Starting phenix.real_space_refine on Wed Mar 20 09:37:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9j_0661/03_2024/6o9j_0661.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9j_0661/03_2024/6o9j_0661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9j_0661/03_2024/6o9j_0661.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9j_0661/03_2024/6o9j_0661.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9j_0661/03_2024/6o9j_0661.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9j_0661/03_2024/6o9j_0661.pdb" } resolution = 3.9 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= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4564 5.49 5 S 149 5.16 5 C 71705 2.51 5 N 26586 2.21 5 O 39678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "V PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 7": "OE1" <-> "OE2" Residue "V GLU 35": "OE1" <-> "OE2" Residue "V GLU 41": "OE1" <-> "OE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "F TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F ASP 146": "OD1" <-> "OD2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "J TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "M PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 104": "OE1" <-> "OE2" Residue "M PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 127": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 93": "OD1" <-> "OD2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P GLU 10": "OE1" <-> "OE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "P PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 90": "OD1" <-> "OD2" Residue "Q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T ASP 37": "OD1" <-> "OD2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 79": "OD1" <-> "OD2" Residue "T PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 9": "OE1" <-> "OE2" Residue "U ASP 17": "OD1" <-> "OD2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 14": "OD1" <-> "OD2" Residue "W ASP 55": "OD1" <-> "OD2" Residue "W PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "Z PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 35": "OE1" <-> "OE2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 20": "OD1" <-> "OD2" Residue "6 ASP 141": "OD1" <-> "OD2" Residue "c GLU 27": "OE1" <-> "OE2" Residue "c PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 109": "OE1" <-> "OE2" Residue "c GLU 165": "OE1" <-> "OE2" Residue "c ASP 182": "OD1" <-> "OD2" Residue "c GLU 187": "OE1" <-> "OE2" Residue "d GLU 56": "OE1" <-> "OE2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 94": "OE1" <-> "OE2" Residue "d ASP 98": "OD1" <-> "OD2" Residue "d TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 173": "OD1" <-> "OD2" Residue "d ASP 193": "OD1" <-> "OD2" Residue "d GLU 201": "OE1" <-> "OE2" Residue "d TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 9": "OE1" <-> "OE2" Residue "e GLU 12": "OE1" <-> "OE2" Residue "e PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 40": "OD1" <-> "OD2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 141": "OD1" <-> "OD2" Residue "f ASP 13": "OD1" <-> "OD2" Residue "f GLU 16": "OE1" <-> "OE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "f PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "g ASP 14": "OD1" <-> "OD2" Residue "g GLU 20": "OE1" <-> "OE2" Residue "g ASP 32": "OD1" <-> "OD2" Residue "g GLU 62": "OE1" <-> "OE2" Residue "g GLU 66": "OE1" <-> "OE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 89": "OE1" <-> "OE2" Residue "g GLU 128": "OE1" <-> "OE2" Residue "g ASP 139": "OD1" <-> "OD2" Residue "g PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 41": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "h GLU 90": "OE1" <-> "OE2" Residue "h ASP 112": "OD1" <-> "OD2" Residue "h GLU 123": "OE1" <-> "OE2" Residue "i TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 35": "OE1" <-> "OE2" Residue "i PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 52": "OE1" <-> "OE2" Residue "i ASP 55": "OD1" <-> "OD2" Residue "i GLU 88": "OE1" <-> "OE2" Residue "i ASP 90": "OD1" <-> "OD2" Residue "i GLU 96": "OE1" <-> "OE2" Residue "i PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 106": "OD1" <-> "OD2" Residue "j PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j GLU 24": "OE1" <-> "OE2" Residue "j GLU 47": "OE1" <-> "OE2" Residue "j TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 81": "OE1" <-> "OE2" Residue "j ASP 91": "OD1" <-> "OD2" Residue "j ASP 97": "OD1" <-> "OD2" Residue "k GLU 67": "OE1" <-> "OE2" Residue "k ASP 71": "OD1" <-> "OD2" Residue "k TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "l GLU 24": "OE1" <-> "OE2" Residue "l GLU 69": "OE1" <-> "OE2" Residue "l ASP 88": "OD1" <-> "OD2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 49": "OE1" <-> "OE2" Residue "m GLU 71": "OE1" <-> "OE2" Residue "n GLU 9": "OE1" <-> "OE2" Residue "n TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 13": "OE1" <-> "OE2" Residue "o PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 17": "OD1" <-> "OD2" Residue "o GLU 25": "OE1" <-> "OE2" Residue "o PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 45": "OE1" <-> "OE2" Residue "p GLU 47": "OE1" <-> "OE2" Residue "p ASP 53": "OD1" <-> "OD2" Residue "q ASP 14": "OD1" <-> "OD2" Residue "q TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 48": "OE1" <-> "OE2" Residue "r TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 24": "OD1" <-> "OD2" Residue "r TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 71": "OD1" <-> "OD2" Residue "s PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 63": "OD1" <-> "OD2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "t GLU 14": "OE1" <-> "OE2" Residue "t GLU 39": "OE1" <-> "OE2" Residue "7 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 55": "OE1" <-> "OE2" Residue "7 GLU 77": "OE1" <-> "OE2" Residue "7 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 132": "OE1" <-> "OE2" Residue "7 ASP 158": "OD1" <-> "OD2" Residue "7 PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 12": "OD1" <-> "OD2" Residue "u GLU 35": "OE1" <-> "OE2" Residue "u PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 142682 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2507 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 58, 'rna3p_pyr': 52} Link IDs: {'rna2p': 7, 'rna3p': 109} Chain: "B" Number of atoms: 60995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2841, 60995 Classifications: {'RNA': 2841} Modifications used: {'rna2p_pur': 250, 'rna2p_pyr': 135, 'rna3p_pur': 1391, 'rna3p_pyr': 1065} Link IDs: {'rna2p': 385, 'rna3p': 2455} Chain breaks: 3 Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "C" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2053 Classifications: {'peptide': 267} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 249} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1420 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 144} Chain: "J" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1112 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "K" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 930 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1008 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "O" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 777 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "W" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 634 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "X" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "Z" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 549 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "2" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 441 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "3" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "4" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "5" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "a" Number of atoms: 32831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1530, 32831 Classifications: {'RNA': 1530} Modifications used: {'rna2p_pur': 108, 'rna2p_pyr': 77, 'rna3p_pur': 764, 'rna3p_pyr': 581} Link IDs: {'rna2p': 185, 'rna3p': 1344} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "f" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "o" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 716 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "s" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "7" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "u" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "v" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 2, 'rna3p_pur': 32, 'rna3p_pyr': 35} Link IDs: {'rna2p': 9, 'rna3p': 66} Time building chain proxies: 53.78, per 1000 atoms: 0.38 Number of scatterers: 142682 At special positions: 0 Unit cell: (232.4, 250.66, 273.9, 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 149 16.00 P 4564 15.00 O 39678 8.00 N 26586 7.00 C 71705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM A0D5Q O4' G a1279 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DZ4 O5' A a1329 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DMC O4' U a1307 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D6A O5' A a1280 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CFV O4' A a1236 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DMC O4' U a1307 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AM7 O4' U a1126 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D80 O5' U a1283 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D6A O5' A a1280 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CR9 O4' G a1255 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D5N O5' G a1279 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AMR O4' G a1127 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DZ7 O4' A a1329 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0WLF O4' C v 56 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DJT O5' C a1303 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CQK O5' A a1254 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C55 O5' C a1218 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0EH4 O4' C a1359 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0ALN O4' U a1125 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D5Q O4' G a1279 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AM7 O4' U a1126 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08D8 O4' U a 989 .*. O " rejected from bonding due to valence issues. Atom "ATOM A088K O4' U a 981 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DZ7 O4' A a1329 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C6E O4' G a1220 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DTZ O5' C a1320 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08TQ O4' U a1017 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0E2S O5' U a1335 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D80 O5' U a1283 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08D8 O4' U a 989 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0ALN O4' U a1125 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C55 O5' C a1218 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0WLF O4' C v 56 .*. O " rejected from bonding due to valence issues. Atom "ATOM A085I O5' G a 976 .*. O " rejected from bonding due to valence issues. Atom "ATOM A088H O5' U a 981 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AZT O5' C a1149 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08RS O5' A a1014 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0EH1 O5' C a1359 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CFV O4' A a1236 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D53 O4' G a1278 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CRT O5' A a1256 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AZW O4' C a1149 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08T1 O5' A a1016 .*. O " rejected from bonding due to valence issues. Atom "ATOM A07OD O4' G a 947 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DM9 O5' U a1307 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DU2 O4' C a1320 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AM7 O4' U a1126 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DMW O4' U a1308 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0WLF O4' C v 56 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C6E O4' G a1220 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D5Q O4' G a1279 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AZW O4' C a1149 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08D8 O4' U a 989 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DL0 O5' G a1305 .*. O " rejected from bonding due to valence issues. Atom "ATOM A07OA O5' G a 947 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0B1O O4' A a1152 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D5N O5' G a1279 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CR9 O4' G a1255 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DZ7 O4' A a1329 .*. O " rejected from bonding due to valence issues. Atom "ATOM A07OA O5' G a 947 .*. O " rejected from bonding due to valence issues. Atom "ATOM A088H O5' U a 981 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0E25 O5' G a1334 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AM4 O5' U a1126 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0EGH O5' U a1358 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0E2S O5' U a1335 .*. O " rejected from bonding due to valence issues. Atom "ATOM 93743 O4' C a 193 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0B0G O4' A a1150 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DSR O5' A a1318 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DKD O5' G a1304 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D53 O4' G a1278 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CF8 O5' U a1235 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CRT O5' A a1256 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C4O O4' C a1217 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0ALN O4' U a1125 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D6D O4' A a1280 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DZQ O5' U a1330 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C55 O5' C a1218 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AMR O4' G a1127 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DZ4 O5' A a1329 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0E1M O4' A a1333 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0ALN O4' U a1125 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DJW O4' C a1303 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08RV O4' A a1014 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0EFV O5' A a1357 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DKD O5' G a1304 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AM7 O4' U a1126 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CQN O4' A a1254 .*. O " rejected from bonding due to valence issues. Atom "ATOM A088K O4' U a 981 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DKD O5' G a1304 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08D8 O4' U a 989 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AZT O5' C a1149 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CTO O5' C a1259 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DSR O5' A a1318 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DMC O4' U a1307 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0C6E O4' G a1220 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08G3 O4' A a 994 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0CR9 O4' G a1255 .*. O " rejected from bonding due to valence issues. Atom "ATOM A07OX O5' C a 948 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D3W O4' G a1276 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0B0Z O5' A a1151 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08TN O5' U a1017 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0EGH O5' U a1358 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AM4 O5' U a1126 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08TQ O4' U a1017 .*. O " rejected from bonding due to valence issues. Atom "ATOM A07OA O5' G a 947 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D53 O4' G a1278 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AKD O5' U a1123 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AKG O4' U a1123 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0D6A O5' A a1280 .*. O " rejected from bonding due to valence issues. Atom "ATOM A07NR O4' A a 946 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0EH4 O4' C a1359 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DLQ O4' A a1306 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0E25 O5' G a1334 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0E28 O4' G a1334 .*. O " rejected from bonding due to valence issues. Atom "ATOM A08TQ O4' U a1017 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0AOF O5' A a1130 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 68.40 Conformation dependent library (CDL) restraints added in 6.9 seconds 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10516 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 37 sheets defined 27.4% alpha, 4.8% beta 1590 base pairs and 2207 stacking pairs defined. Time for finding SS restraints: 49.83 Creating SS restraints... Processing helix chain 'V' and resid 13 through 23 removed outlier: 3.891A pdb=" N ARG V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 48 Processing helix chain 'V' and resid 53 through 57 Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'D' and resid 61 through 67 Processing helix chain 'E' and resid 24 through 36 removed outlier: 4.038A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 103 Processing helix chain 'E' and resid 107 through 112 Processing helix chain 'E' and resid 133 through 139 removed outlier: 4.192A pdb=" N LYS E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 161 removed outlier: 4.129A pdb=" N LEU E 159 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA E 161 " --> pdb=" O PHE E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'F' and resid 3 through 9 removed outlier: 4.124A pdb=" N LYS F 8 " --> pdb=" O HIS F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 61 removed outlier: 3.924A pdb=" N ALA F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP F 55 " --> pdb=" O ASN F 51 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU F 56 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 101 removed outlier: 3.513A pdb=" N GLU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE F 98 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 81 removed outlier: 4.502A pdb=" N TRP G 61 " --> pdb=" O TYR G 57 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLN G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET G 74 " --> pdb=" O LEU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 150 removed outlier: 3.583A pdb=" N GLN G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 Processing helix chain 'H' and resid 51 through 60 removed outlier: 4.239A pdb=" N GLU H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LEU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 67 removed outlier: 3.938A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 72 Processing helix chain 'H' and resid 96 through 101 Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.929A pdb=" N VAL H 115 " --> pdb=" O LYS H 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 28 Processing helix chain 'J' and resid 29 through 34 Processing helix chain 'J' and resid 66 through 71 removed outlier: 3.997A pdb=" N ARG J 69 " --> pdb=" O GLY J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 94 Processing helix chain 'J' and resid 100 through 109 removed outlier: 4.153A pdb=" N VAL J 105 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY J 107 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.897A pdb=" N MET J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 118 Processing helix chain 'L' and resid 128 through 133 Processing helix chain 'M' and resid 43 through 52 Processing helix chain 'M' and resid 109 through 118 removed outlier: 3.776A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA M 116 " --> pdb=" O LEU M 112 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 31 removed outlier: 5.047A pdb=" N MET N 24 " --> pdb=" O MET N 20 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU N 28 " --> pdb=" O MET N 24 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 53 removed outlier: 3.674A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL N 48 " --> pdb=" O LEU N 44 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 61 through 65 removed outlier: 3.934A pdb=" N LEU N 65 " --> pdb=" O ASN N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 82 Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.771A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 12 Processing helix chain 'O' and resid 14 through 18 removed outlier: 4.061A pdb=" N LYS O 17 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU O 18 " --> pdb=" O ARG O 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 14 through 18' Processing helix chain 'O' and resid 68 through 83 removed outlier: 3.577A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL O 74 " --> pdb=" O ALA O 70 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL O 78 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 112 removed outlier: 3.600A pdb=" N ALA O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 18 removed outlier: 5.216A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS Q 13 " --> pdb=" O ALA Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.664A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 68 removed outlier: 4.574A pdb=" N ILE Q 39 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS Q 40 " --> pdb=" O GLN Q 36 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN Q 55 " --> pdb=" O GLN Q 51 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU Q 59 " --> pdb=" O GLN Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 72 Processing helix chain 'Q' and resid 74 through 84 removed outlier: 3.601A pdb=" N ILE Q 79 " --> pdb=" O TYR Q 75 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS Q 84 " --> pdb=" O ASN Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 95 No H-bonds generated for 'chain 'Q' and resid 93 through 95' Processing helix chain 'Q' and resid 96 through 101 removed outlier: 4.046A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 114 removed outlier: 3.631A pdb=" N GLU Q 110 " --> pdb=" O THR Q 106 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA Q 112 " --> pdb=" O LEU Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 24 removed outlier: 3.776A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 57 removed outlier: 3.548A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 10 removed outlier: 4.181A pdb=" N VAL T 10 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 50 removed outlier: 3.636A pdb=" N GLN T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 21 Processing helix chain 'X' and resid 22 through 27 Processing helix chain 'X' and resid 42 through 48 removed outlier: 5.749A pdb=" N ARG X 47 " --> pdb=" O LYS X 44 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG X 48 " --> pdb=" O GLN X 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 60 Processing helix chain 'Y' and resid 17 through 22 removed outlier: 3.981A pdb=" N ALA Y 21 " --> pdb=" O PRO Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 42 No H-bonds generated for 'chain 'Y' and resid 40 through 42' Processing helix chain 'Y' and resid 43 through 50 removed outlier: 3.831A pdb=" N ILE Y 47 " --> pdb=" O ILE Y 43 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA Y 49 " --> pdb=" O GLY Y 45 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL Y 50 " --> pdb=" O MET Y 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 58 removed outlier: 3.935A pdb=" N VAL Z 57 " --> pdb=" O THR Z 53 " (cutoff:3.500A) Processing helix chain '1' and resid 14 through 20 removed outlier: 3.656A pdb=" N ALA 1 20 " --> pdb=" O SER 1 17 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 13 removed outlier: 3.839A pdb=" N ASN 3 13 " --> pdb=" O LEU 3 10 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 23 Processing helix chain '3' and resid 24 through 35 removed outlier: 3.815A pdb=" N LEU 3 31 " --> pdb=" O GLY 3 27 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA 3 32 " --> pdb=" O ARG 3 28 " (cutoff:3.500A) Processing helix chain '4' and resid 5 through 13 removed outlier: 3.778A pdb=" N ALA 4 9 " --> pdb=" O THR 4 5 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA 4 10 " --> pdb=" O VAL 4 6 " (cutoff:3.500A) Processing helix chain '4' and resid 51 through 56 Processing helix chain '6' and resid 24 through 29 Processing helix chain '6' and resid 33 through 49 removed outlier: 3.701A pdb=" N LYS 6 44 " --> pdb=" O ALA 6 40 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER 6 47 " --> pdb=" O ALA 6 43 " (cutoff:3.500A) Processing helix chain '6' and resid 74 through 84 Processing helix chain '6' and resid 102 through 113 Processing helix chain '6' and resid 120 through 136 removed outlier: 3.581A pdb=" N THR 6 131 " --> pdb=" O SER 6 127 " (cutoff:3.500A) Processing helix chain 'c' and resid 7 through 11 Processing helix chain 'c' and resid 24 through 45 removed outlier: 3.749A pdb=" N ALA c 29 " --> pdb=" O THR c 25 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP c 30 " --> pdb=" O LYS c 26 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS c 44 " --> pdb=" O GLN c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.537A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 90 Processing helix chain 'c' and resid 111 through 124 removed outlier: 3.775A pdb=" N ILE c 119 " --> pdb=" O VAL c 115 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 139 removed outlier: 3.513A pdb=" N ALA c 132 " --> pdb=" O MET c 128 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL c 137 " --> pdb=" O MET c 133 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN c 139 " --> pdb=" O ARG c 135 " (cutoff:3.500A) Processing helix chain 'c' and resid 140 through 142 No H-bonds generated for 'chain 'c' and resid 140 through 142' Processing helix chain 'c' and resid 176 through 180 removed outlier: 3.742A pdb=" N ASP c 180 " --> pdb=" O LEU c 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 14 removed outlier: 4.039A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 50 through 65 removed outlier: 3.886A pdb=" N GLU d 56 " --> pdb=" O VAL d 52 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS d 57 " --> pdb=" O GLN d 53 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR d 64 " --> pdb=" O VAL d 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 81 removed outlier: 3.981A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 95 removed outlier: 3.519A pdb=" N LEU d 89 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) Processing helix chain 'd' and resid 96 through 103 removed outlier: 3.746A pdb=" N TYR d 102 " --> pdb=" O ASP d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 119 removed outlier: 3.788A pdb=" N GLN d 115 " --> pdb=" O ALA d 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 158 removed outlier: 3.531A pdb=" N LEU d 158 " --> pdb=" O VAL d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 163 Processing helix chain 'd' and resid 186 through 190 Processing helix chain 'd' and resid 195 through 203 removed outlier: 3.891A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 68 removed outlier: 3.752A pdb=" N ILE e 59 " --> pdb=" O VAL e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 115 Processing helix chain 'e' and resid 131 through 146 removed outlier: 4.484A pdb=" N ARG e 137 " --> pdb=" O ILE e 133 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE e 140 " --> pdb=" O VAL e 136 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY e 142 " --> pdb=" O ALA e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 151 through 156 Processing helix chain 'f' and resid 12 through 16 removed outlier: 3.723A pdb=" N SER f 15 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLU f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 12 through 16' Processing helix chain 'f' and resid 17 through 31 removed outlier: 3.537A pdb=" N GLU f 23 " --> pdb=" O PRO f 19 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 80 removed outlier: 3.518A pdb=" N GLU f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU f 74 " --> pdb=" O VAL f 70 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU f 75 " --> pdb=" O ILE f 71 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR f 76 " --> pdb=" O ASP f 72 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR f 77 " --> pdb=" O GLU f 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 removed outlier: 3.958A pdb=" N PHE g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 48 removed outlier: 3.568A pdb=" N ALA g 38 " --> pdb=" O LYS g 34 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER g 44 " --> pdb=" O SER g 40 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA g 45 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU g 47 " --> pdb=" O TYR g 43 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 53 removed outlier: 3.579A pdb=" N ARG g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 67 removed outlier: 4.572A pdb=" N GLU g 62 " --> pdb=" O LEU g 58 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 106 removed outlier: 4.176A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 128 removed outlier: 3.770A pdb=" N ALA g 120 " --> pdb=" O ALA g 116 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU g 122 " --> pdb=" O ARG g 118 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER g 124 " --> pdb=" O ALA g 120 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 142 removed outlier: 3.775A pdb=" N VAL g 134 " --> pdb=" O LYS g 130 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG g 137 " --> pdb=" O ALA g 133 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU g 138 " --> pdb=" O VAL g 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 19 removed outlier: 3.546A pdb=" N MET h 9 " --> pdb=" O PRO h 5 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU h 10 " --> pdb=" O ILE h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 42 removed outlier: 3.534A pdb=" N VAL h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU h 41 " --> pdb=" O ASN h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 98 Processing helix chain 'h' and resid 112 through 119 Processing helix chain 'i' and resid 48 through 53 Processing helix chain 'i' and resid 70 through 90 removed outlier: 3.709A pdb=" N ILE i 78 " --> pdb=" O GLN i 74 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU i 88 " --> pdb=" O ARG i 84 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR i 89 " --> pdb=" O ALA i 85 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 101 removed outlier: 3.521A pdb=" N ALA i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 28 removed outlier: 5.283A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE j 25 " --> pdb=" O ALA j 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 67 removed outlier: 4.382A pdb=" N VAL k 64 " --> pdb=" O PHE k 60 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA k 65 " --> pdb=" O ALA k 61 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 72 Processing helix chain 'k' and resid 93 through 103 removed outlier: 3.826A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 9 removed outlier: 3.581A pdb=" N LYS l 9 " --> pdb=" O GLN l 5 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 19 Processing helix chain 'm' and resid 27 through 35 removed outlier: 3.987A pdb=" N LEU m 33 " --> pdb=" O SER m 29 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA m 34 " --> pdb=" O LYS m 30 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA m 35 " --> pdb=" O ALA m 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 43 through 47 Processing helix chain 'm' and resid 48 through 56 removed outlier: 5.464A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU m 55 " --> pdb=" O GLN m 51 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG m 56 " --> pdb=" O ILE m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 64 through 81 Processing helix chain 'm' and resid 84 through 91 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 4 through 19 removed outlier: 3.607A pdb=" N GLU n 9 " --> pdb=" O MET n 5 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA n 14 " --> pdb=" O VAL n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 19 through 31 removed outlier: 5.783A pdb=" N GLU n 25 " --> pdb=" O ALA n 21 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU n 26 " --> pdb=" O LYS n 22 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS n 27 " --> pdb=" O ARG n 23 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE n 30 " --> pdb=" O LEU n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 48 Processing helix chain 'n' and resid 80 through 89 Processing helix chain 'o' and resid 3 through 15 removed outlier: 4.153A pdb=" N LYS o 9 " --> pdb=" O GLU o 5 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER o 12 " --> pdb=" O ALA o 8 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 44 removed outlier: 3.545A pdb=" N ALA o 29 " --> pdb=" O GLU o 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA o 33 " --> pdb=" O ALA o 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN o 34 " --> pdb=" O LEU o 30 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU o 44 " --> pdb=" O GLY o 40 " (cutoff:3.500A) Processing helix chain 'o' and resid 51 through 71 removed outlier: 3.641A pdb=" N TYR o 68 " --> pdb=" O LYS o 64 " (cutoff:3.500A) Processing helix chain 'o' and resid 73 through 81 removed outlier: 3.540A pdb=" N TYR o 77 " --> pdb=" O ASP o 73 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR o 78 " --> pdb=" O VAL o 74 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 62 removed outlier: 4.111A pdb=" N HIS p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TRP p 60 " --> pdb=" O ARG p 56 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 78 Processing helix chain 'r' and resid 24 through 28 Processing helix chain 'r' and resid 48 through 64 removed outlier: 3.780A pdb=" N GLN r 53 " --> pdb=" O LYS r 49 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE r 58 " --> pdb=" O LEU r 54 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR r 63 " --> pdb=" O LYS r 59 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU r 64 " --> pdb=" O ARG r 60 " (cutoff:3.500A) Processing helix chain 's' and resid 11 through 24 removed outlier: 4.001A pdb=" N LYS s 17 " --> pdb=" O HIS s 13 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 74 Processing helix chain 't' and resid 5 through 40 removed outlier: 3.648A pdb=" N ARG t 9 " --> pdb=" O SER t 5 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA t 16 " --> pdb=" O GLN t 12 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG t 28 " --> pdb=" O ARG t 24 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE t 30 " --> pdb=" O MET t 26 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 58 removed outlier: 3.575A pdb=" N GLN t 47 " --> pdb=" O LYS t 43 " (cutoff:3.500A) Proline residue: t 55 - end of helix removed outlier: 3.567A pdb=" N ASP t 58 " --> pdb=" O GLN t 54 " (cutoff:3.500A) Processing helix chain 't' and resid 59 through 63 Processing helix chain 't' and resid 69 through 84 removed outlier: 3.519A pdb=" N ARG t 73 " --> pdb=" O ASN t 69 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS t 74 " --> pdb=" O LYS t 70 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS t 75 " --> pdb=" O ALA t 71 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN t 81 " --> pdb=" O ASN t 77 " (cutoff:3.500A) Processing helix chain '7' and resid 41 through 44 Processing helix chain '7' and resid 45 through 61 removed outlier: 3.584A pdb=" N ASN 7 50 " --> pdb=" O VAL 7 46 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA 7 52 " --> pdb=" O MET 7 48 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU 7 53 " --> pdb=" O PHE 7 49 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU 7 55 " --> pdb=" O GLU 7 51 " (cutoff:3.500A) Processing helix chain '7' and resid 72 through 77 removed outlier: 4.279A pdb=" N GLU 7 77 " --> pdb=" O ARG 7 73 " (cutoff:3.500A) Processing helix chain '7' and resid 79 through 83 Processing helix chain '7' and resid 102 through 122 removed outlier: 4.276A pdb=" N GLN 7 108 " --> pdb=" O LYS 7 104 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER 7 109 " --> pdb=" O THR 7 105 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE 7 110 " --> pdb=" O VAL 7 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG 7 112 " --> pdb=" O GLN 7 108 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN 7 119 " --> pdb=" O ASP 7 115 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER 7 120 " --> pdb=" O LEU 7 116 " (cutoff:3.500A) Processing helix chain '7' and resid 123 through 126 Processing helix chain '7' and resid 129 through 147 removed outlier: 3.638A pdb=" N LEU 7 134 " --> pdb=" O LYS 7 130 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU 7 139 " --> pdb=" O MET 7 135 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU 7 140 " --> pdb=" O ARG 7 136 " (cutoff:3.500A) Processing helix chain '7' and resid 168 through 179 removed outlier: 3.534A pdb=" N ALA 7 175 " --> pdb=" O ALA 7 171 " (cutoff:3.500A) Processing helix chain '7' and resid 191 through 195 removed outlier: 3.574A pdb=" N GLY 7 194 " --> pdb=" O ASP 7 191 " (cutoff:3.500A) Processing helix chain '7' and resid 205 through 222 removed outlier: 3.572A pdb=" N THR 7 210 " --> pdb=" O ILE 7 206 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR 7 219 " --> pdb=" O ALA 7 215 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU 7 222 " --> pdb=" O ALA 7 218 " (cutoff:3.500A) Processing helix chain 'u' and resid 15 through 19 Processing helix chain 'u' and resid 28 through 33 removed outlier: 4.538A pdb=" N ARG u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 44 removed outlier: 4.036A pdb=" N THR u 41 " --> pdb=" O TYR u 37 " (cutoff:3.500A) Processing helix chain 'u' and resid 46 through 51 Processing sheet with id=AA1, first strand: chain 'V' and resid 28 through 31 removed outlier: 6.082A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN V 78 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE V 89 " --> pdb=" O ASP V 76 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP V 76 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE V 91 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA V 74 " --> pdb=" O PHE V 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AA3, first strand: chain 'G' and resid 15 through 19 removed outlier: 3.811A pdb=" N LYS G 17 " --> pdb=" O THR G 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.790A pdb=" N LYS G 84 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 95 through 96 removed outlier: 3.691A pdb=" N ILE G 102 " --> pdb=" O HIS G 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'H' and resid 128 through 130 Processing sheet with id=AA8, first strand: chain 'K' and resid 7 through 9 Processing sheet with id=AA9, first strand: chain 'K' and resid 39 through 42 removed outlier: 4.816A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 69 through 70 Processing sheet with id=AB2, first strand: chain 'M' and resid 39 through 41 Processing sheet with id=AB3, first strand: chain 'M' and resid 62 through 63 Processing sheet with id=AB4, first strand: chain 'P' and resid 62 through 63 Processing sheet with id=AB5, first strand: chain 'Y' and resid 6 through 7 Processing sheet with id=AB6, first strand: chain '2' and resid 9 through 10 Processing sheet with id=AB7, first strand: chain '6' and resid 8 through 12 Processing sheet with id=AB8, first strand: chain '6' and resid 98 through 101 Processing sheet with id=AB9, first strand: chain 'c' and resid 51 through 55 removed outlier: 6.392A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE c 54 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR c 66 " --> pdb=" O ILE c 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 168 through 169 Processing sheet with id=AC2, first strand: chain 'd' and resid 127 through 128 Processing sheet with id=AC3, first strand: chain 'e' and resid 11 through 16 removed outlier: 6.683A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL e 38 " --> pdb=" O GLY e 46 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG e 44 " --> pdb=" O ASP e 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 21 through 23 Processing sheet with id=AC5, first strand: chain 'e' and resid 85 through 88 Processing sheet with id=AC6, first strand: chain 'e' and resid 104 through 105 Processing sheet with id=AC7, first strand: chain 'f' and resid 4 through 6 removed outlier: 3.613A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'f' and resid 41 through 46 removed outlier: 7.097A pdb=" N MET f 9 " --> pdb=" O ILE f 85 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 23 through 27 Processing sheet with id=AD1, first strand: chain 'h' and resid 73 through 76 removed outlier: 3.556A pdb=" N SER h 73 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS h 86 " --> pdb=" O GLY h 122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'h' and resid 73 through 76 removed outlier: 3.556A pdb=" N SER h 73 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE h 124 " --> pdb=" O SER h 104 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER h 104 " --> pdb=" O ILE h 124 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'i' and resid 5 through 7 removed outlier: 3.518A pdb=" N GLY i 7 " --> pdb=" O VAL i 18 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL i 18 " --> pdb=" O GLY i 7 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL i 28 " --> pdb=" O ILE i 64 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'j' and resid 10 through 12 removed outlier: 3.983A pdb=" N GLU j 47 " --> pdb=" O ILE j 67 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR j 69 " --> pdb=" O ARG j 45 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'k' and resid 29 through 32 Processing sheet with id=AD6, first strand: chain 'l' and resid 29 through 30 Processing sheet with id=AD7, first strand: chain 'l' and resid 51 through 55 Processing sheet with id=AD8, first strand: chain 'p' and resid 2 through 3 Processing sheet with id=AD9, first strand: chain 'q' and resid 19 through 22 removed outlier: 3.971A pdb=" N ILE q 20 " --> pdb=" O VAL q 45 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '7' and resid 89 through 91 928 hydrogen bonds defined for protein. 2484 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3997 hydrogen bonds 6248 hydrogen bond angles 0 basepair planarities 1590 basepair parallelities 2207 stacking parallelities Total time for adding SS restraints: 205.90 Time building geometry restraints manager: 73.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.19: 4 1.19 - 1.39: 55497 1.39 - 1.59: 90612 1.59 - 1.79: 8726 1.79 - 1.99: 198 Bond restraints: 155037 Sorted by residual: bond pdb=" C LEU u 15 " pdb=" N ARG u 16 " ideal model delta sigma weight residual 1.333 0.989 0.343 1.45e-02 4.76e+03 5.61e+02 bond pdb=" N VAL R 54 " pdb=" CA VAL R 54 " ideal model delta sigma weight residual 1.459 1.226 0.233 1.25e-02 6.40e+03 3.47e+02 bond pdb=" CA VAL R 54 " pdb=" CB VAL R 54 " ideal model delta sigma weight residual 1.540 1.776 -0.236 1.36e-02 5.41e+03 3.01e+02 bond pdb=" CA VAL R 54 " pdb=" C VAL R 54 " ideal model delta sigma weight residual 1.523 1.713 -0.190 1.27e-02 6.20e+03 2.23e+02 bond pdb=" CB PHE R 53 " pdb=" CG PHE R 53 " ideal model delta sigma weight residual 1.502 1.813 -0.311 2.30e-02 1.89e+03 1.82e+02 ... (remaining 155032 not shown) Histogram of bond angle deviations from ideal: 74.98 - 88.01: 4 88.01 - 101.04: 328 101.04 - 114.07: 125163 114.07 - 127.10: 95689 127.10 - 140.13: 10744 Bond angle restraints: 231928 Sorted by residual: angle pdb=" CA PHE R 53 " pdb=" C PHE R 53 " pdb=" N VAL R 54 " ideal model delta sigma weight residual 115.51 79.08 36.43 1.24e+00 6.50e-01 8.63e+02 angle pdb=" N ILE E 73 " pdb=" CA ILE E 73 " pdb=" C ILE E 73 " ideal model delta sigma weight residual 112.43 131.70 -19.27 9.20e-01 1.18e+00 4.39e+02 angle pdb=" N LYS E 74 " pdb=" CA LYS E 74 " pdb=" C LYS E 74 " ideal model delta sigma weight residual 112.72 90.85 21.87 1.14e+00 7.69e-01 3.68e+02 angle pdb=" C VAL R 54 " pdb=" CA VAL R 54 " pdb=" CB VAL R 54 " ideal model delta sigma weight residual 111.29 140.13 -28.84 1.64e+00 3.72e-01 3.09e+02 angle pdb=" N LEU L 6 " pdb=" CA LEU L 6 " pdb=" C LEU L 6 " ideal model delta sigma weight residual 111.90 134.26 -22.36 1.32e+00 5.74e-01 2.87e+02 ... (remaining 231923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 86263 35.79 - 71.58: 11694 71.58 - 107.36: 1301 107.36 - 143.15: 35 143.15 - 178.94: 44 Dihedral angle restraints: 99337 sinusoidal: 83030 harmonic: 16307 Sorted by residual: dihedral pdb=" N VAL R 54 " pdb=" C VAL R 54 " pdb=" CA VAL R 54 " pdb=" CB VAL R 54 " ideal model delta harmonic sigma weight residual 123.40 70.08 53.32 0 2.50e+00 1.60e-01 4.55e+02 dihedral pdb=" C5' C a1397 " pdb=" C4' C a1397 " pdb=" C3' C a1397 " pdb=" O3' C a1397 " ideal model delta sinusoidal sigma weight residual 147.00 73.27 73.73 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C LYS 1 52 " pdb=" N LYS 1 52 " pdb=" CA LYS 1 52 " pdb=" CB LYS 1 52 " ideal model delta harmonic sigma weight residual -122.60 -96.65 -25.95 0 2.50e+00 1.60e-01 1.08e+02 ... (remaining 99334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 28348 0.183 - 0.367: 1155 0.367 - 0.550: 92 0.550 - 0.734: 31 0.734 - 0.917: 13 Chirality restraints: 29639 Sorted by residual: chirality pdb=" CA PRO C 28 " pdb=" N PRO C 28 " pdb=" C PRO C 28 " pdb=" CB PRO C 28 " both_signs ideal model delta sigma weight residual False 2.72 1.80 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CB VAL R 54 " pdb=" CA VAL R 54 " pdb=" CG1 VAL R 54 " pdb=" CG2 VAL R 54 " both_signs ideal model delta sigma weight residual False -2.63 -3.54 0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" C3' G B1250 " pdb=" C4' G B1250 " pdb=" O3' G B1250 " pdb=" C2' G B1250 " both_signs ideal model delta sigma weight residual False -2.74 -1.83 -0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 29636 not shown) Planarity restraints: 12421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 75 " -0.307 2.00e-02 2.50e+03 1.69e-01 5.69e+02 pdb=" CG TYR J 75 " 0.110 2.00e-02 2.50e+03 pdb=" CD1 TYR J 75 " 0.123 2.00e-02 2.50e+03 pdb=" CD2 TYR J 75 " 0.127 2.00e-02 2.50e+03 pdb=" CE1 TYR J 75 " 0.083 2.00e-02 2.50e+03 pdb=" CE2 TYR J 75 " 0.091 2.00e-02 2.50e+03 pdb=" CZ TYR J 75 " 0.042 2.00e-02 2.50e+03 pdb=" OH TYR J 75 " -0.269 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B2272 " -0.068 2.00e-02 2.50e+03 1.57e-01 5.55e+02 pdb=" N1 U B2272 " -0.066 2.00e-02 2.50e+03 pdb=" C2 U B2272 " 0.017 2.00e-02 2.50e+03 pdb=" O2 U B2272 " -0.035 2.00e-02 2.50e+03 pdb=" N3 U B2272 " 0.172 2.00e-02 2.50e+03 pdb=" C4 U B2272 " 0.213 2.00e-02 2.50e+03 pdb=" O4 U B2272 " -0.338 2.00e-02 2.50e+03 pdb=" C5 U B2272 " 0.145 2.00e-02 2.50e+03 pdb=" C6 U B2272 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B1060 " -0.149 2.00e-02 2.50e+03 1.51e-01 5.10e+02 pdb=" N1 U B1060 " -0.034 2.00e-02 2.50e+03 pdb=" C2 U B1060 " 0.031 2.00e-02 2.50e+03 pdb=" O2 U B1060 " 0.007 2.00e-02 2.50e+03 pdb=" N3 U B1060 " 0.135 2.00e-02 2.50e+03 pdb=" C4 U B1060 " 0.168 2.00e-02 2.50e+03 pdb=" O4 U B1060 " -0.331 2.00e-02 2.50e+03 pdb=" C5 U B1060 " 0.150 2.00e-02 2.50e+03 pdb=" C6 U B1060 " 0.023 2.00e-02 2.50e+03 ... (remaining 12418 not shown) Histogram of nonbonded interaction distances: 0.15 - 1.10: 496 1.10 - 2.05: 2629 2.05 - 3.00: 85479 3.00 - 3.95: 488095 3.95 - 4.90: 790612 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1367311 Sorted by model distance: nonbonded pdb=" C VAL c 75 " pdb=" CA SER j 54 " model vdw 0.154 3.700 nonbonded pdb=" N4 C a1262 " pdb=" CZ2 TRP n 100 " model vdw 0.199 3.420 nonbonded pdb=" CA PHE F 137 " pdb=" CB ARG m 112 " model vdw 0.257 3.870 nonbonded pdb=" N1 C a1359 " pdb=" CA PRO n 69 " model vdw 0.309 3.550 nonbonded pdb=" N6 A a1012 " pdb=" CA VAL n 33 " model vdw 0.335 3.550 ... (remaining 1367306 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 9.230 Check model and map are aligned: 1.500 Set scattering table: 0.960 Process input model: 478.850 Find NCS groups from input model: 2.560 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 496.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 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 0.343 155037 Z= 0.358 Angle : 1.253 36.427 231928 Z= 0.798 Chirality : 0.096 0.917 29639 Planarity : 0.014 0.188 12421 Dihedral : 24.374 178.941 88821 Min Nonbonded Distance : 0.154 Molprobity Statistics. All-atom Clashscore : 55.29 Ramachandran Plot: Outliers : 14.74 % Allowed : 26.57 % Favored : 58.69 % Rotamer: Outliers : 23.17 % Allowed : 18.21 % Favored : 58.62 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.52 % 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: -7.10 (0.07), residues: 5631 helix: -4.33 (0.08), residues: 1315 sheet: -4.73 (0.15), residues: 646 loop : -5.23 (0.07), residues: 3670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.007 TRP P 30 HIS 0.013 0.001 HIS J 80 PHE 0.127 0.010 PHE L 66 TYR 0.307 0.013 TYR J 75 ARG 0.041 0.001 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3148 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1082 poor density : 2066 time to evaluate : 5.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 31 TYR cc_start: 0.7044 (p90) cc_final: 0.6688 (p90) REVERT: C 33 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7219 (tp) REVERT: C 36 ASN cc_start: 0.5474 (OUTLIER) cc_final: 0.5044 (p0) REVERT: C 58 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6143 (tptt) REVERT: C 83 ASP cc_start: 0.8089 (t0) cc_final: 0.7631 (t0) REVERT: C 84 PRO cc_start: 0.7675 (OUTLIER) cc_final: 0.7448 (Cg_exo) REVERT: C 102 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7265 (t80) REVERT: C 127 ASN cc_start: 0.0890 (OUTLIER) cc_final: -0.0217 (t0) REVERT: C 235 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5622 (pt0) REVERT: C 237 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.6638 (ptp-170) REVERT: C 250 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: C 261 ARG cc_start: 0.5439 (OUTLIER) cc_final: 0.3172 (ttp80) REVERT: D 28 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.6037 (tt0) REVERT: D 99 GLU cc_start: 0.5516 (OUTLIER) cc_final: 0.5199 (pm20) REVERT: D 161 MET cc_start: 0.6545 (OUTLIER) cc_final: 0.6196 (mmm) REVERT: E 78 TRP cc_start: 0.7734 (OUTLIER) cc_final: 0.7422 (m-10) REVERT: E 90 GLN cc_start: 0.7658 (pt0) cc_final: 0.7167 (mm-40) REVERT: E 109 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8566 (tp) REVERT: E 114 ARG cc_start: 0.5791 (OUTLIER) cc_final: 0.5357 (tpt90) REVERT: E 132 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6083 (ptpt) REVERT: E 148 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7735 (pt) REVERT: E 159 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.5132 (pt) REVERT: G 150 TYR cc_start: 0.5621 (OUTLIER) cc_final: 0.4685 (m-80) REVERT: H 1 MET cc_start: 0.1721 (OUTLIER) cc_final: 0.1109 (ppp) REVERT: H 2 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.6076 (mm-40) REVERT: H 54 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.4826 (pp) REVERT: J 108 MET cc_start: 0.8274 (mtt) cc_final: 0.7904 (mtp) REVERT: K 7 MET cc_start: 0.8585 (mmp) cc_final: 0.8366 (mmp) REVERT: K 32 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: K 64 ARG cc_start: 0.8677 (mpp-170) cc_final: 0.8367 (ptt-90) REVERT: K 86 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7913 (mt) REVERT: K 87 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7992 (mp) REVERT: L 29 LYS cc_start: -0.0174 (OUTLIER) cc_final: -0.1325 (ttpp) REVERT: L 85 VAL cc_start: 0.7004 (p) cc_final: 0.6769 (p) REVERT: L 92 LEU cc_start: 0.4037 (OUTLIER) cc_final: 0.3624 (tt) REVERT: L 105 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.7858 (pt) REVERT: L 106 GLU cc_start: 0.6053 (OUTLIER) cc_final: 0.5554 (pm20) REVERT: M 14 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6674 (pptt) REVERT: M 36 VAL cc_start: 0.6736 (OUTLIER) cc_final: 0.6465 (m) REVERT: M 38 ARG cc_start: 0.7751 (mtt90) cc_final: 0.7457 (mmt90) REVERT: M 71 LYS cc_start: 0.6478 (OUTLIER) cc_final: 0.6095 (tptp) REVERT: M 109 PRO cc_start: 0.7883 (OUTLIER) cc_final: 0.6837 (Cg_endo) REVERT: N 1 MET cc_start: 0.2276 (OUTLIER) cc_final: 0.0928 (ptp) REVERT: N 36 THR cc_start: 0.8288 (t) cc_final: 0.8077 (t) REVERT: N 42 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8069 (pptt) REVERT: N 103 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6328 (ttp80) REVERT: O 3 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6424 (tptp) REVERT: O 12 THR cc_start: 0.7036 (p) cc_final: 0.6475 (t) REVERT: O 32 PRO cc_start: 0.6815 (OUTLIER) cc_final: 0.6518 (Cg_exo) REVERT: O 60 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.5396 (tp30) REVERT: O 85 LYS cc_start: 0.5356 (OUTLIER) cc_final: 0.5126 (mptt) REVERT: P 42 PHE cc_start: 0.5478 (OUTLIER) cc_final: 0.5263 (p90) REVERT: P 63 ILE cc_start: 0.7982 (mp) cc_final: 0.7744 (mp) REVERT: P 71 ARG cc_start: 0.5586 (mmt180) cc_final: 0.5283 (mmt180) REVERT: R 12 HIS cc_start: 0.6566 (OUTLIER) cc_final: 0.5843 (m170) REVERT: R 13 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.5286 (tmt-80) REVERT: R 83 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.6630 (m-80) REVERT: S 1 MET cc_start: -0.1143 (mtm) cc_final: -0.2349 (mtm) REVERT: S 8 ARG cc_start: 0.7050 (mmt180) cc_final: 0.6307 (mtt-85) REVERT: S 13 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8240 (p) REVERT: S 42 LYS cc_start: 0.7487 (ttpt) cc_final: 0.7239 (tptm) REVERT: S 84 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.5684 (tpp-160) REVERT: S 96 ILE cc_start: 0.7927 (mt) cc_final: 0.7633 (mt) REVERT: T 28 ASN cc_start: 0.6862 (OUTLIER) cc_final: 0.6531 (t0) REVERT: T 53 VAL cc_start: 0.6867 (m) cc_final: 0.6658 (m) REVERT: U 32 LYS cc_start: 0.4716 (pttt) cc_final: 0.4237 (mmmt) REVERT: U 61 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5979 (pm20) REVERT: U 72 PHE cc_start: 0.5945 (OUTLIER) cc_final: 0.4744 (p90) REVERT: U 81 ARG cc_start: 0.3589 (OUTLIER) cc_final: 0.2398 (mtp180) REVERT: U 87 GLU cc_start: 0.6165 (tt0) cc_final: 0.4826 (mm-30) REVERT: U 88 ASP cc_start: 0.4714 (OUTLIER) cc_final: 0.2502 (m-30) REVERT: U 94 PHE cc_start: 0.2785 (t80) cc_final: 0.2316 (t80) REVERT: U 95 PHE cc_start: 0.4178 (OUTLIER) cc_final: 0.2079 (m-80) REVERT: W 2 HIS cc_start: 0.3168 (OUTLIER) cc_final: 0.2427 (t70) REVERT: W 13 ARG cc_start: 0.7451 (mmt90) cc_final: 0.6453 (mmp-170) REVERT: W 18 LYS cc_start: 0.2954 (OUTLIER) cc_final: 0.1216 (ttmt) REVERT: X 44 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6790 (mptt) REVERT: Y 39 ASP cc_start: 0.5000 (OUTLIER) cc_final: 0.4711 (p0) REVERT: Z 1 MET cc_start: 0.6542 (ttt) cc_final: 0.6315 (ttm) REVERT: Z 15 SER cc_start: 0.7175 (OUTLIER) cc_final: 0.6925 (p) REVERT: Z 25 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6111 (ttp80) REVERT: Z 35 ASP cc_start: 0.6446 (OUTLIER) cc_final: 0.5731 (m-30) REVERT: Z 47 LYS cc_start: 0.8273 (pttt) cc_final: 0.7701 (pttt) REVERT: Z 60 PHE cc_start: 0.6011 (m-10) cc_final: 0.5767 (m-10) REVERT: 1 49 ARG cc_start: 0.5421 (OUTLIER) cc_final: 0.5191 (ttt90) REVERT: 2 36 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6551 (mttt) REVERT: 3 26 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.7103 (m-40) REVERT: 3 34 ARG cc_start: 0.8285 (ttt90) cc_final: 0.8065 (ttt90) REVERT: 5 23 ILE cc_start: 0.0056 (OUTLIER) cc_final: -0.0548 (pt) REVERT: 5 36 ARG cc_start: 0.5291 (OUTLIER) cc_final: 0.4330 (ttt180) REVERT: c 68 HIS cc_start: 0.7706 (m-70) cc_final: 0.7380 (m170) REVERT: c 88 LYS cc_start: 0.8283 (tmtp) cc_final: 0.7734 (mptt) REVERT: c 183 TYR cc_start: 0.7563 (t80) cc_final: 0.6893 (t80) REVERT: d 136 VAL cc_start: 0.7306 (t) cc_final: 0.7007 (t) REVERT: d 188 SER cc_start: 0.7714 (m) cc_final: 0.6166 (p) REVERT: e 73 VAL cc_start: 0.7956 (t) cc_final: 0.7718 (m) REVERT: e 81 GLN cc_start: 0.4856 (OUTLIER) cc_final: 0.4638 (pm20) REVERT: f 6 ILE cc_start: 0.8957 (tp) cc_final: 0.8639 (tp) REVERT: f 75 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6208 (pp20) REVERT: f 96 VAL cc_start: 0.7545 (t) cc_final: 0.7323 (t) REVERT: g 32 ASP cc_start: 0.6397 (m-30) cc_final: 0.6171 (m-30) REVERT: g 49 LEU cc_start: 0.5548 (mt) cc_final: 0.4994 (mt) REVERT: g 57 GLU cc_start: 0.3213 (mm-30) cc_final: 0.2882 (tm-30) REVERT: g 74 VAL cc_start: 0.7874 (OUTLIER) cc_final: 0.7173 (t) REVERT: g 135 LYS cc_start: 0.7757 (ttmt) cc_final: 0.7511 (mmmm) REVERT: h 29 SER cc_start: 0.8471 (t) cc_final: 0.7909 (m) REVERT: h 55 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6348 (mmmt) REVERT: h 61 THR cc_start: 0.5144 (OUTLIER) cc_final: 0.4695 (p) REVERT: h 107 LYS cc_start: 0.8243 (mptm) cc_final: 0.8014 (mmmt) REVERT: i 38 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: i 58 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6971 (mm-30) REVERT: i 65 THR cc_start: 0.8232 (m) cc_final: 0.7762 (p) REVERT: i 112 ARG cc_start: 0.7993 (ptm160) cc_final: 0.7421 (ttt180) REVERT: k 83 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8070 (m) REVERT: k 115 ILE cc_start: 0.5256 (OUTLIER) cc_final: 0.5020 (pp) REVERT: l 18 SER cc_start: 0.5791 (OUTLIER) cc_final: 0.5168 (p) REVERT: l 20 VAL cc_start: 0.6777 (OUTLIER) cc_final: 0.6565 (p) REVERT: l 48 LEU cc_start: 0.7100 (pt) cc_final: 0.6770 (mm) REVERT: l 74 GLN cc_start: 0.6722 (tm-30) cc_final: 0.6318 (tm-30) REVERT: m 74 MET cc_start: 0.6485 (ttp) cc_final: 0.5972 (mmt) REVERT: m 81 ASP cc_start: -0.2480 (OUTLIER) cc_final: -0.2974 (p0) REVERT: o 64 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7149 (mmmt) REVERT: o 80 LEU cc_start: 0.8388 (tt) cc_final: 0.8171 (tp) REVERT: p 6 LEU cc_start: 0.7869 (mp) cc_final: 0.7523 (mp) REVERT: p 16 PHE cc_start: 0.7185 (t80) cc_final: 0.6754 (t80) REVERT: p 26 ASN cc_start: 0.6355 (OUTLIER) cc_final: 0.5996 (m110) REVERT: q 27 PHE cc_start: 0.7146 (m-80) cc_final: 0.6789 (m-10) REVERT: q 33 TYR cc_start: 0.7662 (m-80) cc_final: 0.6785 (m-80) REVERT: s 20 LYS cc_start: 0.5592 (OUTLIER) cc_final: 0.4937 (mtmt) REVERT: s 59 VAL cc_start: 0.2266 (t) cc_final: 0.1663 (t) REVERT: t 19 HIS cc_start: 0.7503 (t-90) cc_final: 0.7237 (t70) REVERT: t 20 ASN cc_start: 0.7478 (m110) cc_final: 0.7182 (t0) REVERT: t 33 LYS cc_start: 0.8094 (mttt) cc_final: 0.7842 (mmtt) REVERT: t 34 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8740 (t) REVERT: 7 9 LEU cc_start: 0.2267 (OUTLIER) cc_final: 0.0058 (tt) REVERT: 7 47 PRO cc_start: 0.8937 (Cg_exo) cc_final: 0.7640 (Cg_endo) REVERT: 7 99 MET cc_start: 0.7375 (ptp) cc_final: 0.6462 (ptp) REVERT: 7 140 LEU cc_start: 0.8348 (mt) cc_final: 0.7811 (tp) REVERT: 7 180 ILE cc_start: 0.8355 (mm) cc_final: 0.8087 (mm) REVERT: 7 185 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7140 (tt) REVERT: u 5 VAL cc_start: 0.7199 (t) cc_final: 0.6857 (t) REVERT: u 16 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.5292 (mmm160) REVERT: u 36 PHE cc_start: 0.3848 (m-80) cc_final: 0.3563 (m-10) outliers start: 1082 outliers final: 294 residues processed: 2663 average time/residue: 1.4017 time to fit residues: 6135.3073 Evaluate side-chains 1685 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 377 poor density : 1308 time to evaluate : 5.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain C residue 14 HIS Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 28 PRO Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 84 PRO Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 167 ASN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 78 TRP Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 114 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 142 TYR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 47 PHE Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 71 LYS Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 LYS Chi-restraints excluded: chain M residue 109 PRO Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain N residue 112 TYR Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 3 LYS Chi-restraints excluded: chain O residue 32 PRO Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 64 TYR Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 85 LYS Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 42 PHE Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 74 GLN Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 36 GLN Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 13 ARG Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 60 HIS Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 84 ARG Chi-restraints excluded: chain S residue 88 ARG Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 110 ARG Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 72 PHE Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain U residue 85 ARG Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 95 PHE Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 18 LYS Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 45 HIS Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain W residue 76 ARG Chi-restraints excluded: chain W residue 84 GLU Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 38 GLN Chi-restraints excluded: chain X residue 41 HIS Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Z residue 6 HIS Chi-restraints excluded: chain Z residue 8 LYS Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 30 HIS Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 33 ASN Chi-restraints excluded: chain Z residue 35 ASP Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 49 ARG Chi-restraints excluded: chain 1 residue 52 LYS Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 2 residue 5 ARG Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 36 LYS Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 3 residue 26 ASN Chi-restraints excluded: chain 4 residue 4 LYS Chi-restraints excluded: chain 4 residue 21 PHE Chi-restraints excluded: chain 4 residue 25 HIS Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 5 residue 23 ILE Chi-restraints excluded: chain 5 residue 33 HIS Chi-restraints excluded: chain 5 residue 36 ARG Chi-restraints excluded: chain 6 residue 141 ASP Chi-restraints excluded: chain c residue 31 ASN Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 205 GLU Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 25 ARG Chi-restraints excluded: chain d residue 39 GLN Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 154 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 183 ARG Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 81 GLN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 151 MET Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 75 GLU Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 19 SER Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 55 LYS Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 38 PHE Chi-restraints excluded: chain i residue 44 ARG Chi-restraints excluded: chain i residue 58 GLU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 81 GLU Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 89 ARG Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 18 SER Chi-restraints excluded: chain l residue 20 VAL Chi-restraints excluded: chain l residue 103 CYS Chi-restraints excluded: chain m residue 2 ARG Chi-restraints excluded: chain m residue 11 HIS Chi-restraints excluded: chain m residue 18 LEU Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 41 ASP Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 62 PHE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 81 ASP Chi-restraints excluded: chain m residue 99 GLN Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain m residue 102 LYS Chi-restraints excluded: chain m residue 106 ARG Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 45 LEU Chi-restraints excluded: chain n residue 50 LEU Chi-restraints excluded: chain n residue 65 GLN Chi-restraints excluded: chain n residue 73 LEU Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 17 ASP Chi-restraints excluded: chain o residue 64 LYS Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 26 ASN Chi-restraints excluded: chain q residue 10 ARG Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 52 CYS Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 20 LYS Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 72 GLU Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain 7 residue 9 LEU Chi-restraints excluded: chain 7 residue 38 HIS Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 69 VAL Chi-restraints excluded: chain 7 residue 90 PHE Chi-restraints excluded: chain 7 residue 128 LEU Chi-restraints excluded: chain 7 residue 185 ILE Chi-restraints excluded: chain 7 residue 188 THR Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 17 ARG Chi-restraints excluded: chain u residue 33 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 848 optimal weight: 6.9990 chunk 761 optimal weight: 10.0000 chunk 422 optimal weight: 8.9990 chunk 260 optimal weight: 10.0000 chunk 513 optimal weight: 5.9990 chunk 406 optimal weight: 0.6980 chunk 787 optimal weight: 9.9990 chunk 304 optimal weight: 10.0000 chunk 478 optimal weight: 8.9990 chunk 586 optimal weight: 3.9990 chunk 912 optimal weight: 30.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 75 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN C 250 GLN D 32 ASN D 49 GLN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN D 164 GLN D 167 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 97 ASN E 136 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 26 GLN F 36 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS G 138 GLN H 2 GLN H 28 ASN J 128 ASN J 131 ASN ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN K 88 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN O 34 HIS ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN O 104 GLN P 2 ASN ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 GLN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 ASN T 59 ASN U 26 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 38 GLN X 39 GLN Y 8 GLN 1 4 GLN ** 4 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 13 ASN 6 11 GLN 6 29 GLN 6 93 ASN c 5 HIS c 31 ASN d 39 GLN ** d 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 99 ASN ** d 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 147 ASN f 14 GLN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN g 67 ASN g 85 GLN h 15 ASN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 74 GLN i 109 GLN ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 GLN k 23 HIS k 27 ASN k 37 GLN l 5 GLN l 45 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 61 ASN n 65 GLN o 36 ASN o 39 GLN ** p 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 13 HIS ** s 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 51 HIS s 55 GLN t 12 GLN t 20 ASN ** t 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 23 ASN 7 119 GLN 7 169 HIS ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.989 155037 Z= 0.715 Angle : 1.372 60.780 231928 Z= 0.671 Chirality : 0.065 2.763 29639 Planarity : 0.011 0.230 12421 Dihedral : 24.312 179.192 78469 Min Nonbonded Distance : 1.314 Molprobity Statistics. All-atom Clashscore : 35.96 Ramachandran Plot: Outliers : 4.78 % Allowed : 24.77 % Favored : 70.45 % Rotamer: Outliers : 15.72 % Allowed : 25.47 % Favored : 58.81 % Cbeta Deviations : 0.70 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 2.60 % Twisted General : 1.00 % 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: -6.08 (0.08), residues: 5631 helix: -3.11 (0.11), residues: 1375 sheet: -4.11 (0.17), residues: 628 loop : -4.73 (0.08), residues: 3628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP n 100 HIS 0.034 0.003 HIS j 56 PHE 0.164 0.004 PHE F 113 TYR 0.155 0.004 TYR j 65 ARG 0.038 0.002 ARG m 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2152 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 734 poor density : 1418 time to evaluate : 5.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 44 HIS cc_start: 0.7515 (t70) cc_final: 0.7186 (t-170) REVERT: V 48 MET cc_start: 0.5843 (tpt) cc_final: 0.5267 (tpt) REVERT: V 56 PHE cc_start: 0.6308 (t80) cc_final: 0.5833 (t80) REVERT: C 36 ASN cc_start: 0.6941 (OUTLIER) cc_final: 0.6209 (p0) REVERT: C 42 ARG cc_start: 0.5994 (ttt180) cc_final: 0.5700 (ptm160) REVERT: C 44 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8106 (m-40) REVERT: C 58 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7813 (tptp) REVERT: C 83 ASP cc_start: 0.8424 (t0) cc_final: 0.7713 (t0) REVERT: C 102 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7234 (t80) REVERT: C 173 LEU cc_start: 0.7178 (mt) cc_final: 0.6798 (mt) REVERT: C 235 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.6030 (pt0) REVERT: C 250 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6946 (tt0) REVERT: D 28 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6905 (tt0) REVERT: D 35 THR cc_start: 0.4304 (OUTLIER) cc_final: 0.4081 (m) REVERT: D 118 PHE cc_start: 0.9032 (t80) cc_final: 0.8570 (t80) REVERT: E 18 THR cc_start: 0.5083 (OUTLIER) cc_final: 0.4278 (m) REVERT: E 88 ARG cc_start: 0.7688 (mmt90) cc_final: 0.7261 (tpp-160) REVERT: E 148 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8278 (pt) REVERT: E 159 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5680 (pt) REVERT: E 189 THR cc_start: 0.5465 (OUTLIER) cc_final: 0.5173 (p) REVERT: E 199 MET cc_start: 0.6431 (ptp) cc_final: 0.5922 (ptp) REVERT: F 16 MET cc_start: 0.3829 (tpp) cc_final: 0.2815 (mtt) REVERT: F 32 LYS cc_start: 0.7781 (pptt) cc_final: 0.6918 (pptt) REVERT: G 21 GLN cc_start: 0.1291 (tm-30) cc_final: 0.0826 (pm20) REVERT: G 43 LYS cc_start: 0.5869 (OUTLIER) cc_final: 0.5366 (mptt) REVERT: G 84 LYS cc_start: 0.7146 (ptpt) cc_final: 0.6258 (tptt) REVERT: G 150 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.5948 (m-80) REVERT: H 1 MET cc_start: 0.1388 (ppp) cc_final: 0.0799 (ppp) REVERT: H 2 GLN cc_start: 0.6443 (OUTLIER) cc_final: 0.5954 (mm-40) REVERT: H 132 PHE cc_start: 0.2364 (OUTLIER) cc_final: 0.1131 (t80) REVERT: J 98 GLU cc_start: 0.5160 (OUTLIER) cc_final: 0.3977 (mm-30) REVERT: J 108 MET cc_start: 0.8640 (mtt) cc_final: 0.7974 (mtt) REVERT: J 122 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6665 (pp) REVERT: J 125 TYR cc_start: 0.7839 (m-80) cc_final: 0.7388 (m-80) REVERT: J 137 PRO cc_start: 0.5873 (OUTLIER) cc_final: 0.5591 (Cg_exo) REVERT: K 31 ARG cc_start: 0.8526 (mtt90) cc_final: 0.8236 (mtm-85) REVERT: K 79 PHE cc_start: 0.7704 (m-80) cc_final: 0.7414 (m-10) REVERT: K 86 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8471 (mt) REVERT: K 112 PHE cc_start: 0.6798 (m-80) cc_final: 0.6409 (m-10) REVERT: L 61 LEU cc_start: 0.4486 (OUTLIER) cc_final: 0.4274 (mm) REVERT: M 1 MET cc_start: 0.3590 (OUTLIER) cc_final: 0.2033 (tmm) REVERT: M 8 LYS cc_start: 0.4954 (OUTLIER) cc_final: 0.4488 (mmtm) REVERT: M 38 ARG cc_start: 0.7743 (mtt90) cc_final: 0.7313 (mmt90) REVERT: M 71 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6055 (tttp) REVERT: N 1 MET cc_start: 0.2065 (OUTLIER) cc_final: 0.0217 (ptp) REVERT: N 24 MET cc_start: 0.7486 (ttp) cc_final: 0.7054 (ttp) REVERT: N 32 GLU cc_start: 0.7970 (tt0) cc_final: 0.7133 (tt0) REVERT: N 36 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.8076 (t) REVERT: O 8 ILE cc_start: 0.1788 (OUTLIER) cc_final: 0.1579 (mp) REVERT: O 60 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.5927 (tp30) REVERT: O 85 LYS cc_start: 0.4115 (OUTLIER) cc_final: 0.3882 (mptt) REVERT: O 94 ARG cc_start: 0.5083 (ptm160) cc_final: 0.4859 (ptm-80) REVERT: Q 49 ARG cc_start: 0.6864 (tpm-80) cc_final: 0.6572 (tpp-160) REVERT: Q 55 GLN cc_start: 0.7678 (tt0) cc_final: 0.7473 (tm-30) REVERT: Q 82 LEU cc_start: 0.8030 (tt) cc_final: 0.7804 (tp) REVERT: Q 101 ASP cc_start: 0.7300 (t0) cc_final: 0.7061 (t0) REVERT: R 12 HIS cc_start: 0.6390 (OUTLIER) cc_final: 0.5676 (m170) REVERT: R 13 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6033 (tmt-80) REVERT: R 83 TYR cc_start: 0.6554 (OUTLIER) cc_final: 0.5786 (m-80) REVERT: S 53 SER cc_start: 0.8938 (m) cc_final: 0.8562 (t) REVERT: S 82 MET cc_start: 0.5786 (mmm) cc_final: 0.5500 (tpp) REVERT: S 90 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6271 (mptt) REVERT: T 31 VAL cc_start: 0.6803 (OUTLIER) cc_final: 0.6430 (t) REVERT: U 72 PHE cc_start: 0.5316 (OUTLIER) cc_final: 0.3866 (p90) REVERT: U 84 PHE cc_start: 0.4241 (t80) cc_final: 0.3930 (t80) REVERT: U 88 ASP cc_start: 0.4063 (OUTLIER) cc_final: 0.2598 (t0) REVERT: W 66 VAL cc_start: 0.8874 (p) cc_final: 0.8619 (p) REVERT: X 2 LYS cc_start: 0.3714 (OUTLIER) cc_final: 0.3449 (pptt) REVERT: X 31 GLN cc_start: 0.5612 (pp30) cc_final: 0.4902 (tp-100) REVERT: X 44 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7268 (mptt) REVERT: Z 15 SER cc_start: 0.7392 (OUTLIER) cc_final: 0.7107 (p) REVERT: Z 25 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6478 (ttp80) REVERT: 2 6 GLU cc_start: 0.4610 (OUTLIER) cc_final: 0.3757 (tm-30) REVERT: 2 10 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6388 (mp) REVERT: 2 11 VAL cc_start: 0.5403 (OUTLIER) cc_final: 0.4845 (t) REVERT: 2 36 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6805 (mttt) REVERT: 3 26 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7291 (m-40) REVERT: 3 34 ARG cc_start: 0.8435 (ttt90) cc_final: 0.8185 (ttt90) REVERT: 3 35 ARG cc_start: 0.8530 (ttp-110) cc_final: 0.8105 (ttp80) REVERT: 4 51 LYS cc_start: 0.6793 (tttt) cc_final: 0.6521 (ptmt) REVERT: 5 4 ARG cc_start: 0.5947 (ttt-90) cc_final: 0.5742 (ttt-90) REVERT: 6 63 ASP cc_start: -0.0840 (OUTLIER) cc_final: -0.1603 (p0) REVERT: c 13 ILE cc_start: 0.8387 (pt) cc_final: 0.8063 (mp) REVERT: c 58 ARG cc_start: 0.0465 (OUTLIER) cc_final: -0.0163 (mtt-85) REVERT: c 74 ILE cc_start: 0.5894 (tt) cc_final: 0.5572 (mm) REVERT: c 106 ARG cc_start: 0.8677 (mmt180) cc_final: 0.8314 (tpp-160) REVERT: d 25 ARG cc_start: 0.5915 (OUTLIER) cc_final: 0.4486 (ppt-90) REVERT: d 109 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.6962 (p) REVERT: d 143 SER cc_start: 0.8385 (p) cc_final: 0.7778 (m) REVERT: d 167 PRO cc_start: 0.6444 (Cg_exo) cc_final: 0.6203 (Cg_endo) REVERT: e 155 LYS cc_start: 0.6566 (ttmt) cc_final: 0.6239 (mtmm) REVERT: h 9 MET cc_start: 0.7864 (tpt) cc_final: 0.7575 (tpt) REVERT: h 29 SER cc_start: 0.8613 (t) cc_final: 0.8082 (p) REVERT: h 120 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7475 (pp) REVERT: i 35 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: i 44 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.2536 (ppt90) REVERT: i 61 ASP cc_start: 0.7349 (t0) cc_final: 0.6461 (t0) REVERT: i 64 ILE cc_start: 0.8483 (mp) cc_final: 0.8201 (mm) REVERT: i 67 LYS cc_start: 0.9042 (pttm) cc_final: 0.8549 (pttt) REVERT: i 89 TYR cc_start: 0.6985 (t80) cc_final: 0.6778 (t80) REVERT: j 32 THR cc_start: 0.3366 (OUTLIER) cc_final: 0.3116 (p) REVERT: j 35 GLN cc_start: 0.5185 (OUTLIER) cc_final: 0.4349 (mm110) REVERT: j 89 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.5439 (ttm170) REVERT: k 74 LYS cc_start: 0.6945 (ptmm) cc_final: 0.6713 (ptmm) REVERT: k 108 ASN cc_start: 0.7650 (p0) cc_final: 0.7323 (p0) REVERT: l 35 ARG cc_start: 0.7870 (ptm160) cc_final: 0.7535 (ptm-80) REVERT: l 48 LEU cc_start: 0.7546 (pt) cc_final: 0.7093 (mm) REVERT: l 72 ASN cc_start: 0.6508 (t0) cc_final: 0.6143 (t0) REVERT: m 3 ILE cc_start: 0.2316 (OUTLIER) cc_final: 0.1841 (mt) REVERT: n 59 GLN cc_start: -0.1127 (OUTLIER) cc_final: -0.1529 (tp40) REVERT: o 64 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7282 (mmmt) REVERT: o 69 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7119 (mp) REVERT: o 87 ARG cc_start: 0.4347 (tpp80) cc_final: 0.3914 (tpp80) REVERT: p 18 GLN cc_start: 0.8318 (mm-40) cc_final: 0.7551 (mm110) REVERT: p 19 VAL cc_start: 0.8688 (t) cc_final: 0.8429 (t) REVERT: q 33 TYR cc_start: 0.7864 (m-80) cc_final: 0.7292 (m-80) REVERT: q 43 LEU cc_start: 0.8327 (tp) cc_final: 0.8069 (tp) REVERT: t 35 TYR cc_start: 0.8654 (m-80) cc_final: 0.7901 (m-80) REVERT: t 47 GLN cc_start: 0.8336 (tp40) cc_final: 0.8107 (mm-40) REVERT: t 82 ILE cc_start: 0.7198 (pt) cc_final: 0.6861 (pt) REVERT: 7 9 LEU cc_start: 0.2028 (OUTLIER) cc_final: 0.1348 (pp) REVERT: 7 26 MET cc_start: 0.7664 (mmp) cc_final: 0.7436 (mmp) REVERT: 7 47 PRO cc_start: 0.8402 (Cg_exo) cc_final: 0.7756 (Cg_endo) REVERT: 7 51 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8001 (mt-10) REVERT: 7 99 MET cc_start: 0.8130 (ptp) cc_final: 0.7585 (ptm) REVERT: 7 108 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7599 (mp10) REVERT: 7 153 MET cc_start: 0.6610 (tmm) cc_final: 0.6380 (tmm) REVERT: 7 173 LYS cc_start: 0.7415 (tptm) cc_final: 0.6989 (mttp) REVERT: u 16 ARG cc_start: 0.5443 (OUTLIER) cc_final: 0.5150 (mmm160) REVERT: u 19 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7417 (mtmm) REVERT: u 36 PHE cc_start: 0.4858 (OUTLIER) cc_final: 0.3893 (m-80) REVERT: u 44 ARG cc_start: 0.6965 (tpp-160) cc_final: 0.6640 (mmp80) outliers start: 734 outliers final: 370 residues processed: 1917 average time/residue: 1.3059 time to fit residues: 4243.2224 Evaluate side-chains 1640 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 433 poor density : 1207 time to evaluate : 5.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain C residue 14 HIS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 6 TYR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 132 PHE Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 119 PHE Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 137 PRO Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 8 LYS Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 71 LYS Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 LYS Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 112 TYR Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 34 HIS Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 64 TYR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 85 LYS Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 42 PHE Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 74 GLN Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 50 ARG Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 13 ARG Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 7 HIS Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 60 HIS Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 110 ARG Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 72 PHE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 95 PHE Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 45 HIS Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain W residue 84 GLU Chi-restraints excluded: chain X residue 2 LYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Z residue 6 HIS Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 30 HIS Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 33 ASN Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain Z residue 60 PHE Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 52 LYS Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 2 residue 6 GLU Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 22 THR Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 32 LYS Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 36 LYS Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 3 residue 26 ASN Chi-restraints excluded: chain 4 residue 21 PHE Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 10 LEU Chi-restraints excluded: chain 5 residue 16 ILE Chi-restraints excluded: chain 5 residue 26 ILE Chi-restraints excluded: chain 5 residue 33 HIS Chi-restraints excluded: chain 6 residue 63 ASP Chi-restraints excluded: chain 6 residue 141 ASP Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 58 ARG Chi-restraints excluded: chain c residue 99 GLN Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 205 GLU Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 25 ARG Chi-restraints excluded: chain d residue 39 GLN Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain d residue 73 ASN Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 182 LYS Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 87 SER Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 19 SER Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 128 GLU Chi-restraints excluded: chain g residue 148 LYS Chi-restraints excluded: chain h residue 64 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 41 GLU Chi-restraints excluded: chain i residue 44 ARG Chi-restraints excluded: chain i residue 58 GLU Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 35 GLN Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 89 ARG Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 8 ILE Chi-restraints excluded: chain m residue 18 LEU Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 41 ASP Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 51 GLN Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 106 ARG Chi-restraints excluded: chain n residue 40 ARG Chi-restraints excluded: chain n residue 45 LEU Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 48 GLN Chi-restraints excluded: chain n residue 58 ARG Chi-restraints excluded: chain n residue 59 GLN Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain o residue 10 ILE Chi-restraints excluded: chain o residue 17 ASP Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 62 ARG Chi-restraints excluded: chain o residue 64 LYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 69 LEU Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 10 ARG Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 45 VAL Chi-restraints excluded: chain q residue 52 CYS Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 52 ARG Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain 7 residue 9 LEU Chi-restraints excluded: chain 7 residue 30 ILE Chi-restraints excluded: chain 7 residue 40 ILE Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 90 PHE Chi-restraints excluded: chain 7 residue 128 LEU Chi-restraints excluded: chain 7 residue 190 SER Chi-restraints excluded: chain u residue 8 ASN Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 19 LYS Chi-restraints excluded: chain u residue 35 GLU Chi-restraints excluded: chain u residue 36 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 507 optimal weight: 0.9980 chunk 283 optimal weight: 10.0000 chunk 759 optimal weight: 10.0000 chunk 621 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 914 optimal weight: 5.9990 chunk 987 optimal weight: 10.0000 chunk 814 optimal weight: 9.9990 chunk 906 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 733 optimal weight: 20.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 24 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS O 38 GLN P 6 GLN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 36 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 58 ASN Y 48 ASN 1 40 HIS ** 4 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 25 HIS 6 33 ASN 6 93 ASN c 5 HIS c 31 ASN ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 GLN d 99 ASN d 115 GLN d 119 HIS d 135 GLN ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 121 ASN e 134 ASN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN h 15 ASN i 125 GLN j 35 GLN k 27 ASN k 80 ASN m 13 HIS m 90 HIS ** n 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 79 ASN q 50 ASN r 51 GLN ** s 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN 7 17 HIS ** 7 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.6606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.045 155037 Z= 0.692 Angle : 1.236 61.449 231928 Z= 0.614 Chirality : 0.057 1.214 29639 Planarity : 0.010 0.174 12421 Dihedral : 24.335 179.431 78087 Min Nonbonded Distance : 1.347 Molprobity Statistics. All-atom Clashscore : 35.92 Ramachandran Plot: Outliers : 3.98 % Allowed : 25.50 % Favored : 70.52 % Rotamer: Outliers : 16.60 % Allowed : 26.86 % Favored : 56.54 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 2.60 % Twisted General : 0.93 % 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: -5.52 (0.09), residues: 5631 helix: -2.77 (0.11), residues: 1399 sheet: -3.50 (0.18), residues: 578 loop : -4.37 (0.08), residues: 3654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP 7 95 HIS 0.054 0.004 HIS G 110 PHE 0.064 0.005 PHE F 113 TYR 0.125 0.004 TYR j 65 ARG 0.033 0.002 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2153 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 775 poor density : 1378 time to evaluate : 5.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 44 HIS cc_start: 0.7449 (t70) cc_final: 0.7241 (t-170) REVERT: V 46 LYS cc_start: 0.8016 (mtmm) cc_final: 0.7683 (mttm) REVERT: V 48 MET cc_start: 0.7628 (tpt) cc_final: 0.7149 (tpt) REVERT: V 66 ASP cc_start: 0.6156 (t70) cc_final: 0.5919 (t0) REVERT: V 89 ILE cc_start: 0.7868 (mt) cc_final: 0.7664 (mt) REVERT: C 34 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6672 (pp20) REVERT: C 36 ASN cc_start: 0.7280 (OUTLIER) cc_final: 0.6723 (p0) REVERT: C 83 ASP cc_start: 0.8386 (t0) cc_final: 0.8089 (t0) REVERT: C 102 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7113 (t80) REVERT: C 123 ILE cc_start: 0.7741 (pt) cc_final: 0.7330 (pt) REVERT: C 134 ILE cc_start: 0.8270 (mt) cc_final: 0.8026 (mt) REVERT: C 235 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7108 (pt0) REVERT: C 268 ARG cc_start: 0.2727 (OUTLIER) cc_final: 0.2356 (mtm180) REVERT: D 16 THR cc_start: 0.3149 (OUTLIER) cc_final: 0.2747 (t) REVERT: D 33 ARG cc_start: 0.5942 (OUTLIER) cc_final: 0.4432 (mmm160) REVERT: D 165 MET cc_start: 0.5742 (mmm) cc_final: 0.5308 (mtt) REVERT: D 186 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8655 (mt) REVERT: E 27 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8700 (tp) REVERT: E 88 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7522 (tpp-160) REVERT: E 100 MET cc_start: 0.8671 (mmm) cc_final: 0.8319 (tpp) REVERT: E 148 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8461 (pt) REVERT: E 149 ILE cc_start: 0.8560 (pt) cc_final: 0.7736 (mm) REVERT: E 159 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.5979 (pt) REVERT: E 199 MET cc_start: 0.6912 (ptp) cc_final: 0.6452 (ptp) REVERT: F 16 MET cc_start: 0.4188 (tpp) cc_final: 0.3076 (mtt) REVERT: F 19 PHE cc_start: 0.7042 (t80) cc_final: 0.6806 (t80) REVERT: F 70 ARG cc_start: 0.7497 (tmm160) cc_final: 0.6742 (ttp80) REVERT: F 102 LEU cc_start: 0.5596 (tp) cc_final: 0.5373 (tp) REVERT: G 110 HIS cc_start: 0.5773 (OUTLIER) cc_final: 0.5382 (p-80) REVERT: G 142 GLN cc_start: 0.7988 (pm20) cc_final: 0.7751 (pm20) REVERT: G 146 ASP cc_start: 0.7057 (p0) cc_final: 0.6686 (p0) REVERT: G 162 ARG cc_start: 0.6974 (ptp-170) cc_final: 0.6738 (ptp90) REVERT: H 1 MET cc_start: 0.2550 (ppp) cc_final: 0.1568 (ppp) REVERT: H 2 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6345 (mm-40) REVERT: J 53 TYR cc_start: 0.6325 (OUTLIER) cc_final: 0.3394 (t80) REVERT: J 98 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.4945 (tm-30) REVERT: J 102 GLU cc_start: 0.4687 (OUTLIER) cc_final: 0.3446 (pt0) REVERT: J 108 MET cc_start: 0.8780 (mtt) cc_final: 0.8012 (mtt) REVERT: J 122 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6526 (pp) REVERT: J 132 HIS cc_start: 0.5764 (OUTLIER) cc_final: 0.5161 (t-170) REVERT: K 20 MET cc_start: 0.9114 (tpp) cc_final: 0.8704 (tpp) REVERT: K 31 ARG cc_start: 0.8100 (mtt90) cc_final: 0.7768 (mtt90) REVERT: K 32 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: K 45 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8209 (tm-30) REVERT: K 82 ASN cc_start: 0.8895 (m-40) cc_final: 0.8655 (m-40) REVERT: K 112 PHE cc_start: 0.6589 (m-80) cc_final: 0.6332 (m-10) REVERT: K 115 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8167 (mp) REVERT: L 54 GLN cc_start: 0.5718 (OUTLIER) cc_final: 0.5408 (mt0) REVERT: L 58 TYR cc_start: 0.2308 (OUTLIER) cc_final: 0.1489 (m-10) REVERT: L 64 PHE cc_start: 0.4342 (OUTLIER) cc_final: 0.3852 (m-80) REVERT: L 112 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6436 (pt) REVERT: M 1 MET cc_start: 0.4679 (OUTLIER) cc_final: 0.3910 (tpt) REVERT: M 71 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6311 (tptp) REVERT: M 91 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6565 (m-10) REVERT: M 114 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.8036 (ptm160) REVERT: N 1 MET cc_start: 0.3886 (OUTLIER) cc_final: 0.1412 (ptp) REVERT: N 18 GLN cc_start: 0.7333 (mp10) cc_final: 0.7047 (mp10) REVERT: N 51 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8783 (tt) REVERT: N 67 PHE cc_start: 0.4265 (OUTLIER) cc_final: 0.3737 (m-10) REVERT: Q 17 LEU cc_start: 0.8419 (tp) cc_final: 0.8168 (tp) REVERT: Q 101 ASP cc_start: 0.7652 (t0) cc_final: 0.7407 (t0) REVERT: R 1 MET cc_start: 0.6310 (mtm) cc_final: 0.5848 (mtp) REVERT: R 4 VAL cc_start: 0.8628 (p) cc_final: 0.8346 (p) REVERT: R 40 MET cc_start: 0.7568 (tpp) cc_final: 0.7282 (tpp) REVERT: R 83 TYR cc_start: 0.6238 (OUTLIER) cc_final: 0.5428 (m-80) REVERT: R 90 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.3965 (ttp-170) REVERT: S 53 SER cc_start: 0.9201 (m) cc_final: 0.8855 (t) REVERT: S 99 ARG cc_start: 0.8091 (mmt90) cc_final: 0.7837 (mtt90) REVERT: U 20 LYS cc_start: 0.7912 (tppt) cc_final: 0.7212 (mmtt) REVERT: U 44 HIS cc_start: 0.5348 (OUTLIER) cc_final: 0.4476 (m90) REVERT: U 72 PHE cc_start: 0.5868 (OUTLIER) cc_final: 0.4575 (p90) REVERT: U 81 ARG cc_start: 0.5621 (OUTLIER) cc_final: 0.4316 (mtp180) REVERT: U 87 GLU cc_start: 0.6641 (tt0) cc_final: 0.5070 (mm-30) REVERT: U 88 ASP cc_start: 0.4331 (OUTLIER) cc_final: 0.3322 (t0) REVERT: U 94 PHE cc_start: 0.4994 (t80) cc_final: 0.4277 (t80) REVERT: X 2 LYS cc_start: 0.4624 (OUTLIER) cc_final: 0.4258 (pptt) REVERT: X 44 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7606 (mmtt) REVERT: Y 20 LYS cc_start: 0.7434 (mmmt) cc_final: 0.7231 (tppt) REVERT: Z 25 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7174 (ttp80) REVERT: Z 58 ASP cc_start: 0.7497 (m-30) cc_final: 0.6873 (m-30) REVERT: Z 63 ARG cc_start: 0.7441 (mmp80) cc_final: 0.7231 (mmp80) REVERT: 1 37 HIS cc_start: 0.6159 (OUTLIER) cc_final: 0.5953 (m90) REVERT: 2 5 ARG cc_start: -0.0352 (OUTLIER) cc_final: -0.1262 (ttm110) REVERT: 2 10 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6644 (mp) REVERT: 2 26 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7907 (ptpt) REVERT: 3 19 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.5902 (ppt170) REVERT: 3 26 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7519 (m-40) REVERT: 4 24 LYS cc_start: 0.5111 (ptmt) cc_final: 0.4846 (ptmt) REVERT: 6 63 ASP cc_start: -0.0599 (OUTLIER) cc_final: -0.0898 (m-30) REVERT: 6 81 LYS cc_start: -0.0547 (OUTLIER) cc_final: -0.1483 (mttp) REVERT: c 18 ASN cc_start: 0.6535 (OUTLIER) cc_final: 0.6263 (p0) REVERT: c 32 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7838 (tp) REVERT: c 39 ARG cc_start: 0.6270 (ttm170) cc_final: 0.6011 (ttp-110) REVERT: c 45 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7187 (tt0) REVERT: c 63 ILE cc_start: 0.3388 (OUTLIER) cc_final: 0.2293 (pt) REVERT: c 86 LEU cc_start: 0.6864 (mt) cc_final: 0.6097 (mt) REVERT: c 128 MET cc_start: 0.7845 (tpp) cc_final: 0.7492 (mpp) REVERT: c 141 MET cc_start: 0.5711 (OUTLIER) cc_final: 0.5444 (mpm) REVERT: c 156 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8379 (pp) REVERT: d 20 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.5136 (pp) REVERT: d 25 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.4785 (ppt-90) REVERT: d 39 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6685 (tt0) REVERT: d 58 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7301 (tm-30) REVERT: d 71 PHE cc_start: 0.8422 (t80) cc_final: 0.8126 (t80) REVERT: d 85 THR cc_start: 0.8595 (m) cc_final: 0.8381 (p) REVERT: d 115 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6523 (tp40) REVERT: d 143 SER cc_start: 0.8232 (p) cc_final: 0.7845 (m) REVERT: d 190 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7780 (mp) REVERT: e 61 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7736 (mmmm) REVERT: e 68 ARG cc_start: 0.7181 (tpp-160) cc_final: 0.6913 (tpp-160) REVERT: e 84 VAL cc_start: 0.8306 (p) cc_final: 0.8088 (p) REVERT: e 95 MET cc_start: 0.6793 (tpp) cc_final: 0.6410 (ttm) REVERT: f 6 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8761 (tp) REVERT: h 120 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8153 (pp) REVERT: i 44 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.3231 (ppt90) REVERT: i 61 ASP cc_start: 0.7596 (t0) cc_final: 0.7235 (t0) REVERT: i 62 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8427 (mt) REVERT: i 67 LYS cc_start: 0.8791 (pttm) cc_final: 0.8479 (pttt) REVERT: i 106 ASP cc_start: 0.7865 (m-30) cc_final: 0.7536 (m-30) REVERT: j 19 ASP cc_start: 0.7465 (t0) cc_final: 0.7223 (p0) REVERT: j 48 ARG cc_start: 0.1322 (OUTLIER) cc_final: 0.0454 (ptp90) REVERT: j 89 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.5115 (tpp80) REVERT: k 52 ARG cc_start: 0.6100 (OUTLIER) cc_final: 0.5680 (ttt-90) REVERT: l 48 LEU cc_start: 0.7333 (pt) cc_final: 0.6792 (mm) REVERT: l 60 PHE cc_start: 0.8221 (m-80) cc_final: 0.8011 (m-80) REVERT: l 72 ASN cc_start: 0.6981 (t0) cc_final: 0.6449 (t0) REVERT: l 74 GLN cc_start: 0.7512 (tm-30) cc_final: 0.6732 (tt0) REVERT: l 114 SER cc_start: 0.9136 (m) cc_final: 0.8737 (m) REVERT: m 100 ARG cc_start: 0.5608 (ptp-170) cc_final: 0.5402 (ptm160) REVERT: m 104 ASN cc_start: -0.0853 (OUTLIER) cc_final: -0.2129 (p0) REVERT: n 5 MET cc_start: 0.4655 (mmm) cc_final: 0.3933 (mmm) REVERT: n 27 LYS cc_start: 0.2509 (pttp) cc_final: 0.1400 (mttp) REVERT: o 44 GLU cc_start: 0.6997 (tp30) cc_final: 0.6732 (tp30) REVERT: o 64 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7197 (mmmt) REVERT: o 86 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6776 (mm) REVERT: p 5 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.6324 (ppt-90) REVERT: p 18 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7831 (mm110) REVERT: p 60 TRP cc_start: 0.8835 (m100) cc_final: 0.8593 (m100) REVERT: p 70 ARG cc_start: 0.8081 (tpt-90) cc_final: 0.7652 (tpt170) REVERT: q 33 TYR cc_start: 0.7641 (m-80) cc_final: 0.7382 (m-80) REVERT: r 49 LYS cc_start: 0.9106 (tttp) cc_final: 0.7093 (pttm) REVERT: r 60 ARG cc_start: 0.8060 (ptp90) cc_final: 0.7684 (ptp-170) REVERT: t 17 ARG cc_start: 0.8788 (ttp80) cc_final: 0.8351 (tmm-80) REVERT: t 27 MET cc_start: 0.7731 (ttp) cc_final: 0.7188 (ttm) REVERT: 7 14 HIS cc_start: 0.7133 (p-80) cc_final: 0.6677 (p90) REVERT: 7 42 LEU cc_start: 0.7494 (mt) cc_final: 0.7087 (mp) REVERT: 7 43 GLU cc_start: 0.5640 (mp0) cc_final: 0.5346 (pm20) REVERT: 7 49 PHE cc_start: 0.8500 (m-80) cc_final: 0.8295 (m-80) REVERT: 7 108 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7511 (mp10) REVERT: 7 134 LEU cc_start: 0.8208 (mp) cc_final: 0.7629 (tp) REVERT: 7 183 PHE cc_start: 0.7509 (m-80) cc_final: 0.6994 (m-10) REVERT: u 16 ARG cc_start: 0.5283 (OUTLIER) cc_final: 0.4585 (mtm180) REVERT: u 19 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.6891 (mtmt) REVERT: u 24 LYS cc_start: 0.7516 (mmtt) cc_final: 0.7309 (mmtp) REVERT: u 36 PHE cc_start: 0.5565 (OUTLIER) cc_final: 0.4774 (m-80) outliers start: 775 outliers final: 407 residues processed: 1894 average time/residue: 1.3050 time to fit residues: 4265.7488 Evaluate side-chains 1674 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 480 poor density : 1194 time to evaluate : 5.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain C residue 14 HIS Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 113 PHE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 132 PHE Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 132 HIS Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 66 PHE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 71 LYS Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 LYS Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 67 PHE Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 112 TYR Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 42 PHE Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 74 GLN Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 110 LYS Chi-restraints excluded: chain P residue 114 ASN Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 110 ARG Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 44 HIS Chi-restraints excluded: chain U residue 72 PHE Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 84 GLU Chi-restraints excluded: chain X residue 2 LYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 58 ASN Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Z residue 6 HIS Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 33 ASN Chi-restraints excluded: chain Z residue 41 HIS Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain Z residue 60 PHE Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain 1 residue 2 VAL Chi-restraints excluded: chain 1 residue 25 THR Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 37 HIS Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 45 ASP Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 2 residue 5 ARG Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 46 VAL Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 26 ASN Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 21 PHE Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 4 residue 37 THR Chi-restraints excluded: chain 4 residue 43 LEU Chi-restraints excluded: chain 5 residue 13 ASN Chi-restraints excluded: chain 5 residue 33 HIS Chi-restraints excluded: chain 6 residue 23 VAL Chi-restraints excluded: chain 6 residue 63 ASP Chi-restraints excluded: chain 6 residue 70 THR Chi-restraints excluded: chain 6 residue 81 LYS Chi-restraints excluded: chain 6 residue 141 ASP Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 18 ASN Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 25 ARG Chi-restraints excluded: chain d residue 31 CYS Chi-restraints excluded: chain d residue 39 GLN Chi-restraints excluded: chain d residue 50 TYR Chi-restraints excluded: chain d residue 73 ASN Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 135 GLN Chi-restraints excluded: chain d residue 139 ASN Chi-restraints excluded: chain d residue 154 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 182 LYS Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 15 ILE Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 134 ASN Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 6 ILE Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 14 ASP Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 66 GLU Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 4 ASP Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 64 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 44 ARG Chi-restraints excluded: chain i residue 58 GLU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 35 GLN Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 62 ARG Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 89 ARG Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 52 ARG Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 37 TYR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain m residue 8 ILE Chi-restraints excluded: chain m residue 18 LEU Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 51 GLN Chi-restraints excluded: chain m residue 104 ASN Chi-restraints excluded: chain m residue 106 ARG Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 45 LEU Chi-restraints excluded: chain n residue 48 GLN Chi-restraints excluded: chain n residue 50 LEU Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 58 ARG Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain n residue 99 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 10 ILE Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 64 LYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 10 ARG Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 52 CYS Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 43 ILE Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 52 ARG Chi-restraints excluded: chain r residue 58 ILE Chi-restraints excluded: chain r residue 69 TYR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 13 HIS Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 33 TRP Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 66 ILE Chi-restraints excluded: chain 7 residue 30 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 69 VAL Chi-restraints excluded: chain 7 residue 71 THR Chi-restraints excluded: chain 7 residue 172 ILE Chi-restraints excluded: chain 7 residue 185 ILE Chi-restraints excluded: chain 7 residue 186 VAL Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 19 LYS Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 903 optimal weight: 0.0020 chunk 687 optimal weight: 10.0000 chunk 474 optimal weight: 0.0170 chunk 101 optimal weight: 9.9990 chunk 436 optimal weight: 0.0980 chunk 613 optimal weight: 8.9990 chunk 917 optimal weight: 10.0000 chunk 971 optimal weight: 3.9990 chunk 479 optimal weight: 6.9990 chunk 869 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 overall best weight: 2.2230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN D 150 GLN E 90 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN G 21 GLN G 63 GLN G 110 HIS G 114 HIS ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN K 93 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN Y 48 ASN ** Z 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 GLN ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 125 GLN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 ASN n 70 HIS ** p 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 ASN q 50 ASN ** s 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN ** 7 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 119 GLN ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.6933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.981 155037 Z= 0.579 Angle : 0.988 63.843 231928 Z= 0.493 Chirality : 0.046 1.076 29639 Planarity : 0.007 0.158 12421 Dihedral : 24.123 179.057 77969 Min Nonbonded Distance : 1.334 Molprobity Statistics. All-atom Clashscore : 26.65 Ramachandran Plot: Outliers : 3.37 % Allowed : 21.58 % Favored : 75.05 % Rotamer: Outliers : 11.46 % Allowed : 31.46 % Favored : 57.08 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 2.08 % Twisted General : 0.69 % 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: -5.03 (0.09), residues: 5631 helix: -2.17 (0.12), residues: 1354 sheet: -3.17 (0.20), residues: 527 loop : -4.13 (0.09), residues: 3750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 7 95 HIS 0.020 0.002 HIS U 44 PHE 0.059 0.003 PHE F 113 TYR 0.120 0.003 TYR j 65 ARG 0.023 0.001 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1838 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 535 poor density : 1303 time to evaluate : 5.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 5 ASN cc_start: 0.7553 (OUTLIER) cc_final: 0.6828 (p0) REVERT: V 44 HIS cc_start: 0.7647 (t70) cc_final: 0.7069 (t70) REVERT: V 48 MET cc_start: 0.6928 (tpt) cc_final: 0.6031 (tpt) REVERT: C 36 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6537 (p0) REVERT: C 123 ILE cc_start: 0.7897 (pt) cc_final: 0.7688 (pt) REVERT: C 161 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8689 (m) REVERT: C 229 HIS cc_start: 0.7571 (t-90) cc_final: 0.7369 (t-170) REVERT: C 235 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7008 (pt0) REVERT: D 17 GLU cc_start: 0.7455 (pp20) cc_final: 0.7138 (pm20) REVERT: D 18 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: D 30 GLU cc_start: 0.7039 (pm20) cc_final: 0.6320 (pt0) REVERT: D 33 ARG cc_start: 0.7009 (ptt180) cc_final: 0.4802 (mmm160) REVERT: D 64 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6915 (tm-30) REVERT: D 80 TRP cc_start: 0.5744 (m-10) cc_final: 0.5295 (m-10) REVERT: D 113 SER cc_start: 0.7817 (t) cc_final: 0.7538 (p) REVERT: D 165 MET cc_start: 0.6387 (mmm) cc_final: 0.5787 (mtt) REVERT: E 35 TYR cc_start: 0.7488 (t80) cc_final: 0.7205 (t80) REVERT: E 72 SER cc_start: 0.8354 (m) cc_final: 0.7907 (t) REVERT: E 84 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8121 (m) REVERT: E 88 ARG cc_start: 0.8522 (mmt90) cc_final: 0.7685 (tpp-160) REVERT: E 148 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8559 (pt) REVERT: E 149 ILE cc_start: 0.8281 (pt) cc_final: 0.7525 (mm) REVERT: E 159 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.5955 (pt) REVERT: E 199 MET cc_start: 0.6506 (ptp) cc_final: 0.6087 (ptp) REVERT: F 110 ILE cc_start: 0.2578 (OUTLIER) cc_final: 0.2216 (mm) REVERT: F 119 LYS cc_start: 0.3552 (OUTLIER) cc_final: 0.2948 (pptt) REVERT: G 108 PHE cc_start: 0.6918 (m-80) cc_final: 0.6603 (t80) REVERT: G 142 GLN cc_start: 0.8181 (pm20) cc_final: 0.7866 (pm20) REVERT: G 146 ASP cc_start: 0.7161 (p0) cc_final: 0.6445 (p0) REVERT: H 1 MET cc_start: 0.2536 (ppp) cc_final: 0.1742 (ppp) REVERT: H 2 GLN cc_start: 0.6850 (OUTLIER) cc_final: 0.6413 (mm-40) REVERT: H 57 LYS cc_start: 0.0517 (OUTLIER) cc_final: 0.0108 (mmtm) REVERT: H 61 VAL cc_start: 0.1887 (OUTLIER) cc_final: 0.1659 (p) REVERT: J 102 GLU cc_start: 0.4006 (OUTLIER) cc_final: 0.2593 (pt0) REVERT: J 108 MET cc_start: 0.8709 (mtt) cc_final: 0.7985 (mtt) REVERT: J 132 HIS cc_start: 0.5654 (OUTLIER) cc_final: 0.5287 (t-170) REVERT: K 20 MET cc_start: 0.9149 (tpp) cc_final: 0.8927 (tpp) REVERT: K 114 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7686 (mmmm) REVERT: L 64 PHE cc_start: 0.4731 (OUTLIER) cc_final: 0.3981 (m-80) REVERT: L 106 GLU cc_start: 0.4606 (OUTLIER) cc_final: 0.3055 (pm20) REVERT: M 1 MET cc_start: 0.3787 (OUTLIER) cc_final: 0.3494 (tpt) REVERT: M 71 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6194 (tptp) REVERT: M 91 TYR cc_start: 0.7129 (m-10) cc_final: 0.6241 (m-10) REVERT: M 136 MET cc_start: 0.3934 (mtt) cc_final: 0.3618 (mtt) REVERT: N 1 MET cc_start: 0.3569 (OUTLIER) cc_final: 0.1903 (pmm) REVERT: N 24 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6800 (ttp) REVERT: O 38 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7531 (mp10) REVERT: O 87 ILE cc_start: 0.5806 (pt) cc_final: 0.5593 (mt) REVERT: P 5 LYS cc_start: 0.8584 (pttt) cc_final: 0.8027 (tptp) REVERT: P 61 ARG cc_start: 0.7939 (mtm110) cc_final: 0.6077 (mtt180) REVERT: Q 69 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7530 (ptm160) REVERT: Q 70 GLN cc_start: 0.7634 (pt0) cc_final: 0.7390 (pt0) REVERT: R 1 MET cc_start: 0.6213 (mtm) cc_final: 0.5877 (mtm) REVERT: R 38 VAL cc_start: 0.7198 (OUTLIER) cc_final: 0.6897 (t) REVERT: R 74 ILE cc_start: 0.7944 (mp) cc_final: 0.7335 (tp) REVERT: R 83 TYR cc_start: 0.5701 (OUTLIER) cc_final: 0.4949 (m-80) REVERT: R 85 LYS cc_start: 0.8377 (ttpt) cc_final: 0.7971 (ttpp) REVERT: S 1 MET cc_start: -0.1757 (mtm) cc_final: -0.1974 (mtm) REVERT: T 26 LYS cc_start: -0.2014 (OUTLIER) cc_final: -0.2271 (mtmm) REVERT: U 17 ASP cc_start: 0.6879 (t0) cc_final: 0.6356 (t0) REVERT: U 20 LYS cc_start: 0.7695 (tppt) cc_final: 0.7162 (tttt) REVERT: U 44 HIS cc_start: 0.6207 (OUTLIER) cc_final: 0.5766 (m-70) REVERT: U 72 PHE cc_start: 0.5536 (OUTLIER) cc_final: 0.4340 (p90) REVERT: U 81 ARG cc_start: 0.4625 (OUTLIER) cc_final: 0.3472 (mtp180) REVERT: U 84 PHE cc_start: 0.3573 (t80) cc_final: 0.3209 (t80) REVERT: X 2 LYS cc_start: 0.4426 (OUTLIER) cc_final: 0.3933 (pptt) REVERT: X 41 HIS cc_start: 0.7621 (p90) cc_final: 0.7324 (p90) REVERT: X 44 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7509 (mptt) REVERT: Y 6 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8333 (tp) REVERT: Y 20 LYS cc_start: 0.7157 (mmmt) cc_final: 0.6836 (tppt) REVERT: Y 46 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7587 (mpp) REVERT: Z 3 LYS cc_start: 0.6738 (pttt) cc_final: 0.5502 (tptm) REVERT: Z 25 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.7053 (ttp80) REVERT: Z 58 ASP cc_start: 0.7318 (m-30) cc_final: 0.6827 (m-30) REVERT: 1 36 LYS cc_start: 0.7012 (ttpt) cc_final: 0.6804 (ttpt) REVERT: 2 10 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6186 (mp) REVERT: 2 11 VAL cc_start: 0.5424 (OUTLIER) cc_final: 0.4776 (t) REVERT: 3 26 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7408 (m-40) REVERT: 6 63 ASP cc_start: -0.0308 (OUTLIER) cc_final: -0.0563 (m-30) REVERT: 6 81 LYS cc_start: 0.0078 (OUTLIER) cc_final: -0.0845 (mttp) REVERT: c 22 PHE cc_start: 0.5605 (t80) cc_final: 0.5319 (t80) REVERT: c 45 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: c 54 ILE cc_start: 0.5947 (OUTLIER) cc_final: 0.5651 (mt) REVERT: c 88 LYS cc_start: 0.6134 (mmtt) cc_final: 0.5852 (pttm) REVERT: c 101 ASN cc_start: 0.7520 (OUTLIER) cc_final: 0.7296 (m-40) REVERT: c 128 MET cc_start: 0.7830 (tpp) cc_final: 0.7509 (mpp) REVERT: d 20 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.5443 (pp) REVERT: d 25 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.4343 (ppt-90) REVERT: d 39 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6681 (tt0) REVERT: d 58 GLN cc_start: 0.7467 (tm-30) cc_final: 0.7194 (tm-30) REVERT: d 71 PHE cc_start: 0.8133 (t80) cc_final: 0.7927 (t80) REVERT: d 77 GLU cc_start: 0.6317 (mm-30) cc_final: 0.6111 (tp30) REVERT: d 97 LEU cc_start: 0.8597 (tp) cc_final: 0.8342 (tp) REVERT: d 143 SER cc_start: 0.8479 (p) cc_final: 0.8119 (m) REVERT: d 177 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.5711 (mmp) REVERT: d 190 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7866 (mp) REVERT: e 59 ILE cc_start: 0.8979 (pt) cc_final: 0.8761 (tt) REVERT: e 63 MET cc_start: 0.8828 (mmt) cc_final: 0.7737 (mmt) REVERT: e 64 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8037 (mm-30) REVERT: e 155 LYS cc_start: 0.7001 (ttpt) cc_final: 0.6608 (mtpp) REVERT: e 156 ARG cc_start: 0.7207 (ptt180) cc_final: 0.6944 (ptt90) REVERT: f 24 ARG cc_start: 0.8260 (ttp-170) cc_final: 0.7788 (ptp-170) REVERT: f 39 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6882 (tm) REVERT: f 45 ARG cc_start: 0.7893 (ptm-80) cc_final: 0.7156 (mtp-110) REVERT: f 61 LEU cc_start: 0.8369 (tp) cc_final: 0.8168 (tt) REVERT: f 90 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.6223 (mmm) REVERT: h 9 MET cc_start: 0.7923 (tpt) cc_final: 0.7666 (tpt) REVERT: h 120 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8025 (pp) REVERT: i 30 ASN cc_start: 0.8163 (m-40) cc_final: 0.7352 (t0) REVERT: i 44 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.3919 (ppt90) REVERT: i 61 ASP cc_start: 0.7508 (t0) cc_final: 0.7250 (t0) REVERT: i 62 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8425 (mt) REVERT: i 67 LYS cc_start: 0.8669 (pttm) cc_final: 0.8391 (pttt) REVERT: i 106 ASP cc_start: 0.7883 (m-30) cc_final: 0.7422 (m-30) REVERT: j 31 ARG cc_start: 0.3677 (OUTLIER) cc_final: -0.0569 (mtm-85) REVERT: l 48 LEU cc_start: 0.7454 (pt) cc_final: 0.6928 (mm) REVERT: l 60 PHE cc_start: 0.8157 (m-80) cc_final: 0.7941 (m-80) REVERT: l 72 ASN cc_start: 0.6964 (t0) cc_final: 0.6214 (t0) REVERT: l 74 GLN cc_start: 0.8165 (tm-30) cc_final: 0.6851 (tt0) REVERT: m 16 ILE cc_start: 0.4785 (mp) cc_final: 0.4291 (tt) REVERT: n 5 MET cc_start: 0.4861 (mmm) cc_final: 0.4597 (mmm) REVERT: n 8 ARG cc_start: 0.5143 (mmp-170) cc_final: 0.4729 (mmp-170) REVERT: n 27 LYS cc_start: 0.2192 (pttp) cc_final: 0.1145 (mttp) REVERT: o 44 GLU cc_start: 0.7208 (tp30) cc_final: 0.6971 (tp30) REVERT: o 61 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: o 64 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7106 (mmmt) REVERT: p 18 GLN cc_start: 0.8500 (mm-40) cc_final: 0.7957 (mm110) REVERT: p 70 ARG cc_start: 0.8035 (tpt-90) cc_final: 0.7688 (tpt170) REVERT: q 33 TYR cc_start: 0.7628 (m-80) cc_final: 0.7420 (m-80) REVERT: q 43 LEU cc_start: 0.7946 (tp) cc_final: 0.7533 (tp) REVERT: q 56 ASP cc_start: 0.6808 (m-30) cc_final: 0.6468 (t0) REVERT: q 71 SER cc_start: 0.8361 (m) cc_final: 0.7999 (t) REVERT: r 49 LYS cc_start: 0.8985 (tttp) cc_final: 0.6944 (pttm) REVERT: s 65 MET cc_start: -0.1046 (ttt) cc_final: -0.3294 (ptt) REVERT: t 8 LYS cc_start: 0.7686 (tmtt) cc_final: 0.7453 (ttmt) REVERT: t 35 TYR cc_start: 0.8818 (m-80) cc_final: 0.8028 (m-80) REVERT: t 78 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8075 (tt) REVERT: 7 14 HIS cc_start: 0.7095 (p-80) cc_final: 0.6731 (p90) REVERT: 7 43 GLU cc_start: 0.6021 (mp0) cc_final: 0.5535 (pm20) REVERT: 7 51 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7704 (mt-10) REVERT: 7 95 TRP cc_start: 0.7444 (t60) cc_final: 0.6886 (t60) REVERT: 7 108 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7534 (mp10) REVERT: 7 134 LEU cc_start: 0.8323 (mp) cc_final: 0.7689 (tp) REVERT: 7 183 PHE cc_start: 0.7395 (m-80) cc_final: 0.7050 (m-10) REVERT: u 15 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6352 (tp) REVERT: u 16 ARG cc_start: 0.5328 (OUTLIER) cc_final: 0.4858 (mtm180) REVERT: u 19 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7058 (mtmt) REVERT: u 36 PHE cc_start: 0.4759 (OUTLIER) cc_final: 0.4045 (m-80) outliers start: 535 outliers final: 315 residues processed: 1654 average time/residue: 1.2897 time to fit residues: 3641.3457 Evaluate side-chains 1551 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 375 poor density : 1176 time to evaluate : 5.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain C residue 14 HIS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 113 PHE Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 132 PHE Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 119 PHE Chi-restraints excluded: chain J residue 132 HIS Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 71 LYS Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 LYS Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 112 TYR Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 42 PHE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 74 GLN Chi-restraints excluded: chain P residue 114 ASN Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 19 GLN Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 50 ARG Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 110 ARG Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 26 LYS Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 44 HIS Chi-restraints excluded: chain U residue 72 PHE Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain U residue 95 PHE Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain W residue 84 GLU Chi-restraints excluded: chain X residue 2 LYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Y residue 48 ASN Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Z residue 6 HIS Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 33 ASN Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain Z residue 60 PHE Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 41 HIS Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 45 ASP Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 2 residue 9 LYS Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 35 LEU Chi-restraints excluded: chain 2 residue 46 VAL Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 3 residue 26 ASN Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 21 PHE Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 4 residue 37 THR Chi-restraints excluded: chain 4 residue 43 LEU Chi-restraints excluded: chain 5 residue 8 LYS Chi-restraints excluded: chain 5 residue 33 HIS Chi-restraints excluded: chain 6 residue 23 VAL Chi-restraints excluded: chain 6 residue 63 ASP Chi-restraints excluded: chain 6 residue 70 THR Chi-restraints excluded: chain 6 residue 81 LYS Chi-restraints excluded: chain 6 residue 141 ASP Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 25 ARG Chi-restraints excluded: chain d residue 39 GLN Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 15 ILE Chi-restraints excluded: chain e residue 18 ASN Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 19 SER Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain h residue 4 ASP Chi-restraints excluded: chain h residue 64 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 44 ARG Chi-restraints excluded: chain i residue 58 GLU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 5 ARG Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 24 GLU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 31 ARG Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 89 ARG Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 120 CYS Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 37 TYR Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain m residue 8 ILE Chi-restraints excluded: chain m residue 13 HIS Chi-restraints excluded: chain m residue 18 LEU Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 50 LEU Chi-restraints excluded: chain n residue 58 ARG Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain n residue 99 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 64 LYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 10 ARG Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 52 CYS Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 52 ARG Chi-restraints excluded: chain r residue 69 TYR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain 7 residue 30 ILE Chi-restraints excluded: chain 7 residue 40 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 69 VAL Chi-restraints excluded: chain u residue 15 LEU Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 19 LYS Chi-restraints excluded: chain u residue 36 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 809 optimal weight: 20.0000 chunk 551 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 723 optimal weight: 9.9990 chunk 400 optimal weight: 9.9990 chunk 828 optimal weight: 0.5980 chunk 671 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 496 optimal weight: 3.9990 chunk 871 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN G 110 HIS ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 GLN ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 48 ASN Z 30 HIS ** c 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 GLN d 88 ASN d 135 GLN ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 ASN l 71 HIS ** m 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 GLN q 50 ASN ** t 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN ** 7 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 119 GLN ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.7897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.967 155037 Z= 0.629 Angle : 1.045 40.314 231928 Z= 0.522 Chirality : 0.049 1.068 29639 Planarity : 0.008 0.155 12421 Dihedral : 24.149 179.426 77910 Min Nonbonded Distance : 1.284 Molprobity Statistics. All-atom Clashscore : 31.82 Ramachandran Plot: Outliers : 3.29 % Allowed : 23.89 % Favored : 72.83 % Rotamer: Outliers : 13.56 % Allowed : 30.78 % Favored : 55.67 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 2.60 % Twisted General : 0.60 % 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: -5.09 (0.09), residues: 5631 helix: -2.35 (0.12), residues: 1393 sheet: -3.14 (0.19), residues: 585 loop : -4.14 (0.09), residues: 3653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP n 100 HIS 0.055 0.003 HIS G 110 PHE 0.052 0.004 PHE F 113 TYR 0.108 0.003 TYR j 65 ARG 0.027 0.001 ARG Q 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1891 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 633 poor density : 1258 time to evaluate : 6.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 44 HIS cc_start: 0.7490 (t70) cc_final: 0.6854 (t70) REVERT: V 48 MET cc_start: 0.7144 (tpt) cc_final: 0.6261 (tpt) REVERT: V 55 GLU cc_start: 0.7955 (pt0) cc_final: 0.7472 (pt0) REVERT: C 36 ASN cc_start: 0.6920 (OUTLIER) cc_final: 0.6273 (p0) REVERT: C 102 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7081 (t80) REVERT: C 213 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.4440 (ppt170) REVERT: C 268 ARG cc_start: 0.1824 (OUTLIER) cc_final: 0.0487 (mtm-85) REVERT: D 33 ARG cc_start: 0.6196 (ptt180) cc_final: 0.4837 (mmm160) REVERT: D 113 SER cc_start: 0.7645 (t) cc_final: 0.7196 (p) REVERT: E 72 SER cc_start: 0.8521 (m) cc_final: 0.7937 (t) REVERT: E 88 ARG cc_start: 0.8434 (mmt90) cc_final: 0.7893 (tpp-160) REVERT: E 148 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8679 (pt) REVERT: E 149 ILE cc_start: 0.8516 (pt) cc_final: 0.7787 (mm) REVERT: E 159 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6090 (pt) REVERT: E 189 THR cc_start: 0.6214 (OUTLIER) cc_final: 0.5926 (p) REVERT: E 199 MET cc_start: 0.6854 (ptp) cc_final: 0.6491 (ptp) REVERT: F 13 LYS cc_start: 0.6997 (tmtt) cc_final: 0.6323 (pptt) REVERT: F 16 MET cc_start: 0.3227 (tpp) cc_final: 0.2025 (tpp) REVERT: F 87 LYS cc_start: 0.5132 (tppt) cc_final: 0.4762 (tttp) REVERT: F 168 LEU cc_start: 0.3960 (OUTLIER) cc_final: 0.3482 (pt) REVERT: G 2 ARG cc_start: 0.0867 (OUTLIER) cc_final: -0.1034 (ttm110) REVERT: G 34 ARG cc_start: 0.6224 (ttp-170) cc_final: 0.5919 (ttp-170) REVERT: G 142 GLN cc_start: 0.7892 (pm20) cc_final: 0.7446 (pm20) REVERT: G 146 ASP cc_start: 0.7779 (p0) cc_final: 0.7065 (p0) REVERT: G 162 ARG cc_start: 0.7181 (ptp90) cc_final: 0.6937 (ptp90) REVERT: H 1 MET cc_start: 0.2995 (OUTLIER) cc_final: 0.2446 (ptp) REVERT: H 29 PHE cc_start: 0.8129 (t80) cc_final: 0.7849 (t80) REVERT: H 57 LYS cc_start: 0.1194 (OUTLIER) cc_final: 0.0413 (mmtm) REVERT: J 53 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.3611 (t80) REVERT: J 93 ILE cc_start: 0.8223 (tt) cc_final: 0.7896 (pt) REVERT: J 102 GLU cc_start: 0.4583 (OUTLIER) cc_final: 0.3511 (pt0) REVERT: J 108 MET cc_start: 0.8815 (mtt) cc_final: 0.8142 (mtt) REVERT: K 32 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.8020 (m-10) REVERT: K 45 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8088 (tm-30) REVERT: K 112 PHE cc_start: 0.6216 (m-10) cc_final: 0.5937 (m-10) REVERT: L 54 GLN cc_start: 0.5781 (OUTLIER) cc_final: 0.5389 (mt0) REVERT: L 64 PHE cc_start: 0.4913 (OUTLIER) cc_final: 0.4086 (m-80) REVERT: L 66 PHE cc_start: 0.6286 (OUTLIER) cc_final: 0.5367 (p90) REVERT: M 1 MET cc_start: 0.4676 (OUTLIER) cc_final: 0.4081 (tpt) REVERT: M 71 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6669 (tptp) REVERT: M 91 TYR cc_start: 0.7215 (m-10) cc_final: 0.6411 (m-10) REVERT: N 67 PHE cc_start: 0.4465 (OUTLIER) cc_final: 0.3930 (m-10) REVERT: O 40 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7040 (mp) REVERT: O 92 PHE cc_start: 0.7605 (t80) cc_final: 0.6933 (t80) REVERT: P 86 LYS cc_start: 0.6734 (tmtt) cc_final: 0.6436 (tmtt) REVERT: Q 12 ARG cc_start: 0.8850 (mtp-110) cc_final: 0.8598 (ttp80) REVERT: R 1 MET cc_start: 0.6518 (mtm) cc_final: 0.6317 (mtm) REVERT: R 77 PHE cc_start: 0.6592 (m-80) cc_final: 0.6331 (m-80) REVERT: R 83 TYR cc_start: 0.5934 (OUTLIER) cc_final: 0.5243 (m-80) REVERT: R 90 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.3591 (ttp-170) REVERT: S 1 MET cc_start: -0.1211 (mtm) cc_final: -0.1490 (mtm) REVERT: S 52 GLU cc_start: 0.8235 (pp20) cc_final: 0.8028 (pp20) REVERT: S 66 ILE cc_start: 0.7070 (mp) cc_final: 0.6848 (mp) REVERT: S 67 ASP cc_start: 0.7386 (t0) cc_final: 0.5419 (p0) REVERT: S 82 MET cc_start: 0.7220 (tpp) cc_final: 0.6895 (ttm) REVERT: T 80 TRP cc_start: 0.4922 (m-90) cc_final: 0.4567 (m-90) REVERT: T 91 GLN cc_start: 0.3065 (OUTLIER) cc_final: 0.2853 (pm20) REVERT: U 7 ASP cc_start: 0.8521 (t70) cc_final: 0.8293 (t0) REVERT: U 20 LYS cc_start: 0.7629 (tppt) cc_final: 0.7388 (mmtt) REVERT: U 44 HIS cc_start: 0.5646 (OUTLIER) cc_final: 0.4192 (m170) REVERT: U 72 PHE cc_start: 0.6449 (OUTLIER) cc_final: 0.5273 (p90) REVERT: U 81 ARG cc_start: 0.5032 (OUTLIER) cc_final: 0.3867 (mtp180) REVERT: W 20 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7303 (pp) REVERT: X 2 LYS cc_start: 0.5158 (OUTLIER) cc_final: 0.4622 (pptt) REVERT: X 24 GLU cc_start: 0.8021 (mp0) cc_final: 0.7749 (mp0) REVERT: X 44 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7735 (mptt) REVERT: Y 6 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8322 (mt) REVERT: Y 17 PRO cc_start: 0.7277 (Cg_endo) cc_final: 0.7073 (Cg_endo) REVERT: Y 20 LYS cc_start: 0.7474 (mmmt) cc_final: 0.6977 (tppt) REVERT: Y 35 VAL cc_start: 0.8788 (t) cc_final: 0.8558 (t) REVERT: Y 46 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7347 (mpp) REVERT: Z 25 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7294 (ttp80) REVERT: Z 48 GLN cc_start: 0.7199 (mt0) cc_final: 0.6816 (mm-40) REVERT: 2 11 VAL cc_start: 0.5264 (OUTLIER) cc_final: 0.4653 (t) REVERT: 2 27 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6336 (mtp85) REVERT: 3 19 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6483 (ppt170) REVERT: 3 26 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7549 (m-40) REVERT: 5 8 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7880 (ptpt) REVERT: 6 81 LYS cc_start: 0.0051 (OUTLIER) cc_final: -0.1114 (mttp) REVERT: c 22 PHE cc_start: 0.6178 (t80) cc_final: 0.5773 (t80) REVERT: c 45 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: c 54 ILE cc_start: 0.5642 (OUTLIER) cc_final: 0.5204 (mt) REVERT: c 62 SER cc_start: 0.3431 (p) cc_final: 0.2591 (m) REVERT: c 75 VAL cc_start: 0.6699 (t) cc_final: 0.6466 (t) REVERT: c 86 LEU cc_start: 0.6572 (mt) cc_final: 0.6366 (mt) REVERT: c 88 LYS cc_start: 0.5829 (mmtt) cc_final: 0.5580 (pttp) REVERT: c 93 ILE cc_start: 0.6122 (tt) cc_final: 0.5534 (mp) REVERT: c 101 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7396 (m110) REVERT: c 166 TRP cc_start: 0.7427 (m100) cc_final: 0.7147 (m100) REVERT: d 25 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.4179 (ppt-90) REVERT: d 39 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: d 58 GLN cc_start: 0.7545 (tm-30) cc_final: 0.7211 (tm-30) REVERT: d 74 TYR cc_start: 0.7814 (m-80) cc_final: 0.7568 (m-80) REVERT: d 143 SER cc_start: 0.8486 (p) cc_final: 0.8165 (m) REVERT: d 189 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6328 (p0) REVERT: d 190 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7782 (mp) REVERT: e 155 LYS cc_start: 0.7404 (ttpt) cc_final: 0.7036 (mtmt) REVERT: f 39 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7092 (tm) REVERT: f 45 ARG cc_start: 0.7932 (ptm-80) cc_final: 0.7358 (mtp-110) REVERT: f 51 ILE cc_start: 0.5655 (OUTLIER) cc_final: 0.5231 (tt) REVERT: f 61 LEU cc_start: 0.8390 (tp) cc_final: 0.8179 (tt) REVERT: h 2 MET cc_start: 0.5556 (ptm) cc_final: 0.5321 (ptm) REVERT: h 31 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8182 (tt) REVERT: h 94 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8574 (m) REVERT: h 95 MET cc_start: 0.8089 (mmp) cc_final: 0.7830 (mmm) REVERT: h 112 ASP cc_start: 0.7179 (p0) cc_final: 0.6791 (p0) REVERT: h 120 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8083 (pp) REVERT: i 30 ASN cc_start: 0.8196 (m-40) cc_final: 0.7304 (t0) REVERT: i 44 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.4409 (ppt90) REVERT: i 61 ASP cc_start: 0.8031 (t0) cc_final: 0.7765 (t0) REVERT: i 62 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8371 (mt) REVERT: i 106 ASP cc_start: 0.7984 (m-30) cc_final: 0.7501 (m-30) REVERT: k 52 ARG cc_start: 0.6122 (OUTLIER) cc_final: 0.5587 (ttt-90) REVERT: k 82 GLU cc_start: 0.5253 (mp0) cc_final: 0.4914 (mp0) REVERT: l 37 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.7196 (m-10) REVERT: l 43 LYS cc_start: 0.7207 (tppt) cc_final: 0.6327 (tmtt) REVERT: l 72 ASN cc_start: 0.6850 (t0) cc_final: 0.6022 (t0) REVERT: l 107 LYS cc_start: 0.6179 (mmtt) cc_final: 0.5963 (mmtt) REVERT: l 114 SER cc_start: 0.9182 (m) cc_final: 0.8899 (m) REVERT: m 11 HIS cc_start: 0.5049 (OUTLIER) cc_final: 0.4771 (t70) REVERT: n 27 LYS cc_start: 0.3053 (pttp) cc_final: 0.1823 (mtmm) REVERT: o 61 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: o 64 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7257 (mmmt) REVERT: p 5 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.6824 (ppt-90) REVERT: p 18 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8032 (mm110) REVERT: p 70 ARG cc_start: 0.8089 (tpt-90) cc_final: 0.7498 (tpt170) REVERT: q 10 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6008 (tpm-80) REVERT: q 33 TYR cc_start: 0.7579 (m-80) cc_final: 0.7289 (m-80) REVERT: q 43 LEU cc_start: 0.8020 (tp) cc_final: 0.7541 (tt) REVERT: q 56 ASP cc_start: 0.8122 (m-30) cc_final: 0.6837 (m-30) REVERT: r 25 ILE cc_start: 0.8249 (mm) cc_final: 0.8017 (mm) REVERT: r 49 LYS cc_start: 0.9016 (tttp) cc_final: 0.6965 (pttm) REVERT: t 8 LYS cc_start: 0.7877 (tmtt) cc_final: 0.7646 (ttmt) REVERT: t 27 MET cc_start: 0.8214 (ptm) cc_final: 0.7894 (ptp) REVERT: t 79 THR cc_start: 0.8967 (m) cc_final: 0.8703 (p) REVERT: 7 14 HIS cc_start: 0.7491 (p-80) cc_final: 0.7217 (p-80) REVERT: 7 26 MET cc_start: 0.8268 (mmm) cc_final: 0.7782 (mmm) REVERT: 7 43 GLU cc_start: 0.6688 (mp0) cc_final: 0.6141 (pm20) REVERT: 7 49 PHE cc_start: 0.8315 (m-80) cc_final: 0.7996 (m-80) REVERT: 7 134 LEU cc_start: 0.8315 (mp) cc_final: 0.7654 (tp) REVERT: 7 183 PHE cc_start: 0.7742 (m-80) cc_final: 0.7510 (m-80) REVERT: u 16 ARG cc_start: 0.4534 (OUTLIER) cc_final: 0.3762 (mtm180) outliers start: 633 outliers final: 388 residues processed: 1675 average time/residue: 1.2826 time to fit residues: 3656.2240 Evaluate side-chains 1602 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 448 poor density : 1154 time to evaluate : 5.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 14 HIS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 113 PHE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 119 PHE Chi-restraints excluded: chain J residue 132 HIS Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 66 PHE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 71 LYS Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 LYS Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 67 PHE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 112 TYR Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 42 PHE Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 114 ASN Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 7 HIS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 91 GLN Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 44 HIS Chi-restraints excluded: chain U residue 72 PHE Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 24 ARG Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain W residue 80 SER Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 84 GLU Chi-restraints excluded: chain X residue 2 LYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Z residue 6 HIS Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 33 ASN Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain 1 residue 2 VAL Chi-restraints excluded: chain 1 residue 41 HIS Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 45 ASP Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 46 VAL Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 26 ASN Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 21 PHE Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 4 residue 37 THR Chi-restraints excluded: chain 4 residue 42 HIS Chi-restraints excluded: chain 4 residue 43 LEU Chi-restraints excluded: chain 4 residue 58 ILE Chi-restraints excluded: chain 5 residue 8 LYS Chi-restraints excluded: chain 5 residue 13 ASN Chi-restraints excluded: chain 5 residue 33 HIS Chi-restraints excluded: chain 6 residue 23 VAL Chi-restraints excluded: chain 6 residue 32 VAL Chi-restraints excluded: chain 6 residue 70 THR Chi-restraints excluded: chain 6 residue 81 LYS Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 18 ASN Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 68 HIS 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 120 THR Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 25 ARG Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 39 GLN Chi-restraints excluded: chain d residue 73 ASN Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 135 GLN Chi-restraints excluded: chain d residue 139 ASN Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 154 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 15 ILE Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 18 ASN Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 87 SER Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 19 SER Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 66 GLU Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 4 ASP Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 64 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 44 ARG Chi-restraints excluded: chain i residue 58 GLU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain j residue 89 ARG Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 16 SER Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 52 ARG Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 37 TYR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain l residue 69 GLU Chi-restraints excluded: chain l residue 120 ARG Chi-restraints excluded: chain m residue 8 ILE Chi-restraints excluded: chain m residue 11 HIS Chi-restraints excluded: chain m residue 18 LEU Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 52 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 50 LEU Chi-restraints excluded: chain n residue 58 ARG Chi-restraints excluded: chain n residue 76 PHE Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 10 ILE Chi-restraints excluded: chain o residue 37 HIS Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 64 LYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 10 ARG Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 52 CYS Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 68 LYS Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 52 ARG Chi-restraints excluded: chain r residue 58 ILE Chi-restraints excluded: chain r residue 69 TYR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 33 TRP Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain 7 residue 22 TRP Chi-restraints excluded: chain 7 residue 30 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 69 VAL Chi-restraints excluded: chain 7 residue 71 THR Chi-restraints excluded: chain 7 residue 128 LEU Chi-restraints excluded: chain 7 residue 185 ILE Chi-restraints excluded: chain 7 residue 186 VAL Chi-restraints excluded: chain 7 residue 212 TYR Chi-restraints excluded: chain u residue 16 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 326 optimal weight: 0.2980 chunk 874 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 570 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 972 optimal weight: 9.9990 chunk 807 optimal weight: 4.9990 chunk 450 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 321 optimal weight: 1.9990 chunk 510 optimal weight: 0.6980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN U 44 HIS Z 30 HIS 5 33 HIS ** c 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 GLN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 134 ASN f 3 HIS ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 ASN h 15 ASN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 ASN q 50 ASN ** t 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN ** 7 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.8146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.967 155037 Z= 0.562 Angle : 0.905 39.709 231928 Z= 0.455 Chirality : 0.042 0.879 29639 Planarity : 0.007 0.153 12421 Dihedral : 24.047 179.824 77866 Min Nonbonded Distance : 1.292 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 2.89 % Allowed : 20.71 % Favored : 76.40 % Rotamer: Outliers : 10.28 % Allowed : 33.56 % Favored : 56.16 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 2.60 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.10), residues: 5631 helix: -2.05 (0.12), residues: 1395 sheet: -2.91 (0.20), residues: 575 loop : -4.01 (0.09), residues: 3661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP n 100 HIS 0.031 0.002 HIS m 13 PHE 0.052 0.002 PHE F 113 TYR 0.107 0.003 TYR j 65 ARG 0.033 0.001 ARG F 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1731 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 480 poor density : 1251 time to evaluate : 5.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 44 HIS cc_start: 0.7474 (t70) cc_final: 0.6920 (t70) REVERT: V 48 MET cc_start: 0.7032 (tpt) cc_final: 0.6087 (tpt) REVERT: C 261 ARG cc_start: 0.6892 (mmt90) cc_final: 0.4522 (ttp-170) REVERT: C 265 PHE cc_start: 0.6954 (t80) cc_final: 0.5848 (t80) REVERT: C 268 ARG cc_start: 0.1757 (OUTLIER) cc_final: 0.0802 (mtm-85) REVERT: D 30 GLU cc_start: 0.6914 (pm20) cc_final: 0.6517 (pt0) REVERT: D 68 PHE cc_start: 0.6997 (m-10) cc_final: 0.6772 (m-10) REVERT: D 113 SER cc_start: 0.7575 (t) cc_final: 0.7182 (p) REVERT: D 140 HIS cc_start: 0.5780 (OUTLIER) cc_final: 0.5370 (t70) REVERT: E 72 SER cc_start: 0.8444 (m) cc_final: 0.7779 (t) REVERT: E 88 ARG cc_start: 0.8376 (mmt90) cc_final: 0.7815 (tpp-160) REVERT: E 148 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8632 (pt) REVERT: E 149 ILE cc_start: 0.8380 (pt) cc_final: 0.7805 (mm) REVERT: E 154 ASP cc_start: 0.5772 (t0) cc_final: 0.5501 (t0) REVERT: E 159 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.5834 (pp) REVERT: E 189 THR cc_start: 0.6070 (OUTLIER) cc_final: 0.5837 (p) REVERT: E 199 MET cc_start: 0.6436 (ptp) cc_final: 0.6151 (ptp) REVERT: F 13 LYS cc_start: 0.6499 (tmtt) cc_final: 0.6159 (pttp) REVERT: F 16 MET cc_start: 0.3313 (tpp) cc_final: 0.2870 (mpp) REVERT: F 98 PHE cc_start: 0.5637 (t80) cc_final: 0.5282 (t80) REVERT: F 168 LEU cc_start: 0.3776 (OUTLIER) cc_final: 0.3386 (pt) REVERT: G 75 VAL cc_start: 0.6509 (t) cc_final: 0.6235 (m) REVERT: G 85 LYS cc_start: 0.6993 (mppt) cc_final: 0.6188 (mppt) REVERT: G 146 ASP cc_start: 0.7707 (p0) cc_final: 0.7344 (p0) REVERT: H 1 MET cc_start: 0.2217 (ppp) cc_final: 0.1582 (ppp) REVERT: H 2 GLN cc_start: 0.6227 (OUTLIER) cc_final: 0.5953 (mm-40) REVERT: J 14 ASP cc_start: 0.6885 (t70) cc_final: 0.6646 (t70) REVERT: J 90 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.6080 (tm-30) REVERT: J 96 ARG cc_start: 0.5845 (mtm110) cc_final: 0.5471 (mtm180) REVERT: J 102 GLU cc_start: 0.3692 (OUTLIER) cc_final: 0.2284 (pt0) REVERT: J 108 MET cc_start: 0.8546 (mtt) cc_final: 0.8241 (mtt) REVERT: K 20 MET cc_start: 0.8966 (tpp) cc_final: 0.8747 (tpp) REVERT: K 30 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.8083 (mmm-85) REVERT: K 32 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: K 45 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7632 (tm-30) REVERT: K 98 ARG cc_start: 0.7828 (ptm-80) cc_final: 0.7516 (ptm-80) REVERT: L 60 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.4944 (tmm-80) REVERT: L 61 LEU cc_start: 0.5424 (OUTLIER) cc_final: 0.5208 (mp) REVERT: L 64 PHE cc_start: 0.4628 (OUTLIER) cc_final: 0.4052 (m-80) REVERT: L 105 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.6610 (mt) REVERT: L 126 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.5495 (ppp80) REVERT: M 12 MET cc_start: 0.6886 (tpt) cc_final: 0.6293 (tpp) REVERT: M 14 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7323 (mtmm) REVERT: M 71 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6319 (tptp) REVERT: N 51 LEU cc_start: 0.9104 (tp) cc_final: 0.8831 (tt) REVERT: O 40 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7126 (mp) REVERT: O 87 ILE cc_start: 0.5693 (pt) cc_final: 0.5486 (mt) REVERT: O 92 PHE cc_start: 0.7540 (t80) cc_final: 0.7126 (t80) REVERT: P 6 GLN cc_start: 0.7171 (pp30) cc_final: 0.6779 (mp10) REVERT: P 61 ARG cc_start: 0.8087 (mtm110) cc_final: 0.6657 (mtt180) REVERT: Q 15 LYS cc_start: 0.7060 (tptt) cc_final: 0.6843 (mmtt) REVERT: Q 17 LEU cc_start: 0.8096 (tp) cc_final: 0.7590 (tt) REVERT: Q 74 SER cc_start: 0.7861 (p) cc_final: 0.7429 (p) REVERT: R 90 ARG cc_start: 0.6210 (OUTLIER) cc_final: 0.3311 (ttp-170) REVERT: S 52 GLU cc_start: 0.7956 (pp20) cc_final: 0.7698 (pp20) REVERT: S 67 ASP cc_start: 0.7120 (t0) cc_final: 0.5606 (p0) REVERT: S 88 ARG cc_start: 0.7460 (mtp-110) cc_final: 0.7130 (mtp-110) REVERT: T 2 ILE cc_start: 0.2644 (OUTLIER) cc_final: 0.2359 (mp) REVERT: T 6 ARG cc_start: 0.6634 (mmm-85) cc_final: 0.6400 (mmm-85) REVERT: T 80 TRP cc_start: 0.4801 (m-90) cc_final: 0.4505 (m-90) REVERT: U 44 HIS cc_start: 0.5255 (OUTLIER) cc_final: 0.4742 (m90) REVERT: U 72 PHE cc_start: 0.6015 (OUTLIER) cc_final: 0.5634 (p90) REVERT: U 84 PHE cc_start: 0.2699 (t80) cc_final: 0.2480 (t80) REVERT: W 20 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6880 (pp) REVERT: X 2 LYS cc_start: 0.5069 (OUTLIER) cc_final: 0.4565 (pptt) REVERT: X 24 GLU cc_start: 0.7910 (mp0) cc_final: 0.7656 (mp0) REVERT: X 41 HIS cc_start: 0.7761 (p90) cc_final: 0.7344 (p90) REVERT: X 44 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7598 (mptt) REVERT: Y 6 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8109 (mt) REVERT: Y 20 LYS cc_start: 0.7307 (mmmt) cc_final: 0.6806 (tppt) REVERT: Y 46 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.6811 (mpp) REVERT: Z 3 LYS cc_start: 0.6192 (pttt) cc_final: 0.5970 (pttt) REVERT: Z 25 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7204 (ttp80) REVERT: 2 10 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6130 (mp) REVERT: 2 11 VAL cc_start: 0.5054 (OUTLIER) cc_final: 0.4399 (t) REVERT: 2 27 ARG cc_start: 0.7485 (ttm-80) cc_final: 0.6708 (mtp85) REVERT: 3 1 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.6172 (pmm) REVERT: 3 19 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6419 (ppt170) REVERT: 3 26 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7325 (m-40) REVERT: 4 12 ARG cc_start: 0.7700 (ptp-110) cc_final: 0.7442 (ptp-170) REVERT: 6 81 LYS cc_start: 0.0883 (OUTLIER) cc_final: -0.0347 (mttp) REVERT: c 13 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7022 (mt) REVERT: c 45 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7140 (tp30) REVERT: c 54 ILE cc_start: 0.5812 (OUTLIER) cc_final: 0.5319 (mt) REVERT: c 63 ILE cc_start: 0.2002 (OUTLIER) cc_final: 0.1688 (pt) REVERT: c 66 THR cc_start: 0.8017 (m) cc_final: 0.7705 (m) REVERT: c 75 VAL cc_start: 0.6603 (t) cc_final: 0.6278 (t) REVERT: c 101 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7388 (m-40) REVERT: d 25 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.4562 (ppt-90) REVERT: d 58 GLN cc_start: 0.7335 (tm-30) cc_final: 0.6989 (tm-30) REVERT: d 74 TYR cc_start: 0.7738 (m-80) cc_final: 0.7472 (m-80) REVERT: d 143 SER cc_start: 0.8343 (p) cc_final: 0.8008 (m) REVERT: d 190 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7637 (mp) REVERT: e 63 MET cc_start: 0.8322 (mmm) cc_final: 0.7614 (mmt) REVERT: e 155 LYS cc_start: 0.7349 (ttpt) cc_final: 0.7048 (mtmt) REVERT: e 156 ARG cc_start: 0.6979 (ptt180) cc_final: 0.6363 (ptp-170) REVERT: f 2 ARG cc_start: 0.6821 (ttm170) cc_final: 0.5800 (mtp85) REVERT: f 39 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6927 (tm) REVERT: f 45 ARG cc_start: 0.7925 (ptm-80) cc_final: 0.7339 (mtp-110) REVERT: f 51 ILE cc_start: 0.5247 (OUTLIER) cc_final: 0.5043 (tt) REVERT: f 63 ASN cc_start: 0.6270 (OUTLIER) cc_final: 0.6009 (m-40) REVERT: f 70 VAL cc_start: 0.8325 (p) cc_final: 0.8109 (p) REVERT: g 138 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: h 31 LEU cc_start: 0.8377 (tp) cc_final: 0.7979 (tt) REVERT: h 95 MET cc_start: 0.8154 (mmp) cc_final: 0.7858 (mmp) REVERT: h 112 ASP cc_start: 0.6989 (p0) cc_final: 0.6749 (p0) REVERT: h 120 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7977 (pp) REVERT: i 30 ASN cc_start: 0.7792 (m-40) cc_final: 0.7294 (t0) REVERT: i 44 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.3026 (ppt90) REVERT: i 62 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8198 (mt) REVERT: i 106 ASP cc_start: 0.7916 (m-30) cc_final: 0.7371 (m-30) REVERT: i 119 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8401 (ttmt) REVERT: j 65 TYR cc_start: 0.5917 (OUTLIER) cc_final: 0.5339 (m-80) REVERT: k 13 LYS cc_start: 0.7723 (tmtt) cc_final: 0.7450 (tmmt) REVERT: k 45 THR cc_start: 0.8086 (t) cc_final: 0.7740 (p) REVERT: k 52 ARG cc_start: 0.5960 (OUTLIER) cc_final: 0.5531 (ttt-90) REVERT: l 37 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.7127 (m-10) REVERT: l 43 LYS cc_start: 0.7344 (tppt) cc_final: 0.6524 (tmtt) REVERT: l 48 LEU cc_start: 0.7431 (pt) cc_final: 0.6881 (mm) REVERT: l 72 ASN cc_start: 0.6928 (t0) cc_final: 0.6125 (t0) REVERT: l 114 SER cc_start: 0.9006 (m) cc_final: 0.8802 (m) REVERT: m 11 HIS cc_start: 0.4550 (OUTLIER) cc_final: 0.4264 (t70) REVERT: m 104 ASN cc_start: 0.0499 (OUTLIER) cc_final: 0.0296 (p0) REVERT: n 27 LYS cc_start: 0.2885 (OUTLIER) cc_final: 0.2026 (mtmm) REVERT: n 62 ARG cc_start: 0.2167 (mmt90) cc_final: 0.1702 (ptt90) REVERT: o 34 GLN cc_start: 0.8654 (pm20) cc_final: 0.8222 (pm20) REVERT: o 61 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: o 64 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7105 (mmmt) REVERT: p 18 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7705 (mm110) REVERT: q 43 LEU cc_start: 0.7914 (tp) cc_final: 0.7570 (tt) REVERT: q 56 ASP cc_start: 0.7033 (m-30) cc_final: 0.6471 (m-30) REVERT: q 64 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8366 (ttp-110) REVERT: r 47 ARG cc_start: 0.6430 (mtt180) cc_final: 0.6005 (mtm180) REVERT: r 49 LYS cc_start: 0.8920 (tttp) cc_final: 0.6852 (pttm) REVERT: r 63 TYR cc_start: 0.6441 (m-80) cc_final: 0.5654 (t80) REVERT: t 8 LYS cc_start: 0.7834 (tmtt) cc_final: 0.7625 (ttmt) REVERT: t 14 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7404 (mt-10) REVERT: t 27 MET cc_start: 0.8168 (ptm) cc_final: 0.7900 (ptm) REVERT: t 78 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8110 (tt) REVERT: t 79 THR cc_start: 0.8777 (m) cc_final: 0.8442 (p) REVERT: 7 14 HIS cc_start: 0.7463 (p-80) cc_final: 0.7212 (p-80) REVERT: 7 43 GLU cc_start: 0.6823 (mp0) cc_final: 0.6433 (mp0) REVERT: 7 134 LEU cc_start: 0.8302 (mp) cc_final: 0.7621 (tp) REVERT: u 16 ARG cc_start: 0.3867 (OUTLIER) cc_final: 0.3058 (mtm180) outliers start: 480 outliers final: 308 residues processed: 1577 average time/residue: 1.2888 time to fit residues: 3471.9853 Evaluate side-chains 1517 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 1151 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 14 HIS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 113 PHE Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 119 PHE Chi-restraints excluded: chain J residue 132 HIS Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 71 LYS Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 LYS Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 42 PHE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 70 GLN Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 44 HIS Chi-restraints excluded: chain U residue 72 PHE Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 84 GLU Chi-restraints excluded: chain X residue 2 LYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Z residue 6 HIS Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 33 ASN Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain 1 residue 2 VAL Chi-restraints excluded: chain 1 residue 41 HIS Chi-restraints excluded: chain 1 residue 45 ASP Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 2 residue 9 LYS Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 26 ASN Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 21 PHE Chi-restraints excluded: chain 4 residue 23 HIS Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 4 residue 37 THR Chi-restraints excluded: chain 5 residue 13 ASN Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 6 residue 23 VAL Chi-restraints excluded: chain 6 residue 32 VAL Chi-restraints excluded: chain 6 residue 81 LYS Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 68 HIS Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 25 ARG Chi-restraints excluded: chain d residue 73 ASN Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 139 ASN Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 18 ASN Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 19 SER Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 138 GLU Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 4 ASP Chi-restraints excluded: chain h residue 64 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 111 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 44 ARG Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 89 ARG Chi-restraints excluded: chain k residue 16 SER Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 52 ARG Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 37 TYR Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain l residue 103 CYS Chi-restraints excluded: chain l residue 120 ARG Chi-restraints excluded: chain m residue 8 ILE Chi-restraints excluded: chain m residue 11 HIS Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 104 ASN Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 58 ARG Chi-restraints excluded: chain n residue 91 GLU Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain n residue 100 TRP Chi-restraints excluded: chain o residue 37 HIS Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 64 LYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 52 CYS Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 71 SER Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 52 ARG Chi-restraints excluded: chain r residue 69 TYR Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 33 TRP Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain 7 residue 30 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 186 VAL Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 16 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 937 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 554 optimal weight: 7.9990 chunk 710 optimal weight: 10.0000 chunk 550 optimal weight: 0.4980 chunk 818 optimal weight: 0.4980 chunk 542 optimal weight: 0.9980 chunk 968 optimal weight: 7.9990 chunk 606 optimal weight: 0.0570 chunk 590 optimal weight: 0.0970 chunk 447 optimal weight: 5.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS K 3 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN P 74 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 HIS c 122 GLN d 135 GLN e 11 GLN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 3 HIS ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 42 ASN ** t 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 ASN ** 7 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 119 GLN ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.8361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.951 155037 Z= 0.553 Angle : 0.866 39.920 231928 Z= 0.433 Chirality : 0.040 1.427 29639 Planarity : 0.007 0.137 12421 Dihedral : 23.923 179.962 77831 Min Nonbonded Distance : 1.292 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 2.84 % Allowed : 20.17 % Favored : 76.98 % Rotamer: Outliers : 9.17 % Allowed : 35.23 % Favored : 55.60 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 2.60 % Twisted General : 0.62 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.10), residues: 5631 helix: -1.75 (0.13), residues: 1361 sheet: -2.55 (0.21), residues: 538 loop : -3.85 (0.09), residues: 3732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP n 100 HIS 0.056 0.002 HIS U 44 PHE 0.050 0.002 PHE F 113 TYR 0.100 0.002 TYR j 65 ARG 0.025 0.001 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1723 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 428 poor density : 1295 time to evaluate : 6.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 44 HIS cc_start: 0.7398 (t70) cc_final: 0.6888 (t70) REVERT: V 48 MET cc_start: 0.6930 (tpt) cc_final: 0.6023 (tpt) REVERT: V 55 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7008 (tp30) REVERT: C 36 ASN cc_start: 0.6080 (OUTLIER) cc_final: 0.5655 (p0) REVERT: C 53 ILE cc_start: 0.7725 (mt) cc_final: 0.7353 (mt) REVERT: C 124 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7268 (ptmm) REVERT: C 202 ARG cc_start: 0.7332 (ptt90) cc_final: 0.7107 (ptt180) REVERT: C 261 ARG cc_start: 0.6824 (mmt90) cc_final: 0.4503 (ttp-170) REVERT: C 268 ARG cc_start: 0.1992 (OUTLIER) cc_final: 0.1347 (mtm-85) REVERT: D 33 ARG cc_start: 0.6067 (ptt180) cc_final: 0.4915 (mmm160) REVERT: D 68 PHE cc_start: 0.6889 (m-10) cc_final: 0.6658 (m-10) REVERT: D 94 GLN cc_start: 0.8687 (pp30) cc_final: 0.7557 (tm-30) REVERT: D 113 SER cc_start: 0.7532 (t) cc_final: 0.7177 (p) REVERT: D 140 HIS cc_start: 0.5618 (OUTLIER) cc_final: 0.5331 (t70) REVERT: D 169 ARG cc_start: 0.7580 (mmm160) cc_final: 0.6786 (mmm160) REVERT: E 72 SER cc_start: 0.8287 (m) cc_final: 0.7640 (t) REVERT: E 88 ARG cc_start: 0.8250 (mmt90) cc_final: 0.7773 (tpp-160) REVERT: E 148 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8558 (pt) REVERT: E 149 ILE cc_start: 0.8321 (pt) cc_final: 0.7508 (mm) REVERT: E 159 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6073 (pp) REVERT: E 199 MET cc_start: 0.6092 (ptp) cc_final: 0.5644 (ptp) REVERT: F 98 PHE cc_start: 0.5160 (t80) cc_final: 0.4917 (t80) REVERT: F 151 LEU cc_start: 0.8202 (mm) cc_final: 0.7908 (mp) REVERT: F 168 LEU cc_start: 0.4136 (OUTLIER) cc_final: 0.3528 (pt) REVERT: G 23 ILE cc_start: 0.7331 (mm) cc_final: 0.7044 (tt) REVERT: G 72 ASN cc_start: 0.7398 (t0) cc_final: 0.7147 (m110) REVERT: G 87 GLN cc_start: 0.8256 (mp10) cc_final: 0.8024 (mp10) REVERT: H 1 MET cc_start: 0.2310 (ppp) cc_final: 0.1488 (ppp) REVERT: H 53 GLU cc_start: 0.3271 (mp0) cc_final: 0.2994 (tp30) REVERT: J 17 VAL cc_start: 0.8940 (m) cc_final: 0.8674 (m) REVERT: J 37 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.6051 (mtp180) REVERT: J 96 ARG cc_start: 0.5935 (mtm110) cc_final: 0.5537 (mtm180) REVERT: J 108 MET cc_start: 0.8537 (mtt) cc_final: 0.7987 (mtt) REVERT: K 45 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7005 (tm-30) REVERT: K 78 ARG cc_start: 0.8348 (mtm180) cc_final: 0.8090 (mtm180) REVERT: L 61 LEU cc_start: 0.5387 (OUTLIER) cc_final: 0.5107 (mp) REVERT: L 64 PHE cc_start: 0.4281 (OUTLIER) cc_final: 0.3898 (m-80) REVERT: L 96 LYS cc_start: -0.0330 (mmtt) cc_final: -0.0721 (mptt) REVERT: L 105 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6301 (mt) REVERT: L 126 ARG cc_start: 0.6453 (OUTLIER) cc_final: 0.5664 (ppp80) REVERT: M 12 MET cc_start: 0.6599 (tpt) cc_final: 0.6285 (tpp) REVERT: M 14 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7049 (mtmt) REVERT: M 17 ASN cc_start: 0.4796 (m-40) cc_final: 0.4390 (m110) REVERT: M 53 MET cc_start: 0.7886 (mmt) cc_final: 0.7628 (tpp) REVERT: M 65 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7015 (mt) REVERT: M 71 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.5684 (tptt) REVERT: M 105 MET cc_start: 0.5860 (ptm) cc_final: 0.5649 (ttp) REVERT: M 127 LYS cc_start: 0.7962 (tttt) cc_final: 0.7550 (mmtt) REVERT: N 27 SER cc_start: 0.7973 (m) cc_final: 0.6792 (t) REVERT: O 40 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.7002 (mp) REVERT: O 67 ASN cc_start: 0.5910 (p0) cc_final: 0.5259 (m110) REVERT: P 6 GLN cc_start: 0.7170 (pp30) cc_final: 0.6830 (pm20) REVERT: P 61 ARG cc_start: 0.7879 (mtm110) cc_final: 0.6765 (mtt180) REVERT: Q 17 LEU cc_start: 0.7971 (tp) cc_final: 0.7333 (tt) REVERT: Q 51 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: S 52 GLU cc_start: 0.7388 (pp20) cc_final: 0.7116 (pp20) REVERT: S 67 ASP cc_start: 0.7025 (t0) cc_final: 0.5791 (p0) REVERT: T 87 LEU cc_start: 0.8675 (tp) cc_final: 0.8382 (tt) REVERT: U 44 HIS cc_start: 0.6446 (OUTLIER) cc_final: 0.5554 (m-70) REVERT: W 59 PHE cc_start: 0.6474 (t80) cc_final: 0.5766 (t80) REVERT: X 2 LYS cc_start: 0.4941 (OUTLIER) cc_final: 0.4484 (pptt) REVERT: X 41 HIS cc_start: 0.7249 (p90) cc_final: 0.6972 (p90) REVERT: X 44 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7519 (mptt) REVERT: Y 6 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8153 (mt) REVERT: Y 20 LYS cc_start: 0.6943 (mmmt) cc_final: 0.6479 (tppt) REVERT: Z 6 HIS cc_start: 0.4238 (OUTLIER) cc_final: 0.3962 (m-70) REVERT: Z 25 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.7056 (ttp80) REVERT: 1 41 HIS cc_start: 0.2987 (OUTLIER) cc_final: 0.1937 (t-90) REVERT: 1 47 TYR cc_start: 0.6173 (p90) cc_final: 0.5972 (p90) REVERT: 2 10 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6090 (mp) REVERT: 2 27 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.6686 (mtp85) REVERT: 3 19 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6488 (ppt170) REVERT: 3 26 ASN cc_start: 0.7437 (OUTLIER) cc_final: 0.6903 (m110) REVERT: 3 34 ARG cc_start: 0.8079 (ttm170) cc_final: 0.7661 (ttm170) REVERT: 5 24 ARG cc_start: 0.7042 (ttm170) cc_final: 0.6817 (ttm-80) REVERT: 6 81 LYS cc_start: 0.0796 (OUTLIER) cc_final: -0.0402 (mttp) REVERT: c 17 TRP cc_start: 0.7672 (OUTLIER) cc_final: 0.7340 (m-10) REVERT: c 45 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7206 (tp30) REVERT: c 66 THR cc_start: 0.7369 (m) cc_final: 0.7102 (m) REVERT: c 75 VAL cc_start: 0.6089 (t) cc_final: 0.5808 (t) REVERT: c 106 ARG cc_start: 0.8451 (mmt180) cc_final: 0.8063 (ttm110) REVERT: c 141 MET cc_start: 0.5985 (mmp) cc_final: 0.5679 (mmt) REVERT: d 25 ARG cc_start: 0.6220 (OUTLIER) cc_final: 0.5818 (ppt-90) REVERT: d 58 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6881 (tm-30) REVERT: d 138 PRO cc_start: 0.8771 (Cg_endo) cc_final: 0.8524 (Cg_exo) REVERT: d 143 SER cc_start: 0.8326 (p) cc_final: 0.8111 (m) REVERT: d 189 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.6258 (p0) REVERT: d 190 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7441 (mp) REVERT: d 197 HIS cc_start: 0.7111 (p-80) cc_final: 0.6640 (p-80) REVERT: d 198 LEU cc_start: 0.8268 (mt) cc_final: 0.8012 (mp) REVERT: e 111 ARG cc_start: 0.6765 (ttt180) cc_final: 0.6344 (ttt180) REVERT: e 114 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7628 (mp) REVERT: e 155 LYS cc_start: 0.7295 (ttpt) cc_final: 0.6973 (mtmt) REVERT: e 156 ARG cc_start: 0.6768 (ptt180) cc_final: 0.6410 (ptp90) REVERT: f 1 MET cc_start: 0.8850 (mtt) cc_final: 0.8549 (ptp) REVERT: f 39 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6825 (tm) REVERT: f 45 ARG cc_start: 0.7834 (ptm-80) cc_final: 0.7384 (mtp-110) REVERT: f 49 TYR cc_start: 0.7523 (p90) cc_final: 0.7237 (p90) REVERT: f 51 ILE cc_start: 0.4968 (OUTLIER) cc_final: 0.4614 (tt) REVERT: g 68 VAL cc_start: 0.8061 (OUTLIER) cc_final: 0.7839 (p) REVERT: g 138 GLU cc_start: 0.7661 (pm20) cc_final: 0.6790 (tp30) REVERT: h 31 LEU cc_start: 0.8323 (tp) cc_final: 0.7970 (tt) REVERT: h 112 ASP cc_start: 0.6746 (p0) cc_final: 0.6408 (p0) REVERT: h 120 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7972 (pp) REVERT: i 30 ASN cc_start: 0.7753 (m-40) cc_final: 0.7335 (t0) REVERT: i 34 LEU cc_start: 0.7355 (tt) cc_final: 0.7051 (tp) REVERT: i 44 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.3077 (ppt90) REVERT: i 51 LEU cc_start: 0.6461 (mp) cc_final: 0.5864 (mt) REVERT: i 106 ASP cc_start: 0.7785 (m-30) cc_final: 0.7260 (m-30) REVERT: j 8 ILE cc_start: -0.2413 (OUTLIER) cc_final: -0.2970 (tp) REVERT: j 51 VAL cc_start: 0.1157 (OUTLIER) cc_final: 0.0596 (t) REVERT: k 36 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7762 (mtp85) REVERT: l 37 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.7048 (m-10) REVERT: l 43 LYS cc_start: 0.7365 (tppt) cc_final: 0.6600 (tmtt) REVERT: l 48 LEU cc_start: 0.7317 (pt) cc_final: 0.6806 (mm) REVERT: l 58 ASN cc_start: 0.8314 (m110) cc_final: 0.7881 (m110) REVERT: l 88 ASP cc_start: 0.7461 (m-30) cc_final: 0.7188 (m-30) REVERT: l 106 VAL cc_start: 0.8033 (p) cc_final: 0.7756 (p) REVERT: l 120 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7748 (mmm-85) REVERT: n 27 LYS cc_start: 0.1811 (OUTLIER) cc_final: 0.1075 (mttm) REVERT: o 9 LYS cc_start: 0.8640 (tmmt) cc_final: 0.7775 (ttmt) REVERT: o 64 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7103 (mmmt) REVERT: o 68 TYR cc_start: 0.7804 (t80) cc_final: 0.7430 (t80) REVERT: p 18 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7726 (mm110) REVERT: p 19 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.7991 (t) REVERT: q 56 ASP cc_start: 0.6968 (m-30) cc_final: 0.6458 (m-30) REVERT: q 64 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8330 (ttp-110) REVERT: q 71 SER cc_start: 0.8368 (m) cc_final: 0.7869 (t) REVERT: r 47 ARG cc_start: 0.6310 (mtt180) cc_final: 0.5471 (tpp80) REVERT: r 63 TYR cc_start: 0.6413 (m-80) cc_final: 0.5706 (t80) REVERT: r 66 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7525 (mp) REVERT: s 43 MET cc_start: 0.4378 (OUTLIER) cc_final: 0.3920 (mmp) REVERT: s 55 GLN cc_start: -0.0500 (OUTLIER) cc_final: -0.1790 (pt0) REVERT: s 65 MET cc_start: -0.0851 (ttt) cc_final: -0.2382 (ptt) REVERT: t 78 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7974 (tt) REVERT: 7 14 HIS cc_start: 0.7447 (p-80) cc_final: 0.7202 (p-80) REVERT: 7 43 GLU cc_start: 0.6690 (mp0) cc_final: 0.6363 (mp0) REVERT: 7 134 LEU cc_start: 0.8263 (mp) cc_final: 0.7612 (tp) outliers start: 428 outliers final: 249 residues processed: 1577 average time/residue: 1.3089 time to fit residues: 3514.7241 Evaluate side-chains 1474 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1175 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 113 PHE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 78 ARG Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 71 LYS Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 LYS Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 67 PHE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 42 PHE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 74 GLN Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 44 HIS Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain U residue 95 PHE Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 75 ASN Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 84 GLU Chi-restraints excluded: chain X residue 2 LYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 6 HIS Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain Z residue 60 PHE Chi-restraints excluded: chain 1 residue 2 VAL Chi-restraints excluded: chain 1 residue 41 HIS Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 2 residue 9 LYS Chi-restraints excluded: chain 2 residue 10 LEU Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 26 ASN Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 21 PHE Chi-restraints excluded: chain 4 residue 37 THR Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 6 residue 23 VAL Chi-restraints excluded: chain 6 residue 32 VAL Chi-restraints excluded: chain 6 residue 81 LYS Chi-restraints excluded: chain c residue 17 TRP Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 25 ARG Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 19 SER Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 115 MET Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 64 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 44 ARG Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 68 ARG Chi-restraints excluded: chain j residue 70 HIS Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 89 ARG Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 37 TYR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain l residue 103 CYS Chi-restraints excluded: chain l residue 120 ARG Chi-restraints excluded: chain m residue 8 ILE Chi-restraints excluded: chain m residue 11 HIS Chi-restraints excluded: chain m residue 18 LEU Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 58 ARG Chi-restraints excluded: chain n residue 91 GLU Chi-restraints excluded: chain n residue 92 ILE Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain o residue 37 HIS Chi-restraints excluded: chain o residue 64 LYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 52 CYS Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 43 MET Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain 7 residue 30 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 186 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 599 optimal weight: 9.9990 chunk 386 optimal weight: 9.9990 chunk 578 optimal weight: 5.9990 chunk 291 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 615 optimal weight: 9.9990 chunk 659 optimal weight: 20.0000 chunk 478 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 761 optimal weight: 10.0000 overall best weight: 7.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS K 89 ASN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS S 57 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 ASN ** Z 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 29 GLN d 88 ASN ** e 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 ASN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 74 GLN i 125 GLN j 35 GLN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 ASN k 118 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 119 GLN ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.9049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.010 155037 Z= 0.671 Angle : 1.091 40.662 231928 Z= 0.539 Chirality : 0.051 1.779 29639 Planarity : 0.009 0.179 12421 Dihedral : 24.159 179.490 77785 Min Nonbonded Distance : 1.265 Molprobity Statistics. All-atom Clashscore : 34.24 Ramachandran Plot: Outliers : 2.86 % Allowed : 23.46 % Favored : 73.68 % Rotamer: Outliers : 10.47 % Allowed : 34.65 % Favored : 54.87 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 2.60 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.09), residues: 5631 helix: -2.17 (0.12), residues: 1391 sheet: -2.73 (0.20), residues: 555 loop : -4.05 (0.09), residues: 3685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP n 100 HIS 0.025 0.003 HIS s 68 PHE 0.055 0.004 PHE n 76 TYR 0.124 0.004 TYR j 65 ARG 0.027 0.001 ARG u 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1680 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 489 poor density : 1191 time to evaluate : 5.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 44 HIS cc_start: 0.7304 (t70) cc_final: 0.6420 (t70) REVERT: V 48 MET cc_start: 0.7258 (tpt) cc_final: 0.6253 (tpt) REVERT: C 124 LYS cc_start: 0.8246 (mmmm) cc_final: 0.7543 (pttp) REVERT: C 260 LYS cc_start: 0.8373 (mptt) cc_final: 0.8090 (mmmt) REVERT: C 261 ARG cc_start: 0.6819 (mmt90) cc_final: 0.4783 (ttp-170) REVERT: D 2 ILE cc_start: 0.7107 (tp) cc_final: 0.6814 (tp) REVERT: D 22 ILE cc_start: 0.7446 (tp) cc_final: 0.7134 (pt) REVERT: D 33 ARG cc_start: 0.5914 (ptt180) cc_final: 0.5047 (mmm160) REVERT: D 94 GLN cc_start: 0.8695 (pp30) cc_final: 0.7987 (tm-30) REVERT: D 113 SER cc_start: 0.7543 (t) cc_final: 0.7045 (p) REVERT: E 72 SER cc_start: 0.8508 (m) cc_final: 0.7864 (t) REVERT: E 88 ARG cc_start: 0.8397 (mmt90) cc_final: 0.7741 (tpp-160) REVERT: E 116 ASP cc_start: 0.6164 (OUTLIER) cc_final: 0.5770 (m-30) REVERT: E 159 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6150 (pp) REVERT: F 19 PHE cc_start: 0.6528 (t80) cc_final: 0.6312 (t80) REVERT: F 65 LEU cc_start: 0.7105 (tp) cc_final: 0.6760 (tt) REVERT: F 111 ARG cc_start: 0.0641 (ttt90) cc_final: -0.0819 (ptm160) REVERT: G 72 ASN cc_start: 0.8266 (t0) cc_final: 0.7641 (m-40) REVERT: G 146 ASP cc_start: 0.7944 (p0) cc_final: 0.7322 (p0) REVERT: H 132 PHE cc_start: 0.5325 (OUTLIER) cc_final: 0.5107 (m-10) REVERT: J 37 ARG cc_start: 0.6498 (OUTLIER) cc_final: 0.6238 (mtp180) REVERT: J 53 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.3463 (t80) REVERT: J 96 ARG cc_start: 0.6388 (mtm110) cc_final: 0.5987 (mtm180) REVERT: J 108 MET cc_start: 0.8899 (mtt) cc_final: 0.8567 (mtt) REVERT: K 20 MET cc_start: 0.9167 (tpp) cc_final: 0.8963 (tpp) REVERT: K 32 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: K 45 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7909 (tm-30) REVERT: K 56 ASP cc_start: 0.6336 (m-30) cc_final: 0.6121 (m-30) REVERT: K 87 LEU cc_start: 0.8193 (pt) cc_final: 0.7512 (pt) REVERT: K 92 GLU cc_start: 0.6347 (mm-30) cc_final: 0.5866 (mm-30) REVERT: K 98 ARG cc_start: 0.8115 (ptm-80) cc_final: 0.7672 (ptm-80) REVERT: L 60 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6604 (mmt90) REVERT: L 64 PHE cc_start: 0.5102 (OUTLIER) cc_final: 0.4600 (m-80) REVERT: L 105 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.7980 (mt) REVERT: L 126 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6638 (ppp80) REVERT: M 18 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.6286 (ppt170) REVERT: M 33 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6777 (mm) REVERT: M 60 GLN cc_start: 0.7056 (pt0) cc_final: 0.6792 (pt0) REVERT: M 71 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6575 (tptp) REVERT: M 91 TYR cc_start: 0.6744 (m-10) cc_final: 0.6076 (m-10) REVERT: N 1 MET cc_start: 0.5317 (OUTLIER) cc_final: 0.5058 (pp-130) REVERT: N 67 PHE cc_start: 0.4428 (OUTLIER) cc_final: 0.3897 (m-10) REVERT: O 40 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7714 (mp) REVERT: O 74 VAL cc_start: 0.9014 (m) cc_final: 0.8635 (p) REVERT: O 94 ARG cc_start: 0.6905 (ttt180) cc_final: 0.6692 (ttt-90) REVERT: P 114 ASN cc_start: 0.8046 (p0) cc_final: 0.7817 (p0) REVERT: Q 17 LEU cc_start: 0.8190 (tp) cc_final: 0.7758 (tt) REVERT: Q 73 ILE cc_start: 0.7642 (mp) cc_final: 0.7412 (mm) REVERT: R 77 PHE cc_start: 0.6739 (m-80) cc_final: 0.6335 (m-80) REVERT: S 57 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7903 (t0) REVERT: S 67 ASP cc_start: 0.7302 (t0) cc_final: 0.5847 (p0) REVERT: T 53 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7509 (m) REVERT: U 7 ASP cc_start: 0.8635 (t0) cc_final: 0.8398 (t0) REVERT: U 44 HIS cc_start: 0.6117 (OUTLIER) cc_final: 0.5840 (t-170) REVERT: U 72 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.4251 (p90) REVERT: U 81 ARG cc_start: 0.5323 (OUTLIER) cc_final: 0.4191 (ttt180) REVERT: W 24 ARG cc_start: 0.7837 (ptp-170) cc_final: 0.7501 (ptp-170) REVERT: W 43 LYS cc_start: 0.7356 (mtmm) cc_final: 0.7061 (mtmm) REVERT: W 69 GLU cc_start: 0.4292 (OUTLIER) cc_final: 0.3574 (pm20) REVERT: X 2 LYS cc_start: 0.5407 (OUTLIER) cc_final: 0.4889 (pptt) REVERT: X 44 LYS cc_start: 0.7768 (tmmt) cc_final: 0.6810 (mmtt) REVERT: Y 6 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8242 (mt) REVERT: Y 20 LYS cc_start: 0.7169 (mmmt) cc_final: 0.6635 (tppt) REVERT: Z 25 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7417 (ttp80) REVERT: 2 11 VAL cc_start: 0.5113 (OUTLIER) cc_final: 0.4210 (t) REVERT: 2 27 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6523 (mtm110) REVERT: 3 1 MET cc_start: 0.6748 (tpp) cc_final: 0.6049 (pmm) REVERT: 3 19 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6525 (ppt170) REVERT: 4 2 LYS cc_start: 0.7757 (tptt) cc_final: 0.7033 (tttt) REVERT: 6 81 LYS cc_start: 0.0670 (OUTLIER) cc_final: -0.0768 (mttp) REVERT: c 5 HIS cc_start: 0.6442 (t70) cc_final: 0.6233 (t-170) REVERT: c 45 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7263 (tp30) REVERT: c 93 ILE cc_start: 0.6182 (tt) cc_final: 0.5500 (mp) REVERT: c 163 ARG cc_start: 0.6931 (mtp180) cc_final: 0.6032 (mmm-85) REVERT: d 25 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.4453 (ppt-90) REVERT: d 58 GLN cc_start: 0.7313 (tm-30) cc_final: 0.6909 (tm-30) REVERT: d 143 SER cc_start: 0.8429 (p) cc_final: 0.8127 (m) REVERT: d 189 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7100 (p0) REVERT: d 190 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7833 (mp) REVERT: e 155 LYS cc_start: 0.7814 (ttpt) cc_final: 0.7320 (mtmt) REVERT: f 2 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.6167 (mtp180) REVERT: f 39 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7113 (tm) REVERT: f 45 ARG cc_start: 0.7976 (ptm-80) cc_final: 0.7435 (mtp-110) REVERT: f 49 TYR cc_start: 0.7954 (p90) cc_final: 0.7554 (p90) REVERT: h 31 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8217 (tt) REVERT: h 57 GLU cc_start: 0.6895 (pm20) cc_final: 0.6683 (pm20) REVERT: h 95 MET cc_start: 0.7984 (mmp) cc_final: 0.7771 (mmp) REVERT: h 120 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8135 (pp) REVERT: i 30 ASN cc_start: 0.8166 (m-40) cc_final: 0.7342 (t0) REVERT: i 44 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.4086 (ppt90) REVERT: i 51 LEU cc_start: 0.6986 (mp) cc_final: 0.6261 (mt) REVERT: i 61 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.5913 (m-30) REVERT: i 106 ASP cc_start: 0.8082 (m-30) cc_final: 0.7618 (m-30) REVERT: j 65 TYR cc_start: 0.6620 (m-80) cc_final: 0.6212 (m-80) REVERT: k 52 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.5833 (ttt-90) REVERT: l 37 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6937 (m-10) REVERT: l 60 PHE cc_start: 0.8204 (m-80) cc_final: 0.7925 (m-80) REVERT: n 27 LYS cc_start: 0.3568 (OUTLIER) cc_final: 0.2365 (mtmm) REVERT: o 64 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7300 (mmmt) REVERT: p 18 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8026 (mm110) REVERT: q 33 TYR cc_start: 0.7376 (m-80) cc_final: 0.7110 (m-80) REVERT: q 56 ASP cc_start: 0.7594 (m-30) cc_final: 0.4209 (m-30) REVERT: r 49 LYS cc_start: 0.8987 (tttp) cc_final: 0.7322 (pttm) REVERT: r 63 TYR cc_start: 0.6889 (m-80) cc_final: 0.6108 (t80) REVERT: s 55 GLN cc_start: 0.0574 (OUTLIER) cc_final: -0.1121 (pt0) REVERT: t 27 MET cc_start: 0.8125 (ptm) cc_final: 0.7696 (ptp) REVERT: t 78 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8233 (tt) REVERT: 7 134 LEU cc_start: 0.8249 (mp) cc_final: 0.7519 (tp) REVERT: 7 183 PHE cc_start: 0.7700 (m-80) cc_final: 0.7239 (m-10) outliers start: 489 outliers final: 343 residues processed: 1507 average time/residue: 1.2978 time to fit residues: 3346.8437 Evaluate side-chains 1519 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 1131 time to evaluate : 5.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 113 PHE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 174 LYS Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 132 PHE Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 119 PHE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 132 HIS Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 71 LYS Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 LYS Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 67 PHE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 42 PHE Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 71 ASN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 44 HIS Chi-restraints excluded: chain U residue 72 PHE Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain U residue 95 PHE Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 84 GLU Chi-restraints excluded: chain X residue 2 LYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 6 HIS Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 28 VAL Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain 1 residue 2 VAL Chi-restraints excluded: chain 1 residue 41 HIS Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 27 ARG Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 21 PHE Chi-restraints excluded: chain 4 residue 23 HIS Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 4 residue 37 THR Chi-restraints excluded: chain 4 residue 42 HIS Chi-restraints excluded: chain 5 residue 13 ASN Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 6 residue 23 VAL Chi-restraints excluded: chain 6 residue 70 THR Chi-restraints excluded: chain 6 residue 81 LYS Chi-restraints excluded: chain c residue 18 ASN Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 25 ARG Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 73 ASN Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 182 LYS Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 65 GLU Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 64 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 33 SER Chi-restraints excluded: chain i residue 44 ARG Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 70 HIS Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 89 ARG Chi-restraints excluded: chain k residue 16 SER Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 52 ARG Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain k residue 118 ASN Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 4 ASN Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 37 TYR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain l residue 69 GLU Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain l residue 116 TYR Chi-restraints excluded: chain m residue 8 ILE Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 58 ARG Chi-restraints excluded: chain n residue 65 GLN Chi-restraints excluded: chain n residue 91 GLU Chi-restraints excluded: chain n residue 92 ILE Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 64 LYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 52 CYS Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 68 LYS Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 52 ARG Chi-restraints excluded: chain r residue 69 TYR Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 13 HIS Chi-restraints excluded: chain s residue 33 TRP Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain s residue 59 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 20 ASN Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 70 LYS Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain 7 residue 30 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 185 ILE Chi-restraints excluded: chain 7 residue 186 VAL Chi-restraints excluded: chain 7 residue 212 TYR Chi-restraints excluded: chain u residue 42 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 881 optimal weight: 10.0000 chunk 927 optimal weight: 6.9990 chunk 846 optimal weight: 6.9990 chunk 902 optimal weight: 4.9990 chunk 543 optimal weight: 8.9990 chunk 393 optimal weight: 8.9990 chunk 708 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 815 optimal weight: 9.9990 chunk 853 optimal weight: 6.9990 chunk 899 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 24 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS S 57 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 41 HIS 3 29 GLN 6 42 ASN d 135 GLN e 11 GLN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN i 125 GLN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 ASN ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 14 HIS ** 7 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.9421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.963 155037 Z= 0.619 Angle : 0.998 40.602 231928 Z= 0.496 Chirality : 0.048 1.484 29639 Planarity : 0.008 0.156 12421 Dihedral : 24.138 179.253 77766 Min Nonbonded Distance : 1.283 Molprobity Statistics. All-atom Clashscore : 29.62 Ramachandran Plot: Outliers : 2.77 % Allowed : 22.80 % Favored : 74.43 % Rotamer: Outliers : 9.47 % Allowed : 35.77 % Favored : 54.77 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 3.12 % Twisted General : 0.82 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.10), residues: 5631 helix: -2.12 (0.12), residues: 1389 sheet: -2.79 (0.20), residues: 595 loop : -3.98 (0.09), residues: 3647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP n 100 HIS 0.020 0.002 HIS s 68 PHE 0.045 0.003 PHE F 113 TYR 0.104 0.003 TYR j 65 ARG 0.024 0.001 ARG P 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1629 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 442 poor density : 1187 time to evaluate : 5.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 42 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7742 (mp) REVERT: V 44 HIS cc_start: 0.7259 (t70) cc_final: 0.6284 (t70) REVERT: V 48 MET cc_start: 0.7427 (tpt) cc_final: 0.6562 (tpt) REVERT: V 55 GLU cc_start: 0.8008 (pm20) cc_final: 0.7222 (tp30) REVERT: C 124 LYS cc_start: 0.8378 (mmmm) cc_final: 0.7663 (pttp) REVERT: C 260 LYS cc_start: 0.8381 (mptt) cc_final: 0.8164 (mmmt) REVERT: C 261 ARG cc_start: 0.6933 (mmt90) cc_final: 0.4991 (ttp-170) REVERT: D 33 ARG cc_start: 0.6328 (ptt180) cc_final: 0.5527 (mmm160) REVERT: D 94 GLN cc_start: 0.8733 (pp30) cc_final: 0.8059 (tm-30) REVERT: D 113 SER cc_start: 0.7558 (t) cc_final: 0.7066 (p) REVERT: E 23 PHE cc_start: 0.6131 (t80) cc_final: 0.5725 (t80) REVERT: E 72 SER cc_start: 0.8420 (m) cc_final: 0.8029 (t) REVERT: E 88 ARG cc_start: 0.8365 (mmt90) cc_final: 0.7753 (tpp-160) REVERT: E 114 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6839 (tpt170) REVERT: E 116 ASP cc_start: 0.6411 (OUTLIER) cc_final: 0.6211 (m-30) REVERT: E 159 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6322 (pp) REVERT: F 19 PHE cc_start: 0.6517 (t80) cc_final: 0.6274 (t80) REVERT: F 50 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6816 (p0) REVERT: F 65 LEU cc_start: 0.7155 (tp) cc_final: 0.6950 (tt) REVERT: F 111 ARG cc_start: 0.0312 (ttt90) cc_final: -0.0512 (ptm160) REVERT: G 74 MET cc_start: 0.5697 (ptp) cc_final: 0.5351 (ptp) REVERT: G 146 ASP cc_start: 0.7817 (p0) cc_final: 0.7206 (p0) REVERT: J 17 VAL cc_start: 0.8943 (m) cc_final: 0.8638 (m) REVERT: J 37 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6373 (mtp180) REVERT: J 96 ARG cc_start: 0.6569 (mtm110) cc_final: 0.6035 (ptp-170) REVERT: J 108 MET cc_start: 0.8852 (mtt) cc_final: 0.8594 (mtt) REVERT: K 17 ARG cc_start: 0.8670 (mmt180) cc_final: 0.8465 (mmt180) REVERT: K 31 ARG cc_start: 0.8190 (mtt-85) cc_final: 0.7906 (mtt90) REVERT: K 32 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: K 45 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7640 (tm-30) REVERT: K 67 LYS cc_start: 0.6687 (mttt) cc_final: 0.6430 (tptm) REVERT: K 87 LEU cc_start: 0.8111 (pt) cc_final: 0.7763 (pt) REVERT: K 89 ASN cc_start: 0.8306 (m-40) cc_final: 0.8074 (m-40) REVERT: K 98 ARG cc_start: 0.7960 (ptm-80) cc_final: 0.7544 (ptm-80) REVERT: L 60 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.4881 (ptt180) REVERT: L 105 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.7983 (mt) REVERT: L 126 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6257 (ppp80) REVERT: L 136 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6638 (pp20) REVERT: M 18 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.6277 (ppt170) REVERT: M 71 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6612 (tptp) REVERT: N 67 PHE cc_start: 0.4393 (OUTLIER) cc_final: 0.3785 (m-10) REVERT: O 30 ARG cc_start: 0.8288 (tpp80) cc_final: 0.6646 (tpp80) REVERT: O 40 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7748 (mp) REVERT: O 74 VAL cc_start: 0.8900 (m) cc_final: 0.8594 (t) REVERT: O 92 PHE cc_start: 0.7859 (t80) cc_final: 0.7573 (t80) REVERT: P 61 ARG cc_start: 0.7892 (mtm110) cc_final: 0.6572 (mtt180) REVERT: P 114 ASN cc_start: 0.8422 (p0) cc_final: 0.8161 (p0) REVERT: Q 17 LEU cc_start: 0.7896 (tp) cc_final: 0.7671 (tt) REVERT: R 77 PHE cc_start: 0.6535 (m-80) cc_final: 0.6275 (m-80) REVERT: R 90 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.3467 (ttp-170) REVERT: S 57 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8098 (t0) REVERT: S 67 ASP cc_start: 0.6886 (t0) cc_final: 0.5643 (p0) REVERT: U 7 ASP cc_start: 0.8698 (t0) cc_final: 0.8461 (t0) REVERT: U 38 ILE cc_start: 0.7643 (mm) cc_final: 0.7423 (tt) REVERT: U 44 HIS cc_start: 0.6120 (OUTLIER) cc_final: 0.5426 (m170) REVERT: U 72 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.3793 (p90) REVERT: U 81 ARG cc_start: 0.5574 (OUTLIER) cc_final: 0.4132 (ttt180) REVERT: W 20 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7095 (pp) REVERT: W 43 LYS cc_start: 0.7368 (mtmm) cc_final: 0.7138 (mtmm) REVERT: W 69 GLU cc_start: 0.3961 (OUTLIER) cc_final: 0.2492 (pm20) REVERT: W 70 VAL cc_start: 0.6666 (t) cc_final: 0.6308 (t) REVERT: X 2 LYS cc_start: 0.5359 (OUTLIER) cc_final: 0.4847 (pptt) REVERT: X 44 LYS cc_start: 0.7651 (tmmt) cc_final: 0.6687 (mmtt) REVERT: Y 6 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7960 (mt) REVERT: Y 20 LYS cc_start: 0.6973 (mmmt) cc_final: 0.6436 (tppt) REVERT: Y 46 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7584 (mmm) REVERT: 1 12 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6823 (ptm160) REVERT: 2 27 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6614 (mtm110) REVERT: 3 1 MET cc_start: 0.6648 (tpp) cc_final: 0.6285 (tpp) REVERT: 3 19 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6679 (ppt170) REVERT: 4 2 LYS cc_start: 0.7675 (tptt) cc_final: 0.7024 (tttt) REVERT: 6 81 LYS cc_start: 0.0420 (OUTLIER) cc_final: -0.0959 (mtmt) REVERT: c 13 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7579 (mt) REVERT: c 45 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7178 (tp30) REVERT: c 93 ILE cc_start: 0.5680 (tt) cc_final: 0.5010 (mp) REVERT: c 106 ARG cc_start: 0.8633 (mmt180) cc_final: 0.8257 (ttm110) REVERT: c 141 MET cc_start: 0.6015 (mmp) cc_final: 0.5806 (mmt) REVERT: c 163 ARG cc_start: 0.6871 (mtp180) cc_final: 0.6004 (mmm-85) REVERT: d 25 ARG cc_start: 0.6358 (OUTLIER) cc_final: 0.4684 (ppt-90) REVERT: d 58 GLN cc_start: 0.7211 (tm-30) cc_final: 0.6876 (tm-30) REVERT: d 143 SER cc_start: 0.8391 (p) cc_final: 0.8174 (t) REVERT: d 189 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7103 (p0) REVERT: d 190 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7786 (mp) REVERT: e 64 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8089 (mm-30) REVERT: e 95 MET cc_start: 0.7405 (tpp) cc_final: 0.7163 (tpp) REVERT: e 155 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7522 (mtmm) REVERT: f 2 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.5900 (mtp-110) REVERT: f 39 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7262 (tm) REVERT: f 45 ARG cc_start: 0.7983 (ptm-80) cc_final: 0.7415 (mtp-110) REVERT: f 49 TYR cc_start: 0.7968 (p90) cc_final: 0.7557 (p90) REVERT: f 65 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6672 (pp20) REVERT: g 138 GLU cc_start: 0.7875 (pm20) cc_final: 0.6687 (tp30) REVERT: h 31 LEU cc_start: 0.8576 (tp) cc_final: 0.8219 (tt) REVERT: h 95 MET cc_start: 0.8029 (mmp) cc_final: 0.7806 (mmp) REVERT: h 120 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8044 (pp) REVERT: i 30 ASN cc_start: 0.7996 (m-40) cc_final: 0.7325 (t0) REVERT: i 44 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.4431 (ppt90) REVERT: i 51 LEU cc_start: 0.6937 (mp) cc_final: 0.6270 (mt) REVERT: i 61 ASP cc_start: 0.6162 (m-30) cc_final: 0.5641 (m-30) REVERT: j 56 HIS cc_start: 0.4825 (OUTLIER) cc_final: 0.4098 (p-80) REVERT: k 45 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8152 (m) REVERT: k 52 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.6275 (ttt-90) REVERT: l 37 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.7205 (m-10) REVERT: l 43 LYS cc_start: 0.7600 (tppt) cc_final: 0.6767 (tmtt) REVERT: l 48 LEU cc_start: 0.7771 (pt) cc_final: 0.7230 (mm) REVERT: l 60 PHE cc_start: 0.8112 (m-80) cc_final: 0.7903 (m-80) REVERT: l 85 ARG cc_start: 0.7836 (ptm-80) cc_final: 0.7467 (ptt180) REVERT: l 88 ASP cc_start: 0.7330 (m-30) cc_final: 0.7125 (m-30) REVERT: m 11 HIS cc_start: 0.5244 (OUTLIER) cc_final: 0.4578 (t70) REVERT: m 51 GLN cc_start: 0.4326 (OUTLIER) cc_final: 0.4109 (mm-40) REVERT: n 27 LYS cc_start: 0.2644 (OUTLIER) cc_final: 0.1498 (mttp) REVERT: o 34 GLN cc_start: 0.8606 (pm20) cc_final: 0.8324 (pm20) REVERT: o 64 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7229 (mmmt) REVERT: p 5 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.6774 (ppt-90) REVERT: p 18 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8019 (mm110) REVERT: q 33 TYR cc_start: 0.7421 (m-80) cc_final: 0.6707 (m-80) REVERT: r 63 TYR cc_start: 0.7449 (m-80) cc_final: 0.6222 (t80) REVERT: s 2 ARG cc_start: 0.3597 (OUTLIER) cc_final: 0.3054 (ptm160) REVERT: s 43 MET cc_start: 0.5548 (mmp) cc_final: 0.5047 (mmp) REVERT: s 55 GLN cc_start: 0.0583 (OUTLIER) cc_final: -0.0804 (pt0) REVERT: t 27 MET cc_start: 0.8139 (ptm) cc_final: 0.7725 (ptp) REVERT: t 78 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8294 (tt) REVERT: 7 134 LEU cc_start: 0.8405 (mp) cc_final: 0.7690 (tp) outliers start: 442 outliers final: 328 residues processed: 1463 average time/residue: 1.2431 time to fit residues: 3111.5688 Evaluate side-chains 1509 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1131 time to evaluate : 5.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 114 ARG Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 113 PHE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 174 LYS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 119 PHE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 71 LYS Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 LYS Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 67 PHE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 42 PHE Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 71 ASN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 44 HIS Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 72 PHE Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain U residue 95 PHE Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain W residue 80 SER Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 84 GLU Chi-restraints excluded: chain X residue 2 LYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Z residue 6 HIS Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 28 VAL Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain 1 residue 12 ARG Chi-restraints excluded: chain 1 residue 41 HIS Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 9 LYS Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 27 ARG Chi-restraints excluded: chain 2 residue 32 LYS Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 21 PHE Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 4 residue 37 THR Chi-restraints excluded: chain 4 residue 42 HIS Chi-restraints excluded: chain 5 residue 13 ASN Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 6 residue 23 VAL Chi-restraints excluded: chain 6 residue 70 THR Chi-restraints excluded: chain 6 residue 81 LYS Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 18 ASN Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 25 ARG Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain d residue 104 MET Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 135 GLN Chi-restraints excluded: chain d residue 139 ASN Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 18 ASN Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 110 MET Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 147 ASN Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 87 SER Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 115 MET Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 64 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 33 SER Chi-restraints excluded: chain i residue 44 ARG Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 59 LYS Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 70 HIS Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 89 ARG Chi-restraints excluded: chain k residue 16 SER Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 52 ARG Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 37 TYR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain l residue 116 TYR Chi-restraints excluded: chain l residue 120 ARG Chi-restraints excluded: chain m residue 8 ILE Chi-restraints excluded: chain m residue 11 HIS Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 51 GLN Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 58 ARG Chi-restraints excluded: chain n residue 65 GLN Chi-restraints excluded: chain n residue 91 GLU Chi-restraints excluded: chain n residue 92 ILE Chi-restraints excluded: chain o residue 10 ILE Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 64 LYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 74 VAL Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 52 CYS Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 28 LEU Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 69 TYR Chi-restraints excluded: chain s residue 2 ARG Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 34 SER Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain 7 residue 30 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 186 VAL Chi-restraints excluded: chain 7 residue 198 VAL Chi-restraints excluded: chain 7 residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 592 optimal weight: 10.0000 chunk 954 optimal weight: 1.9990 chunk 582 optimal weight: 0.6980 chunk 452 optimal weight: 6.9990 chunk 663 optimal weight: 10.0000 chunk 1001 optimal weight: 10.0000 chunk 921 optimal weight: 3.9990 chunk 797 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 615 optimal weight: 9.9990 chunk 488 optimal weight: 0.0010 overall best weight: 2.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 24 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS S 57 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 GLN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN i 125 GLN ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 HIS ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 55 GLN ** t 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.9593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.040 155037 Z= 0.567 Angle : 0.912 43.115 231928 Z= 0.456 Chirality : 0.043 1.441 29639 Planarity : 0.007 0.145 12421 Dihedral : 24.033 179.965 77755 Min Nonbonded Distance : 1.300 Molprobity Statistics. All-atom Clashscore : 25.46 Ramachandran Plot: Outliers : 2.73 % Allowed : 21.22 % Favored : 76.04 % Rotamer: Outliers : 7.24 % Allowed : 38.47 % Favored : 54.29 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 2.60 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.10), residues: 5631 helix: -1.98 (0.13), residues: 1411 sheet: -2.68 (0.21), residues: 570 loop : -3.87 (0.09), residues: 3650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP n 100 HIS 0.015 0.002 HIS 4 23 PHE 0.046 0.003 PHE F 113 TYR 0.110 0.002 TYR j 65 ARG 0.022 0.001 ARG j 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11262 Ramachandran restraints generated. 5631 Oldfield, 0 Emsley, 5631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1542 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1204 time to evaluate : 5.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 42 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7500 (mp) REVERT: V 44 HIS cc_start: 0.7316 (t70) cc_final: 0.6893 (t70) REVERT: V 48 MET cc_start: 0.7323 (tpt) cc_final: 0.6506 (tpt) REVERT: C 53 ILE cc_start: 0.7596 (mt) cc_final: 0.7268 (mt) REVERT: C 124 LYS cc_start: 0.8206 (mmmm) cc_final: 0.7610 (pttp) REVERT: C 260 LYS cc_start: 0.8279 (mptt) cc_final: 0.8073 (mmmt) REVERT: C 261 ARG cc_start: 0.6504 (mmt90) cc_final: 0.4477 (ttp-170) REVERT: D 22 ILE cc_start: 0.7129 (tp) cc_final: 0.6852 (pt) REVERT: D 169 ARG cc_start: 0.7749 (mmm160) cc_final: 0.6953 (mmm160) REVERT: E 18 THR cc_start: 0.5305 (m) cc_final: 0.4965 (p) REVERT: E 23 PHE cc_start: 0.5984 (t80) cc_final: 0.5325 (t80) REVERT: E 72 SER cc_start: 0.8403 (m) cc_final: 0.7792 (t) REVERT: E 88 ARG cc_start: 0.8271 (mmt90) cc_final: 0.7742 (tpp-160) REVERT: E 114 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6787 (tpt170) REVERT: E 116 ASP cc_start: 0.5949 (OUTLIER) cc_final: 0.5506 (m-30) REVERT: E 159 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.5996 (pp) REVERT: E 199 MET cc_start: 0.6623 (mtm) cc_final: 0.6316 (mpp) REVERT: F 19 PHE cc_start: 0.6498 (t80) cc_final: 0.6238 (t80) REVERT: F 50 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6823 (p0) REVERT: F 65 LEU cc_start: 0.7244 (tp) cc_final: 0.7002 (tt) REVERT: F 93 GLU cc_start: 0.8397 (pp20) cc_final: 0.7835 (pp20) REVERT: F 147 ARG cc_start: 0.7603 (ptt-90) cc_final: 0.7335 (ptp90) REVERT: G 146 ASP cc_start: 0.7753 (p0) cc_final: 0.7126 (p0) REVERT: H 53 GLU cc_start: 0.5350 (mp0) cc_final: 0.4880 (tp30) REVERT: J 17 VAL cc_start: 0.8921 (m) cc_final: 0.8629 (m) REVERT: J 37 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.6123 (mtp180) REVERT: J 96 ARG cc_start: 0.6409 (mtm110) cc_final: 0.6082 (ptp-170) REVERT: K 87 LEU cc_start: 0.8149 (pt) cc_final: 0.7753 (pt) REVERT: K 98 ARG cc_start: 0.7916 (ptm-80) cc_final: 0.7537 (ptm-80) REVERT: L 60 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.5011 (ptp90) REVERT: L 105 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7758 (mt) REVERT: M 17 ASN cc_start: 0.4966 (m110) cc_final: 0.4486 (m-40) REVERT: M 18 ARG cc_start: 0.6197 (OUTLIER) cc_final: 0.5994 (ppt170) REVERT: M 71 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6417 (tptp) REVERT: N 67 PHE cc_start: 0.4287 (OUTLIER) cc_final: 0.3684 (m-10) REVERT: O 30 ARG cc_start: 0.8280 (tpp80) cc_final: 0.6560 (tpp80) REVERT: O 40 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7644 (mp) REVERT: O 74 VAL cc_start: 0.8615 (m) cc_final: 0.8229 (t) REVERT: P 61 ARG cc_start: 0.7444 (mtm110) cc_final: 0.6617 (mmt90) REVERT: P 114 ASN cc_start: 0.8295 (p0) cc_final: 0.8003 (p0) REVERT: Q 17 LEU cc_start: 0.7968 (tp) cc_final: 0.7586 (tt) REVERT: R 77 PHE cc_start: 0.6393 (m-80) cc_final: 0.6139 (m-80) REVERT: R 90 ARG cc_start: 0.6012 (OUTLIER) cc_final: 0.3179 (ttp-170) REVERT: S 1 MET cc_start: -0.1645 (mtm) cc_final: -0.2315 (mtm) REVERT: S 67 ASP cc_start: 0.7057 (t0) cc_final: 0.5897 (p0) REVERT: T 1 MET cc_start: 0.5192 (mmm) cc_final: 0.4918 (mmm) REVERT: U 7 ASP cc_start: 0.8806 (t0) cc_final: 0.8514 (t0) REVERT: U 38 ILE cc_start: 0.7499 (mm) cc_final: 0.7288 (tt) REVERT: U 44 HIS cc_start: 0.5647 (OUTLIER) cc_final: 0.4768 (m170) REVERT: U 72 PHE cc_start: 0.6204 (OUTLIER) cc_final: 0.4438 (p90) REVERT: W 20 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6713 (pp) REVERT: W 43 LYS cc_start: 0.7219 (mtmm) cc_final: 0.6669 (mtmm) REVERT: W 69 GLU cc_start: 0.4024 (OUTLIER) cc_final: 0.2573 (pm20) REVERT: W 70 VAL cc_start: 0.6536 (t) cc_final: 0.6149 (t) REVERT: X 2 LYS cc_start: 0.5186 (OUTLIER) cc_final: 0.4695 (pptt) REVERT: Y 6 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7936 (mt) REVERT: Y 20 LYS cc_start: 0.7087 (mmmt) cc_final: 0.6485 (tppt) REVERT: 1 41 HIS cc_start: 0.3020 (OUTLIER) cc_final: 0.1795 (t-90) REVERT: 2 27 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6593 (mtp85) REVERT: 3 1 MET cc_start: 0.6659 (tpp) cc_final: 0.6207 (tpp) REVERT: 3 19 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6586 (ppt170) REVERT: 4 2 LYS cc_start: 0.7772 (tptt) cc_final: 0.6999 (tttt) REVERT: 4 18 LYS cc_start: 0.6793 (ptpp) cc_final: 0.6325 (pptt) REVERT: 6 81 LYS cc_start: 0.0456 (OUTLIER) cc_final: -0.0997 (mtmt) REVERT: c 13 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7549 (mt) REVERT: c 45 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7341 (tp30) REVERT: c 63 ILE cc_start: 0.0698 (OUTLIER) cc_final: 0.0419 (pp) REVERT: c 79 LYS cc_start: 0.4347 (mmmt) cc_final: 0.3645 (mmtm) REVERT: c 100 ILE cc_start: 0.2390 (OUTLIER) cc_final: 0.1939 (tt) REVERT: c 101 ASN cc_start: 0.7295 (OUTLIER) cc_final: 0.7031 (m-40) REVERT: c 106 ARG cc_start: 0.8269 (mmt180) cc_final: 0.7880 (ttm110) REVERT: d 25 ARG cc_start: 0.6295 (OUTLIER) cc_final: 0.4741 (ppt-90) REVERT: d 58 GLN cc_start: 0.7078 (tm-30) cc_final: 0.6787 (tm-30) REVERT: d 74 TYR cc_start: 0.7862 (m-80) cc_final: 0.7660 (m-80) REVERT: d 143 SER cc_start: 0.8381 (p) cc_final: 0.8078 (m) REVERT: d 189 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6808 (p0) REVERT: d 190 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7653 (mp) REVERT: e 111 ARG cc_start: 0.7190 (ttt180) cc_final: 0.6885 (ttt180) REVERT: e 155 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7353 (mtmm) REVERT: f 1 MET cc_start: 0.8392 (ptp) cc_final: 0.7880 (ptp) REVERT: f 2 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.5814 (mtp-110) REVERT: f 21 MET cc_start: 0.6481 (tpp) cc_final: 0.6174 (mmm) REVERT: f 25 TYR cc_start: 0.7735 (m-80) cc_final: 0.6643 (m-80) REVERT: f 39 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7232 (tm) REVERT: f 45 ARG cc_start: 0.8080 (ptm-80) cc_final: 0.7519 (mtp-110) REVERT: f 49 TYR cc_start: 0.7876 (p90) cc_final: 0.7448 (p90) REVERT: f 68 GLN cc_start: 0.8711 (pp30) cc_final: 0.8502 (pp30) REVERT: g 138 GLU cc_start: 0.7896 (pm20) cc_final: 0.6927 (tp30) REVERT: g 150 PHE cc_start: 0.6271 (m-80) cc_final: 0.6049 (m-80) REVERT: h 31 LEU cc_start: 0.8460 (tp) cc_final: 0.8148 (tt) REVERT: h 95 MET cc_start: 0.7968 (mmp) cc_final: 0.7509 (mmm) REVERT: h 120 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7955 (pp) REVERT: i 30 ASN cc_start: 0.7722 (m-40) cc_final: 0.7402 (t0) REVERT: i 44 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.4402 (ppt90) REVERT: i 51 LEU cc_start: 0.6717 (mp) cc_final: 0.6269 (tp) REVERT: i 61 ASP cc_start: 0.6298 (OUTLIER) cc_final: 0.5853 (m-30) REVERT: j 51 VAL cc_start: 0.1627 (OUTLIER) cc_final: 0.1027 (t) REVERT: j 56 HIS cc_start: 0.3259 (OUTLIER) cc_final: 0.3021 (p-80) REVERT: j 87 LEU cc_start: 0.4056 (tp) cc_final: 0.3606 (tp) REVERT: l 37 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.7101 (m-10) REVERT: l 43 LYS cc_start: 0.7606 (tppt) cc_final: 0.6729 (tmtt) REVERT: l 48 LEU cc_start: 0.7692 (pt) cc_final: 0.7243 (mm) REVERT: l 60 PHE cc_start: 0.8031 (m-80) cc_final: 0.7648 (m-80) REVERT: l 85 ARG cc_start: 0.7840 (ptm-80) cc_final: 0.7446 (ptt180) REVERT: l 114 SER cc_start: 0.9073 (m) cc_final: 0.8837 (m) REVERT: m 11 HIS cc_start: 0.5008 (OUTLIER) cc_final: 0.4572 (t70) REVERT: n 27 LYS cc_start: 0.2068 (OUTLIER) cc_final: 0.1206 (mtmm) REVERT: p 18 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8109 (mm110) REVERT: q 16 MET cc_start: 0.6515 (mtm) cc_final: 0.6141 (mtp) REVERT: q 64 ARG cc_start: 0.8490 (ttp-110) cc_final: 0.8269 (ttp-110) REVERT: r 47 ARG cc_start: 0.6238 (mtt180) cc_final: 0.5760 (mtm180) REVERT: r 63 TYR cc_start: 0.7209 (m-80) cc_final: 0.5865 (t80) REVERT: s 43 MET cc_start: 0.5462 (mmp) cc_final: 0.4970 (mmp) REVERT: s 55 GLN cc_start: 0.0176 (OUTLIER) cc_final: -0.1057 (pt0) REVERT: s 68 HIS cc_start: 0.4171 (OUTLIER) cc_final: 0.3906 (t70) REVERT: t 27 MET cc_start: 0.7992 (ptm) cc_final: 0.7609 (ptp) REVERT: 7 134 LEU cc_start: 0.8468 (mp) cc_final: 0.7876 (tp) outliers start: 338 outliers final: 258 residues processed: 1422 average time/residue: 1.2832 time to fit residues: 3114.2475 Evaluate side-chains 1446 residues out of total 4669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1145 time to evaluate : 5.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 114 ARG Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 113 PHE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 15 TRP Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 132 HIS Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 71 LYS Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 100 LYS Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 67 PHE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 80 PHE Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 42 PHE Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 69 ARG Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 44 HIS Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 72 PHE Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain U residue 95 PHE Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 2 LYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 32 LEU Chi-restraints excluded: chain 1 residue 41 HIS Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 9 LYS Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 27 ARG Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 5 THR Chi-restraints excluded: chain 4 residue 21 PHE Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 4 residue 37 THR Chi-restraints excluded: chain 4 residue 42 HIS Chi-restraints excluded: chain 5 residue 13 ASN Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 33 HIS Chi-restraints excluded: chain 6 residue 23 VAL Chi-restraints excluded: chain 6 residue 70 THR Chi-restraints excluded: chain 6 residue 81 LYS Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 25 ARG Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 139 ASN Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 40 ASP Chi-restraints excluded: chain e residue 54 GLU Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 110 MET Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 115 MET Chi-restraints excluded: chain g residue 140 VAL Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 64 TYR Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 44 ARG Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 70 HIS Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 89 ARG Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 37 TYR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 66 ILE Chi-restraints excluded: chain m residue 8 ILE Chi-restraints excluded: chain m residue 11 HIS Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain n residue 27 LYS Chi-restraints excluded: chain n residue 58 ARG Chi-restraints excluded: chain n residue 65 GLN Chi-restraints excluded: chain n residue 91 GLU Chi-restraints excluded: chain n residue 92 ILE Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 25 GLU Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 28 LEU Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 68 HIS Chi-restraints excluded: chain t residue 78 LEU Chi-restraints excluded: chain 7 residue 30 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 91 VAL Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 185 ILE Chi-restraints excluded: chain 7 residue 186 VAL Chi-restraints excluded: chain 7 residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1005 random chunks: chunk 633 optimal weight: 10.0000 chunk 849 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 735 optimal weight: 20.0000 chunk 117 optimal weight: 30.0000 chunk 221 optimal weight: 20.0000 chunk 798 optimal weight: 4.9990 chunk 334 optimal weight: 9.9990 chunk 819 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 ASN E 94 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 6 HIS Z 41 HIS d 135 GLN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN i 125 GLN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 80 ASN ** m 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 39 GLN ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.127186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.110685 restraints weight = 399849.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113024 restraints weight = 163758.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.114369 restraints weight = 90577.902| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 1.0016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.980 155037 Z= 0.686 Angle : 1.111 43.080 231928 Z= 0.548 Chirality : 0.052 1.307 29639 Planarity : 0.009 0.140 12421 Dihedral : 24.275 179.764 77744 Min Nonbonded Distance : 1.282 Molprobity Statistics. All-atom Clashscore : 34.98 Ramachandran Plot: Outliers : 2.86 % Allowed : 24.93 % Favored : 72.21 % Rotamer: Outliers : 8.67 % Allowed : 37.42 % Favored : 53.91 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 3.12 % Twisted General : 0.93 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.10), residues: 5631 helix: -2.23 (0.12), residues: 1391 sheet: -2.91 (0.19), residues: 627 loop : -4.03 (0.09), residues: 3613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP n 100 HIS 0.025 0.003 HIS d 197 PHE 0.058 0.004 PHE n 76 TYR 0.118 0.004 TYR j 65 ARG 0.020 0.001 ARG W 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47327.22 seconds wall clock time: 823 minutes 40.80 seconds (49420.80 seconds total)