Starting phenix.real_space_refine on Fri Mar 22 08:38:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r55_18901/03_2024/8r55_18901.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r55_18901/03_2024/8r55_18901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r55_18901/03_2024/8r55_18901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r55_18901/03_2024/8r55_18901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r55_18901/03_2024/8r55_18901.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r55_18901/03_2024/8r55_18901.pdb" } resolution = 3.57 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= 0.014 sd= 0.132 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1560 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 4713 5.49 5 S 134 5.16 5 C 71855 2.51 5 N 26712 2.21 5 O 40453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 35": "OE1" <-> "OE2" Residue "4 GLU 12": "OE1" <-> "OE2" Residue "6 GLU 21": "OE1" <-> "OE2" Residue "6 GLU 23": "OE1" <-> "OE2" Residue "6 GLU 29": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "G PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 50": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "I GLU 56": "OE1" <-> "OE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "K GLU 19": "OE1" <-> "OE2" Residue "K GLU 85": "OE1" <-> "OE2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "P GLU 35": "OE1" <-> "OE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q GLU 51": "OE1" <-> "OE2" Residue "Q PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 24": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "T GLU 43": "OE1" <-> "OE2" Residue "Z GLU 82": "OE1" <-> "OE2" Residue "Z GLU 100": "OE1" <-> "OE2" Residue "Z GLU 115": "OE1" <-> "OE2" Residue "Z GLU 168": "OE1" <-> "OE2" Residue "a GLU 29": "OE1" <-> "OE2" Residue "a GLU 65": "OE1" <-> "OE2" Residue "a GLU 87": "OE1" <-> "OE2" Residue "a GLU 92": "OE1" <-> "OE2" Residue "a GLU 167": "OE1" <-> "OE2" Residue "a GLU 175": "OE1" <-> "OE2" Residue "b GLU 149": "OE1" <-> "OE2" Residue "b GLU 204": "OE1" <-> "OE2" Residue "c GLU 56": "OE1" <-> "OE2" Residue "c GLU 94": "OE1" <-> "OE2" Residue "c GLU 134": "OE1" <-> "OE2" Residue "c GLU 165": "OE1" <-> "OE2" Residue "c GLU 168": "OE1" <-> "OE2" Residue "d GLU 10": "OE1" <-> "OE2" Residue "d GLU 89": "OE1" <-> "OE2" Residue "d GLU 125": "OE1" <-> "OE2" Residue "d GLU 140": "OE1" <-> "OE2" Residue "e PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 130": "OE1" <-> "OE2" Residue "e GLU 134": "OE1" <-> "OE2" Residue "f GLU 56": "OE1" <-> "OE2" Residue "f GLU 120": "OE1" <-> "OE2" Residue "i GLU 51": "OE1" <-> "OE2" Residue "i GLU 73": "OE1" <-> "OE2" Residue "i GLU 94": "OE1" <-> "OE2" Residue "i GLU 98": "OE1" <-> "OE2" Residue "i GLU 134": "OE1" <-> "OE2" Residue "j GLU 12": "OE1" <-> "OE2" Residue "j GLU 26": "OE1" <-> "OE2" Residue "j GLU 80": "OE1" <-> "OE2" Residue "j GLU 91": "OE1" <-> "OE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "j GLU 135": "OE1" <-> "OE2" Residue "k GLU 31": "OE1" <-> "OE2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 115": "OE1" <-> "OE2" Residue "m GLU 34": "OE1" <-> "OE2" Residue "m GLU 38": "OE1" <-> "OE2" Residue "m GLU 57": "OE1" <-> "OE2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "o GLU 28": "OE1" <-> "OE2" Residue "o GLU 31": "OE1" <-> "OE2" Residue "o GLU 36": "OE1" <-> "OE2" Residue "o GLU 98": "OE1" <-> "OE2" Residue "r GLU 48": "OE1" <-> "OE2" Residue "r GLU 78": "OE1" <-> "OE2" Residue "s GLU 15": "OE1" <-> "OE2" Residue "s GLU 29": "OE1" <-> "OE2" Residue "s GLU 38": "OE1" <-> "OE2" Residue "s GLU 44": "OE1" <-> "OE2" Residue "s GLU 89": "OE1" <-> "OE2" Residue "t GLU 60": "OE1" <-> "OE2" Residue "u GLU 25": "OE1" <-> "OE2" Residue "u GLU 78": "OE1" <-> "OE2" Residue "w GLU 5": "OE1" <-> "OE2" Residue "w GLU 23": "OE1" <-> "OE2" Residue "w GLU 38": "OE1" <-> "OE2" Residue "w GLU 45": "OE1" <-> "OE2" Residue "w GLU 61": "OE1" <-> "OE2" Residue "z GLU 682": "OE1" <-> "OE2" Residue "z GLU 783": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143867 Number of models: 1 Model: "" Number of chains: 53 Chain: "0" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "1" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 402 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "2" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 368 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "4" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 499 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "7" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1560 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 59} Chain: "A" Number of atoms: 32891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1533, 32891 Classifications: {'RNA': 1533} Modifications used: {'rna2p_pur': 130, 'rna2p_pyr': 90, 'rna3p_pur': 740, 'rna3p_pyr': 573} Link IDs: {'rna2p': 219, 'rna3p': 1313} Chain: "B" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1757 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "C" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 3, 'TRANS': 202} Chain: "D" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1569 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "E" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1219 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "F" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 755 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1181 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "H" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1037 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "I" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "J" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 761 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "K" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 839 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "L" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1052 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "M" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 868 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "N" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 498 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "O" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 710 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "P" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "Q" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 691 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "R" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "S" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 637 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain: "U" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "V" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 704 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 12, 'rna3p_pyr': 8} Link IDs: {'rna2p': 13, 'rna3p': 19} Chain: "Y" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2392 Classifications: {'RNA': 112} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 51, 'rna3p_pyr': 45} Link IDs: {'rna2p': 16, 'rna3p': 95} Chain: "Z" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "a" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "b" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1562 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "c" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1386 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "d" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1343 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "e" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1124 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "f" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 921 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "i" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1082 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "j" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "k" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 954 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "l" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 913 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 945 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "n" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 941 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "o" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 787 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "r" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "s" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 725 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "t" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "u" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 631 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "w" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 531 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'TRANS': 64} Chain: "x" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 456 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "X" Number of atoms: 62005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2887, 62005 Classifications: {'RNA': 2887} Modifications used: {'5*END': 1, 'rna2p_pur': 303, 'rna2p_pyr': 158, 'rna3p_pur': 1375, 'rna3p_pyr': 1051} Link IDs: {'rna2p': 461, 'rna3p': 2425} Chain breaks: 5 Chain: "z" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1083 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 1 Time building chain proxies: 54.62, per 1000 atoms: 0.38 Number of scatterers: 143867 At special positions: 0 Unit cell: (234.08, 244.53, 323.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 134 16.00 P 4713 15.00 O 40453 8.00 N 26712 7.00 C 71855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 27 " - pdb=" SG CYS N 43 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 68.07 Conformation dependent library (CDL) restraints added in 6.1 seconds 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9940 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 70 sheets defined 34.1% alpha, 18.1% beta 1561 base pairs and 2385 stacking pairs defined. Time for finding SS restraints: 52.35 Creating SS restraints... Processing helix chain '0' and resid 9 through 18 Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 4.059A pdb=" N SER 2 24 " --> pdb=" O SER 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 Processing helix chain '3' and resid 7 through 12 Processing helix chain '3' and resid 18 through 20 No H-bonds generated for 'chain '3' and resid 18 through 20' Processing helix chain '3' and resid 37 through 46 removed outlier: 3.920A pdb=" N LYS 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 59 Processing helix chain '3' and resid 60 through 63 Processing helix chain '4' and resid 29 through 32 Processing helix chain 'B' and resid 41 through 64 removed outlier: 4.478A pdb=" N VAL B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 103 through 124 removed outlier: 4.325A pdb=" N ARG B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 149 removed outlier: 4.106A pdb=" N GLU B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 179 removed outlier: 3.752A pdb=" N VAL B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 226 removed outlier: 4.038A pdb=" N LEU B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 214 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 27 through 46 Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 79 through 95 removed outlier: 3.510A pdb=" N GLY C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 removed outlier: 3.521A pdb=" N LEU C 110 " --> pdb=" O ARG C 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 107 through 110' Processing helix chain 'C' and resid 111 through 126 Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'D' and resid 7 through 16 Processing helix chain 'D' and resid 47 through 60 Processing helix chain 'D' and resid 64 through 78 Processing helix chain 'D' and resid 83 through 93 Processing helix chain 'D' and resid 93 through 101 Processing helix chain 'D' and resid 106 through 117 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 148 through 154 removed outlier: 3.938A pdb=" N LYS D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 Processing helix chain 'E' and resid 55 through 70 Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.744A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 146 removed outlier: 3.674A pdb=" N GLU E 146 " --> pdb=" O GLN E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 removed outlier: 3.889A pdb=" N VAL E 153 " --> pdb=" O ARG E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 166 Processing helix chain 'F' and resid 15 through 33 Processing helix chain 'F' and resid 70 through 82 removed outlier: 4.335A pdb=" N GLU F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 39 through 49 removed outlier: 3.502A pdb=" N LEU G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 Processing helix chain 'G' and resid 92 through 111 Processing helix chain 'G' and resid 115 through 129 Processing helix chain 'G' and resid 132 through 149 Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.988A pdb=" N VAL H 94 " --> pdb=" O SER H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 101 Processing helix chain 'H' and resid 115 through 121 Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 50 removed outlier: 4.748A pdb=" N ASP I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE I 48 " --> pdb=" O LEU I 44 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS I 49 " --> pdb=" O ILE I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 55 Processing helix chain 'I' and resid 71 through 91 removed outlier: 3.627A pdb=" N ALA I 78 " --> pdb=" O GLY I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 102 removed outlier: 3.613A pdb=" N ALA I 101 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 32 removed outlier: 4.812A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 85 removed outlier: 4.366A pdb=" N ASP J 85 " --> pdb=" O PRO J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 90 removed outlier: 4.051A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 60 removed outlier: 3.611A pdb=" N SER K 60 " --> pdb=" O SER K 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 57 through 60' Processing helix chain 'K' and resid 61 through 76 Processing helix chain 'K' and resid 93 through 105 removed outlier: 3.726A pdb=" N ALA K 97 " --> pdb=" O SER K 93 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA K 98 " --> pdb=" O GLY K 94 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE K 99 " --> pdb=" O ARG K 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Processing helix chain 'L' and resid 21 through 24 removed outlier: 4.030A pdb=" N LEU L 24 " --> pdb=" O SER L 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 21 through 24' Processing helix chain 'M' and resid 14 through 19 Processing helix chain 'M' and resid 20 through 22 No H-bonds generated for 'chain 'M' and resid 20 through 22' Processing helix chain 'M' and resid 26 through 38 removed outlier: 3.501A pdb=" N GLN M 32 " --> pdb=" O THR M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 48 removed outlier: 3.907A pdb=" N LEU M 48 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 63 removed outlier: 4.570A pdb=" N ILE M 56 " --> pdb=" O GLU M 52 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG M 57 " --> pdb=" O LEU M 53 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP M 58 " --> pdb=" O GLY M 54 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE M 59 " --> pdb=" O LYS M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 removed outlier: 4.990A pdb=" N ARG M 71 " --> pdb=" O GLY M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'N' and resid 3 through 12 removed outlier: 3.658A pdb=" N ILE N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 20 removed outlier: 4.009A pdb=" N GLU N 20 " --> pdb=" O LYS N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 51 removed outlier: 3.855A pdb=" N LEU N 47 " --> pdb=" O CYS N 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.745A pdb=" N ALA O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE O 31 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 4.230A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 removed outlier: 4.363A pdb=" N LYS O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 64 removed outlier: 4.056A pdb=" N ALA P 64 " --> pdb=" O LEU P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 69 No H-bonds generated for 'chain 'P' and resid 67 through 69' Processing helix chain 'P' and resid 70 through 77 Processing helix chain 'P' and resid 80 through 88 removed outlier: 3.860A pdb=" N GLN P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 21 Processing helix chain 'R' and resid 31 through 38 removed outlier: 3.519A pdb=" N LYS R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 51 Processing helix chain 'R' and resid 53 through 70 removed outlier: 4.102A pdb=" N ARG R 58 " --> pdb=" O ALA R 54 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 26 removed outlier: 3.701A pdb=" N MET S 16 " --> pdb=" O ASP S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 75 removed outlier: 3.713A pdb=" N PHE S 74 " --> pdb=" O LEU S 71 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA S 75 " --> pdb=" O GLY S 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 41 removed outlier: 3.881A pdb=" N ARG T 10 " --> pdb=" O SER T 6 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS T 12 " --> pdb=" O ILE T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 65 removed outlier: 4.772A pdb=" N THR T 52 " --> pdb=" O LYS T 48 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU T 53 " --> pdb=" O THR T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 83 removed outlier: 3.777A pdb=" N ALA T 72 " --> pdb=" O HIS T 68 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA T 73 " --> pdb=" O LYS T 69 " (cutoff:3.500A) Processing helix chain 'Z' and resid 30 through 32 No H-bonds generated for 'chain 'Z' and resid 30 through 32' Processing helix chain 'Z' and resid 197 through 203 removed outlier: 4.226A pdb=" N GLU Z 201 " --> pdb=" O GLU Z 198 " (cutoff:3.500A) Processing helix chain 'Z' and resid 207 through 215 removed outlier: 3.784A pdb=" N SER Z 211 " --> pdb=" O LYS Z 207 " (cutoff:3.500A) Processing helix chain 'Z' and resid 266 through 271 removed outlier: 3.703A pdb=" N ILE Z 270 " --> pdb=" O SER Z 266 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL Z 271 " --> pdb=" O ASP Z 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 266 through 271' Processing helix chain 'a' and resid 40 through 45 Processing helix chain 'a' and resid 62 through 70 Processing helix chain 'a' and resid 121 through 127 Processing helix chain 'b' and resid 20 through 25 Processing helix chain 'b' and resid 29 through 45 removed outlier: 4.147A pdb=" N ARG b 45 " --> pdb=" O ARG b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 53 through 57 removed outlier: 3.994A pdb=" N VAL b 57 " --> pdb=" O ARG b 54 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 121 Processing helix chain 'b' and resid 135 through 147 removed outlier: 4.196A pdb=" N MET b 139 " --> pdb=" O LYS b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 159 through 168 removed outlier: 4.765A pdb=" N LEU b 165 " --> pdb=" O GLU b 161 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER b 166 " --> pdb=" O ALA b 162 " (cutoff:3.500A) Processing helix chain 'b' and resid 183 through 189 Processing helix chain 'b' and resid 195 through 206 Processing helix chain 'c' and resid 3 through 11 Processing helix chain 'c' and resid 11 through 21 Processing helix chain 'c' and resid 24 through 28 removed outlier: 3.593A pdb=" N VAL c 28 " --> pdb=" O VAL c 25 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 61 removed outlier: 5.145A pdb=" N GLU c 55 " --> pdb=" O ASP c 51 " (cutoff:3.500A) Processing helix chain 'c' and resid 74 through 78 removed outlier: 3.716A pdb=" N PHE c 77 " --> pdb=" O ILE c 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 107 removed outlier: 4.371A pdb=" N TYR c 97 " --> pdb=" O GLY c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 111 Processing helix chain 'c' and resid 162 through 174 removed outlier: 3.920A pdb=" N ALA c 166 " --> pdb=" O THR c 162 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR c 171 " --> pdb=" O ARG c 167 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN c 172 " --> pdb=" O GLU c 168 " (cutoff:3.500A) Processing helix chain 'd' and resid 59 through 83 Processing helix chain 'd' and resid 138 through 151 Processing helix chain 'e' and resid 25 through 39 Processing helix chain 'e' and resid 59 through 63 removed outlier: 3.590A pdb=" N LYS e 62 " --> pdb=" O ASN e 59 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE e 63 " --> pdb=" O ALA e 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 59 through 63' Processing helix chain 'e' and resid 68 through 73 Processing helix chain 'e' and resid 97 through 110 removed outlier: 4.102A pdb=" N MET e 101 " --> pdb=" O TYR e 97 " (cutoff:3.500A) Processing helix chain 'e' and resid 113 through 121 Processing helix chain 'f' and resid 104 through 109 removed outlier: 4.163A pdb=" N GLU f 108 " --> pdb=" O ARG f 104 " (cutoff:3.500A) Processing helix chain 'f' and resid 111 through 118 Processing helix chain 'i' and resid 2 through 6 Processing helix chain 'i' and resid 56 through 61 Processing helix chain 'i' and resid 80 through 85 removed outlier: 3.654A pdb=" N GLY i 84 " --> pdb=" O LYS i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 99 Processing helix chain 'i' and resid 129 through 140 Processing helix chain 'j' and resid 44 through 59 removed outlier: 3.952A pdb=" N TYR j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 110 through 123 removed outlier: 3.927A pdb=" N HIS j 123 " --> pdb=" O ARG j 119 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 28 Processing helix chain 'k' and resid 34 through 54 removed outlier: 4.370A pdb=" N SER k 42 " --> pdb=" O LYS k 38 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL k 43 " --> pdb=" O GLU k 39 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 64 Processing helix chain 'k' and resid 79 through 91 removed outlier: 5.026A pdb=" N ALA k 88 " --> pdb=" O PHE k 84 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR k 89 " --> pdb=" O SER k 85 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 20 removed outlier: 3.938A pdb=" N LYS l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG l 14 " --> pdb=" O ALA l 10 " (cutoff:3.500A) Processing helix chain 'l' and resid 70 through 88 removed outlier: 4.198A pdb=" N LYS l 88 " --> pdb=" O ARG l 84 " (cutoff:3.500A) Processing helix chain 'l' and resid 104 through 117 Processing helix chain 'm' and resid 2 through 10 Processing helix chain 'm' and resid 97 through 102 removed outlier: 3.506A pdb=" N LEU m 100 " --> pdb=" O LEU m 97 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG m 101 " --> pdb=" O TYR m 98 " (cutoff:3.500A) Processing helix chain 'n' and resid 7 through 21 removed outlier: 4.572A pdb=" N ARG n 11 " --> pdb=" O GLY n 7 " (cutoff:3.500A) Processing helix chain 'n' and resid 25 through 30 Processing helix chain 'n' and resid 31 through 71 removed outlier: 3.999A pdb=" N GLN n 37 " --> pdb=" O LYS n 33 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS n 41 " --> pdb=" O GLN n 37 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS n 54 " --> pdb=" O ARG n 50 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG n 55 " --> pdb=" O ARG n 51 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 87 Processing helix chain 'n' and resid 92 through 101 Processing helix chain 'n' and resid 102 through 118 removed outlier: 3.738A pdb=" N PHE n 106 " --> pdb=" O ASP n 102 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA n 112 " --> pdb=" O GLN n 108 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN n 118 " --> pdb=" O LYS n 114 " (cutoff:3.500A) Processing helix chain 'r' and resid 13 through 22 removed outlier: 4.147A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) Processing helix chain 'r' and resid 23 through 25 No H-bonds generated for 'chain 'r' and resid 23 through 25' Processing helix chain 'r' and resid 28 through 39 removed outlier: 4.214A pdb=" N SER r 34 " --> pdb=" O GLY r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 43 through 57 Processing helix chain 's' and resid 3 through 6 Processing helix chain 's' and resid 14 through 23 removed outlier: 3.699A pdb=" N THR s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU s 23 " --> pdb=" O ASP s 19 " (cutoff:3.500A) Processing helix chain 's' and resid 35 through 48 removed outlier: 3.809A pdb=" N VAL s 39 " --> pdb=" O ASN s 35 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS s 40 " --> pdb=" O LYS s 36 " (cutoff:3.500A) Processing helix chain 'v' and resid 20 through 22 No H-bonds generated for 'chain 'v' and resid 20 through 22' Processing helix chain 'v' and resid 51 through 56 removed outlier: 3.722A pdb=" N SER v 56 " --> pdb=" O ARG v 52 " (cutoff:3.500A) Processing helix chain 'w' and resid 3 through 8 Processing helix chain 'w' and resid 11 through 34 removed outlier: 3.811A pdb=" N GLU w 15 " --> pdb=" O THR w 11 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN w 16 " --> pdb=" O ALA w 12 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 65 removed outlier: 4.158A pdb=" N ARG w 47 " --> pdb=" O ILE w 43 " (cutoff:3.500A) Processing helix chain 'x' and resid 16 through 26 Processing helix chain 'x' and resid 40 through 51 Processing helix chain 'z' and resid 716 through 734 removed outlier: 4.356A pdb=" N SER z 722 " --> pdb=" O GLU z 718 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG z 723 " --> pdb=" O ASN z 719 " (cutoff:3.500A) Processing helix chain 'z' and resid 748 through 760 removed outlier: 4.483A pdb=" N GLN z 755 " --> pdb=" O ARG z 751 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP z 756 " --> pdb=" O LYS z 752 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU z 757 " --> pdb=" O GLY z 753 " (cutoff:3.500A) Processing helix chain 'z' and resid 775 through 778 Processing sheet with id=AA1, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain '0' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain '1' and resid 18 through 22 removed outlier: 3.569A pdb=" N LYS 1 41 " --> pdb=" O CYS 1 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 15 through 16 Processing sheet with id=AA5, first strand: chain '4' and resid 2 through 4 removed outlier: 6.435A pdb=" N LYS 4 2 " --> pdb=" O LYS 4 35 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN 4 34 " --> pdb=" O VAL 4 25 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL 4 23 " --> pdb=" O GLN 4 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '6' and resid 10 through 11 Processing sheet with id=AA7, first strand: chain '6' and resid 13 through 16 removed outlier: 6.839A pdb=" N THR 6 13 " --> pdb=" O VAL 6 31 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL 6 33 " --> pdb=" O THR 6 13 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS 6 15 " --> pdb=" O VAL 6 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.175A pdb=" N ILE B 67 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N VAL B 92 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE B 69 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU B 68 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 162 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU B 161 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE B 186 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE B 163 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 198 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 54 through 57 Processing sheet with id=AB1, first strand: chain 'C' and resid 163 through 170 removed outlier: 3.845A pdb=" N TYR C 167 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU C 169 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 198 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ASP C 180 " --> pdb=" O ARG C 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 12 through 25 removed outlier: 5.585A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR E 17 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 85 through 86 removed outlier: 3.589A pdb=" N LYS E 126 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU E 124 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE E 106 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N SER E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 36 through 47 removed outlier: 5.462A pdb=" N ILE F 37 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN F 66 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR F 60 " --> pdb=" O TRP F 43 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS F 45 " --> pdb=" O GLY F 58 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLY F 58 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 10 " --> pdb=" O PHE F 59 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN F 61 " --> pdb=" O TYR F 8 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR F 8 " --> pdb=" O GLN F 61 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU F 5 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N MET F 7 " --> pdb=" O HIS F 88 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N HIS F 88 " --> pdb=" O MET F 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE F 9 " --> pdb=" O ILE F 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 73 through 77 Processing sheet with id=AB6, first strand: chain 'H' and resid 26 through 28 Processing sheet with id=AB7, first strand: chain 'H' and resid 77 through 79 removed outlier: 6.740A pdb=" N ILE H 105 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR H 130 " --> pdb=" O ILE H 103 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE H 103 " --> pdb=" O TYR H 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 6 through 11 Processing sheet with id=AB9, first strand: chain 'I' and resid 29 through 30 Processing sheet with id=AC1, first strand: chain 'J' and resid 40 through 45 removed outlier: 4.485A pdb=" N LYS J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 49 through 52 Processing sheet with id=AC3, first strand: chain 'K' and resid 43 through 48 removed outlier: 6.043A pdb=" N ALA K 43 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASP K 38 " --> pdb=" O ALA K 43 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER K 45 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY K 21 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR K 87 " --> pdb=" O GLY K 21 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA K 23 " --> pdb=" O THR K 87 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LYS K 89 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE K 25 " --> pdb=" O LYS K 89 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU K 84 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE K 112 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL K 86 " --> pdb=" O ILE K 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 26 through 29 removed outlier: 3.582A pdb=" N GLU L 34 " --> pdb=" O ASN L 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 43 through 53 removed outlier: 6.627A pdb=" N ARG L 67 " --> pdb=" O THR L 48 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL L 50 " --> pdb=" O TYR L 65 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N TYR L 65 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR L 52 " --> pdb=" O ARG L 63 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG L 63 " --> pdb=" O THR L 52 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL L 68 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL L 76 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 13.711A pdb=" N GLU L 75 " --> pdb=" O VAL L 106 " (cutoff:3.500A) removed outlier: 10.663A pdb=" N TYR L 108 " --> pdb=" O GLU L 75 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR L 77 " --> pdb=" O TYR L 108 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE L 110 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR L 79 " --> pdb=" O ILE L 110 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 3 through 11 removed outlier: 6.388A pdb=" N VAL P 22 " --> pdb=" O THR P 36 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR P 36 " --> pdb=" O VAL P 22 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Q' and resid 44 through 45 removed outlier: 5.754A pdb=" N ARG Q 74 " --> pdb=" O THR Q 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET Q 64 " --> pdb=" O ARG Q 76 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LYS Q 62 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL Q 80 " --> pdb=" O ILE Q 60 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE Q 60 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR Q 24 " --> pdb=" O VAL Q 15 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Q' and resid 31 through 32 Processing sheet with id=AC9, first strand: chain 'S' and resid 31 through 32 removed outlier: 6.769A pdb=" N VAL S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N TYR S 52 " --> pdb=" O VAL S 31 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 3 through 5 Processing sheet with id=AD2, first strand: chain 'Z' and resid 34 through 35 Processing sheet with id=AD3, first strand: chain 'Z' and resid 101 through 105 Processing sheet with id=AD4, first strand: chain 'Z' and resid 129 through 131 removed outlier: 5.763A pdb=" N VAL Z 164 " --> pdb=" O ARG Z 175 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG Z 175 " --> pdb=" O VAL Z 164 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Z 174 " --> pdb=" O ARG Z 182 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'a' and resid 4 through 16 removed outlier: 4.918A pdb=" N LYS a 9 " --> pdb=" O GLU a 29 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU a 29 " --> pdb=" O LYS a 9 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE a 23 " --> pdb=" O VAL a 15 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LYS a 189 " --> pdb=" O ILE a 176 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE a 176 " --> pdb=" O LYS a 189 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR a 170 " --> pdb=" O GLY a 112 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLY a 112 " --> pdb=" O THR a 170 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N GLN a 172 " --> pdb=" O VAL a 110 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL a 110 " --> pdb=" O GLN a 172 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'a' and resid 34 through 39 removed outlier: 5.394A pdb=" N VAL a 35 " --> pdb=" O GLY a 52 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY a 52 " --> pdb=" O VAL a 35 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE a 49 " --> pdb=" O LEU a 83 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'a' and resid 118 through 120 removed outlier: 4.017A pdb=" N GLY a 118 " --> pdb=" O MET a 164 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'b' and resid 13 through 18 removed outlier: 3.957A pdb=" N LEU b 6 " --> pdb=" O ALA b 14 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASP b 16 " --> pdb=" O VAL b 4 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL b 4 " --> pdb=" O ASP b 16 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N ILE b 123 " --> pdb=" O LYS b 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA b 5 " --> pdb=" O ILE b 123 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL b 125 " --> pdb=" O ALA b 5 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU b 153 " --> pdb=" O LEU b 193 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR b 174 " --> pdb=" O ALA b 152 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE b 154 " --> pdb=" O THR b 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'c' and resid 66 through 67 removed outlier: 6.582A pdb=" N VAL c 157 " --> pdb=" O GLU c 32 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE c 34 " --> pdb=" O VAL c 155 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL c 155 " --> pdb=" O ILE c 34 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE c 36 " --> pdb=" O ASP c 153 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP c 153 " --> pdb=" O ILE c 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 16 through 19 Processing sheet with id=AE2, first strand: chain 'd' and resid 46 through 47 Processing sheet with id=AE3, first strand: chain 'd' and resid 84 through 88 removed outlier: 7.104A pdb=" N LYS d 131 " --> pdb=" O PRO d 127 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 96 through 100 removed outlier: 3.933A pdb=" N LYS d 103 " --> pdb=" O SER d 100 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU d 106 " --> pdb=" O VAL d 114 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'e' and resid 54 through 58 removed outlier: 6.393A pdb=" N TRP e 16 " --> pdb=" O GLU e 139 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'e' and resid 74 through 77 Processing sheet with id=AE7, first strand: chain 'f' and resid 92 through 93 removed outlier: 4.100A pdb=" N SER f 92 " --> pdb=" O ARG f 88 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG f 88 " --> pdb=" O SER f 92 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL f 85 " --> pdb=" O ILE f 62 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE f 62 " --> pdb=" O VAL f 85 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE f 87 " --> pdb=" O ALA f 60 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA f 60 " --> pdb=" O ILE f 87 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N VAL f 38 " --> pdb=" O VAL f 24 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL f 24 " --> pdb=" O VAL f 38 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL f 40 " --> pdb=" O ILE f 22 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU f 18 " --> pdb=" O LYS f 44 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA f 46 " --> pdb=" O ALA f 16 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA f 16 " --> pdb=" O ALA f 46 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG f 17 " --> pdb=" O VAL f 10 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS f 84 " --> pdb=" O ARG f 7 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS f 9 " --> pdb=" O CYS f 84 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE f 86 " --> pdb=" O LYS f 9 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'f' and resid 69 through 70 removed outlier: 3.533A pdb=" N TYR f 76 " --> pdb=" O THR m 73 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS m 49 " --> pdb=" O THR m 60 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG m 62 " --> pdb=" O VAL m 47 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VAL m 47 " --> pdb=" O ARG m 62 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE m 64 " --> pdb=" O GLY m 45 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N GLY m 45 " --> pdb=" O ILE m 64 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR m 25 " --> pdb=" O VAL m 87 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG m 27 " --> pdb=" O GLU m 85 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU m 85 " --> pdb=" O ARG m 27 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS m 83 " --> pdb=" O HIS m 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'f' and resid 101 through 102 Processing sheet with id=AF1, first strand: chain 'i' and resid 74 through 78 Processing sheet with id=AF2, first strand: chain 'i' and resid 89 through 91 removed outlier: 7.161A pdb=" N THR i 89 " --> pdb=" O THR i 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LYS i 124 " --> pdb=" O THR i 89 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL i 91 " --> pdb=" O LYS i 124 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU i 121 " --> pdb=" O THR i 142 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU i 144 " --> pdb=" O LEU i 121 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL i 123 " --> pdb=" O GLU i 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'j' and resid 63 through 66 removed outlier: 6.465A pdb=" N ILE j 34 " --> pdb=" O LEU j 103 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU j 105 " --> pdb=" O PHE j 32 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE j 32 " --> pdb=" O GLU j 105 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'j' and resid 40 through 43 removed outlier: 3.578A pdb=" N SER j 40 " --> pdb=" O VAL j 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY j 92 " --> pdb=" O TYR j 74 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'k' and resid 29 through 33 removed outlier: 3.544A pdb=" N GLU k 118 " --> pdb=" O ARG k 100 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'k' and resid 70 through 72 Processing sheet with id=AF7, first strand: chain 'l' and resid 30 through 35 removed outlier: 6.832A pdb=" N ILE l 40 " --> pdb=" O SER l 57 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER l 57 " --> pdb=" O ILE l 40 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA l 42 " --> pdb=" O SER l 55 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER l 55 " --> pdb=" O ALA l 42 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE l 44 " --> pdb=" O LEU l 53 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'm' and resid 90 through 91 removed outlier: 4.148A pdb=" N LYS m 111 " --> pdb=" O LYS m 91 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'o' and resid 12 through 14 Processing sheet with id=AG1, first strand: chain 'o' and resid 19 through 22 Processing sheet with id=AG2, first strand: chain 'o' and resid 19 through 22 Processing sheet with id=AG3, first strand: chain 'o' and resid 73 through 77 removed outlier: 3.695A pdb=" N LYS o 77 " --> pdb=" O VAL o 82 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL o 82 " --> pdb=" O LYS o 77 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'r' and resid 3 through 6 removed outlier: 7.086A pdb=" N ILE r 96 " --> pdb=" O LYS r 83 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS r 83 " --> pdb=" O ILE r 96 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS r 98 " --> pdb=" O THR r 81 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THR r 81 " --> pdb=" O LYS r 98 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR r 100 " --> pdb=" O GLY r 79 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N SER r 108 " --> pdb=" O ILE r 71 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE r 71 " --> pdb=" O SER r 108 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 's' and resid 8 through 11 removed outlier: 4.449A pdb=" N ARG s 77 " --> pdb=" O VAL s 30 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 't' and resid 20 through 22 removed outlier: 3.584A pdb=" N GLY t 21 " --> pdb=" O VAL t 9 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 't' and resid 32 through 33 Processing sheet with id=AG8, first strand: chain 't' and resid 41 through 45 Processing sheet with id=AG9, first strand: chain 't' and resid 81 through 85 Processing sheet with id=AH1, first strand: chain 'u' and resid 30 through 31 removed outlier: 7.397A pdb=" N LEU u 67 " --> pdb=" O LEU u 45 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'u' and resid 53 through 55 removed outlier: 7.141A pdb=" N TYR u 54 " --> pdb=" O VAL u 87 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL u 89 " --> pdb=" O TYR u 54 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'v' and resid 13 through 18 Processing sheet with id=AH4, first strand: chain 'v' and resid 33 through 39 removed outlier: 4.027A pdb=" N VAL v 36 " --> pdb=" O VAL v 47 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'x' and resid 34 through 38 Processing sheet with id=AH6, first strand: chain 'z' and resid 675 through 677 removed outlier: 6.735A pdb=" N GLU z 664 " --> pdb=" O LYS z 659 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS z 659 " --> pdb=" O GLU z 664 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASN z 666 " --> pdb=" O LEU z 657 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU z 644 " --> pdb=" O ILE z 684 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'z' and resid 709 through 711 removed outlier: 6.764A pdb=" N LEU z 710 " --> pdb=" O ILE z 742 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR z 780 " --> pdb=" O ILE z 741 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER z 766 " --> pdb=" O GLU z 783 " (cutoff:3.500A) 1628 hydrogen bonds defined for protein. 4584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3973 hydrogen bonds 6430 hydrogen bond angles 0 basepair planarities 1561 basepair parallelities 2385 stacking parallelities Total time for adding SS restraints: 245.64 Time building geometry restraints manager: 72.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 13222 1.31 - 1.44: 70304 1.44 - 1.57: 63341 1.57 - 1.70: 9453 1.70 - 1.83: 242 Bond restraints: 156562 Sorted by residual: bond pdb=" CA ALA w 49 " pdb=" C ALA w 49 " ideal model delta sigma weight residual 1.523 1.441 0.082 1.30e-02 5.92e+03 3.96e+01 bond pdb=" CA LYS w 54 " pdb=" C LYS w 54 " ideal model delta sigma weight residual 1.524 1.446 0.078 1.27e-02 6.20e+03 3.77e+01 bond pdb=" C LYS w 54 " pdb=" O LYS w 54 " ideal model delta sigma weight residual 1.236 1.175 0.062 1.15e-02 7.56e+03 2.91e+01 bond pdb=" CA SER P 76 " pdb=" C SER P 76 " ideal model delta sigma weight residual 1.522 1.447 0.075 1.41e-02 5.03e+03 2.86e+01 bond pdb=" CA THR w 55 " pdb=" C THR w 55 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.30e-02 5.92e+03 2.74e+01 ... (remaining 156557 not shown) Histogram of bond angle deviations from ideal: 37.83 - 57.87: 1 57.87 - 77.91: 0 77.91 - 97.94: 10 97.94 - 117.98: 147920 117.98 - 138.02: 86782 Bond angle restraints: 234713 Sorted by residual: angle pdb=" O3' U X 138 " pdb=" P A X 139 " pdb=" OP1 A X 139 " ideal model delta sigma weight residual 108.00 37.83 70.17 3.00e+00 1.11e-01 5.47e+02 angle pdb=" CA PRO J 81 " pdb=" N PRO J 81 " pdb=" CD PRO J 81 " ideal model delta sigma weight residual 112.00 95.02 16.98 1.40e+00 5.10e-01 1.47e+02 angle pdb=" CA PRO P 42 " pdb=" N PRO P 42 " pdb=" CD PRO P 42 " ideal model delta sigma weight residual 112.00 96.87 15.13 1.40e+00 5.10e-01 1.17e+02 angle pdb=" CA GLN N 11 " pdb=" CB GLN N 11 " pdb=" CG GLN N 11 " ideal model delta sigma weight residual 114.10 134.35 -20.25 2.00e+00 2.50e-01 1.03e+02 angle pdb=" CA PRO 1 37 " pdb=" N PRO 1 37 " pdb=" CD PRO 1 37 " ideal model delta sigma weight residual 112.00 98.13 13.87 1.40e+00 5.10e-01 9.82e+01 ... (remaining 234708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 87065 35.92 - 71.83: 12012 71.83 - 107.75: 1378 107.75 - 143.66: 31 143.66 - 179.58: 39 Dihedral angle restraints: 100525 sinusoidal: 85062 harmonic: 15463 Sorted by residual: dihedral pdb=" C5' U X1507 " pdb=" C4' U X1507 " pdb=" C3' U X1507 " pdb=" O3' U X1507 " ideal model delta sinusoidal sigma weight residual 147.00 78.78 68.22 1 8.00e+00 1.56e-02 9.43e+01 dihedral pdb=" C4' U X1507 " pdb=" C3' U X1507 " pdb=" C2' U X1507 " pdb=" C1' U X1507 " ideal model delta sinusoidal sigma weight residual -35.00 30.71 -65.71 1 8.00e+00 1.56e-02 8.83e+01 dihedral pdb=" O4' U X2906 " pdb=" C1' U X2906 " pdb=" N1 U X2906 " pdb=" C2 U X2906 " ideal model delta sinusoidal sigma weight residual 200.00 32.75 167.25 1 1.50e+01 4.44e-03 8.43e+01 ... (remaining 100522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 29636 0.151 - 0.302: 387 0.302 - 0.452: 27 0.452 - 0.603: 6 0.603 - 0.754: 1 Chirality restraints: 30057 Sorted by residual: chirality pdb=" CG LEU k 20 " pdb=" CB LEU k 20 " pdb=" CD1 LEU k 20 " pdb=" CD2 LEU k 20 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA MET w 53 " pdb=" N MET w 53 " pdb=" C MET w 53 " pdb=" CB MET w 53 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CB VAL P 70 " pdb=" CA VAL P 70 " pdb=" CG1 VAL P 70 " pdb=" CG2 VAL P 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.09 -0.54 2.00e-01 2.50e+01 7.21e+00 ... (remaining 30054 not shown) Planarity restraints: 12181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN P 41 " -0.157 5.00e-02 4.00e+02 2.20e-01 7.75e+01 pdb=" N PRO P 42 " 0.379 5.00e-02 4.00e+02 pdb=" CA PRO P 42 " -0.134 5.00e-02 4.00e+02 pdb=" CD PRO P 42 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS 1 36 " -0.136 5.00e-02 4.00e+02 1.93e-01 5.96e+01 pdb=" N PRO 1 37 " 0.333 5.00e-02 4.00e+02 pdb=" CA PRO 1 37 " -0.109 5.00e-02 4.00e+02 pdb=" CD PRO 1 37 " -0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 24 " 0.132 5.00e-02 4.00e+02 1.88e-01 5.65e+01 pdb=" N PRO B 25 " -0.324 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.107 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.085 5.00e-02 4.00e+02 ... (remaining 12178 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 1424 2.53 - 3.12: 100174 3.12 - 3.71: 308144 3.71 - 4.31: 392014 4.31 - 4.90: 527944 Nonbonded interactions: 1329700 Sorted by model distance: nonbonded pdb=" O LEU M 34 " pdb=" OE2 GLU M 41 " model vdw 1.933 3.040 nonbonded pdb=" CD2 LEU M 34 " pdb=" CG GLU M 41 " model vdw 1.953 3.860 nonbonded pdb=" OG SER M 40 " pdb=" OG1 THR M 43 " model vdw 2.038 2.440 nonbonded pdb=" N GLN G 40 " pdb=" OE1 GLN G 40 " model vdw 2.091 2.520 nonbonded pdb=" O2' U X2334 " pdb=" O2 U X2335 " model vdw 2.145 2.440 ... (remaining 1329695 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=1.00 max=1.00 mean=1.00 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: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.620 Construct map_model_manager: 0.110 Extract box with map and model: 28.850 Check model and map are aligned: 1.550 Set scattering table: 0.970 Process input model: 521.960 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 565.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.159 156562 Z= 0.385 Angle : 1.014 70.169 234713 Z= 0.514 Chirality : 0.049 0.754 30057 Planarity : 0.008 0.220 12181 Dihedral : 24.528 179.576 90582 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.89 % Favored : 92.91 % Rotamer: Outliers : 1.40 % Allowed : 34.33 % Favored : 64.27 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.10), residues: 5342 helix: -1.54 (0.11), residues: 1610 sheet: -0.94 (0.16), residues: 977 loop : -1.97 (0.11), residues: 2755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.005 TRP G 103 HIS 0.021 0.002 HIS j 13 PHE 0.061 0.004 PHE Z 257 TYR 0.046 0.003 TYR u 54 ARG 0.040 0.001 ARG w 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1507 time to evaluate : 5.927 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: 0 36 MET cc_start: 0.8044 (tpt) cc_final: 0.7467 (tpt) REVERT: 0 52 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8251 (ttpt) REVERT: 1 24 ARG cc_start: 0.8754 (mmp80) cc_final: 0.8273 (ttt90) REVERT: 4 8 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8112 (mttt) REVERT: 4 13 LYS cc_start: 0.8646 (pttp) cc_final: 0.8082 (ptmm) REVERT: 4 35 LYS cc_start: 0.7633 (mtmt) cc_final: 0.7302 (mttt) REVERT: 6 2 LYS cc_start: 0.6677 (mtmt) cc_final: 0.6157 (tptt) REVERT: B 90 TYR cc_start: 0.7373 (m-80) cc_final: 0.7068 (m-80) REVERT: B 94 GLN cc_start: 0.5792 (mt0) cc_final: 0.5530 (tt0) REVERT: B 134 VAL cc_start: 0.8418 (m) cc_final: 0.8033 (m) REVERT: B 140 GLU cc_start: 0.8731 (tp30) cc_final: 0.8526 (tp30) REVERT: B 143 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.7749 (tmt170) REVERT: B 156 ASP cc_start: 0.6690 (t0) cc_final: 0.5792 (p0) REVERT: C 16 ARG cc_start: 0.6739 (tpp80) cc_final: 0.6080 (mmm160) REVERT: C 48 ASP cc_start: 0.8319 (p0) cc_final: 0.8110 (p0) REVERT: C 61 ASN cc_start: 0.7987 (t0) cc_final: 0.7785 (t0) REVERT: C 97 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7397 (mtt180) REVERT: C 133 GLN cc_start: 0.7047 (mt0) cc_final: 0.6814 (mt0) REVERT: C 165 GLU cc_start: 0.7806 (tp30) cc_final: 0.7514 (tp30) REVERT: C 191 THR cc_start: 0.8500 (p) cc_final: 0.8184 (t) REVERT: D 41 ARG cc_start: 0.6225 (OUTLIER) cc_final: 0.4895 (ptp90) REVERT: D 50 GLN cc_start: 0.8287 (pm20) cc_final: 0.7694 (pm20) REVERT: D 95 ASP cc_start: 0.5930 (m-30) cc_final: 0.5323 (m-30) REVERT: D 153 GLU cc_start: 0.6136 (tp30) cc_final: 0.5839 (mt-10) REVERT: E 19 ASN cc_start: 0.8188 (t0) cc_final: 0.7873 (t0) REVERT: E 149 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.6971 (mtp-110) REVERT: F 37 ILE cc_start: 0.7025 (mp) cc_final: 0.6712 (mp) REVERT: F 84 ASP cc_start: 0.7428 (m-30) cc_final: 0.7219 (m-30) REVERT: G 42 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8650 (tp) REVERT: H 57 GLN cc_start: 0.7867 (pt0) cc_final: 0.7402 (pt0) REVERT: I 7 TYR cc_start: 0.6260 (t80) cc_final: 0.5839 (t80) REVERT: I 61 TYR cc_start: 0.7967 (m-80) cc_final: 0.7657 (m-80) REVERT: I 81 HIS cc_start: 0.6224 (t-90) cc_final: 0.5997 (t70) REVERT: J 10 LEU cc_start: 0.7041 (pt) cc_final: 0.6595 (mp) REVERT: J 73 LEU cc_start: 0.7058 (tp) cc_final: 0.6768 (tt) REVERT: K 29 PHE cc_start: 0.7997 (m-80) cc_final: 0.7451 (m-80) REVERT: K 33 ILE cc_start: 0.8158 (mm) cc_final: 0.7825 (mm) REVERT: K 89 LYS cc_start: 0.7768 (tppt) cc_final: 0.7137 (mttm) REVERT: L 34 GLU cc_start: 0.8055 (tp30) cc_final: 0.7651 (tt0) REVERT: L 53 MET cc_start: 0.5958 (tpp) cc_final: 0.5679 (tmm) REVERT: L 129 LYS cc_start: 0.8397 (tppt) cc_final: 0.8174 (ttpt) REVERT: M 78 LYS cc_start: 0.8431 (mmtt) cc_final: 0.8086 (mmtp) REVERT: O 78 TYR cc_start: 0.8420 (t80) cc_final: 0.8184 (t80) REVERT: P 30 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6507 (t0) REVERT: P 32 ARG cc_start: 0.6721 (ttt180) cc_final: 0.6509 (ttt-90) REVERT: Q 19 MET cc_start: 0.7127 (pmm) cc_final: 0.5686 (ptp) REVERT: R 30 ASP cc_start: 0.6705 (t0) cc_final: 0.6336 (m-30) REVERT: S 6 LYS cc_start: 0.6635 (mmmm) cc_final: 0.5934 (mmmm) REVERT: S 7 LYS cc_start: 0.6980 (mmtm) cc_final: 0.6581 (pttt) REVERT: S 18 LYS cc_start: 0.6268 (pttt) cc_final: 0.5937 (mtpp) REVERT: S 29 GLN cc_start: 0.7050 (pm20) cc_final: 0.6562 (pp30) REVERT: S 31 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7569 (m) REVERT: T 45 ASP cc_start: 0.7960 (p0) cc_final: 0.7357 (m-30) REVERT: T 57 ARG cc_start: 0.7850 (mmp80) cc_final: 0.6859 (mmt90) REVERT: Z 16 MET cc_start: 0.8760 (tpt) cc_final: 0.8226 (tpp) REVERT: Z 43 ARG cc_start: 0.8344 (mmt-90) cc_final: 0.7947 (mmt90) REVERT: Z 84 ASP cc_start: 0.7938 (t0) cc_final: 0.7669 (t0) REVERT: Z 160 THR cc_start: 0.8467 (p) cc_final: 0.8170 (p) REVERT: Z 191 SER cc_start: 0.7806 (t) cc_final: 0.7581 (t) REVERT: Z 261 LYS cc_start: 0.7221 (mmmt) cc_final: 0.6995 (tptt) REVERT: Z 268 LYS cc_start: 0.8727 (pttm) cc_final: 0.8221 (mmtm) REVERT: a 50 GLN cc_start: 0.7922 (pp30) cc_final: 0.7632 (pt0) REVERT: b 111 LYS cc_start: 0.9081 (mttt) cc_final: 0.8817 (mtmm) REVERT: b 138 GLU cc_start: 0.8591 (mp0) cc_final: 0.8204 (mp0) REVERT: c 32 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7361 (mm-30) REVERT: c 33 LYS cc_start: 0.8436 (pttt) cc_final: 0.8068 (ttpt) REVERT: c 37 ASN cc_start: 0.6048 (t0) cc_final: 0.5770 (t0) REVERT: c 38 MET cc_start: 0.6844 (tpp) cc_final: 0.6480 (tpp) REVERT: c 130 LEU cc_start: 0.6814 (mm) cc_final: 0.5923 (mp) REVERT: c 152 MET cc_start: 0.7915 (mmm) cc_final: 0.7591 (mmt) REVERT: d 41 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8155 (p0) REVERT: d 84 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: d 124 ILE cc_start: 0.6993 (pt) cc_final: 0.6240 (pt) REVERT: d 131 LYS cc_start: 0.7057 (tptp) cc_final: 0.6590 (mptt) REVERT: d 135 LYS cc_start: 0.8985 (tptp) cc_final: 0.8636 (mttp) REVERT: e 6 MET cc_start: 0.8121 (mmm) cc_final: 0.7826 (mtt) REVERT: e 13 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8132 (mp0) REVERT: e 118 GLN cc_start: 0.8984 (tp40) cc_final: 0.8759 (tp40) REVERT: f 1 MET cc_start: 0.7937 (pmm) cc_final: 0.7735 (ptm) REVERT: f 110 ASN cc_start: 0.7957 (t0) cc_final: 0.7662 (p0) REVERT: i 59 GLN cc_start: 0.8595 (mm110) cc_final: 0.8124 (mt0) REVERT: i 80 ASP cc_start: 0.7622 (p0) cc_final: 0.7381 (t0) REVERT: j 26 GLU cc_start: 0.8556 (pm20) cc_final: 0.8256 (pm20) REVERT: j 48 GLU cc_start: 0.8424 (tp30) cc_final: 0.7762 (tt0) REVERT: j 105 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7363 (mt-10) REVERT: j 110 SER cc_start: 0.8224 (p) cc_final: 0.7978 (p) REVERT: k 31 GLU cc_start: 0.7578 (tp30) cc_final: 0.7293 (mp0) REVERT: k 39 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8694 (mt-10) REVERT: k 50 LEU cc_start: 0.8919 (tp) cc_final: 0.8640 (tt) REVERT: k 92 GLU cc_start: 0.8588 (pp20) cc_final: 0.7927 (pt0) REVERT: l 55 SER cc_start: 0.7443 (p) cc_final: 0.6926 (m) REVERT: l 76 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7659 (mtpt) REVERT: l 79 GLU cc_start: 0.8380 (pp20) cc_final: 0.7763 (mt-10) REVERT: n 19 LYS cc_start: 0.9263 (tptm) cc_final: 0.9026 (tptm) REVERT: n 45 TYR cc_start: 0.8209 (m-10) cc_final: 0.7722 (m-10) REVERT: n 48 ARG cc_start: 0.8239 (tmm160) cc_final: 0.7867 (tmm160) REVERT: o 71 ILE cc_start: 0.9103 (mm) cc_final: 0.8894 (mt) REVERT: r 16 LYS cc_start: 0.9038 (mttp) cc_final: 0.8673 (mtmt) REVERT: s 10 ARG cc_start: 0.7107 (ptt180) cc_final: 0.6277 (ptp-110) REVERT: t 83 TYR cc_start: 0.8596 (m-80) cc_final: 0.8333 (m-10) REVERT: u 48 GLN cc_start: 0.7702 (pt0) cc_final: 0.7420 (pt0) REVERT: v 29 TRP cc_start: 0.7623 (m100) cc_final: 0.7236 (m100) REVERT: v 45 LYS cc_start: 0.7598 (mtpp) cc_final: 0.7351 (mtpt) REVERT: w 27 ASN cc_start: 0.8694 (m-40) cc_final: 0.8380 (m110) REVERT: w 31 GLN cc_start: 0.9432 (pt0) cc_final: 0.9077 (pt0) REVERT: x 4 LEU cc_start: 0.8703 (pt) cc_final: 0.8489 (pp) REVERT: x 11 SER cc_start: 0.8756 (t) cc_final: 0.7972 (p) REVERT: z 684 ILE cc_start: 0.4903 (mt) cc_final: 0.4576 (mt) REVERT: z 765 LYS cc_start: 0.4961 (OUTLIER) cc_final: 0.4529 (mmtp) outliers start: 64 outliers final: 23 residues processed: 1538 average time/residue: 1.3267 time to fit residues: 3518.4694 Evaluate side-chains 1217 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1187 time to evaluate : 5.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain Z residue 65 ILE Chi-restraints excluded: chain c residue 45 GLN Chi-restraints excluded: chain c residue 59 PHE Chi-restraints excluded: chain d residue 41 ASP Chi-restraints excluded: chain d residue 84 PHE Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 81 VAL Chi-restraints excluded: chain l residue 81 VAL Chi-restraints excluded: chain m residue 74 PHE Chi-restraints excluded: chain n residue 118 ASN Chi-restraints excluded: chain r residue 67 ASN Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain w residue 30 PHE Chi-restraints excluded: chain w residue 50 ILE Chi-restraints excluded: chain w residue 52 ARG Chi-restraints excluded: chain w residue 54 LYS Chi-restraints excluded: chain z residue 765 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 835 optimal weight: 10.0000 chunk 750 optimal weight: 10.0000 chunk 416 optimal weight: 20.0000 chunk 256 optimal weight: 9.9990 chunk 506 optimal weight: 9.9990 chunk 400 optimal weight: 5.9990 chunk 775 optimal weight: 10.0000 chunk 300 optimal weight: 20.0000 chunk 471 optimal weight: 1.9990 chunk 577 optimal weight: 5.9990 chunk 899 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 19 HIS 0 55 ASN 3 64 ASN 4 36 GLN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 ASN K 24 HIS L 125 GLN M 101 ASN ** Z 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 111 GLN Z 153 GLN b 9 GLN ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 75 ASN e 81 HIS f 3 GLN ** i 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN k 77 GLN m 41 GLN ** v 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 41 ASN x 48 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 156562 Z= 0.347 Angle : 0.760 12.053 234713 Z= 0.387 Chirality : 0.041 0.299 30057 Planarity : 0.006 0.107 12181 Dihedral : 24.669 179.839 79662 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.49 % Favored : 92.42 % Rotamer: Outliers : 8.01 % Allowed : 27.79 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.14 (0.11), residues: 5342 helix: -0.88 (0.12), residues: 1637 sheet: -0.93 (0.16), residues: 937 loop : -1.94 (0.11), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP G 103 HIS 0.013 0.002 HIS j 13 PHE 0.038 0.002 PHE j 69 TYR 0.028 0.002 TYR B 54 ARG 0.022 0.001 ARG H 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 1206 time to evaluate : 5.918 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: 0 36 MET cc_start: 0.7840 (tpt) cc_final: 0.7293 (mmt) REVERT: 0 52 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8202 (ttpt) REVERT: 1 1 MET cc_start: 0.7940 (ppp) cc_final: 0.7682 (ppp) REVERT: 1 23 LYS cc_start: 0.8369 (mtmt) cc_final: 0.8102 (mtmt) REVERT: 1 24 ARG cc_start: 0.8867 (mmp80) cc_final: 0.8108 (ttt90) REVERT: 4 31 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7916 (mttm) REVERT: 4 35 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7461 (mttt) REVERT: 6 1 MET cc_start: 0.7617 (mmm) cc_final: 0.6762 (mmm) REVERT: B 69 PHE cc_start: 0.8356 (m-10) cc_final: 0.7920 (m-10) REVERT: B 89 MET cc_start: 0.6397 (pmm) cc_final: 0.5719 (pmm) REVERT: B 94 GLN cc_start: 0.5840 (mt0) cc_final: 0.5360 (tt0) REVERT: B 143 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.7981 (tmt170) REVERT: C 16 ARG cc_start: 0.6985 (tpp80) cc_final: 0.6765 (ttt180) REVERT: C 17 ASP cc_start: 0.7373 (t0) cc_final: 0.7074 (t0) REVERT: C 97 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7460 (mtt180) REVERT: C 111 ASP cc_start: 0.7367 (m-30) cc_final: 0.7122 (m-30) REVERT: C 151 MET cc_start: 0.8293 (tpp) cc_final: 0.7998 (mmm) REVERT: C 165 GLU cc_start: 0.7511 (tp30) cc_final: 0.7260 (tp30) REVERT: C 182 ASP cc_start: 0.7944 (t0) cc_final: 0.7588 (t0) REVERT: C 191 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8119 (t) REVERT: D 46 GLU cc_start: 0.8523 (tp30) cc_final: 0.8265 (tp30) REVERT: D 68 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: E 19 ASN cc_start: 0.8197 (t0) cc_final: 0.7991 (t0) REVERT: E 149 ARG cc_start: 0.7343 (ttm-80) cc_final: 0.6884 (mtp-110) REVERT: F 5 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5936 (mp0) REVERT: F 11 ARG cc_start: 0.7532 (pmt-80) cc_final: 0.6818 (pmt-80) REVERT: H 35 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7939 (pp20) REVERT: H 51 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6497 (m-80) REVERT: H 97 VAL cc_start: 0.4716 (OUTLIER) cc_final: 0.3392 (p) REVERT: I 7 TYR cc_start: 0.6392 (t80) cc_final: 0.6055 (t80) REVERT: I 116 TYR cc_start: 0.7373 (p90) cc_final: 0.6946 (p90) REVERT: J 44 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7323 (p) REVERT: J 57 LYS cc_start: 0.8013 (pttm) cc_final: 0.7519 (pttm) REVERT: J 63 GLU cc_start: 0.7234 (mm-30) cc_final: 0.7032 (tp30) REVERT: J 64 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7358 (mm-40) REVERT: J 66 GLU cc_start: 0.8129 (pm20) cc_final: 0.7730 (pm20) REVERT: K 29 PHE cc_start: 0.8126 (m-80) cc_final: 0.7524 (m-80) REVERT: K 55 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6979 (mmt-90) REVERT: K 89 LYS cc_start: 0.7657 (tppt) cc_final: 0.7451 (tppt) REVERT: L 34 GLU cc_start: 0.7802 (tp30) cc_final: 0.7363 (tt0) REVERT: L 42 GLN cc_start: 0.7529 (mt0) cc_final: 0.7059 (mt0) REVERT: L 53 MET cc_start: 0.6290 (tpp) cc_final: 0.5441 (ttt) REVERT: L 58 PRO cc_start: 0.6785 (OUTLIER) cc_final: 0.6579 (Cg_endo) REVERT: L 94 LEU cc_start: 0.8549 (tp) cc_final: 0.8087 (tp) REVERT: M 35 LYS cc_start: 0.7590 (tptp) cc_final: 0.7376 (tppt) REVERT: N 11 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8215 (mp10) REVERT: N 12 ARG cc_start: 0.6967 (ptt-90) cc_final: 0.6631 (ptt-90) REVERT: O 6 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7550 (tm-30) REVERT: P 33 PHE cc_start: 0.7474 (p90) cc_final: 0.7265 (p90) REVERT: P 71 ARG cc_start: 0.4313 (OUTLIER) cc_final: 0.4107 (tpt170) REVERT: Q 19 MET cc_start: 0.7043 (pmm) cc_final: 0.6095 (ptp) REVERT: Q 39 ARG cc_start: 0.8725 (mtt180) cc_final: 0.8454 (mtt180) REVERT: Q 64 MET cc_start: 0.8639 (tmm) cc_final: 0.7819 (tmm) REVERT: R 30 ASP cc_start: 0.7144 (t0) cc_final: 0.6699 (m-30) REVERT: R 56 TYR cc_start: 0.7783 (m-80) cc_final: 0.7550 (m-80) REVERT: S 18 LYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5985 (mtpp) REVERT: T 45 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7341 (m-30) REVERT: T 57 ARG cc_start: 0.7809 (mmp80) cc_final: 0.6938 (mmt90) REVERT: Z 43 ARG cc_start: 0.8477 (mmt-90) cc_final: 0.8097 (mmt90) REVERT: Z 247 MET cc_start: 0.7590 (mtt) cc_final: 0.7272 (mtt) REVERT: Z 257 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8084 (p90) REVERT: Z 261 LYS cc_start: 0.7229 (mmmt) cc_final: 0.6906 (tptt) REVERT: Z 268 LYS cc_start: 0.8880 (pttm) cc_final: 0.8249 (mmtm) REVERT: a 130 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.6605 (pmt-80) REVERT: a 146 MET cc_start: 0.9036 (mmp) cc_final: 0.8768 (mmm) REVERT: a 175 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: b 62 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7406 (ptp90) REVERT: b 83 TRP cc_start: 0.9075 (m100) cc_final: 0.8813 (m100) REVERT: b 111 LYS cc_start: 0.9134 (mttt) cc_final: 0.8834 (mtmm) REVERT: b 138 GLU cc_start: 0.8681 (mp0) cc_final: 0.8419 (mp0) REVERT: b 190 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: c 26 MET cc_start: 0.7750 (tmm) cc_final: 0.7483 (tmm) REVERT: c 33 LYS cc_start: 0.8465 (pttt) cc_final: 0.7970 (ttpt) REVERT: c 37 ASN cc_start: 0.7256 (t0) cc_final: 0.6669 (t0) REVERT: c 38 MET cc_start: 0.7246 (tpp) cc_final: 0.5590 (tmm) REVERT: c 63 GLN cc_start: 0.7764 (pm20) cc_final: 0.7518 (pm20) REVERT: c 96 MET cc_start: 0.7099 (ptm) cc_final: 0.6752 (ppp) REVERT: c 127 ASN cc_start: 0.8197 (m-40) cc_final: 0.7988 (m110) REVERT: c 153 ASP cc_start: 0.8583 (t0) cc_final: 0.8208 (t0) REVERT: c 163 ASP cc_start: 0.7656 (m-30) cc_final: 0.7342 (t0) REVERT: d 84 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: d 131 LYS cc_start: 0.7281 (tptp) cc_final: 0.6620 (mptt) REVERT: e 6 MET cc_start: 0.8107 (mmm) cc_final: 0.7854 (mtt) REVERT: e 118 GLN cc_start: 0.9144 (tp40) cc_final: 0.8911 (tp40) REVERT: f 91 LYS cc_start: 0.8461 (mmmt) cc_final: 0.7692 (mmmt) REVERT: f 105 GLU cc_start: 0.9007 (mp0) cc_final: 0.8794 (mp0) REVERT: f 108 GLU cc_start: 0.7656 (pm20) cc_final: 0.7263 (mm-30) REVERT: f 110 ASN cc_start: 0.7968 (t0) cc_final: 0.7582 (p0) REVERT: i 80 ASP cc_start: 0.7822 (p0) cc_final: 0.7388 (t0) REVERT: k 28 GLU cc_start: 0.8475 (pm20) cc_final: 0.8045 (pm20) REVERT: l 27 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7310 (pp20) REVERT: l 55 SER cc_start: 0.6239 (p) cc_final: 0.5840 (m) REVERT: l 76 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7734 (mtmt) REVERT: l 79 GLU cc_start: 0.8541 (pp20) cc_final: 0.7891 (mt-10) REVERT: l 80 LEU cc_start: 0.8810 (mt) cc_final: 0.8078 (mt) REVERT: l 84 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6982 (mpt-90) REVERT: m 11 GLU cc_start: 0.8830 (pm20) cc_final: 0.8554 (pm20) REVERT: m 65 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7828 (p) REVERT: m 80 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7450 (ptpp) REVERT: m 85 GLU cc_start: 0.7860 (pm20) cc_final: 0.7581 (pm20) REVERT: m 98 TYR cc_start: 0.9022 (m-80) cc_final: 0.8741 (m-80) REVERT: n 94 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7580 (ttm) REVERT: o 31 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7582 (tm-30) REVERT: o 71 ILE cc_start: 0.9185 (mm) cc_final: 0.8690 (tt) REVERT: r 16 LYS cc_start: 0.9069 (mttp) cc_final: 0.8741 (mttt) REVERT: s 3 ASP cc_start: 0.6781 (t0) cc_final: 0.6574 (t0) REVERT: s 10 ARG cc_start: 0.7168 (ptt180) cc_final: 0.6299 (ptp-110) REVERT: s 15 GLU cc_start: 0.8508 (tp30) cc_final: 0.8181 (tp30) REVERT: s 57 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8148 (ptm) REVERT: t 60 GLU cc_start: 0.7552 (mp0) cc_final: 0.7337 (mp0) REVERT: t 83 TYR cc_start: 0.8687 (m-80) cc_final: 0.8317 (m-10) REVERT: u 85 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7864 (mttp) REVERT: v 29 TRP cc_start: 0.7635 (m100) cc_final: 0.7332 (m100) REVERT: v 45 LYS cc_start: 0.7912 (mtpp) cc_final: 0.7638 (mtpt) REVERT: w 27 ASN cc_start: 0.8886 (m-40) cc_final: 0.8648 (m-40) REVERT: w 59 GLU cc_start: 0.8906 (pt0) cc_final: 0.8573 (pt0) REVERT: x 11 SER cc_start: 0.8688 (t) cc_final: 0.7987 (p) REVERT: x 38 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7832 (tm-30) REVERT: x 47 ILE cc_start: 0.9056 (mm) cc_final: 0.8854 (pt) REVERT: z 765 LYS cc_start: 0.5133 (OUTLIER) cc_final: 0.4929 (tppt) outliers start: 365 outliers final: 238 residues processed: 1410 average time/residue: 1.2762 time to fit residues: 3151.6425 Evaluate side-chains 1356 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1090 time to evaluate : 6.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 9 SER Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 0 residue 55 ASN Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 17 THR Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 23 VAL Chi-restraints excluded: chain 4 residue 31 LYS Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 31 VAL Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 4 TYR Chi-restraints excluded: chain F residue 5 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 51 PHE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 68 HIS Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 58 PRO Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 TYR Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain N residue 4 LYS Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 71 ARG Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 53 ASN Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 18 LYS Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 157 SER Chi-restraints excluded: chain Z residue 241 ILE Chi-restraints excluded: chain Z residue 257 PHE Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain a residue 130 ARG Chi-restraints excluded: chain a residue 137 SER Chi-restraints excluded: chain a residue 145 SER Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 175 GLU Chi-restraints excluded: chain a residue 177 VAL Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 185 ASP Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain c residue 45 GLN Chi-restraints excluded: chain c residue 77 PHE Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain c residue 162 THR Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 84 PHE Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 114 VAL Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 134 VAL Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 35 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 89 ASP Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 61 LEU Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 123 VAL Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 9 THR Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 42 SER Chi-restraints excluded: chain k residue 78 ASP Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 81 VAL Chi-restraints excluded: chain l residue 84 ARG Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain l residue 118 LEU Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 39 ARG Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 78 THR Chi-restraints excluded: chain m residue 80 LYS Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 86 VAL Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 94 MET Chi-restraints excluded: chain n residue 118 ASN Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 93 THR Chi-restraints excluded: chain r residue 12 ILE Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 67 ASN Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 107 VAL Chi-restraints excluded: chain s residue 7 VAL Chi-restraints excluded: chain s residue 14 THR Chi-restraints excluded: chain s residue 44 GLU Chi-restraints excluded: chain s residue 57 MET Chi-restraints excluded: chain s residue 58 ASN Chi-restraints excluded: chain t residue 1 MET Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain t residue 36 GLU Chi-restraints excluded: chain t residue 71 LEU Chi-restraints excluded: chain u residue 18 THR Chi-restraints excluded: chain u residue 65 ASP Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 72 ASP Chi-restraints excluded: chain u residue 75 VAL Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain u residue 87 VAL Chi-restraints excluded: chain v residue 7 ILE Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 16 ASN Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 41 ASN Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 18 VAL Chi-restraints excluded: chain w residue 52 ARG Chi-restraints excluded: chain w residue 54 LYS Chi-restraints excluded: chain w residue 57 ILE Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 21 VAL Chi-restraints excluded: chain x residue 34 THR Chi-restraints excluded: chain x residue 37 HIS Chi-restraints excluded: chain z residue 672 LEU Chi-restraints excluded: chain z residue 764 VAL Chi-restraints excluded: chain z residue 765 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 499 optimal weight: 5.9990 chunk 279 optimal weight: 0.9990 chunk 748 optimal weight: 10.0000 chunk 612 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 900 optimal weight: 50.0000 chunk 972 optimal weight: 10.0000 chunk 802 optimal weight: 30.0000 chunk 893 optimal weight: 8.9990 chunk 307 optimal weight: 0.8980 chunk 722 optimal weight: 20.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN F 73 GLN H 57 GLN I 66 ASN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 ASN b 67 GLN ** d 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 59 ASN e 131 HIS f 109 ASN ** i 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN o 18 GLN ** o 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 719 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 156562 Z= 0.253 Angle : 0.673 11.591 234713 Z= 0.345 Chirality : 0.038 0.287 30057 Planarity : 0.005 0.077 12181 Dihedral : 24.522 179.632 79640 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.41 % Favored : 92.53 % Rotamer: Outliers : 8.27 % Allowed : 28.82 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.11), residues: 5342 helix: -0.58 (0.12), residues: 1650 sheet: -1.06 (0.16), residues: 997 loop : -1.91 (0.11), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 103 HIS 0.012 0.001 HIS j 13 PHE 0.030 0.002 PHE j 69 TYR 0.027 0.002 TYR B 54 ARG 0.009 0.001 ARG 2 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1590 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 377 poor density : 1213 time to evaluate : 6.066 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: 0 36 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.6762 (mmt) REVERT: 0 52 LYS cc_start: 0.8528 (mmmm) cc_final: 0.8215 (ttpt) REVERT: 1 1 MET cc_start: 0.8045 (ppp) cc_final: 0.7828 (ppp) REVERT: 1 24 ARG cc_start: 0.8983 (mmp80) cc_final: 0.8740 (mmp80) REVERT: 1 47 GLU cc_start: 0.7894 (pm20) cc_final: 0.7127 (pm20) REVERT: 4 8 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8322 (mtmt) REVERT: 4 31 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8086 (mttm) REVERT: 4 35 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7580 (mttt) REVERT: 6 29 GLU cc_start: 0.7379 (tp30) cc_final: 0.6390 (tp30) REVERT: B 69 PHE cc_start: 0.8326 (m-10) cc_final: 0.7664 (m-80) REVERT: B 89 MET cc_start: 0.6592 (pmm) cc_final: 0.5780 (pmm) REVERT: B 94 GLN cc_start: 0.6108 (mt0) cc_final: 0.5668 (tt0) REVERT: B 132 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8072 (mtpt) REVERT: B 143 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7790 (tpt90) REVERT: C 16 ARG cc_start: 0.7170 (tpp80) cc_final: 0.6862 (ttm-80) REVERT: C 17 ASP cc_start: 0.7643 (t0) cc_final: 0.7302 (t0) REVERT: C 78 LYS cc_start: 0.7050 (tmtt) cc_final: 0.6689 (pttm) REVERT: C 97 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7324 (mtt180) REVERT: C 191 THR cc_start: 0.8318 (p) cc_final: 0.7981 (t) REVERT: D 60 MET cc_start: 0.7804 (ppp) cc_final: 0.7537 (tmm) REVERT: D 68 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8444 (m-80) REVERT: E 149 ARG cc_start: 0.7235 (ttm-80) cc_final: 0.7035 (ttm-80) REVERT: F 5 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.5757 (mp0) REVERT: F 11 ARG cc_start: 0.7501 (pmt-80) cc_final: 0.6747 (pmt-80) REVERT: G 59 MET cc_start: 0.8278 (tpp) cc_final: 0.7886 (tmm) REVERT: H 35 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7896 (pp20) REVERT: H 51 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6744 (m-80) REVERT: H 110 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6278 (mp10) REVERT: J 18 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7928 (mp) REVERT: J 57 LYS cc_start: 0.7669 (pttm) cc_final: 0.7379 (pttm) REVERT: J 64 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7343 (mm-40) REVERT: J 66 GLU cc_start: 0.8294 (pm20) cc_final: 0.8068 (pm20) REVERT: J 87 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6124 (tt) REVERT: J 88 MET cc_start: 0.6875 (tpt) cc_final: 0.6498 (tpp) REVERT: K 29 PHE cc_start: 0.8268 (m-80) cc_final: 0.7701 (m-80) REVERT: K 55 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6989 (mmt-90) REVERT: K 124 ARG cc_start: 0.8781 (mtp-110) cc_final: 0.7968 (ptm160) REVERT: K 127 LYS cc_start: 0.8424 (pptt) cc_final: 0.7807 (pptt) REVERT: L 34 GLU cc_start: 0.7759 (tp30) cc_final: 0.7275 (tt0) REVERT: L 42 GLN cc_start: 0.7758 (mt0) cc_final: 0.7210 (mt0) REVERT: L 53 MET cc_start: 0.6606 (tpp) cc_final: 0.6148 (ttm) REVERT: L 60 SER cc_start: 0.7157 (OUTLIER) cc_final: 0.6926 (t) REVERT: L 94 LEU cc_start: 0.8501 (tp) cc_final: 0.8018 (tp) REVERT: M 35 LYS cc_start: 0.7591 (tptp) cc_final: 0.7390 (tppt) REVERT: N 12 ARG cc_start: 0.6801 (ptt-90) cc_final: 0.6569 (ptt-90) REVERT: O 6 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7569 (tm-30) REVERT: P 33 PHE cc_start: 0.7483 (p90) cc_final: 0.7136 (p90) REVERT: Q 19 MET cc_start: 0.7036 (pmm) cc_final: 0.6232 (ptp) REVERT: Q 39 ARG cc_start: 0.8657 (mtt180) cc_final: 0.8354 (mtt180) REVERT: Q 64 MET cc_start: 0.8673 (tmm) cc_final: 0.7897 (tmm) REVERT: R 30 ASP cc_start: 0.7459 (t0) cc_final: 0.7047 (m-30) REVERT: T 17 ARG cc_start: 0.8487 (ttm170) cc_final: 0.7370 (ttp-170) REVERT: T 45 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: T 57 ARG cc_start: 0.7926 (mmp80) cc_final: 0.7218 (mmt90) REVERT: T 75 TYR cc_start: 0.8795 (m-80) cc_final: 0.8429 (m-80) REVERT: T 78 ARG cc_start: 0.8576 (ptt90) cc_final: 0.8141 (ptt180) REVERT: Z 43 ARG cc_start: 0.8439 (mmt-90) cc_final: 0.7938 (mmt90) REVERT: Z 87 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7300 (ptp-170) REVERT: Z 225 MET cc_start: 0.8044 (mmt) cc_final: 0.7840 (mmt) REVERT: Z 247 MET cc_start: 0.7642 (mtt) cc_final: 0.7188 (mtt) REVERT: Z 261 LYS cc_start: 0.7274 (mmmt) cc_final: 0.6905 (mttp) REVERT: b 131 LEU cc_start: 0.8299 (mp) cc_final: 0.8028 (mp) REVERT: b 138 GLU cc_start: 0.8729 (mp0) cc_final: 0.8477 (pt0) REVERT: b 190 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8283 (tm-30) REVERT: c 33 LYS cc_start: 0.8557 (pttt) cc_final: 0.8031 (ttmt) REVERT: c 37 ASN cc_start: 0.7373 (t0) cc_final: 0.6956 (t0) REVERT: c 38 MET cc_start: 0.7117 (tpp) cc_final: 0.6898 (tmm) REVERT: c 63 GLN cc_start: 0.7637 (pm20) cc_final: 0.7252 (pm20) REVERT: c 96 MET cc_start: 0.7072 (ptm) cc_final: 0.6861 (ppp) REVERT: c 127 ASN cc_start: 0.8252 (m-40) cc_final: 0.7857 (m110) REVERT: c 128 TYR cc_start: 0.6928 (t80) cc_final: 0.6632 (t80) REVERT: c 148 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7275 (ttpt) REVERT: c 163 ASP cc_start: 0.7831 (m-30) cc_final: 0.7179 (t0) REVERT: d 84 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7416 (m-10) REVERT: e 13 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8231 (mp0) REVERT: f 108 GLU cc_start: 0.7593 (pm20) cc_final: 0.7346 (mm-30) REVERT: i 80 ASP cc_start: 0.7784 (p0) cc_final: 0.7336 (t0) REVERT: k 28 GLU cc_start: 0.8544 (pm20) cc_final: 0.8170 (pm20) REVERT: l 27 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7418 (pp20) REVERT: l 76 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7770 (mmmt) REVERT: l 79 GLU cc_start: 0.8470 (pp20) cc_final: 0.7937 (mm-30) REVERT: m 24 ASP cc_start: 0.8255 (m-30) cc_final: 0.7689 (m-30) REVERT: m 31 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6997 (ptpp) REVERT: m 98 TYR cc_start: 0.8991 (m-80) cc_final: 0.8694 (m-80) REVERT: n 101 ASN cc_start: 0.7118 (OUTLIER) cc_final: 0.6559 (t0) REVERT: o 31 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7577 (tm-30) REVERT: o 71 ILE cc_start: 0.9234 (mm) cc_final: 0.8670 (tt) REVERT: r 16 LYS cc_start: 0.9052 (mttp) cc_final: 0.8728 (mttt) REVERT: r 48 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8600 (tm-30) REVERT: r 64 MET cc_start: 0.7737 (mpp) cc_final: 0.7378 (mtm) REVERT: s 10 ARG cc_start: 0.7161 (ptt180) cc_final: 0.6311 (ptp-110) REVERT: s 15 GLU cc_start: 0.8575 (tp30) cc_final: 0.8200 (tp30) REVERT: u 48 GLN cc_start: 0.7413 (pt0) cc_final: 0.7045 (pt0) REVERT: u 85 LYS cc_start: 0.8483 (mmtp) cc_final: 0.7913 (mttp) REVERT: v 18 ARG cc_start: 0.8546 (mmt90) cc_final: 0.8278 (mmt90) REVERT: w 27 ASN cc_start: 0.8896 (m-40) cc_final: 0.8663 (m-40) REVERT: w 47 ARG cc_start: 0.8178 (ptm-80) cc_final: 0.7743 (ptm-80) REVERT: w 54 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7436 (mptm) REVERT: w 59 GLU cc_start: 0.8808 (pt0) cc_final: 0.8454 (pt0) REVERT: x 11 SER cc_start: 0.8680 (t) cc_final: 0.7992 (p) REVERT: x 38 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7950 (tm-30) REVERT: x 47 ILE cc_start: 0.9033 (mm) cc_final: 0.8787 (pt) REVERT: z 765 LYS cc_start: 0.5343 (OUTLIER) cc_final: 0.5094 (tppt) outliers start: 377 outliers final: 239 residues processed: 1419 average time/residue: 1.2274 time to fit residues: 3050.1165 Evaluate side-chains 1359 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1100 time to evaluate : 7.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 MET Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 0 residue 55 ASN Chi-restraints excluded: chain 1 residue 9 CYS Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 17 THR Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 23 VAL Chi-restraints excluded: chain 4 residue 31 LYS Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 31 VAL Chi-restraints excluded: chain 6 residue 59 PHE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 5 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 55 PHE Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 PHE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 30 ASN Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 4 LYS Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 69 HIS Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 87 ARG Chi-restraints excluded: chain Z residue 146 LEU Chi-restraints excluded: chain Z residue 157 SER Chi-restraints excluded: chain Z residue 167 LYS Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain a residue 137 SER Chi-restraints excluded: chain a residue 145 SER Chi-restraints excluded: chain a residue 177 VAL Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 39 MET Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 156 THR Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 45 GLN Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain c residue 77 PHE Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 101 ASP Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain c residue 162 THR Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 35 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 84 PHE Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 59 ASN Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain f residue 35 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 51 VAL Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 89 ASP Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 61 LEU Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 123 VAL Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 42 ILE Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain k residue 9 THR Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 78 ASP Chi-restraints excluded: chain k residue 110 ASP Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 81 VAL Chi-restraints excluded: chain l residue 84 ARG Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 31 LYS Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 74 PHE Chi-restraints excluded: chain m residue 78 THR Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 86 VAL Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 101 ASN Chi-restraints excluded: chain n residue 118 ASN Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 93 THR Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 38 LEU Chi-restraints excluded: chain r residue 44 SER Chi-restraints excluded: chain r residue 67 ASN Chi-restraints excluded: chain r residue 77 ASP Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain s residue 12 VAL Chi-restraints excluded: chain s residue 14 THR Chi-restraints excluded: chain s residue 44 GLU Chi-restraints excluded: chain s residue 58 ASN Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain u residue 18 THR Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 65 ASP Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 72 ASP Chi-restraints excluded: chain u residue 75 VAL Chi-restraints excluded: chain v residue 7 ILE Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 16 ASN Chi-restraints excluded: chain v residue 59 VAL Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 18 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 30 PHE Chi-restraints excluded: chain w residue 52 ARG Chi-restraints excluded: chain w residue 54 LYS Chi-restraints excluded: chain w residue 57 ILE Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 37 HIS Chi-restraints excluded: chain x residue 48 ASN Chi-restraints excluded: chain z residue 672 LEU Chi-restraints excluded: chain z residue 750 LEU Chi-restraints excluded: chain z residue 764 VAL Chi-restraints excluded: chain z residue 765 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 889 optimal weight: 10.0000 chunk 677 optimal weight: 10.0000 chunk 467 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 429 optimal weight: 7.9990 chunk 604 optimal weight: 10.0000 chunk 903 optimal weight: 50.0000 chunk 956 optimal weight: 10.0000 chunk 472 optimal weight: 0.9990 chunk 856 optimal weight: 10.0000 chunk 257 optimal weight: 0.4980 overall best weight: 5.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 55 ASN ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 GLN H 57 GLN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 37 ASN M 32 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN ** o 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 156562 Z= 0.278 Angle : 0.689 11.846 234713 Z= 0.352 Chirality : 0.038 0.285 30057 Planarity : 0.005 0.066 12181 Dihedral : 24.464 179.115 79638 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.88 % Favored : 92.08 % Rotamer: Outliers : 9.20 % Allowed : 29.26 % Favored : 61.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.11), residues: 5342 helix: -0.46 (0.12), residues: 1652 sheet: -1.15 (0.15), residues: 1028 loop : -1.91 (0.11), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 103 HIS 0.008 0.001 HIS j 13 PHE 0.024 0.002 PHE c 138 TYR 0.024 0.002 TYR B 54 ARG 0.011 0.001 ARG O 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1593 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 419 poor density : 1174 time to evaluate : 7.966 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: 0 52 LYS cc_start: 0.8521 (mmmm) cc_final: 0.8143 (ttpt) REVERT: 1 32 PHE cc_start: 0.8216 (m-80) cc_final: 0.7708 (m-80) REVERT: 1 47 GLU cc_start: 0.7697 (pm20) cc_final: 0.7405 (pm20) REVERT: 3 60 GLN cc_start: 0.8347 (tp-100) cc_final: 0.8134 (tp-100) REVERT: 4 12 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8443 (mm-30) REVERT: 4 31 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8039 (mttm) REVERT: 4 35 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7664 (mttt) REVERT: 6 29 GLU cc_start: 0.7594 (tp30) cc_final: 0.6686 (tp30) REVERT: B 24 ASN cc_start: 0.8642 (t0) cc_final: 0.8267 (m-40) REVERT: B 69 PHE cc_start: 0.8374 (m-10) cc_final: 0.7581 (m-10) REVERT: B 89 MET cc_start: 0.6681 (pmm) cc_final: 0.5858 (pmm) REVERT: B 94 GLN cc_start: 0.5862 (mt0) cc_final: 0.5331 (tt0) REVERT: B 132 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8233 (mtpt) REVERT: B 143 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.7864 (tpt90) REVERT: C 16 ARG cc_start: 0.7117 (tpp80) cc_final: 0.6786 (ttm-80) REVERT: C 17 ASP cc_start: 0.7613 (t0) cc_final: 0.7151 (t0) REVERT: C 78 LYS cc_start: 0.7088 (tmtt) cc_final: 0.6763 (pttm) REVERT: C 97 ARG cc_start: 0.7623 (mtm-85) cc_final: 0.7290 (mtt180) REVERT: C 111 ASP cc_start: 0.7195 (m-30) cc_final: 0.6824 (m-30) REVERT: C 122 GLN cc_start: 0.8151 (mp10) cc_final: 0.7895 (mp10) REVERT: C 191 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8012 (t) REVERT: D 46 GLU cc_start: 0.8522 (tp30) cc_final: 0.8320 (tp30) REVERT: D 60 MET cc_start: 0.7851 (ppp) cc_final: 0.7495 (tmm) REVERT: D 68 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: E 15 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8292 (tp) REVERT: E 73 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8401 (tm-30) REVERT: E 84 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8072 (pp20) REVERT: E 142 GLN cc_start: 0.8982 (tp40) cc_final: 0.8769 (tp40) REVERT: E 149 ARG cc_start: 0.7175 (ttm-80) cc_final: 0.6878 (mtp-110) REVERT: G 53 ARG cc_start: 0.6538 (mmt180) cc_final: 0.6053 (mmt90) REVERT: G 120 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8581 (mp) REVERT: H 51 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6756 (m-80) REVERT: H 98 LEU cc_start: 0.7225 (mt) cc_final: 0.6890 (mt) REVERT: J 63 GLU cc_start: 0.7491 (tp30) cc_final: 0.7020 (tp30) REVERT: J 64 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7490 (mm-40) REVERT: J 88 MET cc_start: 0.6935 (tpt) cc_final: 0.6542 (tpp) REVERT: K 29 PHE cc_start: 0.8261 (m-80) cc_final: 0.7645 (m-80) REVERT: K 124 ARG cc_start: 0.8790 (mtp-110) cc_final: 0.8043 (ptm160) REVERT: K 127 LYS cc_start: 0.8606 (pptt) cc_final: 0.7921 (pptt) REVERT: K 131 VAL cc_start: 0.8477 (t) cc_final: 0.8205 (p) REVERT: L 34 GLU cc_start: 0.7727 (tp30) cc_final: 0.7305 (tt0) REVERT: L 53 MET cc_start: 0.6808 (tpp) cc_final: 0.6596 (ttm) REVERT: L 58 PRO cc_start: 0.6932 (OUTLIER) cc_final: 0.6696 (Cg_endo) REVERT: L 65 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6625 (p90) REVERT: L 69 ARG cc_start: 0.7009 (ttm110) cc_final: 0.6561 (tpt-90) REVERT: L 94 LEU cc_start: 0.8504 (tp) cc_final: 0.8208 (tt) REVERT: M 35 LYS cc_start: 0.7608 (tptp) cc_final: 0.7388 (tppt) REVERT: M 95 LEU cc_start: 0.8263 (mm) cc_final: 0.8005 (mp) REVERT: O 6 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7593 (tm-30) REVERT: O 41 GLU cc_start: 0.8566 (mp0) cc_final: 0.8293 (mp0) REVERT: O 44 ARG cc_start: 0.8791 (ttm110) cc_final: 0.8309 (mtm110) REVERT: Q 19 MET cc_start: 0.7094 (pmm) cc_final: 0.6497 (ptp) REVERT: Q 64 MET cc_start: 0.8693 (tmm) cc_final: 0.7825 (tmm) REVERT: R 30 ASP cc_start: 0.7738 (t0) cc_final: 0.7222 (m-30) REVERT: S 36 ARG cc_start: 0.6785 (ptm160) cc_final: 0.6139 (ptm-80) REVERT: T 45 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7315 (m-30) REVERT: T 57 ARG cc_start: 0.7945 (mmp80) cc_final: 0.7227 (mmt90) REVERT: Z 43 ARG cc_start: 0.8385 (mmt-90) cc_final: 0.7892 (mmt90) REVERT: Z 87 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7540 (ptp-170) REVERT: Z 225 MET cc_start: 0.8157 (mmt) cc_final: 0.7946 (mmt) REVERT: Z 261 LYS cc_start: 0.7293 (mmmt) cc_final: 0.6938 (tptt) REVERT: a 133 MET cc_start: 0.8840 (tpp) cc_final: 0.8559 (mmm) REVERT: b 37 ILE cc_start: 0.9391 (mm) cc_final: 0.9130 (mt) REVERT: b 62 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7601 (ptp90) REVERT: b 83 TRP cc_start: 0.9281 (m100) cc_final: 0.9011 (m100) REVERT: b 190 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8348 (tm-30) REVERT: c 17 MET cc_start: 0.8835 (ppp) cc_final: 0.8431 (ppp) REVERT: c 26 MET cc_start: 0.7768 (tmm) cc_final: 0.7503 (tmm) REVERT: c 33 LYS cc_start: 0.8554 (pttt) cc_final: 0.8096 (ttmt) REVERT: c 37 ASN cc_start: 0.7534 (t0) cc_final: 0.7124 (t0) REVERT: c 63 GLN cc_start: 0.7562 (pm20) cc_final: 0.7258 (pm20) REVERT: c 96 MET cc_start: 0.7141 (ptm) cc_final: 0.6922 (ppp) REVERT: c 112 ARG cc_start: 0.6547 (ttt180) cc_final: 0.6122 (ttt-90) REVERT: c 127 ASN cc_start: 0.8309 (m-40) cc_final: 0.7969 (m110) REVERT: c 148 LYS cc_start: 0.8100 (mmtm) cc_final: 0.7279 (ttpt) REVERT: c 153 ASP cc_start: 0.7977 (t0) cc_final: 0.7728 (t0) REVERT: d 65 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7878 (pp) REVERT: d 84 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7189 (m-10) REVERT: d 140 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7495 (tt0) REVERT: e 13 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8204 (mp0) REVERT: f 108 GLU cc_start: 0.7582 (pm20) cc_final: 0.7354 (mm-30) REVERT: i 51 GLU cc_start: 0.8765 (pt0) cc_final: 0.8553 (pt0) REVERT: i 80 ASP cc_start: 0.7849 (p0) cc_final: 0.7368 (t0) REVERT: j 63 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8073 (pttp) REVERT: j 79 LEU cc_start: 0.8490 (tt) cc_final: 0.8266 (tt) REVERT: k 19 ASP cc_start: 0.7283 (t0) cc_final: 0.7014 (t0) REVERT: k 50 LEU cc_start: 0.8916 (tp) cc_final: 0.8621 (tt) REVERT: l 76 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7812 (mmmt) REVERT: l 79 GLU cc_start: 0.8328 (pp20) cc_final: 0.7784 (mm-30) REVERT: m 31 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6978 (ptpp) REVERT: m 62 ARG cc_start: 0.7233 (ttt-90) cc_final: 0.7025 (ttt-90) REVERT: m 94 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8358 (mmp80) REVERT: m 98 TYR cc_start: 0.8979 (m-80) cc_final: 0.8648 (m-80) REVERT: n 57 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: n 94 MET cc_start: 0.7956 (ttm) cc_final: 0.7360 (ttm) REVERT: n 101 ASN cc_start: 0.6906 (OUTLIER) cc_final: 0.6631 (t0) REVERT: o 31 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7651 (tm-30) REVERT: o 71 ILE cc_start: 0.9283 (mm) cc_final: 0.8699 (tt) REVERT: o 75 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.7915 (mmt90) REVERT: r 16 LYS cc_start: 0.9052 (mttp) cc_final: 0.8759 (mttt) REVERT: r 48 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8778 (tm-30) REVERT: r 61 ASN cc_start: 0.7678 (t0) cc_final: 0.7438 (t0) REVERT: r 64 MET cc_start: 0.7803 (mpp) cc_final: 0.7459 (mtm) REVERT: s 10 ARG cc_start: 0.7261 (ptt180) cc_final: 0.6367 (ptp-110) REVERT: s 15 GLU cc_start: 0.8635 (tp30) cc_final: 0.8206 (tp30) REVERT: s 38 GLU cc_start: 0.8409 (pm20) cc_final: 0.8177 (pm20) REVERT: u 48 GLN cc_start: 0.7477 (pt0) cc_final: 0.7131 (pt0) REVERT: u 85 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7995 (mttp) REVERT: v 22 MET cc_start: 0.7132 (mtt) cc_final: 0.6425 (mmm) REVERT: w 27 ASN cc_start: 0.8946 (m-40) cc_final: 0.8729 (m-40) REVERT: w 37 LEU cc_start: 0.8904 (tp) cc_final: 0.8524 (tt) REVERT: w 38 GLU cc_start: 0.8835 (mp0) cc_final: 0.7964 (tm-30) REVERT: w 47 ARG cc_start: 0.8290 (ptm-80) cc_final: 0.7852 (ptm-80) REVERT: w 52 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7882 (mtp85) REVERT: w 55 THR cc_start: 0.8373 (m) cc_final: 0.8069 (p) REVERT: x 11 SER cc_start: 0.8689 (t) cc_final: 0.8010 (p) REVERT: x 32 ASN cc_start: 0.8043 (m-40) cc_final: 0.7660 (m110) REVERT: x 47 ILE cc_start: 0.9051 (mm) cc_final: 0.8781 (pt) REVERT: z 765 LYS cc_start: 0.5345 (OUTLIER) cc_final: 0.5036 (tppt) outliers start: 419 outliers final: 307 residues processed: 1421 average time/residue: 1.2722 time to fit residues: 3194.8297 Evaluate side-chains 1459 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 1129 time to evaluate : 5.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 THR Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 17 THR Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 23 VAL Chi-restraints excluded: chain 4 residue 31 LYS Chi-restraints excluded: chain 6 residue 5 ILE Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 31 VAL Chi-restraints excluded: chain 6 residue 59 PHE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 55 PHE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 51 PHE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 30 ASN Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 58 PRO Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 TYR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 32 GLN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 4 LYS Chi-restraints excluded: chain N residue 20 GLU Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 42 ASN Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 53 HIS Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 87 ARG Chi-restraints excluded: chain Z residue 93 LEU Chi-restraints excluded: chain Z residue 146 LEU Chi-restraints excluded: chain Z residue 157 SER Chi-restraints excluded: chain Z residue 167 LYS Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain Z residue 241 ILE Chi-restraints excluded: chain Z residue 257 PHE Chi-restraints excluded: chain Z residue 270 ILE Chi-restraints excluded: chain Z residue 271 VAL Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 50 GLN Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain a residue 137 SER Chi-restraints excluded: chain a residue 145 SER Chi-restraints excluded: chain a residue 167 GLU Chi-restraints excluded: chain a residue 177 VAL Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 40 GLN Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 156 THR Chi-restraints excluded: chain b residue 185 ASP Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 2 ASN Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain c residue 45 GLN Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain c residue 77 PHE Chi-restraints excluded: chain c residue 90 THR Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 101 ASP Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain c residue 162 THR Chi-restraints excluded: chain c residue 172 GLN Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 84 PHE Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 114 VAL Chi-restraints excluded: chain d residue 116 ILE Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 35 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 89 ASP Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 61 LEU Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 123 VAL Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 37 LEU Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 42 ILE Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 63 LYS Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 9 THR Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 23 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 110 ASP Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 81 VAL Chi-restraints excluded: chain l residue 84 ARG Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain m residue 31 LYS Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 78 THR Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 86 VAL Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 55 ARG Chi-restraints excluded: chain n residue 57 PHE Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 101 ASN Chi-restraints excluded: chain n residue 118 ASN Chi-restraints excluded: chain o residue 19 THR Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 93 THR Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 44 SER Chi-restraints excluded: chain r residue 67 ASN Chi-restraints excluded: chain r residue 71 ILE Chi-restraints excluded: chain r residue 77 ASP Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 107 VAL Chi-restraints excluded: chain s residue 12 VAL Chi-restraints excluded: chain s residue 14 THR Chi-restraints excluded: chain s residue 44 GLU Chi-restraints excluded: chain s residue 46 ILE Chi-restraints excluded: chain s residue 58 ASN Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain t residue 71 LEU Chi-restraints excluded: chain u residue 18 THR Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 65 ASP Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 72 ASP Chi-restraints excluded: chain u residue 75 VAL Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain u residue 87 VAL Chi-restraints excluded: chain v residue 7 ILE Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 16 ASN Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 18 VAL Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 52 ARG Chi-restraints excluded: chain w residue 57 ILE Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 21 VAL Chi-restraints excluded: chain x residue 34 THR Chi-restraints excluded: chain x residue 37 HIS Chi-restraints excluded: chain x residue 48 ASN Chi-restraints excluded: chain z residue 672 LEU Chi-restraints excluded: chain z residue 684 ILE Chi-restraints excluded: chain z residue 750 LEU Chi-restraints excluded: chain z residue 764 VAL Chi-restraints excluded: chain z residue 765 LYS Chi-restraints excluded: chain z residue 781 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 796 optimal weight: 30.0000 chunk 543 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 712 optimal weight: 10.0000 chunk 394 optimal weight: 0.0970 chunk 816 optimal weight: 10.0000 chunk 661 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 488 optimal weight: 10.0000 chunk 858 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 overall best weight: 6.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 GLN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 37 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 GLN ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 HIS e 59 ASN ** i 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN k 68 ASN n 72 ASN ** n 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 156562 Z= 0.321 Angle : 0.726 10.608 234713 Z= 0.369 Chirality : 0.040 0.341 30057 Planarity : 0.005 0.061 12181 Dihedral : 24.478 179.469 79634 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.63 % Favored : 91.33 % Rotamer: Outliers : 10.45 % Allowed : 28.62 % Favored : 60.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.11), residues: 5342 helix: -0.45 (0.12), residues: 1653 sheet: -1.18 (0.15), residues: 1058 loop : -1.99 (0.11), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP j 65 HIS 0.008 0.002 HIS D 59 PHE 0.026 0.002 PHE j 69 TYR 0.027 0.002 TYR B 54 ARG 0.015 0.001 ARG m 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1640 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 476 poor density : 1164 time to evaluate : 5.324 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: 0 27 MET cc_start: 0.8654 (mtm) cc_final: 0.8417 (mtm) REVERT: 0 36 MET cc_start: 0.7930 (mmt) cc_final: 0.7606 (mmt) REVERT: 0 52 LYS cc_start: 0.8527 (mmmm) cc_final: 0.8137 (ttpt) REVERT: 1 32 PHE cc_start: 0.8296 (m-80) cc_final: 0.7793 (m-80) REVERT: 1 47 GLU cc_start: 0.7675 (pm20) cc_final: 0.7423 (pm20) REVERT: 4 8 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8200 (mtpt) REVERT: 4 31 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7540 (mttm) REVERT: 4 35 LYS cc_start: 0.8264 (mtmt) cc_final: 0.7884 (mttt) REVERT: 6 29 GLU cc_start: 0.7577 (tp30) cc_final: 0.6831 (tp30) REVERT: B 24 ASN cc_start: 0.8553 (t0) cc_final: 0.8270 (m-40) REVERT: B 28 LYS cc_start: 0.4115 (OUTLIER) cc_final: 0.2609 (mmtm) REVERT: B 69 PHE cc_start: 0.8380 (m-10) cc_final: 0.7409 (m-10) REVERT: B 89 MET cc_start: 0.6643 (pmm) cc_final: 0.5346 (pmm) REVERT: B 94 GLN cc_start: 0.5858 (mt0) cc_final: 0.5305 (tt0) REVERT: B 132 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8212 (mtpt) REVERT: C 16 ARG cc_start: 0.7344 (tpp80) cc_final: 0.7049 (ttt90) REVERT: C 17 ASP cc_start: 0.7815 (t0) cc_final: 0.7300 (t0) REVERT: C 74 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.4786 (ppp) REVERT: C 78 LYS cc_start: 0.7103 (tmtt) cc_final: 0.6785 (pttm) REVERT: C 97 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.7182 (mtt180) REVERT: C 111 ASP cc_start: 0.7369 (m-30) cc_final: 0.6996 (m-30) REVERT: D 60 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7497 (tmm) REVERT: D 68 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: D 120 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.5945 (tp) REVERT: E 15 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8303 (tp) REVERT: E 73 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8373 (tm-30) REVERT: E 84 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8231 (pp20) REVERT: E 136 MET cc_start: 0.8951 (mmt) cc_final: 0.8690 (mmt) REVERT: E 149 ARG cc_start: 0.7094 (ttm-80) cc_final: 0.6805 (mtp-110) REVERT: G 120 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8582 (mp) REVERT: H 19 MET cc_start: 0.8386 (ptm) cc_final: 0.7612 (ptt) REVERT: H 51 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6861 (m-80) REVERT: H 90 LYS cc_start: 0.6317 (mmtt) cc_final: 0.5390 (mmtm) REVERT: H 110 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6768 (mp10) REVERT: I 41 SER cc_start: 0.7923 (m) cc_final: 0.7429 (p) REVERT: I 107 ASP cc_start: 0.5999 (OUTLIER) cc_final: 0.5767 (p0) REVERT: J 63 GLU cc_start: 0.7529 (tp30) cc_final: 0.6787 (tp30) REVERT: J 64 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7537 (mm-40) REVERT: J 66 GLU cc_start: 0.8384 (pm20) cc_final: 0.8151 (pm20) REVERT: J 88 MET cc_start: 0.7289 (tpt) cc_final: 0.6992 (tpp) REVERT: K 29 PHE cc_start: 0.8223 (m-80) cc_final: 0.7584 (m-80) REVERT: K 124 ARG cc_start: 0.8819 (mtp-110) cc_final: 0.8017 (ptm160) REVERT: K 127 LYS cc_start: 0.8672 (pptt) cc_final: 0.8213 (pptt) REVERT: L 34 GLU cc_start: 0.7833 (tp30) cc_final: 0.7387 (tt0) REVERT: L 69 ARG cc_start: 0.7048 (ttm110) cc_final: 0.6735 (tpt-90) REVERT: M 61 ASP cc_start: 0.8258 (t0) cc_final: 0.7622 (m-30) REVERT: M 95 LEU cc_start: 0.8369 (mm) cc_final: 0.8159 (mp) REVERT: O 6 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7556 (tm-30) REVERT: O 41 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: O 44 ARG cc_start: 0.8789 (ttm110) cc_final: 0.8366 (mtm110) REVERT: O 80 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6861 (mt-10) REVERT: Q 64 MET cc_start: 0.8702 (tmm) cc_final: 0.7857 (tmm) REVERT: R 19 THR cc_start: 0.7913 (p) cc_final: 0.7645 (t) REVERT: S 20 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: S 36 ARG cc_start: 0.6674 (ptm160) cc_final: 0.6032 (ptm-80) REVERT: S 66 MET cc_start: 0.8544 (mmm) cc_final: 0.8325 (tpp) REVERT: T 17 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.7883 (ttm170) REVERT: T 45 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: T 57 ARG cc_start: 0.7984 (mmp80) cc_final: 0.7017 (mmt90) REVERT: T 78 ARG cc_start: 0.8622 (ptt90) cc_final: 0.8101 (ptt180) REVERT: Z 43 ARG cc_start: 0.8333 (mmt-90) cc_final: 0.7910 (mmt90) REVERT: Z 87 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7457 (ptp-170) REVERT: Z 225 MET cc_start: 0.8223 (mmt) cc_final: 0.7954 (mmt) REVERT: Z 261 LYS cc_start: 0.7289 (mmmt) cc_final: 0.6955 (tptt) REVERT: b 37 ILE cc_start: 0.9336 (mm) cc_final: 0.9112 (mt) REVERT: b 58 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.9038 (tpp80) REVERT: b 62 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7753 (ptp90) REVERT: b 83 TRP cc_start: 0.9254 (m100) cc_final: 0.8974 (m100) REVERT: b 190 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8352 (tm-30) REVERT: c 33 LYS cc_start: 0.8500 (pttt) cc_final: 0.8000 (ttmt) REVERT: c 37 ASN cc_start: 0.7612 (t0) cc_final: 0.7113 (t0) REVERT: c 63 GLN cc_start: 0.7669 (pm20) cc_final: 0.7260 (pm20) REVERT: c 112 ARG cc_start: 0.6538 (ttt180) cc_final: 0.6127 (ttt-90) REVERT: c 148 LYS cc_start: 0.8075 (mmtm) cc_final: 0.7096 (ttpt) REVERT: c 153 ASP cc_start: 0.7834 (t0) cc_final: 0.7610 (t0) REVERT: d 84 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7302 (m-10) REVERT: e 13 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8219 (mp0) REVERT: i 51 GLU cc_start: 0.8681 (pt0) cc_final: 0.8047 (pt0) REVERT: l 76 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7775 (mmmt) REVERT: l 79 GLU cc_start: 0.8358 (pp20) cc_final: 0.7849 (mm-30) REVERT: m 31 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.7057 (ptpp) REVERT: m 65 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7902 (p) REVERT: m 80 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7478 (ptpp) REVERT: m 94 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8394 (mmp80) REVERT: m 98 TYR cc_start: 0.8986 (m-80) cc_final: 0.8714 (m-80) REVERT: m 104 ARG cc_start: 0.8040 (tpp80) cc_final: 0.7763 (tpp80) REVERT: n 55 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7625 (ptp-170) REVERT: n 57 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8265 (m-80) REVERT: n 94 MET cc_start: 0.7928 (ttm) cc_final: 0.7129 (ttm) REVERT: n 101 ASN cc_start: 0.6919 (OUTLIER) cc_final: 0.6544 (t0) REVERT: o 31 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: o 44 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6489 (t0) REVERT: r 48 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8785 (tm-30) REVERT: r 61 ASN cc_start: 0.7591 (t0) cc_final: 0.7310 (t0) REVERT: s 2 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7906 (mmmt) REVERT: s 3 ASP cc_start: 0.8047 (m-30) cc_final: 0.7478 (m-30) REVERT: s 6 ASP cc_start: 0.8588 (p0) cc_final: 0.8385 (p0) REVERT: s 10 ARG cc_start: 0.7308 (ptt180) cc_final: 0.6389 (ptp-110) REVERT: s 15 GLU cc_start: 0.8654 (tp30) cc_final: 0.8129 (tp30) REVERT: s 31 ASP cc_start: 0.8688 (t0) cc_final: 0.8469 (t0) REVERT: s 38 GLU cc_start: 0.8415 (pm20) cc_final: 0.8132 (pm20) REVERT: u 35 ASP cc_start: 0.7757 (t0) cc_final: 0.6940 (p0) REVERT: u 48 GLN cc_start: 0.7469 (pt0) cc_final: 0.7119 (pt0) REVERT: u 85 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8060 (mttp) REVERT: v 22 MET cc_start: 0.7273 (mtt) cc_final: 0.6594 (mmm) REVERT: v 43 LYS cc_start: 0.6319 (ptpp) cc_final: 0.5393 (mtmm) REVERT: w 5 GLU cc_start: 0.8765 (mp0) cc_final: 0.8445 (mp0) REVERT: w 27 ASN cc_start: 0.8956 (m-40) cc_final: 0.8755 (m-40) REVERT: w 42 ARG cc_start: 0.8446 (tpt90) cc_final: 0.7942 (tpp80) REVERT: w 45 GLU cc_start: 0.9187 (tp30) cc_final: 0.8970 (tp30) REVERT: w 47 ARG cc_start: 0.8290 (ptm-80) cc_final: 0.7820 (ptm-80) REVERT: w 52 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7809 (mtp85) REVERT: x 11 SER cc_start: 0.8744 (t) cc_final: 0.8016 (p) REVERT: x 32 ASN cc_start: 0.8032 (m-40) cc_final: 0.7607 (m110) REVERT: z 716 ARG cc_start: 0.5330 (OUTLIER) cc_final: 0.4991 (mmm-85) REVERT: z 765 LYS cc_start: 0.5131 (OUTLIER) cc_final: 0.4908 (tppt) outliers start: 476 outliers final: 340 residues processed: 1445 average time/residue: 1.2232 time to fit residues: 3096.7242 Evaluate side-chains 1486 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 375 poor density : 1111 time to evaluate : 5.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 MET Chi-restraints excluded: chain 0 residue 18 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 0 residue 55 ASN Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 17 THR Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 23 VAL Chi-restraints excluded: chain 4 residue 31 LYS Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 31 VAL Chi-restraints excluded: chain 6 residue 39 CYS Chi-restraints excluded: chain 6 residue 59 PHE Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 55 PHE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 142 HIS Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 51 PHE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 30 ASN Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 4 LYS Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 20 GLU Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 41 GLU Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 42 ASN Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 53 HIS Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 87 ARG Chi-restraints excluded: chain Z residue 93 LEU Chi-restraints excluded: chain Z residue 146 LEU Chi-restraints excluded: chain Z residue 157 SER Chi-restraints excluded: chain Z residue 167 LYS Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain Z residue 257 PHE Chi-restraints excluded: chain Z residue 271 VAL Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 50 GLN Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 97 VAL Chi-restraints excluded: chain a residue 137 SER Chi-restraints excluded: chain a residue 145 SER Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 167 GLU Chi-restraints excluded: chain a residue 176 ILE Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 40 GLN Chi-restraints excluded: chain b residue 58 ARG Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 185 ASP Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 2 ASN Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain c residue 45 GLN Chi-restraints excluded: chain c residue 57 LEU Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 101 ASP Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain c residue 162 THR Chi-restraints excluded: chain c residue 172 GLN Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 35 THR Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 84 PHE Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 114 VAL Chi-restraints excluded: chain d residue 116 ILE Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 59 ASN Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 35 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 66 LYS Chi-restraints excluded: chain f residue 89 ASP Chi-restraints excluded: chain f residue 122 ILE Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 61 LEU Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 69 ILE Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 109 VAL Chi-restraints excluded: chain i residue 123 VAL Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 17 MET Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 42 ILE Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 81 VAL Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 9 THR Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 23 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 42 SER Chi-restraints excluded: chain k residue 83 LEU Chi-restraints excluded: chain k residue 110 ASP Chi-restraints excluded: chain l residue 17 ARG Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 75 THR Chi-restraints excluded: chain l residue 81 VAL Chi-restraints excluded: chain l residue 84 ARG Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain m residue 31 LYS Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 78 THR Chi-restraints excluded: chain m residue 80 LYS Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 86 VAL Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 55 ARG Chi-restraints excluded: chain n residue 57 PHE Chi-restraints excluded: chain n residue 97 ASP Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 101 ASN Chi-restraints excluded: chain n residue 118 ASN Chi-restraints excluded: chain o residue 19 THR Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 44 ASP Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 93 THR Chi-restraints excluded: chain r residue 12 ILE Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 44 SER Chi-restraints excluded: chain r residue 48 GLU Chi-restraints excluded: chain r residue 67 ASN Chi-restraints excluded: chain r residue 71 ILE Chi-restraints excluded: chain r residue 77 ASP Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 107 VAL Chi-restraints excluded: chain s residue 7 VAL Chi-restraints excluded: chain s residue 12 VAL Chi-restraints excluded: chain s residue 14 THR Chi-restraints excluded: chain s residue 44 GLU Chi-restraints excluded: chain s residue 46 ILE Chi-restraints excluded: chain s residue 58 ASN Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain t residue 36 GLU Chi-restraints excluded: chain t residue 71 LEU Chi-restraints excluded: chain u residue 18 THR Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 65 ASP Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 72 ASP Chi-restraints excluded: chain u residue 75 VAL Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain u residue 87 VAL Chi-restraints excluded: chain v residue 7 ILE Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 16 ASN Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 18 VAL Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 52 ARG Chi-restraints excluded: chain w residue 57 ILE Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 34 THR Chi-restraints excluded: chain x residue 48 ASN Chi-restraints excluded: chain z residue 672 LEU Chi-restraints excluded: chain z residue 684 ILE Chi-restraints excluded: chain z residue 716 ARG Chi-restraints excluded: chain z residue 750 LEU Chi-restraints excluded: chain z residue 764 VAL Chi-restraints excluded: chain z residue 765 LYS Chi-restraints excluded: chain z residue 780 THR Chi-restraints excluded: chain z residue 781 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 321 optimal weight: 50.0000 chunk 861 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 561 optimal weight: 5.9990 chunk 236 optimal weight: 0.0170 chunk 957 optimal weight: 10.0000 chunk 795 optimal weight: 20.0000 chunk 443 optimal weight: 8.9990 chunk 79 optimal weight: 30.0000 chunk 316 optimal weight: 4.9990 chunk 502 optimal weight: 0.0770 overall best weight: 3.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 6 GLN ** 6 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN F 73 GLN I 81 HIS K 42 ASN K 79 HIS ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 40 GLN ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN k 68 ASN ** n 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 18 GLN ** v 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 156562 Z= 0.208 Angle : 0.640 12.923 234713 Z= 0.327 Chirality : 0.037 0.350 30057 Planarity : 0.005 0.077 12181 Dihedral : 24.395 179.237 79634 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.94 % Favored : 93.02 % Rotamer: Outliers : 8.52 % Allowed : 31.19 % Favored : 60.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.11), residues: 5342 helix: -0.28 (0.12), residues: 1658 sheet: -1.16 (0.16), residues: 997 loop : -1.94 (0.11), residues: 2687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 200 HIS 0.007 0.001 HIS j 13 PHE 0.021 0.002 PHE c 138 TYR 0.025 0.002 TYR B 54 ARG 0.014 0.001 ARG E 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1586 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 1198 time to evaluate : 5.938 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: 0 52 LYS cc_start: 0.8529 (mmmm) cc_final: 0.8135 (ttpt) REVERT: 1 32 PHE cc_start: 0.8260 (m-80) cc_final: 0.7771 (m-80) REVERT: 1 47 GLU cc_start: 0.7601 (pm20) cc_final: 0.7036 (pm20) REVERT: 4 8 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8184 (mtpt) REVERT: 4 31 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8060 (mttm) REVERT: 6 29 GLU cc_start: 0.7578 (tp30) cc_final: 0.6706 (tp30) REVERT: B 9 LEU cc_start: 0.5045 (OUTLIER) cc_final: 0.4479 (mp) REVERT: B 24 ASN cc_start: 0.8556 (m-40) cc_final: 0.8183 (m-40) REVERT: B 28 LYS cc_start: 0.3587 (OUTLIER) cc_final: 0.3181 (mmtm) REVERT: B 69 PHE cc_start: 0.8338 (m-10) cc_final: 0.7577 (m-10) REVERT: B 89 MET cc_start: 0.6859 (pmm) cc_final: 0.6241 (pmm) REVERT: B 94 GLN cc_start: 0.5893 (mt0) cc_final: 0.5316 (tt0) REVERT: B 132 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8464 (mttt) REVERT: B 216 LYS cc_start: 0.3727 (tttt) cc_final: 0.3385 (tptt) REVERT: C 16 ARG cc_start: 0.7250 (tpp80) cc_final: 0.6993 (ttt90) REVERT: C 17 ASP cc_start: 0.7848 (t0) cc_final: 0.7351 (t0) REVERT: C 74 MET cc_start: 0.5154 (OUTLIER) cc_final: 0.4737 (ppp) REVERT: C 78 LYS cc_start: 0.7041 (tmtt) cc_final: 0.6662 (pttm) REVERT: C 111 ASP cc_start: 0.7221 (m-30) cc_final: 0.6913 (m-30) REVERT: C 129 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7429 (p90) REVERT: C 182 ASP cc_start: 0.7989 (t0) cc_final: 0.7472 (t0) REVERT: D 46 GLU cc_start: 0.8459 (tp30) cc_final: 0.8255 (tp30) REVERT: D 60 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7459 (tmm) REVERT: D 66 ARG cc_start: 0.8829 (mtt180) cc_final: 0.8361 (mmm-85) REVERT: D 68 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8556 (m-80) REVERT: D 120 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6379 (tp) REVERT: E 73 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: E 84 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8216 (pp20) REVERT: E 149 ARG cc_start: 0.6955 (ttm-80) cc_final: 0.6718 (mtp-110) REVERT: G 59 MET cc_start: 0.8468 (tpp) cc_final: 0.8147 (tpp) REVERT: G 116 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6452 (tpt) REVERT: G 120 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8585 (mp) REVERT: H 19 MET cc_start: 0.8301 (ptm) cc_final: 0.7544 (ptt) REVERT: H 45 PHE cc_start: 0.8629 (m-80) cc_final: 0.8309 (m-80) REVERT: H 51 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: H 90 LYS cc_start: 0.6251 (mmtt) cc_final: 0.5457 (mmtm) REVERT: H 98 LEU cc_start: 0.7456 (mt) cc_final: 0.7207 (mt) REVERT: H 110 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6706 (mp10) REVERT: I 29 VAL cc_start: 0.6943 (OUTLIER) cc_final: 0.6583 (p) REVERT: I 41 SER cc_start: 0.7937 (m) cc_final: 0.7461 (p) REVERT: J 63 GLU cc_start: 0.7336 (tp30) cc_final: 0.7104 (tp30) REVERT: J 88 MET cc_start: 0.7309 (tpt) cc_final: 0.7025 (tpp) REVERT: K 29 PHE cc_start: 0.8194 (m-80) cc_final: 0.7519 (m-80) REVERT: K 89 LYS cc_start: 0.7257 (tppt) cc_final: 0.6181 (mttm) REVERT: K 124 ARG cc_start: 0.8808 (mtp-110) cc_final: 0.8066 (ptm160) REVERT: K 127 LYS cc_start: 0.8667 (pptt) cc_final: 0.8243 (pptt) REVERT: L 34 GLU cc_start: 0.7820 (tp30) cc_final: 0.7313 (tt0) REVERT: L 69 ARG cc_start: 0.7101 (ttm110) cc_final: 0.6671 (tpt-90) REVERT: M 61 ASP cc_start: 0.8441 (t0) cc_final: 0.7780 (m-30) REVERT: O 6 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7470 (tm-30) REVERT: O 79 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7763 (mtm-85) REVERT: O 80 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: Q 64 MET cc_start: 0.8643 (tmm) cc_final: 0.7816 (tmm) REVERT: S 20 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: S 66 MET cc_start: 0.8530 (mmm) cc_final: 0.8315 (tpp) REVERT: T 17 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.8213 (mtp180) REVERT: T 45 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: T 57 ARG cc_start: 0.8045 (mmp80) cc_final: 0.7116 (mmt90) REVERT: Z 43 ARG cc_start: 0.8304 (mmt-90) cc_final: 0.8009 (mmt90) REVERT: Z 87 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7554 (ptp-170) REVERT: Z 225 MET cc_start: 0.8156 (mmt) cc_final: 0.7881 (mmt) REVERT: Z 261 LYS cc_start: 0.7348 (mmmt) cc_final: 0.6956 (tptt) REVERT: a 61 SER cc_start: 0.8192 (OUTLIER) cc_final: 0.7938 (t) REVERT: b 83 TRP cc_start: 0.9257 (m100) cc_final: 0.9003 (m100) REVERT: b 90 PHE cc_start: 0.8382 (m-10) cc_final: 0.8125 (m-80) REVERT: b 190 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: c 33 LYS cc_start: 0.8574 (pttt) cc_final: 0.8022 (ttmt) REVERT: c 37 ASN cc_start: 0.7452 (t0) cc_final: 0.6986 (t0) REVERT: c 63 GLN cc_start: 0.7573 (pm20) cc_final: 0.7121 (pm20) REVERT: c 112 ARG cc_start: 0.6524 (ttt180) cc_final: 0.6132 (ttt-90) REVERT: c 148 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7147 (ttpt) REVERT: d 84 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: d 140 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7552 (tt0) REVERT: e 13 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8200 (mp0) REVERT: e 38 ARG cc_start: 0.9073 (ttt90) cc_final: 0.8355 (ttt90) REVERT: e 96 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.6979 (p0) REVERT: i 50 PHE cc_start: 0.8821 (t80) cc_final: 0.8245 (t80) REVERT: i 51 GLU cc_start: 0.8600 (pt0) cc_final: 0.7592 (pt0) REVERT: i 54 GLN cc_start: 0.8385 (tt0) cc_final: 0.8105 (tt0) REVERT: j 63 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8268 (pttp) REVERT: k 50 LEU cc_start: 0.8912 (tp) cc_final: 0.8641 (tt) REVERT: l 76 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7788 (mmmt) REVERT: l 79 GLU cc_start: 0.8312 (pp20) cc_final: 0.7811 (mm-30) REVERT: m 31 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6989 (ptpp) REVERT: m 65 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.7974 (p) REVERT: m 80 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7273 (ptpp) REVERT: m 98 TYR cc_start: 0.8925 (m-80) cc_final: 0.8653 (m-80) REVERT: m 104 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7915 (tpp80) REVERT: n 55 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7483 (ptp-170) REVERT: n 57 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: o 31 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: r 48 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8733 (tm-30) REVERT: s 2 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7902 (mmmt) REVERT: s 3 ASP cc_start: 0.7951 (m-30) cc_final: 0.7517 (m-30) REVERT: s 6 ASP cc_start: 0.8534 (p0) cc_final: 0.8317 (p0) REVERT: s 10 ARG cc_start: 0.7294 (ptt180) cc_final: 0.6401 (ptp-110) REVERT: s 15 GLU cc_start: 0.8604 (tp30) cc_final: 0.8082 (tp30) REVERT: s 31 ASP cc_start: 0.8718 (t0) cc_final: 0.8479 (t0) REVERT: u 35 ASP cc_start: 0.7828 (t0) cc_final: 0.6925 (p0) REVERT: u 48 GLN cc_start: 0.7495 (pt0) cc_final: 0.7124 (pt0) REVERT: u 52 LYS cc_start: 0.8710 (tppt) cc_final: 0.8474 (tppt) REVERT: u 85 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8027 (mttp) REVERT: v 22 MET cc_start: 0.7280 (mtt) cc_final: 0.6570 (mmm) REVERT: w 5 GLU cc_start: 0.8774 (mp0) cc_final: 0.8438 (mp0) REVERT: w 16 GLN cc_start: 0.5995 (OUTLIER) cc_final: 0.4895 (tt0) REVERT: w 38 GLU cc_start: 0.8849 (mp0) cc_final: 0.7943 (tm-30) REVERT: w 42 ARG cc_start: 0.8358 (tpt90) cc_final: 0.7921 (tpp80) REVERT: w 45 GLU cc_start: 0.9179 (tp30) cc_final: 0.8961 (tp30) REVERT: w 52 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7630 (mtp85) REVERT: w 55 THR cc_start: 0.8393 (m) cc_final: 0.8117 (p) REVERT: x 11 SER cc_start: 0.8849 (t) cc_final: 0.8087 (p) REVERT: x 32 ASN cc_start: 0.7972 (m-40) cc_final: 0.7589 (m110) REVERT: z 785 LYS cc_start: 0.1718 (OUTLIER) cc_final: 0.1364 (tptm) outliers start: 388 outliers final: 281 residues processed: 1426 average time/residue: 1.3487 time to fit residues: 3405.0528 Evaluate side-chains 1451 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 1137 time to evaluate : 5.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 MET Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 28 THR Chi-restraints excluded: chain 0 residue 55 ASN Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 17 THR Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 31 LYS Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 39 CYS Chi-restraints excluded: chain 6 residue 59 PHE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 PHE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 GLN Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 51 PHE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 30 ASN Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 4 LYS Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 42 ASN Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 39 LYS Chi-restraints excluded: chain Z residue 53 HIS Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 82 GLU Chi-restraints excluded: chain Z residue 87 ARG Chi-restraints excluded: chain Z residue 93 LEU Chi-restraints excluded: chain Z residue 146 LEU Chi-restraints excluded: chain Z residue 157 SER Chi-restraints excluded: chain Z residue 257 PHE Chi-restraints excluded: chain Z residue 271 VAL Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 50 GLN Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 137 SER Chi-restraints excluded: chain a residue 145 SER Chi-restraints excluded: chain a residue 167 GLU Chi-restraints excluded: chain a residue 176 ILE Chi-restraints excluded: chain a residue 177 VAL Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 40 GLN Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 2 ASN Chi-restraints excluded: chain c residue 26 MET Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain c residue 45 GLN Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain c residue 77 PHE Chi-restraints excluded: chain c residue 85 ILE Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 101 ASP Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain c residue 162 THR Chi-restraints excluded: chain c residue 172 GLN Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 35 THR Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 84 PHE Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 96 ASN Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain e residue 143 LEU Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 35 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 89 ASP Chi-restraints excluded: chain f residue 122 ILE Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 61 LEU Chi-restraints excluded: chain i residue 69 ILE Chi-restraints excluded: chain i residue 103 SER Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 123 VAL Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 63 LYS Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 9 THR Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 78 ASP Chi-restraints excluded: chain k residue 110 ASP Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 81 VAL Chi-restraints excluded: chain l residue 84 ARG Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain m residue 31 LYS Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 80 LYS Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 86 VAL Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 55 ARG Chi-restraints excluded: chain n residue 57 PHE Chi-restraints excluded: chain n residue 97 ASP Chi-restraints excluded: chain n residue 118 ASN Chi-restraints excluded: chain o residue 11 GLN Chi-restraints excluded: chain o residue 19 THR Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 57 THR Chi-restraints excluded: chain o residue 93 THR Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 44 SER Chi-restraints excluded: chain r residue 67 ASN Chi-restraints excluded: chain r residue 77 ASP Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 107 VAL Chi-restraints excluded: chain s residue 7 VAL Chi-restraints excluded: chain s residue 12 VAL Chi-restraints excluded: chain s residue 14 THR Chi-restraints excluded: chain s residue 44 GLU Chi-restraints excluded: chain s residue 46 ILE Chi-restraints excluded: chain s residue 58 ASN Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 36 GLU Chi-restraints excluded: chain t residue 71 LEU Chi-restraints excluded: chain u residue 18 THR Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 65 ASP Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 72 ASP Chi-restraints excluded: chain u residue 75 VAL Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain v residue 7 ILE Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 16 ASN Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 16 GLN Chi-restraints excluded: chain w residue 18 VAL Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 52 ARG Chi-restraints excluded: chain w residue 57 ILE Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 48 ASN Chi-restraints excluded: chain z residue 667 VAL Chi-restraints excluded: chain z residue 672 LEU Chi-restraints excluded: chain z residue 750 LEU Chi-restraints excluded: chain z residue 764 VAL Chi-restraints excluded: chain z residue 785 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 923 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 545 optimal weight: 4.9990 chunk 699 optimal weight: 20.0000 chunk 541 optimal weight: 10.0000 chunk 806 optimal weight: 10.0000 chunk 534 optimal weight: 10.0000 chunk 954 optimal weight: 20.0000 chunk 597 optimal weight: 10.0000 chunk 581 optimal weight: 10.0000 chunk 440 optimal weight: 1.9990 overall best weight: 7.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 6 GLN ** 6 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 137 GLN F 73 GLN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 GLN ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 68 ASN ** r 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 20 GLN ** v 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 156562 Z= 0.363 Angle : 0.761 12.327 234713 Z= 0.385 Chirality : 0.041 0.372 30057 Planarity : 0.006 0.064 12181 Dihedral : 24.467 179.592 79627 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.97 % Favored : 90.96 % Rotamer: Outliers : 9.79 % Allowed : 30.51 % Favored : 59.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.09 (0.11), residues: 5342 helix: -0.44 (0.12), residues: 1641 sheet: -1.31 (0.15), residues: 1080 loop : -2.03 (0.11), residues: 2621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP j 65 HIS 0.019 0.002 HIS C 99 PHE 0.026 0.002 PHE j 69 TYR 0.027 0.002 TYR B 54 ARG 0.021 0.001 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1592 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 446 poor density : 1146 time to evaluate : 6.064 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: 0 52 LYS cc_start: 0.8520 (mmmm) cc_final: 0.8056 (ttpt) REVERT: 1 32 PHE cc_start: 0.8328 (m-80) cc_final: 0.7797 (m-80) REVERT: 1 47 GLU cc_start: 0.7507 (pm20) cc_final: 0.6903 (pm20) REVERT: 4 8 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8244 (mmmm) REVERT: 4 31 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7641 (mttm) REVERT: 4 35 LYS cc_start: 0.8321 (mttt) cc_final: 0.8058 (mttt) REVERT: B 24 ASN cc_start: 0.8324 (m-40) cc_final: 0.7988 (m-40) REVERT: B 28 LYS cc_start: 0.3954 (OUTLIER) cc_final: 0.2681 (mmtm) REVERT: B 69 PHE cc_start: 0.8328 (m-10) cc_final: 0.7420 (m-10) REVERT: B 89 MET cc_start: 0.6872 (pmm) cc_final: 0.5615 (pmm) REVERT: B 94 GLN cc_start: 0.5840 (mt0) cc_final: 0.5223 (tt0) REVERT: B 132 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8399 (mttt) REVERT: B 216 LYS cc_start: 0.3877 (tttt) cc_final: 0.3515 (tptt) REVERT: C 16 ARG cc_start: 0.7291 (tpp80) cc_final: 0.7008 (ttt90) REVERT: C 17 ASP cc_start: 0.7882 (t0) cc_final: 0.7295 (t0) REVERT: C 74 MET cc_start: 0.5277 (OUTLIER) cc_final: 0.4850 (ppp) REVERT: C 78 LYS cc_start: 0.7107 (tmtt) cc_final: 0.6822 (pttm) REVERT: C 84 GLU cc_start: 0.7357 (tp30) cc_final: 0.7151 (tp30) REVERT: C 105 ILE cc_start: 0.8036 (tp) cc_final: 0.7652 (pt) REVERT: C 111 ASP cc_start: 0.7481 (m-30) cc_final: 0.7122 (m-30) REVERT: C 129 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7504 (p90) REVERT: D 60 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7532 (tmm) REVERT: D 66 ARG cc_start: 0.8882 (mtt180) cc_final: 0.8423 (mmm-85) REVERT: D 68 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: D 173 GLU cc_start: 0.3211 (tp30) cc_final: 0.2849 (tp30) REVERT: E 73 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8630 (tm-30) REVERT: E 84 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8152 (pp20) REVERT: F 43 TRP cc_start: 0.7606 (m-10) cc_final: 0.7377 (m-10) REVERT: F 60 TYR cc_start: 0.7498 (m-10) cc_final: 0.7172 (m-10) REVERT: G 59 MET cc_start: 0.8437 (tpp) cc_final: 0.7844 (tmm) REVERT: G 116 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6716 (tpt) REVERT: H 19 MET cc_start: 0.8409 (ptm) cc_final: 0.7584 (ptt) REVERT: H 45 PHE cc_start: 0.8717 (m-80) cc_final: 0.8408 (m-80) REVERT: H 50 GLU cc_start: 0.7938 (pm20) cc_final: 0.7536 (pm20) REVERT: H 51 PHE cc_start: 0.7205 (m-80) cc_final: 0.6682 (m-80) REVERT: H 90 LYS cc_start: 0.6345 (mmtt) cc_final: 0.5613 (mmtm) REVERT: H 110 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7017 (mp10) REVERT: I 27 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7781 (tmm-80) REVERT: I 29 VAL cc_start: 0.6834 (OUTLIER) cc_final: 0.6590 (p) REVERT: I 41 SER cc_start: 0.7973 (m) cc_final: 0.7491 (p) REVERT: J 63 GLU cc_start: 0.7354 (tp30) cc_final: 0.7038 (tp30) REVERT: J 64 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7652 (mm-40) REVERT: J 88 MET cc_start: 0.7378 (tpt) cc_final: 0.7154 (tpp) REVERT: K 26 ARG cc_start: 0.7681 (tpp80) cc_final: 0.7371 (ttt90) REVERT: K 29 PHE cc_start: 0.8259 (m-80) cc_final: 0.7588 (m-80) REVERT: K 89 LYS cc_start: 0.7467 (tppt) cc_final: 0.6509 (mttm) REVERT: K 124 ARG cc_start: 0.8849 (mtp-110) cc_final: 0.8049 (ptm160) REVERT: K 127 LYS cc_start: 0.8666 (pptt) cc_final: 0.8282 (pptt) REVERT: L 34 GLU cc_start: 0.7901 (tp30) cc_final: 0.7378 (tt0) REVERT: L 42 GLN cc_start: 0.8075 (mt0) cc_final: 0.7843 (mt0) REVERT: L 69 ARG cc_start: 0.7177 (ttm110) cc_final: 0.6792 (tpt-90) REVERT: M 61 ASP cc_start: 0.8150 (t0) cc_final: 0.7561 (m-30) REVERT: O 6 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7545 (tm-30) REVERT: O 44 ARG cc_start: 0.8782 (mtm110) cc_final: 0.8514 (mtm110) REVERT: O 79 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7807 (mtm-85) REVERT: O 80 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6812 (mt-10) REVERT: Q 64 MET cc_start: 0.8674 (tmm) cc_final: 0.7832 (tmm) REVERT: R 19 THR cc_start: 0.7833 (p) cc_final: 0.7555 (t) REVERT: S 20 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: S 36 ARG cc_start: 0.6633 (ptm160) cc_final: 0.6056 (ptm-80) REVERT: T 57 ARG cc_start: 0.8030 (mmp80) cc_final: 0.7107 (mmt90) REVERT: T 78 ARG cc_start: 0.8542 (ptt90) cc_final: 0.8124 (ptt180) REVERT: Z 43 ARG cc_start: 0.8326 (mmt-90) cc_final: 0.8051 (mmt90) REVERT: Z 87 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7479 (ptp-170) REVERT: Z 225 MET cc_start: 0.8258 (mmt) cc_final: 0.7976 (mmt) REVERT: Z 261 LYS cc_start: 0.7341 (mmmt) cc_final: 0.6996 (tptt) REVERT: b 62 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7778 (ptp90) REVERT: b 83 TRP cc_start: 0.9244 (m100) cc_final: 0.9008 (m100) REVERT: b 190 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8386 (tm-30) REVERT: c 33 LYS cc_start: 0.8572 (pttt) cc_final: 0.7985 (ttmt) REVERT: c 37 ASN cc_start: 0.7555 (t0) cc_final: 0.7075 (t0) REVERT: c 38 MET cc_start: 0.7119 (tmm) cc_final: 0.6251 (tmm) REVERT: c 63 GLN cc_start: 0.7648 (pm20) cc_final: 0.7182 (pm20) REVERT: c 148 LYS cc_start: 0.8062 (mmtm) cc_final: 0.7075 (ttpt) REVERT: d 84 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7114 (m-80) REVERT: e 13 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8212 (mp0) REVERT: f 86 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8454 (mp) REVERT: f 105 GLU cc_start: 0.9319 (mp0) cc_final: 0.8802 (mp0) REVERT: i 51 GLU cc_start: 0.8526 (pt0) cc_final: 0.7827 (pt0) REVERT: i 129 SER cc_start: 0.8894 (p) cc_final: 0.8430 (t) REVERT: i 144 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7313 (pp20) REVERT: j 63 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8366 (pttp) REVERT: j 80 GLU cc_start: 0.8462 (pm20) cc_final: 0.8164 (pm20) REVERT: k 19 ASP cc_start: 0.7525 (t0) cc_final: 0.7322 (t0) REVERT: k 50 LEU cc_start: 0.8949 (tp) cc_final: 0.8647 (tt) REVERT: k 65 TYR cc_start: 0.8452 (t80) cc_final: 0.8233 (t80) REVERT: k 68 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8443 (p0) REVERT: l 76 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7736 (mmmt) REVERT: l 79 GLU cc_start: 0.8377 (pp20) cc_final: 0.7849 (mm-30) REVERT: m 40 ILE cc_start: 0.8858 (mm) cc_final: 0.8642 (tp) REVERT: m 65 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7740 (p) REVERT: m 80 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7543 (ptpp) REVERT: m 94 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8382 (mmp80) REVERT: m 98 TYR cc_start: 0.8985 (m-80) cc_final: 0.8696 (m-80) REVERT: n 57 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: n 101 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.6594 (t0) REVERT: o 31 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: o 44 ASP cc_start: 0.6793 (OUTLIER) cc_final: 0.6567 (t0) REVERT: r 48 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8778 (tm-30) REVERT: s 2 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7948 (mmmt) REVERT: s 3 ASP cc_start: 0.8087 (m-30) cc_final: 0.7603 (m-30) REVERT: s 10 ARG cc_start: 0.7332 (ptt180) cc_final: 0.6420 (ptp-110) REVERT: s 15 GLU cc_start: 0.8703 (tp30) cc_final: 0.8129 (tp30) REVERT: s 31 ASP cc_start: 0.8789 (t0) cc_final: 0.8546 (t0) REVERT: u 35 ASP cc_start: 0.7745 (t0) cc_final: 0.7079 (p0) REVERT: u 48 GLN cc_start: 0.7379 (pt0) cc_final: 0.6963 (pt0) REVERT: u 85 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8128 (mttp) REVERT: v 22 MET cc_start: 0.7330 (mtt) cc_final: 0.6651 (mmm) REVERT: v 27 ARG cc_start: 0.8377 (ptm-80) cc_final: 0.8151 (ptm-80) REVERT: w 5 GLU cc_start: 0.8789 (mp0) cc_final: 0.8403 (mp0) REVERT: w 16 GLN cc_start: 0.6144 (OUTLIER) cc_final: 0.5313 (tt0) REVERT: w 38 GLU cc_start: 0.8781 (mp0) cc_final: 0.7803 (tm-30) REVERT: w 42 ARG cc_start: 0.8409 (tpt90) cc_final: 0.7973 (tpp80) REVERT: w 45 GLU cc_start: 0.9230 (tp30) cc_final: 0.8961 (tp30) REVERT: w 52 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7558 (mtp85) REVERT: w 55 THR cc_start: 0.8410 (m) cc_final: 0.8089 (p) REVERT: w 59 GLU cc_start: 0.8833 (pt0) cc_final: 0.8555 (pt0) REVERT: x 11 SER cc_start: 0.8746 (t) cc_final: 0.8020 (p) REVERT: x 32 ASN cc_start: 0.8085 (m-40) cc_final: 0.7679 (m110) REVERT: z 784 LEU cc_start: 0.4512 (OUTLIER) cc_final: 0.4273 (pp) outliers start: 446 outliers final: 343 residues processed: 1413 average time/residue: 1.2303 time to fit residues: 3045.6330 Evaluate side-chains 1482 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 376 poor density : 1106 time to evaluate : 5.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 MET Chi-restraints excluded: chain 0 residue 18 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 28 THR Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 0 residue 55 ASN Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 17 THR Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 31 LYS Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 39 CYS Chi-restraints excluded: chain 6 residue 59 PHE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 55 PHE Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 30 ASN Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 TYR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 4 LYS Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 20 GLU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 42 ASN Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 39 LYS Chi-restraints excluded: chain Z residue 53 HIS Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 82 GLU Chi-restraints excluded: chain Z residue 87 ARG Chi-restraints excluded: chain Z residue 93 LEU Chi-restraints excluded: chain Z residue 94 ILE Chi-restraints excluded: chain Z residue 118 SER Chi-restraints excluded: chain Z residue 146 LEU Chi-restraints excluded: chain Z residue 157 SER Chi-restraints excluded: chain Z residue 167 LYS Chi-restraints excluded: chain Z residue 177 ASN Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain Z residue 247 MET Chi-restraints excluded: chain Z residue 257 PHE Chi-restraints excluded: chain Z residue 270 ILE Chi-restraints excluded: chain Z residue 271 VAL Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 50 GLN Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 97 VAL Chi-restraints excluded: chain a residue 137 SER Chi-restraints excluded: chain a residue 145 SER Chi-restraints excluded: chain a residue 167 GLU Chi-restraints excluded: chain a residue 176 ILE Chi-restraints excluded: chain a residue 177 VAL Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 10 ASN Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 26 MET Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain c residue 77 PHE Chi-restraints excluded: chain c residue 85 ILE Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 101 ASP Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain c residue 162 THR Chi-restraints excluded: chain c residue 172 GLN Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 35 THR Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 84 PHE Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 114 VAL Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 35 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 66 LYS Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 89 ASP Chi-restraints excluded: chain f residue 122 ILE Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 61 LEU Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 103 SER Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 123 VAL Chi-restraints excluded: chain i residue 144 GLU Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 42 ILE Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 63 LYS Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 9 THR Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 23 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 68 ASN Chi-restraints excluded: chain k residue 110 ASP Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 17 ARG Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 84 ARG Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 78 THR Chi-restraints excluded: chain m residue 80 LYS Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 86 VAL Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 55 ARG Chi-restraints excluded: chain n residue 57 PHE Chi-restraints excluded: chain n residue 97 ASP Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 101 ASN Chi-restraints excluded: chain n residue 118 ASN Chi-restraints excluded: chain o residue 11 GLN Chi-restraints excluded: chain o residue 19 THR Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 44 ASP Chi-restraints excluded: chain o residue 48 VAL Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 93 THR Chi-restraints excluded: chain r residue 10 VAL Chi-restraints excluded: chain r residue 12 ILE Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 48 GLU Chi-restraints excluded: chain r residue 67 ASN Chi-restraints excluded: chain r residue 71 ILE Chi-restraints excluded: chain r residue 77 ASP Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 97 ASN Chi-restraints excluded: chain r residue 107 VAL Chi-restraints excluded: chain s residue 7 VAL Chi-restraints excluded: chain s residue 12 VAL Chi-restraints excluded: chain s residue 14 THR Chi-restraints excluded: chain s residue 44 GLU Chi-restraints excluded: chain s residue 46 ILE Chi-restraints excluded: chain s residue 58 ASN Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain t residue 36 GLU Chi-restraints excluded: chain t residue 71 LEU Chi-restraints excluded: chain u residue 18 THR Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 65 ASP Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 72 ASP Chi-restraints excluded: chain u residue 75 VAL Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain v residue 7 ILE Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 16 ASN Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 16 GLN Chi-restraints excluded: chain w residue 18 VAL Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 43 ILE Chi-restraints excluded: chain w residue 52 ARG Chi-restraints excluded: chain w residue 57 ILE Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 37 HIS Chi-restraints excluded: chain x residue 48 ASN Chi-restraints excluded: chain z residue 655 THR Chi-restraints excluded: chain z residue 667 VAL Chi-restraints excluded: chain z residue 672 LEU Chi-restraints excluded: chain z residue 750 LEU Chi-restraints excluded: chain z residue 764 VAL Chi-restraints excluded: chain z residue 780 THR Chi-restraints excluded: chain z residue 781 VAL Chi-restraints excluded: chain z residue 784 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 590 optimal weight: 5.9990 chunk 381 optimal weight: 3.9990 chunk 569 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 606 optimal weight: 1.9990 chunk 650 optimal weight: 1.9990 chunk 471 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 750 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 45 HIS ** 6 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 ASN ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 85 ASN ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 156562 Z= 0.208 Angle : 0.655 13.513 234713 Z= 0.334 Chirality : 0.037 0.354 30057 Planarity : 0.005 0.067 12181 Dihedral : 24.405 179.084 79623 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.24 % Favored : 92.72 % Rotamer: Outliers : 8.12 % Allowed : 32.73 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.11), residues: 5342 helix: -0.31 (0.12), residues: 1665 sheet: -1.29 (0.15), residues: 1052 loop : -1.95 (0.11), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 103 HIS 0.006 0.001 HIS j 13 PHE 0.023 0.002 PHE j 69 TYR 0.036 0.002 TYR o 21 ARG 0.012 0.001 ARG I 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1536 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 370 poor density : 1166 time to evaluate : 5.974 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: 0 52 LYS cc_start: 0.8438 (mmmm) cc_final: 0.8067 (ttpt) REVERT: 1 32 PHE cc_start: 0.8337 (m-80) cc_final: 0.7799 (m-80) REVERT: 4 8 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8358 (mmmm) REVERT: 4 31 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8097 (mttm) REVERT: 4 35 LYS cc_start: 0.8370 (mttt) cc_final: 0.8111 (mttt) REVERT: 6 29 GLU cc_start: 0.8001 (tp30) cc_final: 0.7280 (tp30) REVERT: B 24 ASN cc_start: 0.8426 (m-40) cc_final: 0.7998 (m-40) REVERT: B 28 LYS cc_start: 0.3334 (OUTLIER) cc_final: 0.2781 (mmtm) REVERT: B 69 PHE cc_start: 0.8288 (m-10) cc_final: 0.7487 (m-10) REVERT: B 89 MET cc_start: 0.6920 (pmm) cc_final: 0.6262 (pmm) REVERT: B 94 GLN cc_start: 0.5804 (mt0) cc_final: 0.5226 (tt0) REVERT: B 132 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8355 (mtmt) REVERT: B 216 LYS cc_start: 0.3815 (tttt) cc_final: 0.3445 (tptt) REVERT: C 16 ARG cc_start: 0.7315 (tpp80) cc_final: 0.7041 (ttt90) REVERT: C 17 ASP cc_start: 0.7948 (t0) cc_final: 0.7429 (t0) REVERT: C 74 MET cc_start: 0.5255 (OUTLIER) cc_final: 0.4864 (ppp) REVERT: C 78 LYS cc_start: 0.7053 (tmtt) cc_final: 0.6781 (pttm) REVERT: C 105 ILE cc_start: 0.7908 (tp) cc_final: 0.7688 (pt) REVERT: C 111 ASP cc_start: 0.7303 (m-30) cc_final: 0.6963 (m-30) REVERT: C 129 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7431 (p90) REVERT: C 135 GLN cc_start: 0.8964 (pp30) cc_final: 0.8457 (pp30) REVERT: C 182 ASP cc_start: 0.7944 (t0) cc_final: 0.7438 (t0) REVERT: C 183 TYR cc_start: 0.8155 (t80) cc_final: 0.7904 (t80) REVERT: D 60 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7465 (tmm) REVERT: D 66 ARG cc_start: 0.8839 (mtt180) cc_final: 0.8351 (mmm-85) REVERT: D 120 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6548 (tp) REVERT: D 163 GLU cc_start: 0.5205 (tm-30) cc_final: 0.4309 (tm-30) REVERT: D 173 GLU cc_start: 0.3016 (tp30) cc_final: 0.2700 (mm-30) REVERT: E 73 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: F 7 MET cc_start: 0.7293 (tpt) cc_final: 0.6855 (tpt) REVERT: G 59 MET cc_start: 0.8448 (tpp) cc_final: 0.7792 (tmm) REVERT: H 19 MET cc_start: 0.8290 (ptm) cc_final: 0.7580 (ptt) REVERT: H 45 PHE cc_start: 0.8710 (m-80) cc_final: 0.8484 (m-80) REVERT: H 51 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6550 (m-80) REVERT: H 90 LYS cc_start: 0.6450 (mmtt) cc_final: 0.5656 (mmtm) REVERT: H 98 LEU cc_start: 0.7479 (mt) cc_final: 0.7250 (mt) REVERT: H 110 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6747 (mp10) REVERT: I 41 SER cc_start: 0.7949 (m) cc_final: 0.7460 (p) REVERT: J 88 MET cc_start: 0.7340 (tpt) cc_final: 0.7127 (tpp) REVERT: K 26 ARG cc_start: 0.7706 (tpp80) cc_final: 0.7377 (ttt90) REVERT: K 29 PHE cc_start: 0.8169 (m-80) cc_final: 0.7507 (m-80) REVERT: K 89 LYS cc_start: 0.7449 (tppt) cc_final: 0.6433 (mttm) REVERT: K 124 ARG cc_start: 0.8822 (mtp-110) cc_final: 0.8067 (ptm160) REVERT: K 127 LYS cc_start: 0.8727 (pptt) cc_final: 0.8334 (pptt) REVERT: L 34 GLU cc_start: 0.7863 (tp30) cc_final: 0.7351 (tt0) REVERT: L 42 GLN cc_start: 0.7962 (mt0) cc_final: 0.7683 (mt0) REVERT: L 60 SER cc_start: 0.7882 (t) cc_final: 0.7464 (m) REVERT: L 69 ARG cc_start: 0.7129 (ttm110) cc_final: 0.6760 (tpt-90) REVERT: M 61 ASP cc_start: 0.8183 (t0) cc_final: 0.7621 (m-30) REVERT: O 6 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7492 (tm-30) REVERT: O 44 ARG cc_start: 0.8641 (mtm110) cc_final: 0.8363 (mtm110) REVERT: O 53 ARG cc_start: 0.8681 (ttm110) cc_final: 0.8452 (ttm110) REVERT: O 79 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7883 (mtm-85) REVERT: O 80 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6935 (mt-10) REVERT: Q 64 MET cc_start: 0.8614 (tmm) cc_final: 0.7760 (tmm) REVERT: R 19 THR cc_start: 0.8009 (p) cc_final: 0.7757 (t) REVERT: S 20 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: S 29 GLN cc_start: 0.7304 (pm20) cc_final: 0.6937 (pp30) REVERT: T 45 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: T 57 ARG cc_start: 0.8072 (mmp80) cc_final: 0.7166 (mmt90) REVERT: Z 43 ARG cc_start: 0.8289 (mmt-90) cc_final: 0.7981 (mmt90) REVERT: Z 87 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7542 (ptp-170) REVERT: Z 225 MET cc_start: 0.8211 (mmt) cc_final: 0.7881 (mmt) REVERT: Z 261 LYS cc_start: 0.7317 (mmmt) cc_final: 0.6930 (tptt) REVERT: a 3 LYS cc_start: 0.8687 (pttt) cc_final: 0.8476 (pttm) REVERT: a 61 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.8105 (t) REVERT: b 37 ILE cc_start: 0.9481 (mt) cc_final: 0.9231 (mt) REVERT: b 62 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7642 (ptp90) REVERT: b 83 TRP cc_start: 0.9213 (m100) cc_final: 0.8887 (m100) REVERT: b 90 PHE cc_start: 0.8377 (m-10) cc_final: 0.8155 (m-80) REVERT: b 190 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: c 33 LYS cc_start: 0.8584 (pttt) cc_final: 0.7972 (ttmt) REVERT: c 37 ASN cc_start: 0.7490 (t0) cc_final: 0.6970 (t0) REVERT: c 148 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7059 (ttpt) REVERT: d 84 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: d 140 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7562 (tt0) REVERT: e 13 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8196 (mp0) REVERT: e 26 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7647 (pt) REVERT: e 38 ARG cc_start: 0.8918 (ttt90) cc_final: 0.8428 (ttt90) REVERT: e 66 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7641 (p) REVERT: e 96 ASN cc_start: 0.7310 (OUTLIER) cc_final: 0.6727 (p0) REVERT: e 118 GLN cc_start: 0.8948 (tp40) cc_final: 0.8688 (tp40) REVERT: f 86 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8499 (mp) REVERT: f 105 GLU cc_start: 0.9317 (mp0) cc_final: 0.8552 (mp0) REVERT: i 50 PHE cc_start: 0.8746 (t80) cc_final: 0.8194 (t80) REVERT: i 51 GLU cc_start: 0.8376 (pt0) cc_final: 0.7589 (pt0) REVERT: i 54 GLN cc_start: 0.8464 (tt0) cc_final: 0.8084 (tt0) REVERT: i 144 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7344 (pp20) REVERT: j 63 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8423 (pttp) REVERT: k 19 ASP cc_start: 0.7578 (t0) cc_final: 0.7363 (t0) REVERT: l 45 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7461 (mp) REVERT: l 76 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7709 (mmmt) REVERT: l 79 GLU cc_start: 0.8304 (pp20) cc_final: 0.7795 (mm-30) REVERT: m 24 ASP cc_start: 0.8145 (m-30) cc_final: 0.7713 (m-30) REVERT: m 40 ILE cc_start: 0.8901 (mm) cc_final: 0.8681 (tp) REVERT: m 65 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7896 (p) REVERT: m 80 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.7146 (ptpp) REVERT: m 94 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8301 (mmp80) REVERT: m 98 TYR cc_start: 0.8913 (m-80) cc_final: 0.8663 (m-80) REVERT: n 55 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7512 (ptp-170) REVERT: n 57 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: n 101 ASN cc_start: 0.6916 (OUTLIER) cc_final: 0.6594 (t0) REVERT: o 31 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: r 48 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8743 (tm-30) REVERT: r 64 MET cc_start: 0.8022 (mpp) cc_final: 0.7634 (mtm) REVERT: s 2 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7925 (mmmt) REVERT: s 3 ASP cc_start: 0.8118 (m-30) cc_final: 0.7640 (m-30) REVERT: s 6 ASP cc_start: 0.8599 (p0) cc_final: 0.8377 (p0) REVERT: s 10 ARG cc_start: 0.7283 (ptt180) cc_final: 0.6397 (ptp-110) REVERT: s 15 GLU cc_start: 0.8613 (tp30) cc_final: 0.8067 (tp30) REVERT: s 31 ASP cc_start: 0.8775 (t0) cc_final: 0.8503 (t0) REVERT: s 47 PHE cc_start: 0.8417 (m-10) cc_final: 0.8102 (m-10) REVERT: t 58 ASN cc_start: 0.7523 (t0) cc_final: 0.7322 (t0) REVERT: t 80 ARG cc_start: 0.3202 (ttp-110) cc_final: 0.2673 (ttp-170) REVERT: u 35 ASP cc_start: 0.7814 (t0) cc_final: 0.6877 (p0) REVERT: u 48 GLN cc_start: 0.7332 (pt0) cc_final: 0.7053 (pt0) REVERT: u 52 LYS cc_start: 0.8742 (tppt) cc_final: 0.8530 (tppt) REVERT: u 85 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7996 (mttp) REVERT: w 16 GLN cc_start: 0.6229 (OUTLIER) cc_final: 0.5496 (tt0) REVERT: w 38 GLU cc_start: 0.8805 (mp0) cc_final: 0.7824 (tm-30) REVERT: w 42 ARG cc_start: 0.8352 (tpt90) cc_final: 0.7908 (tpp80) REVERT: w 45 GLU cc_start: 0.9227 (tp30) cc_final: 0.8980 (tp30) REVERT: w 55 THR cc_start: 0.8402 (m) cc_final: 0.8116 (p) REVERT: w 59 GLU cc_start: 0.8743 (pt0) cc_final: 0.8449 (pt0) REVERT: x 11 SER cc_start: 0.8848 (t) cc_final: 0.8080 (p) REVERT: x 32 ASN cc_start: 0.7951 (m-40) cc_final: 0.7572 (m110) REVERT: z 784 LEU cc_start: 0.4372 (OUTLIER) cc_final: 0.4150 (pp) outliers start: 370 outliers final: 288 residues processed: 1388 average time/residue: 1.3348 time to fit residues: 3281.0964 Evaluate side-chains 1439 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 1116 time to evaluate : 5.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 18 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 55 ASN Chi-restraints excluded: chain 1 residue 16 ASN Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 17 THR Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 31 LYS Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 39 CYS Chi-restraints excluded: chain 6 residue 59 PHE Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 55 PHE Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 51 PHE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 30 ASN Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 TYR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 4 LYS Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 42 ASN Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 69 LYS Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 39 LYS Chi-restraints excluded: chain Z residue 53 HIS Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 82 GLU Chi-restraints excluded: chain Z residue 87 ARG Chi-restraints excluded: chain Z residue 93 LEU Chi-restraints excluded: chain Z residue 94 ILE Chi-restraints excluded: chain Z residue 146 LEU Chi-restraints excluded: chain Z residue 157 SER Chi-restraints excluded: chain Z residue 177 ASN Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain Z residue 247 MET Chi-restraints excluded: chain Z residue 257 PHE Chi-restraints excluded: chain Z residue 271 VAL Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 50 GLN Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 137 SER Chi-restraints excluded: chain a residue 145 SER Chi-restraints excluded: chain a residue 167 GLU Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 2 ASN Chi-restraints excluded: chain c residue 26 MET Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain c residue 77 PHE Chi-restraints excluded: chain c residue 85 ILE Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 101 ASP Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain c residue 162 THR Chi-restraints excluded: chain c residue 172 GLN Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 35 THR Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 84 PHE Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain e residue 26 LEU Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 96 ASN Chi-restraints excluded: chain e residue 97 TYR Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 35 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 89 ASP Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 61 LEU Chi-restraints excluded: chain i residue 103 SER Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 123 VAL Chi-restraints excluded: chain i residue 129 SER Chi-restraints excluded: chain i residue 144 GLU Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 63 LYS Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain k residue 9 THR Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 23 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 110 ASP Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 45 ILE Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 75 THR Chi-restraints excluded: chain l residue 84 ARG Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 80 LYS Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 86 VAL Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 55 ARG Chi-restraints excluded: chain n residue 57 PHE Chi-restraints excluded: chain n residue 97 ASP Chi-restraints excluded: chain n residue 101 ASN Chi-restraints excluded: chain n residue 118 ASN Chi-restraints excluded: chain o residue 11 GLN Chi-restraints excluded: chain o residue 19 THR Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 36 GLU Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 93 THR Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 44 SER Chi-restraints excluded: chain r residue 48 GLU Chi-restraints excluded: chain r residue 67 ASN Chi-restraints excluded: chain r residue 77 ASP Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 97 ASN Chi-restraints excluded: chain r residue 107 VAL Chi-restraints excluded: chain s residue 12 VAL Chi-restraints excluded: chain s residue 14 THR Chi-restraints excluded: chain s residue 44 GLU Chi-restraints excluded: chain s residue 46 ILE Chi-restraints excluded: chain s residue 58 ASN Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain t residue 36 GLU Chi-restraints excluded: chain t residue 71 LEU Chi-restraints excluded: chain u residue 18 THR Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 65 ASP Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 72 ASP Chi-restraints excluded: chain u residue 75 VAL Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain v residue 7 ILE Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 16 ASN Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 16 GLN Chi-restraints excluded: chain w residue 18 VAL Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 30 PHE Chi-restraints excluded: chain w residue 57 ILE Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 37 HIS Chi-restraints excluded: chain x residue 48 ASN Chi-restraints excluded: chain z residue 647 VAL Chi-restraints excluded: chain z residue 655 THR Chi-restraints excluded: chain z residue 667 VAL Chi-restraints excluded: chain z residue 672 LEU Chi-restraints excluded: chain z residue 750 LEU Chi-restraints excluded: chain z residue 780 THR Chi-restraints excluded: chain z residue 784 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 868 optimal weight: 10.0000 chunk 914 optimal weight: 10.0000 chunk 834 optimal weight: 10.0000 chunk 889 optimal weight: 10.0000 chunk 913 optimal weight: 10.0000 chunk 535 optimal weight: 5.9990 chunk 387 optimal weight: 6.9990 chunk 698 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 803 optimal weight: 10.0000 chunk 840 optimal weight: 20.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 6 GLN ** 6 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 ASN j 35 GLN k 61 GLN ** r 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 156562 Z= 0.409 Angle : 0.802 14.607 234713 Z= 0.403 Chirality : 0.043 0.388 30057 Planarity : 0.006 0.073 12181 Dihedral : 24.493 179.753 79619 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.19 % Favored : 90.75 % Rotamer: Outliers : 9.06 % Allowed : 31.80 % Favored : 59.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.18 (0.11), residues: 5342 helix: -0.51 (0.12), residues: 1662 sheet: -1.33 (0.15), residues: 1068 loop : -2.11 (0.11), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP j 65 HIS 0.007 0.002 HIS j 123 PHE 0.025 0.002 PHE S 44 TYR 0.042 0.003 TYR d 95 ARG 0.009 0.001 ARG d 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1514 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 413 poor density : 1101 time to evaluate : 5.887 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: 1 32 PHE cc_start: 0.8244 (m-80) cc_final: 0.7822 (m-80) REVERT: 4 8 LYS cc_start: 0.8549 (mmmm) cc_final: 0.8233 (mmmm) REVERT: 4 12 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8467 (mm-30) REVERT: 4 31 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7725 (mttm) REVERT: 6 15 LYS cc_start: 0.8015 (mmmm) cc_final: 0.7634 (mmmm) REVERT: B 24 ASN cc_start: 0.8360 (m-40) cc_final: 0.7983 (m-40) REVERT: B 28 LYS cc_start: 0.3963 (OUTLIER) cc_final: 0.3238 (mmtm) REVERT: B 69 PHE cc_start: 0.8328 (m-10) cc_final: 0.7366 (m-10) REVERT: B 89 MET cc_start: 0.6889 (pmm) cc_final: 0.5650 (pmm) REVERT: B 94 GLN cc_start: 0.5903 (mt0) cc_final: 0.5226 (tt0) REVERT: B 108 GLN cc_start: 0.8402 (pp30) cc_final: 0.7951 (pp30) REVERT: B 132 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8354 (mtmt) REVERT: B 216 LYS cc_start: 0.3973 (tttt) cc_final: 0.3628 (tptt) REVERT: C 16 ARG cc_start: 0.7289 (tpp80) cc_final: 0.7067 (ttt90) REVERT: C 62 ARG cc_start: 0.6861 (tpt-90) cc_final: 0.6221 (tpp80) REVERT: C 74 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.4763 (ppp) REVERT: C 78 LYS cc_start: 0.7163 (tmtt) cc_final: 0.6873 (pttm) REVERT: C 105 ILE cc_start: 0.7861 (tp) cc_final: 0.7593 (pt) REVERT: C 111 ASP cc_start: 0.7717 (m-30) cc_final: 0.7368 (m-30) REVERT: C 129 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7529 (p90) REVERT: C 183 TYR cc_start: 0.8269 (t80) cc_final: 0.7941 (t80) REVERT: D 60 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7653 (tmm) REVERT: D 66 ARG cc_start: 0.8922 (mtt180) cc_final: 0.8438 (mmm-85) REVERT: D 163 GLU cc_start: 0.5208 (tm-30) cc_final: 0.4313 (tm-30) REVERT: D 173 GLU cc_start: 0.3181 (tp30) cc_final: 0.2793 (tp30) REVERT: E 73 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8571 (tm-30) REVERT: G 59 MET cc_start: 0.8493 (tpp) cc_final: 0.8008 (tpt) REVERT: H 45 PHE cc_start: 0.8740 (m-80) cc_final: 0.8510 (m-80) REVERT: H 51 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6463 (m-80) REVERT: H 90 LYS cc_start: 0.6497 (mmtt) cc_final: 0.5780 (mmtm) REVERT: H 110 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6769 (mp10) REVERT: I 41 SER cc_start: 0.8003 (m) cc_final: 0.7501 (p) REVERT: I 100 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7127 (mmp80) REVERT: J 27 GLU cc_start: 0.8144 (tp30) cc_final: 0.7860 (tp30) REVERT: J 31 ARG cc_start: 0.7529 (ttp-110) cc_final: 0.7280 (ptp90) REVERT: J 64 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7567 (mm-40) REVERT: J 88 MET cc_start: 0.7464 (tpt) cc_final: 0.7233 (tpp) REVERT: K 26 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7418 (ttt90) REVERT: K 29 PHE cc_start: 0.8274 (m-80) cc_final: 0.7607 (m-80) REVERT: K 124 ARG cc_start: 0.8858 (mtp-110) cc_final: 0.8022 (ptm160) REVERT: K 127 LYS cc_start: 0.8738 (pptt) cc_final: 0.8347 (pptt) REVERT: L 34 GLU cc_start: 0.7993 (tp30) cc_final: 0.7490 (tt0) REVERT: M 55 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7240 (mtmm) REVERT: M 61 ASP cc_start: 0.8202 (t0) cc_final: 0.7612 (m-30) REVERT: O 6 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7524 (tm-30) REVERT: O 16 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.7765 (mmmm) REVERT: O 44 ARG cc_start: 0.8674 (mtm110) cc_final: 0.8428 (mtm110) REVERT: O 53 ARG cc_start: 0.8559 (ttm110) cc_final: 0.8318 (ttm110) REVERT: O 79 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7978 (mtm-85) REVERT: O 80 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6787 (mt-10) REVERT: P 42 PRO cc_start: 0.7913 (Cg_exo) cc_final: 0.7699 (Cg_exo) REVERT: Q 64 MET cc_start: 0.8590 (tmm) cc_final: 0.7728 (tmm) REVERT: R 19 THR cc_start: 0.7792 (p) cc_final: 0.7538 (t) REVERT: S 36 ARG cc_start: 0.6588 (ptm160) cc_final: 0.6027 (ptm-80) REVERT: T 57 ARG cc_start: 0.8038 (mmp80) cc_final: 0.7155 (mmt90) REVERT: Z 43 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.7984 (mmt90) REVERT: Z 87 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7600 (ptp-170) REVERT: Z 225 MET cc_start: 0.8311 (mmt) cc_final: 0.8004 (mmt) REVERT: Z 261 LYS cc_start: 0.7320 (mmmt) cc_final: 0.6984 (tptt) REVERT: a 3 LYS cc_start: 0.8663 (pttt) cc_final: 0.8433 (pttm) REVERT: b 62 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7742 (ptp90) REVERT: b 190 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8396 (tm-30) REVERT: c 33 LYS cc_start: 0.8465 (pttt) cc_final: 0.7911 (ttmt) REVERT: c 37 ASN cc_start: 0.7634 (t0) cc_final: 0.7041 (t0) REVERT: c 38 MET cc_start: 0.7092 (tmm) cc_final: 0.6365 (tmm) REVERT: c 148 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7148 (ttpt) REVERT: c 154 ILE cc_start: 0.8792 (mt) cc_final: 0.8459 (tp) REVERT: d 84 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.6932 (m-80) REVERT: e 13 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8212 (mp0) REVERT: e 26 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7703 (pt) REVERT: e 96 ASN cc_start: 0.7488 (OUTLIER) cc_final: 0.7014 (p0) REVERT: e 118 GLN cc_start: 0.9007 (tp40) cc_final: 0.8750 (tp40) REVERT: f 86 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8441 (mp) REVERT: f 105 GLU cc_start: 0.9333 (mp0) cc_final: 0.8819 (mp0) REVERT: i 51 GLU cc_start: 0.8369 (pt0) cc_final: 0.7402 (pt0) REVERT: i 54 GLN cc_start: 0.8564 (tt0) cc_final: 0.8123 (tt0) REVERT: i 129 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8420 (t) REVERT: i 144 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7329 (pp20) REVERT: j 63 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8376 (pttp) REVERT: k 19 ASP cc_start: 0.7914 (t0) cc_final: 0.7627 (t0) REVERT: k 50 LEU cc_start: 0.8852 (tp) cc_final: 0.8632 (tt) REVERT: l 76 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7756 (mmmt) REVERT: l 79 GLU cc_start: 0.8372 (pp20) cc_final: 0.7778 (mm-30) REVERT: l 119 LYS cc_start: 0.7185 (tptp) cc_final: 0.6781 (tptt) REVERT: m 24 ASP cc_start: 0.8263 (m-30) cc_final: 0.7802 (m-30) REVERT: m 27 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7422 (mtm-85) REVERT: m 65 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7766 (p) REVERT: m 94 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8402 (mmp80) REVERT: m 98 TYR cc_start: 0.8981 (m-80) cc_final: 0.8742 (m-80) REVERT: n 55 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7667 (ptp-170) REVERT: n 57 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8173 (m-80) REVERT: o 31 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: o 44 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6573 (t0) REVERT: r 48 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8787 (tm-30) REVERT: r 64 MET cc_start: 0.8091 (mpp) cc_final: 0.7678 (mtm) REVERT: s 2 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7970 (mmmt) REVERT: s 3 ASP cc_start: 0.8212 (m-30) cc_final: 0.7587 (m-30) REVERT: s 6 ASP cc_start: 0.8636 (p0) cc_final: 0.8392 (p0) REVERT: s 10 ARG cc_start: 0.7329 (ptt180) cc_final: 0.6408 (ptp-110) REVERT: s 15 GLU cc_start: 0.8729 (tp30) cc_final: 0.8192 (tp30) REVERT: s 31 ASP cc_start: 0.8797 (t0) cc_final: 0.8523 (t0) REVERT: t 80 ARG cc_start: 0.3360 (ttp-110) cc_final: 0.2812 (ttp-110) REVERT: u 35 ASP cc_start: 0.7745 (t0) cc_final: 0.7061 (p0) REVERT: u 48 GLN cc_start: 0.7394 (pt0) cc_final: 0.7093 (pt0) REVERT: u 85 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8170 (mttp) REVERT: w 16 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.5635 (tt0) REVERT: w 42 ARG cc_start: 0.8460 (tpt90) cc_final: 0.8011 (tpp80) REVERT: w 45 GLU cc_start: 0.9264 (tp30) cc_final: 0.8958 (tp30) REVERT: w 59 GLU cc_start: 0.8838 (pt0) cc_final: 0.8558 (pt0) REVERT: x 32 ASN cc_start: 0.8084 (m-40) cc_final: 0.7669 (m110) REVERT: z 784 LEU cc_start: 0.4561 (OUTLIER) cc_final: 0.4306 (pp) outliers start: 413 outliers final: 342 residues processed: 1351 average time/residue: 1.2206 time to fit residues: 2890.0508 Evaluate side-chains 1457 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 373 poor density : 1084 time to evaluate : 5.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 MET Chi-restraints excluded: chain 0 residue 18 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 0 residue 55 ASN Chi-restraints excluded: chain 1 residue 11 GLU Chi-restraints excluded: chain 1 residue 16 ASN Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 17 THR Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 23 VAL Chi-restraints excluded: chain 4 residue 31 LYS Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 39 CYS Chi-restraints excluded: chain 6 residue 59 PHE Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 55 PHE Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 51 PHE Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 30 ASN Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 TYR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 4 LYS Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 20 GLU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 42 ASN Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 39 LYS Chi-restraints excluded: chain Z residue 53 HIS Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 65 ILE Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 87 ARG Chi-restraints excluded: chain Z residue 93 LEU Chi-restraints excluded: chain Z residue 94 ILE Chi-restraints excluded: chain Z residue 146 LEU Chi-restraints excluded: chain Z residue 157 SER Chi-restraints excluded: chain Z residue 167 LYS Chi-restraints excluded: chain Z residue 173 LEU Chi-restraints excluded: chain Z residue 177 ASN Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain Z residue 247 MET Chi-restraints excluded: chain Z residue 257 PHE Chi-restraints excluded: chain Z residue 270 ILE Chi-restraints excluded: chain Z residue 271 VAL Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 50 GLN Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 97 VAL Chi-restraints excluded: chain a residue 137 SER Chi-restraints excluded: chain a residue 145 SER Chi-restraints excluded: chain a residue 167 GLU Chi-restraints excluded: chain a residue 176 ILE Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 10 ASN Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 37 ILE Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 26 MET Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain c residue 77 PHE Chi-restraints excluded: chain c residue 85 ILE Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 101 ASP Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain c residue 162 THR Chi-restraints excluded: chain c residue 172 GLN Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 35 THR Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 84 PHE Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 114 VAL Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain e residue 26 LEU Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 96 ASN Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 35 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 66 LYS Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 89 ASP Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 61 LEU Chi-restraints excluded: chain i residue 67 THR Chi-restraints excluded: chain i residue 95 LEU Chi-restraints excluded: chain i residue 103 SER Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 123 VAL Chi-restraints excluded: chain i residue 129 SER Chi-restraints excluded: chain i residue 144 GLU Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 63 LYS Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 9 THR Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 23 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 110 ASP Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 75 THR Chi-restraints excluded: chain l residue 84 ARG Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain l residue 109 LEU Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 27 ARG Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 78 THR Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 86 VAL Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 27 SER Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 55 ARG Chi-restraints excluded: chain n residue 57 PHE Chi-restraints excluded: chain n residue 97 ASP Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 118 ASN Chi-restraints excluded: chain o residue 19 THR Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 44 ASP Chi-restraints excluded: chain o residue 48 VAL Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 59 THR Chi-restraints excluded: chain o residue 93 THR Chi-restraints excluded: chain r residue 12 ILE Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 44 SER Chi-restraints excluded: chain r residue 48 GLU Chi-restraints excluded: chain r residue 67 ASN Chi-restraints excluded: chain r residue 71 ILE Chi-restraints excluded: chain r residue 77 ASP Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 97 ASN Chi-restraints excluded: chain r residue 107 VAL Chi-restraints excluded: chain s residue 7 VAL Chi-restraints excluded: chain s residue 12 VAL Chi-restraints excluded: chain s residue 14 THR Chi-restraints excluded: chain s residue 44 GLU Chi-restraints excluded: chain s residue 58 ASN Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain t residue 36 GLU Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain t residue 71 LEU Chi-restraints excluded: chain u residue 18 THR Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 65 ASP Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 72 ASP Chi-restraints excluded: chain u residue 75 VAL Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain u residue 87 VAL Chi-restraints excluded: chain v residue 7 ILE Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 16 ASN Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 59 VAL Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 16 GLN Chi-restraints excluded: chain w residue 18 VAL Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 43 ILE Chi-restraints excluded: chain w residue 57 ILE Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 22 THR Chi-restraints excluded: chain x residue 37 HIS Chi-restraints excluded: chain x residue 48 ASN Chi-restraints excluded: chain z residue 647 VAL Chi-restraints excluded: chain z residue 655 THR Chi-restraints excluded: chain z residue 667 VAL Chi-restraints excluded: chain z residue 672 LEU Chi-restraints excluded: chain z residue 750 LEU Chi-restraints excluded: chain z residue 764 VAL Chi-restraints excluded: chain z residue 780 THR Chi-restraints excluded: chain z residue 781 VAL Chi-restraints excluded: chain z residue 784 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 886 optimal weight: 10.0000 chunk 583 optimal weight: 2.9990 chunk 940 optimal weight: 10.0000 chunk 573 optimal weight: 9.9990 chunk 446 optimal weight: 0.6980 chunk 653 optimal weight: 0.8980 chunk 986 optimal weight: 30.0000 chunk 907 optimal weight: 20.0000 chunk 785 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 606 optimal weight: 3.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 156562 Z= 0.225 Angle : 0.675 18.331 234713 Z= 0.344 Chirality : 0.038 0.378 30057 Planarity : 0.005 0.070 12181 Dihedral : 24.420 179.783 79619 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.66 % Favored : 92.31 % Rotamer: Outliers : 7.62 % Allowed : 33.38 % Favored : 59.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.03 (0.11), residues: 5342 helix: -0.37 (0.12), residues: 1657 sheet: -1.24 (0.16), residues: 1024 loop : -2.03 (0.11), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP j 65 HIS 0.009 0.001 HIS l 103 PHE 0.026 0.002 PHE S 44 TYR 0.032 0.002 TYR o 21 ARG 0.007 0.001 ARG e 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1486 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 1139 time to evaluate : 5.958 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: 0 52 LYS cc_start: 0.8399 (mmmm) cc_final: 0.8018 (ttpt) REVERT: 1 32 PHE cc_start: 0.8276 (m-80) cc_final: 0.7821 (m-80) REVERT: 4 8 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8292 (mmmm) REVERT: 4 31 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7886 (mttm) REVERT: 6 15 LYS cc_start: 0.7986 (mmmm) cc_final: 0.7586 (mmmm) REVERT: 6 29 GLU cc_start: 0.7982 (tp30) cc_final: 0.7397 (tp30) REVERT: B 24 ASN cc_start: 0.8507 (m-40) cc_final: 0.8147 (m-40) REVERT: B 28 LYS cc_start: 0.3495 (OUTLIER) cc_final: 0.3014 (mmtm) REVERT: B 69 PHE cc_start: 0.8135 (m-10) cc_final: 0.7386 (m-10) REVERT: B 89 MET cc_start: 0.7043 (pmm) cc_final: 0.5717 (pmm) REVERT: B 94 GLN cc_start: 0.5830 (mt0) cc_final: 0.5262 (tt0) REVERT: B 132 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8352 (mttt) REVERT: B 216 LYS cc_start: 0.3892 (tttt) cc_final: 0.3551 (tptt) REVERT: C 16 ARG cc_start: 0.7199 (tpp80) cc_final: 0.6974 (ttt90) REVERT: C 17 ASP cc_start: 0.7958 (t0) cc_final: 0.7425 (t0) REVERT: C 74 MET cc_start: 0.5255 (OUTLIER) cc_final: 0.4872 (ppp) REVERT: C 78 LYS cc_start: 0.7068 (tmtt) cc_final: 0.6805 (pttm) REVERT: C 105 ILE cc_start: 0.7917 (tp) cc_final: 0.7671 (pt) REVERT: C 111 ASP cc_start: 0.7359 (m-30) cc_final: 0.7039 (m-30) REVERT: C 129 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.6911 (p90) REVERT: C 135 GLN cc_start: 0.8964 (pp30) cc_final: 0.8476 (pp30) REVERT: C 182 ASP cc_start: 0.7991 (t0) cc_final: 0.7454 (t0) REVERT: C 183 TYR cc_start: 0.8178 (t80) cc_final: 0.7878 (t80) REVERT: D 60 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7449 (tmm) REVERT: D 66 ARG cc_start: 0.8885 (mtt180) cc_final: 0.8378 (mmm-85) REVERT: D 120 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6589 (tp) REVERT: D 163 GLU cc_start: 0.5238 (tm-30) cc_final: 0.4381 (tm-30) REVERT: D 173 GLU cc_start: 0.2792 (tp30) cc_final: 0.2475 (tp30) REVERT: E 73 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8467 (tm-30) REVERT: E 76 MET cc_start: 0.8080 (tpp) cc_final: 0.7803 (tpp) REVERT: F 7 MET cc_start: 0.7311 (tpt) cc_final: 0.6973 (tpt) REVERT: G 59 MET cc_start: 0.8380 (tpp) cc_final: 0.7734 (tmm) REVERT: H 19 MET cc_start: 0.8306 (ptm) cc_final: 0.7598 (ptt) REVERT: H 51 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6403 (m-80) REVERT: H 90 LYS cc_start: 0.6540 (mmtt) cc_final: 0.5848 (mmtm) REVERT: H 110 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6629 (mp10) REVERT: I 41 SER cc_start: 0.7956 (m) cc_final: 0.7462 (p) REVERT: J 64 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7810 (mm-40) REVERT: J 88 MET cc_start: 0.7277 (tpt) cc_final: 0.7057 (tpp) REVERT: K 26 ARG cc_start: 0.7675 (tpp80) cc_final: 0.7310 (ttt90) REVERT: K 29 PHE cc_start: 0.8216 (m-80) cc_final: 0.7547 (m-80) REVERT: K 124 ARG cc_start: 0.8813 (mtp-110) cc_final: 0.8034 (ptm160) REVERT: K 127 LYS cc_start: 0.8767 (pptt) cc_final: 0.8343 (pptt) REVERT: L 24 LEU cc_start: 0.8801 (mm) cc_final: 0.8563 (mp) REVERT: L 34 GLU cc_start: 0.7957 (tp30) cc_final: 0.7464 (tt0) REVERT: L 60 SER cc_start: 0.8050 (t) cc_final: 0.7565 (m) REVERT: M 55 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7137 (mtmm) REVERT: M 61 ASP cc_start: 0.8201 (t0) cc_final: 0.7627 (m-30) REVERT: O 6 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7468 (tm-30) REVERT: O 16 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.7716 (mmmm) REVERT: O 41 GLU cc_start: 0.8521 (mp0) cc_final: 0.8309 (mp0) REVERT: O 44 ARG cc_start: 0.8633 (mtm110) cc_final: 0.8423 (mtm110) REVERT: O 53 ARG cc_start: 0.8538 (ttm110) cc_final: 0.8279 (ttm110) REVERT: O 79 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.7962 (mtm-85) REVERT: O 80 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6803 (mt-10) REVERT: P 71 ARG cc_start: 0.6350 (tpt170) cc_final: 0.5893 (tpt170) REVERT: Q 64 MET cc_start: 0.8597 (tmm) cc_final: 0.7758 (tmm) REVERT: R 19 THR cc_start: 0.7956 (p) cc_final: 0.7693 (t) REVERT: R 41 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7926 (mtm-85) REVERT: S 29 GLN cc_start: 0.7125 (pm20) cc_final: 0.6807 (pp30) REVERT: T 57 ARG cc_start: 0.8053 (mmp80) cc_final: 0.7193 (mmt90) REVERT: T 78 ARG cc_start: 0.8642 (ptt180) cc_final: 0.8411 (ptt180) REVERT: Z 43 ARG cc_start: 0.8367 (mmt-90) cc_final: 0.8089 (mmt90) REVERT: Z 87 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7551 (ptp-170) REVERT: Z 225 MET cc_start: 0.8248 (mmt) cc_final: 0.7901 (mmt) REVERT: Z 261 LYS cc_start: 0.7326 (mmmt) cc_final: 0.6949 (tptt) REVERT: a 3 LYS cc_start: 0.8733 (pttt) cc_final: 0.8514 (pttm) REVERT: b 37 ILE cc_start: 0.9462 (mt) cc_final: 0.9206 (mt) REVERT: b 62 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7662 (ptp90) REVERT: b 90 PHE cc_start: 0.8412 (m-10) cc_final: 0.8152 (m-80) REVERT: b 190 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: c 33 LYS cc_start: 0.8448 (pttt) cc_final: 0.7899 (ttmt) REVERT: c 37 ASN cc_start: 0.7522 (t0) cc_final: 0.6943 (t0) REVERT: c 38 MET cc_start: 0.7072 (tmm) cc_final: 0.6442 (tmm) REVERT: c 148 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7078 (ttpt) REVERT: c 154 ILE cc_start: 0.8753 (mt) cc_final: 0.8446 (tp) REVERT: d 84 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.6670 (m-80) REVERT: e 13 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8195 (mp0) REVERT: e 26 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7656 (pt) REVERT: e 66 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7582 (p) REVERT: e 96 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6829 (p0) REVERT: e 118 GLN cc_start: 0.8943 (tp40) cc_final: 0.8668 (tp40) REVERT: f 86 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8525 (mp) REVERT: f 105 GLU cc_start: 0.9253 (mp0) cc_final: 0.8501 (mp0) REVERT: i 50 PHE cc_start: 0.8844 (t80) cc_final: 0.8170 (t80) REVERT: i 51 GLU cc_start: 0.8265 (pt0) cc_final: 0.7722 (pt0) REVERT: i 54 GLN cc_start: 0.8473 (tt0) cc_final: 0.8108 (tt0) REVERT: i 144 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7346 (pp20) REVERT: j 63 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8379 (pttp) REVERT: k 19 ASP cc_start: 0.7736 (t0) cc_final: 0.7473 (t0) REVERT: k 50 LEU cc_start: 0.8859 (tp) cc_final: 0.8581 (tt) REVERT: l 45 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7466 (mp) REVERT: l 76 LYS cc_start: 0.8158 (ttmt) cc_final: 0.7714 (mmmt) REVERT: l 79 GLU cc_start: 0.8334 (pp20) cc_final: 0.7801 (mm-30) REVERT: m 24 ASP cc_start: 0.8154 (m-30) cc_final: 0.7720 (m-30) REVERT: m 65 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.7962 (p) REVERT: m 94 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8337 (mmp80) REVERT: m 98 TYR cc_start: 0.8916 (m-80) cc_final: 0.8664 (m-80) REVERT: m 104 ARG cc_start: 0.8235 (tpp80) cc_final: 0.7949 (tpp80) REVERT: n 57 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: o 31 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: o 44 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6510 (t0) REVERT: r 48 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8741 (tm-30) REVERT: r 64 MET cc_start: 0.8006 (mpp) cc_final: 0.7660 (mtm) REVERT: s 2 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7947 (mmmt) REVERT: s 3 ASP cc_start: 0.8213 (m-30) cc_final: 0.7737 (m-30) REVERT: s 10 ARG cc_start: 0.7272 (ptt180) cc_final: 0.6375 (ptp-110) REVERT: s 15 GLU cc_start: 0.8622 (tp30) cc_final: 0.8042 (tp30) REVERT: s 31 ASP cc_start: 0.8774 (t0) cc_final: 0.8487 (t0) REVERT: s 47 PHE cc_start: 0.8487 (m-10) cc_final: 0.8211 (m-80) REVERT: u 35 ASP cc_start: 0.7817 (t0) cc_final: 0.7021 (p0) REVERT: u 48 GLN cc_start: 0.7371 (pt0) cc_final: 0.7064 (pt0) REVERT: u 52 LYS cc_start: 0.8740 (tppt) cc_final: 0.8505 (tppt) REVERT: u 85 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8105 (mttp) REVERT: v 18 ARG cc_start: 0.8476 (mmt90) cc_final: 0.8221 (mmt90) REVERT: v 43 LYS cc_start: 0.6459 (ptpp) cc_final: 0.5557 (mtmm) REVERT: w 16 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.5560 (tt0) REVERT: w 38 GLU cc_start: 0.8813 (mp0) cc_final: 0.7904 (tm-30) REVERT: w 42 ARG cc_start: 0.8393 (tpt90) cc_final: 0.7945 (tpp80) REVERT: w 45 GLU cc_start: 0.9228 (tp30) cc_final: 0.8968 (tp30) REVERT: w 55 THR cc_start: 0.8384 (m) cc_final: 0.8097 (p) REVERT: w 59 GLU cc_start: 0.8748 (pt0) cc_final: 0.8468 (pt0) REVERT: x 32 ASN cc_start: 0.7949 (m-40) cc_final: 0.7573 (m110) REVERT: z 784 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.4192 (pp) outliers start: 347 outliers final: 298 residues processed: 1344 average time/residue: 1.1939 time to fit residues: 2815.4852 Evaluate side-chains 1442 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1114 time to evaluate : 5.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 18 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 36 MET Chi-restraints excluded: chain 0 residue 42 VAL Chi-restraints excluded: chain 0 residue 55 ASN Chi-restraints excluded: chain 1 residue 16 ASN Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 17 THR Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 23 VAL Chi-restraints excluded: chain 4 residue 31 LYS Chi-restraints excluded: chain 6 residue 8 ASN Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 39 CYS Chi-restraints excluded: chain 6 residue 59 PHE Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 55 PHE Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 51 PHE Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 75 GLN Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 30 ASN Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 65 TYR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 4 LYS Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 79 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 42 ASN Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain Z residue 30 GLU Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 39 LYS Chi-restraints excluded: chain Z residue 53 HIS Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 82 GLU Chi-restraints excluded: chain Z residue 87 ARG Chi-restraints excluded: chain Z residue 93 LEU Chi-restraints excluded: chain Z residue 94 ILE Chi-restraints excluded: chain Z residue 118 SER Chi-restraints excluded: chain Z residue 146 LEU Chi-restraints excluded: chain Z residue 157 SER Chi-restraints excluded: chain Z residue 167 LYS Chi-restraints excluded: chain Z residue 177 ASN Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain Z residue 247 MET Chi-restraints excluded: chain Z residue 257 PHE Chi-restraints excluded: chain Z residue 271 VAL Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 50 GLN Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 89 ASP Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 137 SER Chi-restraints excluded: chain a residue 145 SER Chi-restraints excluded: chain a residue 167 GLU Chi-restraints excluded: chain a residue 176 ILE Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 123 ILE Chi-restraints excluded: chain b residue 153 LEU Chi-restraints excluded: chain b residue 190 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 26 MET Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain c residue 77 PHE Chi-restraints excluded: chain c residue 85 ILE Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 101 ASP Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain c residue 162 THR Chi-restraints excluded: chain c residue 172 GLN Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 35 THR Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 84 PHE Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 114 VAL Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain e residue 26 LEU Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 96 ASN Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 35 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 89 ASP Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 61 LEU Chi-restraints excluded: chain i residue 103 SER Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 123 VAL Chi-restraints excluded: chain i residue 129 SER Chi-restraints excluded: chain i residue 144 GLU Chi-restraints excluded: chain j residue 3 LEU Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 63 LYS Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 9 THR Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain k residue 23 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 110 ASP Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 45 ILE Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 75 THR Chi-restraints excluded: chain l residue 84 ARG Chi-restraints excluded: chain l residue 94 VAL Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 25 THR Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 76 VAL Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 86 VAL Chi-restraints excluded: chain m residue 94 ARG Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 9 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 40 MET Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 57 PHE Chi-restraints excluded: chain n residue 97 ASP Chi-restraints excluded: chain n residue 118 ASN Chi-restraints excluded: chain o residue 19 THR Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 44 ASP Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 93 THR Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 20 VAL Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 44 SER Chi-restraints excluded: chain r residue 67 ASN Chi-restraints excluded: chain r residue 77 ASP Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain r residue 82 LEU Chi-restraints excluded: chain r residue 97 ASN Chi-restraints excluded: chain r residue 107 VAL Chi-restraints excluded: chain s residue 7 VAL Chi-restraints excluded: chain s residue 12 VAL Chi-restraints excluded: chain s residue 14 THR Chi-restraints excluded: chain s residue 44 GLU Chi-restraints excluded: chain s residue 58 ASN Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain t residue 36 GLU Chi-restraints excluded: chain t residue 71 LEU Chi-restraints excluded: chain u residue 18 THR Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 65 ASP Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 72 ASP Chi-restraints excluded: chain u residue 75 VAL Chi-restraints excluded: chain u residue 85 LYS Chi-restraints excluded: chain v residue 7 ILE Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 16 ASN Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 16 GLN Chi-restraints excluded: chain w residue 18 VAL Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 30 PHE Chi-restraints excluded: chain w residue 43 ILE Chi-restraints excluded: chain w residue 57 ILE Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 37 HIS Chi-restraints excluded: chain x residue 48 ASN Chi-restraints excluded: chain z residue 647 VAL Chi-restraints excluded: chain z residue 655 THR Chi-restraints excluded: chain z residue 667 VAL Chi-restraints excluded: chain z residue 672 LEU Chi-restraints excluded: chain z residue 750 LEU Chi-restraints excluded: chain z residue 780 THR Chi-restraints excluded: chain z residue 781 VAL Chi-restraints excluded: chain z residue 784 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 481 optimal weight: 0.0980 chunk 623 optimal weight: 0.8980 chunk 836 optimal weight: 10.0000 chunk 240 optimal weight: 30.0000 chunk 724 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 218 optimal weight: 0.6980 chunk 786 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 807 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 HIS ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 109 ASN ** i 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN k 68 ASN ** n 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.090958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.072781 restraints weight = 530650.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.074476 restraints weight = 162725.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.075412 restraints weight = 82782.530| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 156562 Z= 0.243 Angle : 0.679 17.838 234713 Z= 0.345 Chirality : 0.038 0.367 30057 Planarity : 0.005 0.068 12181 Dihedral : 24.408 179.221 79619 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.33 % Favored : 91.63 % Rotamer: Outliers : 7.95 % Allowed : 33.17 % Favored : 58.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.00 (0.11), residues: 5342 helix: -0.32 (0.12), residues: 1649 sheet: -1.19 (0.16), residues: 1028 loop : -2.03 (0.11), residues: 2665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP j 65 HIS 0.026 0.002 HIS L 90 PHE 0.029 0.002 PHE H 45 TYR 0.044 0.002 TYR d 95 ARG 0.013 0.001 ARG j 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40996.77 seconds wall clock time: 715 minutes 53.01 seconds (42953.01 seconds total)