x 291 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7220 (mptt) REVERT: F 19 GLN cc_start: 0.8944 (mt0) cc_final: 0.8626 (pp30) REVERT: F 21 LYS cc_start: 0.8746 (mttt) cc_final: 0.8466 (tptt) REVERT: F 121 LYS cc_start: 0.9177 (tttt) cc_final: 0.8742 (mttp) REVERT: F 225 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8597 (pt0) REVERT: 3 4 GLU cc_start: 0.9415 (tp30) cc_final: 0.9157 (tp30) REVERT: 3 131 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8591 (mm-30) REVERT: 3 143 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7032 (tpt-90) REVERT: 3 150 ARG cc_start: 0.8649 (mtt180) cc_final: 0.8224 (tpt-90) REVERT: 3 167 MET cc_start: 0.9193 (mmm) cc_final: 0.8930 (mmm) REVERT: 4 8 LYS cc_start: 0.9281 (pttt) cc_final: 0.8829 (mmtt) REVERT: 4 38 LYS cc_start: 0.8424 (mttm) cc_final: 0.8206 (mtmm) REVERT: 4 75 LEU cc_start: 0.7633 (tp) cc_final: 0.7428 (tp) REVERT: 4 111 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8340 (t80) REVERT: 4 164 LYS cc_start: 0.8540 (mtpp) cc_final: 0.8157 (mmtt) REVERT: 4 178 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8648 (tt) REVERT: 5 1 MET cc_start: 0.8276 (ptp) cc_final: 0.7089 (mtm) REVERT: 5 112 SER cc_start: 0.8458 (t) cc_final: 0.8255 (p) REVERT: 5 204 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7810 (tp) REVERT: 5 220 ASP cc_start: 0.8588 (t70) cc_final: 0.8150 (p0) REVERT: 5 366 TYR cc_start: 0.8731 (t80) cc_final: 0.8437 (t80) REVERT: 5 412 ASP cc_start: 0.7833 (p0) cc_final: 0.7406 (p0) REVERT: A 79 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8863 (mt-10) REVERT: A 156 LEU cc_start: 0.5706 (tp) cc_final: 0.5231 (pp) REVERT: A 172 PHE cc_start: 0.3509 (OUTLIER) cc_final: 0.2724 (t80) REVERT: b 48 ARG cc_start: 0.8000 (tmt-80) cc_final: 0.7522 (ttm110) REVERT: b 189 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7524 (pttt) REVERT: b 232 MET cc_start: 0.5688 (mtm) cc_final: 0.3676 (mmt) REVERT: r 5 ASP cc_start: 0.7897 (t0) cc_final: 0.7345 (t0) REVERT: r 9 ARG cc_start: 0.9268 (mtm-85) cc_final: 0.8762 (mtm-85) REVERT: r 12 LYS cc_start: 0.8806 (mttt) cc_final: 0.8552 (mmmt) REVERT: r 24 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8593 (tptt) REVERT: r 28 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8669 (mp0) REVERT: u 5 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7495 (mm110) REVERT: u 20 MET cc_start: 0.5951 (OUTLIER) cc_final: 0.5265 (mtp) REVERT: u 28 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7780 (pp20) REVERT: u 43 ARG cc_start: 0.8731 (mtp180) cc_final: 0.8000 (tpt90) REVERT: u 52 THR cc_start: 0.7312 (t) cc_final: 0.7084 (t) REVERT: u 93 MET cc_start: 0.5815 (mpp) cc_final: 0.5516 (mpp) REVERT: v 27 LYS cc_start: 0.8124 (mttt) cc_final: 0.7817 (ttpp) REVERT: v 29 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8135 (t0) REVERT: v 41 ASP cc_start: 0.8855 (t70) cc_final: 0.8422 (t0) REVERT: v 195 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7749 (t0) REVERT: W 5 LYS cc_start: 0.8979 (pttm) cc_final: 0.8615 (ptmm) REVERT: W 66 ILE cc_start: 0.8862 (mm) cc_final: 0.8427 (mp) REVERT: W 67 MET cc_start: 0.7874 (mtp) cc_final: 0.7264 (mmm) REVERT: W 87 GLU cc_start: 0.9203 (mp0) cc_final: 0.8881 (tt0) REVERT: W 88 ASN cc_start: 0.7512 (m110) cc_final: 0.6665 (t0) REVERT: W 110 ASN cc_start: 0.9415 (m-40) cc_final: 0.9113 (p0) REVERT: W 157 MET cc_start: 0.8910 (ttm) cc_final: 0.8049 (mtp) REVERT: y 50 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7679 (m-70) REVERT: y 127 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8276 (mm-30) REVERT: y 215 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8507 (mt) REVERT: B 53 MET cc_start: 0.7349 (tpp) cc_final: 0.6918 (mmm) REVERT: B 66 LYS cc_start: 0.8420 (mtpp) cc_final: 0.7903 (mptt) REVERT: B 74 GLU cc_start: 0.8304 (pt0) cc_final: 0.7461 (tp30) REVERT: B 277 SER cc_start: 0.8232 (m) cc_final: 0.7908 (p) REVERT: B 323 MET cc_start: 0.9175 (mmm) cc_final: 0.8792 (tpp) REVERT: C 73 ARG cc_start: 0.8785 (mtt180) cc_final: 0.8161 (ptt-90) REVERT: C 164 GLU cc_start: 0.9346 (tt0) cc_final: 0.9036 (tp30) REVERT: C 177 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8412 (m-30) REVERT: C 220 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8810 (ptp90) REVERT: C 294 GLU cc_start: 0.8916 (tp30) cc_final: 0.8585 (tm-30) REVERT: e 23 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8668 (p0) REVERT: e 24 ARG cc_start: 0.8409 (tpp80) cc_final: 0.7735 (tpt170) REVERT: e 27 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8297 (ptt180) REVERT: e 34 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8664 (ttpt) REVERT: e 81 ASP cc_start: 0.8924 (m-30) cc_final: 0.8645 (t0) REVERT: E 88 SER cc_start: 0.8779 (p) cc_final: 0.8389 (m) REVERT: f 19 SER cc_start: 0.9652 (m) cc_final: 0.9446 (t) REVERT: f 33 GLU cc_start: 0.9038 (tt0) cc_final: 0.8837 (tm-30) REVERT: G 100 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9026 (mt-10) REVERT: G 173 MET cc_start: 0.9373 (mmm) cc_final: 0.8697 (mmm) REVERT: G 228 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6905 (pp20) REVERT: h 45 LYS cc_start: 0.8556 (tttt) cc_final: 0.8336 (ptpt) REVERT: h 60 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8969 (tm-30) REVERT: h 104 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8852 (mp10) REVERT: H 1 MET cc_start: 0.7566 (ppp) cc_final: 0.6938 (ppp) REVERT: H 116 ASN cc_start: 0.9192 (t0) cc_final: 0.8704 (t0) REVERT: H 162 GLN cc_start: 0.8805 (tt0) cc_final: 0.8472 (tm-30) REVERT: i 38 LYS cc_start: 0.9068 (mttm) cc_final: 0.8823 (mttp) REVERT: j 30 GLN cc_start: 0.8406 (mt0) cc_final: 0.8047 (tt0) REVERT: j 31 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8435 (mtpt) REVERT: j 75 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8898 (tttp) REVERT: L 49 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8405 (mtp-110) REVERT: L 67 ARG cc_start: 0.9523 (ptm-80) cc_final: 0.8862 (mtm180) REVERT: L 102 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: L 104 ARG cc_start: 0.8381 (ttt-90) cc_final: 0.7788 (mtm180) REVERT: M 56 GLN cc_start: 0.8779 (pt0) cc_final: 0.8309 (pm20) REVERT: M 62 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8744 (mp10) REVERT: N 7 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9059 (mp) REVERT: N 119 TYR cc_start: 0.9323 (p90) cc_final: 0.8972 (p90) REVERT: N 126 THR cc_start: 0.9129 (m) cc_final: 0.8903 (p) REVERT: N 143 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8561 (mtt180) REVERT: O 53 LYS cc_start: 0.9017 (mttt) cc_final: 0.8628 (tmtt) REVERT: O 60 LYS cc_start: 0.6568 (mttt) cc_final: 0.5546 (mmtt) REVERT: O 65 ASN cc_start: 0.7894 (t0) cc_final: 0.7562 (t0) REVERT: O 122 GLN cc_start: 0.7743 (pt0) cc_final: 0.7276 (tt0) REVERT: P 23 ARG cc_start: 0.9076 (mtp180) cc_final: 0.8513 (mtm180) REVERT: P 52 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8435 (mm) REVERT: P 120 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8452 (p0) REVERT: P 145 HIS cc_start: 0.9008 (OUTLIER) cc_final: 0.8372 (m-70) REVERT: P 152 GLU cc_start: 0.8513 (tt0) cc_final: 0.7815 (tp30) REVERT: P 154 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8097 (mp0) REVERT: S 117 ARG cc_start: 0.9286 (mtm110) cc_final: 0.8919 (mtt90) REVERT: V 40 LYS cc_start: 0.6295 (mtpp) cc_final: 0.6050 (mtmm) REVERT: V 109 MET cc_start: 0.7665 (mmm) cc_final: 0.6891 (mmm) REVERT: Y 54 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8515 (m-30) REVERT: Y 66 GLN cc_start: 0.9176 (mt0) cc_final: 0.8938 (mt0) REVERT: Y 67 GLU cc_start: 0.8967 (pt0) cc_final: 0.8557 (pp20) REVERT: K 76 LYS cc_start: 0.7899 (ptmt) cc_final: 0.7500 (mmtp) REVERT: K 121 PHE cc_start: 0.6017 (OUTLIER) cc_final: 0.4015 (t80) REVERT: K 179 LEU cc_start: 0.7531 (mm) cc_final: 0.7181 (mm) REVERT: K 293 TYR cc_start: 0.6379 (t80) cc_final: 0.5805 (t80) REVERT: D 392 MET cc_start: 0.8022 (mmm) cc_final: 0.7604 (mmt) REVERT: D 463 TYR cc_start: 0.5665 (m-80) cc_final: 0.5408 (m-80) REVERT: o 194 LYS cc_start: 0.8631 (mttt) cc_final: 0.8410 (mmmm) REVERT: o 200 MET cc_start: 0.4557 (ttp) cc_final: 0.3774 (ppp) REVERT: n 260 SER cc_start: 0.7903 (OUTLIER) cc_final: 0.7591 (m) REVERT: n 445 ASN cc_start: 0.6284 (m-40) cc_final: 0.6021 (p0) REVERT: t 160 PHE cc_start: 0.7062 (OUTLIER) cc_final: 0.6786 (t80) outliers start: 313 outliers final: 257 residues processed: 1023 average time/residue: 0.9082 time to fit residues: 1603.8581 Evaluate side-chains 1055 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 762 time to evaluate : 6.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 95 ILE Chi-restraints excluded: chain x residue 104 LYS Chi-restraints excluded: chain x residue 121 VAL Chi-restraints excluded: chain x residue 125 LYS Chi-restraints excluded: chain x residue 132 LEU Chi-restraints excluded: chain x residue 148 VAL Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 157 VAL Chi-restraints excluded: chain x residue 163 ILE Chi-restraints excluded: chain x residue 165 LEU Chi-restraints excluded: chain x residue 215 GLN Chi-restraints excluded: chain x residue 234 ASN Chi-restraints excluded: chain x residue 254 VAL Chi-restraints excluded: chain x residue 263 PHE Chi-restraints excluded: chain x residue 291 LYS Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 28 CYS Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 52 THR Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 3 residue 72 THR Chi-restraints excluded: chain 3 residue 76 LEU Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain 3 residue 129 GLU Chi-restraints excluded: chain 3 residue 131 GLU Chi-restraints excluded: chain 3 residue 137 VAL Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 158 ILE Chi-restraints excluded: chain 4 residue 17 THR Chi-restraints excluded: chain 4 residue 92 ASP Chi-restraints excluded: chain 4 residue 105 VAL Chi-restraints excluded: chain 4 residue 107 CYS Chi-restraints excluded: chain 4 residue 111 PHE Chi-restraints excluded: chain 4 residue 138 SER Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 171 ILE Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 5 residue 137 VAL Chi-restraints excluded: chain 5 residue 176 ILE Chi-restraints excluded: chain 5 residue 204 ILE Chi-restraints excluded: chain 5 residue 225 SER Chi-restraints excluded: chain 5 residue 280 THR Chi-restraints excluded: chain 5 residue 303 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 17 LEU Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 122 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain b residue 189 LYS Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 256 LEU Chi-restraints excluded: chain b residue 277 LEU Chi-restraints excluded: chain b residue 287 ILE Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain J residue 222 SER Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain r residue 11 ILE Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 59 VAL Chi-restraints excluded: chain s residue 7 GLN Chi-restraints excluded: chain s residue 8 SER Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain u residue 5 GLN Chi-restraints excluded: chain u residue 20 MET Chi-restraints excluded: chain u residue 88 THR Chi-restraints excluded: chain v residue 4 VAL Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 35 ILE Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 156 THR Chi-restraints excluded: chain v residue 195 ASP Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 124 TYR Chi-restraints excluded: chain W residue 128 ASN Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain y residue 50 HIS Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 161 VAL Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 208 LEU Chi-restraints excluded: chain y residue 211 THR Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain z residue 34 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain e residue 11 LYS Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 27 ARG Chi-restraints excluded: chain e residue 34 LYS Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 35 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 53 TYR Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 104 GLN Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 165 CYS Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 59 THR Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 143 ARG Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 144 SER Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 145 HIS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain P residue 157 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain S residue 154 HIS Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 256 LEU Chi-restraints excluded: chain m residue 257 THR Chi-restraints excluded: chain m residue 384 ILE Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain o residue 90 SER Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 137 LEU Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 209 LYS Chi-restraints excluded: chain n residue 83 HIS Chi-restraints excluded: chain n residue 85 THR Chi-restraints excluded: chain n residue 116 HIS Chi-restraints excluded: chain n residue 134 ASP Chi-restraints excluded: chain n residue 148 THR Chi-restraints excluded: chain n residue 152 SER Chi-restraints excluded: chain n residue 164 ASN Chi-restraints excluded: chain n residue 183 ILE Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 238 THR Chi-restraints excluded: chain n residue 260 SER Chi-restraints excluded: chain n residue 263 ILE Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain n residue 407 VAL Chi-restraints excluded: chain n residue 412 VAL Chi-restraints excluded: chain t residue 104 THR Chi-restraints excluded: chain t residue 134 THR Chi-restraints excluded: chain t residue 160 PHE Chi-restraints excluded: chain t residue 172 ASN Chi-restraints excluded: chain t residue 177 VAL Chi-restraints excluded: chain t residue 180 THR Chi-restraints excluded: chain t residue 242 HIS Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 286 LEU Chi-restraints excluded: chain t residue 302 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 560 optimal weight: 10.0000 chunk 751 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 650 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 706 optimal weight: 30.0000 chunk 295 optimal weight: 8.9990 chunk 725 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 178 HIS ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS Y 26 GLN ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 189 GLN ** t 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.094814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.074604 restraints weight = 381829.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075919 restraints weight = 316147.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.075476 restraints weight = 244442.061| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.231 106125 Z= 0.308 Angle : 0.691 59.200 152938 Z= 0.362 Chirality : 0.040 0.556 18691 Planarity : 0.005 0.144 11918 Dihedral : 23.168 179.948 38945 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.34 % Favored : 92.39 % Rotamer: Outliers : 5.12 % Allowed : 25.92 % Favored : 68.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.10), residues: 6938 helix: -0.01 (0.10), residues: 2648 sheet: -1.20 (0.16), residues: 969 loop : -1.57 (0.10), residues: 3321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP m 246 HIS 0.020 0.001 HIS A 94 PHE 0.056 0.002 PHE n 142 TYR 0.037 0.002 TYR 4 76 ARG 0.017 0.000 ARG K 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28320.55 seconds wall clock time: 497 minutes 39.82 seconds (29859.82 seconds total)