Starting phenix.real_space_refine on Thu Mar 21 10:39:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nso_12573/03_2024/7nso_12573_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nso_12573/03_2024/7nso_12573.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nso_12573/03_2024/7nso_12573_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nso_12573/03_2024/7nso_12573_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nso_12573/03_2024/7nso_12573_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nso_12573/03_2024/7nso_12573.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nso_12573/03_2024/7nso_12573.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nso_12573/03_2024/7nso_12573_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nso_12573/03_2024/7nso_12573_updated.pdb" } resolution = 2.9 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= 0.018 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 4653 5.49 5 S 149 5.16 5 C 72465 2.51 5 N 26918 2.21 5 O 40269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D ASP 103": "OD1" <-> "OD2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G ASP 39": "OD1" <-> "OD2" Residue "G ASP 114": "OD1" <-> "OD2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ASP 7": "OD1" <-> "OD2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 90": "OE1" <-> "OE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 129": "OE1" <-> "OE2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ASP 70": "OD1" <-> "OD2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N GLU 49": "OE1" <-> "OE2" Residue "N ASP 58": "OD1" <-> "OD2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ASP 2": "OD1" <-> "OD2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O GLU 84": "OE1" <-> "OE2" Residue "O ASP 89": "OD1" <-> "OD2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 9": "OE1" <-> "OE2" Residue "P PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P ARG 39": "NH1" <-> "NH2" Residue "P PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ASP 82": "OD1" <-> "OD2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ASP 34": "OD1" <-> "OD2" Residue "S TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S ASP 65": "OD1" <-> "OD2" Residue "S ASP 68": "OD1" <-> "OD2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 77": "OD1" <-> "OD2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 42": "OE1" <-> "OE2" Residue "T ARG 69": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 7": "NH1" <-> "NH2" Residue "U ASP 8": "OD1" <-> "OD2" Residue "U ASP 9": "OD1" <-> "OD2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 11": "OE1" <-> "OE2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 35": "OE1" <-> "OE2" Residue "V GLU 41": "OE1" <-> "OE2" Residue "V GLU 59": "OE1" <-> "OE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 70": "OE1" <-> "OE2" Residue "W PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 43": "OE1" <-> "OE2" Residue "X PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "Z PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 10": "NH1" <-> "NH2" Residue "0 ARG 16": "NH1" <-> "NH2" Residue "0 ARG 40": "NH1" <-> "NH2" Residue "0 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 52": "NH1" <-> "NH2" Residue "1 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 40": "OD1" <-> "OD2" Residue "1 ARG 44": "NH1" <-> "NH2" Residue "1 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 13": "NH1" <-> "NH2" Residue "3 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 30": "NH1" <-> "NH2" Residue "3 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 42": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "5 ASP 35": "OD1" <-> "OD2" Residue "5 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 50": "OD1" <-> "OD2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "5 ASP 58": "OD1" <-> "OD2" Residue "5 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 63": "NH1" <-> "NH2" Residue "b PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 82": "OD1" <-> "OD2" Residue "b ARG 113": "NH1" <-> "NH2" Residue "b PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 142": "OE1" <-> "OE2" Residue "b ASP 165": "OD1" <-> "OD2" Residue "b ASP 188": "OD1" <-> "OD2" Residue "b PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 208": "NH1" <-> "NH2" Residue "b ARG 222": "NH1" <-> "NH2" Residue "b GLU 223": "OE1" <-> "OE2" Residue "c ARG 107": "NH1" <-> "NH2" Residue "c PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "d ASP 18": "OD1" <-> "OD2" Residue "d ASP 50": "OD1" <-> "OD2" Residue "d GLU 57": "OE1" <-> "OE2" Residue "d ASP 141": "OD1" <-> "OD2" Residue "d GLU 163": "OE1" <-> "OE2" Residue "d GLU 179": "OE1" <-> "OE2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "e ARG 20": "NH1" <-> "NH2" Residue "e GLU 65": "OE1" <-> "OE2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 93": "NH1" <-> "NH2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e ASP 142": "OD1" <-> "OD2" Residue "e ARG 157": "NH1" <-> "NH2" Residue "f TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 13": "OD1" <-> "OD2" Residue "f GLU 69": "OE1" <-> "OE2" Residue "f ARG 91": "NH1" <-> "NH2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "g ASP 15": "OD1" <-> "OD2" Residue "g PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "g GLU 67": "OE1" <-> "OE2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g ASP 113": "OD1" <-> "OD2" Residue "h ASP 5": "OD1" <-> "OD2" Residue "h ASP 9": "OD1" <-> "OD2" Residue "h PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 54": "OD1" <-> "OD2" Residue "h GLU 91": "OE1" <-> "OE2" Residue "i TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 36": "OE1" <-> "OE2" Residue "i PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i ARG 49": "NH1" <-> "NH2" Residue "i ARG 99": "NH1" <-> "NH2" Residue "i ARG 124": "NH1" <-> "NH2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j ASP 63": "OD1" <-> "OD2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ASP 75": "OD1" <-> "OD2" Residue "j ASP 85": "OD1" <-> "OD2" Residue "j ASP 91": "OD1" <-> "OD2" Residue "k ASP 36": "OD1" <-> "OD2" Residue "k PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 72": "OD1" <-> "OD2" Residue "k TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 93": "NH1" <-> "NH2" Residue "k GLU 94": "OE1" <-> "OE2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 14": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "l ARG 83": "NH1" <-> "NH2" Residue "l ASP 89": "OD1" <-> "OD2" Residue "m TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m ASP 54": "OD1" <-> "OD2" Residue "m PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 68": "OD1" <-> "OD2" Residue "n ASP 18": "OD1" <-> "OD2" Residue "n TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 90": "NH1" <-> "NH2" Residue "o PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 45": "OE1" <-> "OE2" Residue "o ASP 74": "OD1" <-> "OD2" Residue "p ARG 8": "NH1" <-> "NH2" Residue "p ASP 23": "OD1" <-> "OD2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 45": "OE1" <-> "OE2" Residue "p ASP 55": "OD1" <-> "OD2" Residue "p ASP 69": "OD1" <-> "OD2" Residue "q ARG 11": "NH1" <-> "NH2" Residue "q ASP 15": "OD1" <-> "OD2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 12": "NH1" <-> "NH2" Residue "r GLU 20": "OE1" <-> "OE2" Residue "r ASP 22": "OD1" <-> "OD2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 61": "NH1" <-> "NH2" Residue "s ARG 32": "NH1" <-> "NH2" Residue "s GLU 73": "OE1" <-> "OE2" Residue "t ARG 24": "NH1" <-> "NH2" Residue "t GLU 40": "OE1" <-> "OE2" Residue "t PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 60": "NH1" <-> "NH2" Residue "t ARG 74": "NH1" <-> "NH2" Residue "u ASP 13": "OD1" <-> "OD2" Residue "u PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u ARG 45": "NH1" <-> "NH2" Residue "u ARG 55": "NH1" <-> "NH2" Residue "u ARG 66": "NH1" <-> "NH2" Residue "u ARG 69": "NH1" <-> "NH2" Residue "u TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 144454 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 62321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62321 Classifications: {'RNA': 2903} Modifications used: {'p5*END': 1, 'rna2p_pur': 253, 'rna2p_pyr': 131, 'rna3p_pur': 1421, 'rna3p_pyr': 1098} Link IDs: {'rna2p': 384, 'rna3p': 2518} Chain: "B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2570 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 59, 'rna3p_pyr': 52} Link IDs: {'rna2p': 9, 'rna3p': 110} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} 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: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1304 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} 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: {'PTRANS': 3, 'TRANS': 145} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} 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: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} 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: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 709 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} 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: "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: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" 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: "Z" 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: "0" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" 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: "3" 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: "4" 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: "5" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "6" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "7" Number of atoms: 69 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Conformer: "B" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} bond proxies already assigned to first conformer: 46 Chain: "8" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1861 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 39, 'rna3p_pyr': 34} Link IDs: {'rna2p': 13, 'rna3p': 73} Chain: "a" Number of atoms: 33037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33037 Classifications: {'RNA': 1540} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 66, 'rna3p_pur': 763, 'rna3p_pyr': 599} Link IDs: {'rna2p': 178, 'rna3p': 1361} Chain: "b" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} 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: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "f" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 811 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "g" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} 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: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 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: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "s" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "t" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 590 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "7" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ERY': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG 7 6 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG 7 6 " occ=0.50 Time building chain proxies: 55.41, per 1000 atoms: 0.38 Number of scatterers: 144454 At special positions: 0 Unit cell: (268.136, 275.892, 228.248, 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 4653 15.00 O 40269 8.00 N 26918 7.00 C 72465 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 14 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 27 " distance=2.04 Simple disulfide: pdb=" SG CYS 5 16 " - pdb=" SG CYS 5 37 " distance=2.04 Simple disulfide: pdb=" SG CYS 5 18 " - pdb=" SG CYS 5 40 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 57.61 Conformation dependent library (CDL) restraints added in 7.0 seconds 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10458 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 173 helices and 71 sheets defined 39.0% alpha, 19.6% beta 1526 base pairs and 2740 stacking pairs defined. Time for finding SS restraints: 73.33 Creating SS restraints... Processing helix chain 'C' and resid 10 through 16 removed outlier: 4.886A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.790A pdb=" N LEU C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 removed outlier: 4.389A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.719A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.044A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 6.440A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.988A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.572A pdb=" N VAL D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 61' Processing helix chain 'D' and resid 62 through 72 removed outlier: 4.382A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY D 72 " --> pdb=" O PHE D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 5.723A pdb=" N LYS D 105 " --> pdb=" O PHE D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 39 through 44 removed outlier: 3.786A pdb=" N GLY D 44 " --> pdb=" O ASP D 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 39 through 44' Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.887A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.551A pdb=" N ASP E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.766A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.745A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.523A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 2 through 20 removed outlier: 3.557A pdb=" N ASP F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 62 removed outlier: 4.718A pdb=" N LEU F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.447A pdb=" N VAL F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 142 through 147 removed outlier: 6.867A pdb=" N VAL F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 147' Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.722A pdb=" N GLY F 166 " --> pdb=" O SER F 162 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 5.253A pdb=" N ALA F 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 45 " --> pdb=" O GLU F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.776A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 134 through 139' Processing helix chain 'G' and resid 2 through 7 removed outlier: 4.628A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 81 removed outlier: 4.464A pdb=" N GLN G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 4.339A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 50 removed outlier: 6.606A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 73 removed outlier: 4.944A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 4.108A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.568A pdb=" N LEU J 28 " --> pdb=" O THR J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.182A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 4.115A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 120 removed outlier: 4.694A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA K 119 " --> pdb=" O ILE K 115 " (cutoff:3.500A) Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.568A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.529A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.925A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.980A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 removed outlier: 3.609A pdb=" N ASN L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.583A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 Proline residue: N 50 - end of helix removed outlier: 3.634A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.905A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 20 removed outlier: 3.788A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE O 8 " --> pdb=" O LYS O 4 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG O 9 " --> pdb=" O SER O 5 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.629A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 removed outlier: 4.544A pdb=" N ALA O 105 " --> pdb=" O GLY O 101 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 removed outlier: 3.869A pdb=" N LYS P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN P 7 " --> pdb=" O ASN P 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.139A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.835A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.690A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.866A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.990A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.878A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 11 removed outlier: 3.582A pdb=" N ARG T 6 " --> pdb=" O ILE T 2 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.691A pdb=" N SER T 21 " --> pdb=" O SER T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.796A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.784A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 52 removed outlier: 3.551A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 4.057A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 removed outlier: 4.180A pdb=" N GLY X 63 " --> pdb=" O ILE X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 10 removed outlier: 3.629A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 35 Processing helix chain 'Y' and resid 40 through 60 removed outlier: 4.307A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain '0' and resid 9 through 19 removed outlier: 4.804A pdb=" N HIS 0 19 " --> pdb=" O MET 0 15 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.371A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 7 through 14 Processing helix chain '3' and resid 32 through 37 removed outlier: 4.603A pdb=" N LYS 3 36 " --> pdb=" O ILE 3 32 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ALA 3 37 " --> pdb=" O LEU 3 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 32 through 37' Processing helix chain '3' and resid 38 through 46 Proline residue: 3 46 - end of helix Processing helix chain '3' and resid 52 through 63 removed outlier: 3.859A pdb=" N ALA 3 60 " --> pdb=" O GLY 3 56 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS 3 61 " --> pdb=" O LEU 3 57 " (cutoff:3.500A) Proline residue: 3 63 - end of helix Processing helix chain '5' and resid 41 through 46 Processing helix chain '5' and resid 55 through 64 Processing helix chain 'b' and resid 5 through 13 removed outlier: 4.726A pdb=" N MET b 9 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY b 13 " --> pdb=" O MET b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 32 removed outlier: 4.048A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) Proline residue: b 29 - end of helix removed outlier: 5.519A pdb=" N PHE b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 32' Processing helix chain 'b' and resid 42 through 64 removed outlier: 3.759A pdb=" N THR b 46 " --> pdb=" O ASN b 42 " (cutoff:3.500A) Proline residue: b 48 - end of helix removed outlier: 4.132A pdb=" N ARG b 63 " --> pdb=" O LYS b 59 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS b 64 " --> pdb=" O ILE b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 88 removed outlier: 3.508A pdb=" N GLU b 78 " --> pdb=" O ARG b 74 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP b 82 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N CYS b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 122 removed outlier: 3.857A pdb=" N VAL b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR b 119 " --> pdb=" O LYS b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 removed outlier: 6.184A pdb=" N ALA b 134 " --> pdb=" O THR b 130 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG b 139 " --> pdb=" O LEU b 135 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU b 140 " --> pdb=" O MET b 136 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU b 142 " --> pdb=" O THR b 138 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER b 147 " --> pdb=" O LYS b 143 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 removed outlier: 3.729A pdb=" N GLU b 169 " --> pdb=" O ASP b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 227 Processing helix chain 'c' and resid 6 through 15 removed outlier: 3.916A pdb=" N GLY c 13 " --> pdb=" O GLY c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 51 removed outlier: 4.042A pdb=" N LYS c 45 " --> pdb=" O GLN c 41 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU c 46 " --> pdb=" O TYR c 42 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA c 50 " --> pdb=" O GLU c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.560A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 4.039A pdb=" N ASP c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY c 96 " --> pdb=" O ALA c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 127 removed outlier: 3.549A pdb=" N ARG c 127 " --> pdb=" O GLN c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.663A pdb=" N ALA c 133 " --> pdb=" O MET c 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 3.895A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU d 15 " --> pdb=" O LEU d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 32 removed outlier: 3.657A pdb=" N CYS d 32 " --> pdb=" O ILE d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.534A pdb=" N TYR d 65 " --> pdb=" O VAL d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 83 removed outlier: 5.373A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 removed outlier: 3.833A pdb=" N ARG d 97 " --> pdb=" O LEU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 106 Processing helix chain 'd' and resid 110 through 121 removed outlier: 3.987A pdb=" N LYS d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 152 removed outlier: 4.076A pdb=" N LYS d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLN d 152 " --> pdb=" O LYS d 148 " (cutoff:3.500A) Processing helix chain 'd' and resid 153 through 166 removed outlier: 4.491A pdb=" N GLU d 166 " --> pdb=" O ALA d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 3.534A pdb=" N LEU d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 187 through 192' Processing helix chain 'd' and resid 196 through 206 removed outlier: 3.676A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 71 removed outlier: 4.061A pdb=" N ARG e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN e 70 " --> pdb=" O LYS e 66 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 removed outlier: 3.560A pdb=" N GLY e 119 " --> pdb=" O LEU e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 148 removed outlier: 5.797A pdb=" N ASN e 148 " --> pdb=" O LEU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 Processing helix chain 'e' and resid 160 through 166 removed outlier: 3.691A pdb=" N ILE e 164 " --> pdb=" O SER e 160 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 33 removed outlier: 3.764A pdb=" N MET f 21 " --> pdb=" O GLN f 17 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 3.925A pdb=" N ILE f 71 " --> pdb=" O PRO f 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE f 80 " --> pdb=" O THR f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.906A pdb=" N ALA g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 4.114A pdb=" N THR g 49 " --> pdb=" O SER g 45 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN g 52 " --> pdb=" O GLU g 48 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG g 53 " --> pdb=" O THR g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 6.074A pdb=" N ASN g 68 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG g 70 " --> pdb=" O LEU g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.960A pdb=" N LYS g 110 " --> pdb=" O GLU g 106 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.541A pdb=" N ARG g 119 " --> pdb=" O SER g 115 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER g 125 " --> pdb=" O ALA g 121 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN g 130 " --> pdb=" O ASP g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.891A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.701A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 112 through 120 Processing helix chain 'i' and resid 34 through 39 Processing helix chain 'i' and resid 41 through 54 removed outlier: 4.528A pdb=" N ARG i 45 " --> pdb=" O ARG i 41 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL i 47 " --> pdb=" O THR i 43 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL i 48 " --> pdb=" O ALA i 44 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Proline residue: i 51 - end of helix Processing helix chain 'i' and resid 71 through 92 removed outlier: 4.152A pdb=" N TYR i 90 " --> pdb=" O ALA i 86 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU i 92 " --> pdb=" O MET i 88 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 102 removed outlier: 4.282A pdb=" N LYS i 100 " --> pdb=" O SER i 96 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA i 101 " --> pdb=" O GLU i 97 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY i 102 " --> pdb=" O LEU i 98 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.007A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.170A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 59 removed outlier: 4.047A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 54 through 59' Processing helix chain 'k' and resid 60 through 76 removed outlier: 3.642A pdb=" N ASP k 72 " --> pdb=" O GLU k 68 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL k 74 " --> pdb=" O CYS k 70 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU k 76 " --> pdb=" O ASP k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 93 through 104 removed outlier: 3.819A pdb=" N ASN k 101 " --> pdb=" O ILE k 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA k 102 " --> pdb=" O ARG k 98 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.047A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.927A pdb=" N SER m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 49 removed outlier: 5.285A pdb=" N SER m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 64 removed outlier: 4.513A pdb=" N PHE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N VAL m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 7 through 25 removed outlier: 3.677A pdb=" N ALA n 15 " --> pdb=" O VAL n 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU n 16 " --> pdb=" O LYS n 12 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS n 19 " --> pdb=" O ALA n 15 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 51 removed outlier: 3.903A pdb=" N ARG n 41 " --> pdb=" O SER n 37 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU n 46 " --> pdb=" O TRP n 42 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'n' and resid 52 through 57 removed outlier: 4.688A pdb=" N SER n 55 " --> pdb=" O PRO n 52 " (cutoff:3.500A) Proline residue: n 57 - end of helix Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.689A pdb=" N GLU o 14 " --> pdb=" O LYS o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 44 removed outlier: 3.718A pdb=" N ALA o 44 " --> pdb=" O GLN o 40 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.892A pdb=" N GLN o 80 " --> pdb=" O ALA o 76 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.537A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 82 removed outlier: 3.600A pdb=" N ALA p 82 " --> pdb=" O VAL p 78 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 17 removed outlier: 3.598A pdb=" N ALA r 15 " --> pdb=" O CYS r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 25 through 34 removed outlier: 4.179A pdb=" N LEU r 29 " --> pdb=" O ASP r 25 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.648A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 Processing helix chain 's' and resid 71 through 76 removed outlier: 4.628A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 71 through 76' Processing helix chain 't' and resid 4 through 41 Processing helix chain 't' and resid 44 through 65 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 87 removed outlier: 4.367A pdb=" N ALA t 87 " --> pdb=" O ILE t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 removed outlier: 3.731A pdb=" N ALA u 15 " --> pdb=" O PRO u 11 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 37 removed outlier: 3.831A pdb=" N ARG u 35 " --> pdb=" O GLU u 31 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 68 removed outlier: 4.181A pdb=" N ALA u 61 " --> pdb=" O ALA u 57 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG u 66 " --> pdb=" O ARG u 62 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ARG u 67 " --> pdb=" O GLU u 63 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR u 68 " --> pdb=" O ASN u 64 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 5 Processing sheet with id= 2, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.686A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 139 through 142 removed outlier: 4.488A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 91 through 96 removed outlier: 4.004A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id= 6, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.926A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 79 through 83 removed outlier: 6.664A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 1 through 6 removed outlier: 3.616A pdb=" N LEU E 12 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU E 5 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.569A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.765A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR F 158 " --> pdb=" O GLY F 126 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLY F 126 " --> pdb=" O THR F 158 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 16 through 19 removed outlier: 4.382A pdb=" N ASP G 16 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS G 27 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 13, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.783A pdb=" N ALA G 97 " --> pdb=" O ASN G 104 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 121 through 125 removed outlier: 5.899A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 3 through 6 removed outlier: 6.928A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 76 through 81 removed outlier: 7.645A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN H 145 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER H 131 " --> pdb=" O ARG H 116 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 18, first strand: chain 'J' and resid 74 through 77 Processing sheet with id= 19, first strand: chain 'K' and resid 56 through 60 removed outlier: 4.692A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.934A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.538A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 73 through 76 removed outlier: 6.665A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.851A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.702A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR N 94 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.900A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.727A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.825A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS P 56 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 11 through 15 Processing sheet with id= 30, first strand: chain 'R' and resid 18 through 21 removed outlier: 4.419A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.181A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.364A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'S' and resid 74 through 88 No H-bonds generated for sheet with id= 33 Processing sheet with id= 34, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.403A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'U' and resid 40 through 46 No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 37, first strand: chain 'V' and resid 6 through 9 removed outlier: 6.039A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU V 38 " --> pdb=" O ILE V 30 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'V' and resid 61 through 64 Processing sheet with id= 39, first strand: chain 'W' and resid 34 through 37 removed outlier: 4.181A pdb=" N SER W 35 " --> pdb=" O ALA W 61 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU W 59 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN W 50 " --> pdb=" O LYS W 62 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'W' and resid 45 through 48 removed outlier: 6.555A pdb=" N ILE W 82 " --> pdb=" O GLY W 48 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'X' and resid 12 through 19 removed outlier: 5.122A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 43, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.152A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '0' and resid 28 through 31 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain '1' and resid 20 through 26 removed outlier: 3.637A pdb=" N GLN 1 45 " --> pdb=" O ASP 1 40 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR 1 49 " --> pdb=" O LEU 1 36 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU 1 36 " --> pdb=" O TYR 1 49 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLU 1 51 " --> pdb=" O LEU 1 34 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU 1 34 " --> pdb=" O GLU 1 51 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '3' and resid 22 through 25 removed outlier: 5.587A pdb=" N PHE 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '4' and resid 24 through 27 removed outlier: 4.704A pdb=" N CYS 4 27 " --> pdb=" O HIS 4 33 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS 4 33 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '5' and resid 20 through 25 removed outlier: 4.380A pdb=" N LEU 5 32 " --> pdb=" O THR 5 13 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU 5 34 " --> pdb=" O SER 5 15 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'b' and resid 15 through 18 removed outlier: 5.892A pdb=" N HIS b 15 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N HIS b 39 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'b' and resid 89 through 92 removed outlier: 3.767A pdb=" N LEU b 68 " --> pdb=" O ALA b 160 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE b 186 " --> pdb=" O VAL b 163 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'c' and resid 53 through 59 removed outlier: 3.668A pdb=" N ARG c 54 " --> pdb=" O HIS c 69 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR c 70 " --> pdb=" O ALA c 104 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'c' and resid 164 through 170 removed outlier: 6.440A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU c 206 " --> pdb=" O ARG c 179 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ARG c 179 " --> pdb=" O GLU c 206 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'd' and resid 141 through 144 removed outlier: 3.888A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU d 179 " --> pdb=" O ASP d 174 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 11 through 16 removed outlier: 6.690A pdb=" N LEU e 36 " --> pdb=" O ILE e 16 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 83 through 88 removed outlier: 7.509A pdb=" N HIS e 83 " --> pdb=" O PRO e 98 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR e 128 " --> pdb=" O ARG e 93 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA e 99 " --> pdb=" O ASN e 122 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASN e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'e' and resid 32 through 41 removed outlier: 6.776A pdb=" N ARG e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 38 through 42 removed outlier: 5.733A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'f' and resid 43 through 47 removed outlier: 5.865A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'g' and resid 73 through 77 Processing sheet with id= 60, first strand: chain 'h' and resid 24 through 29 removed outlier: 5.875A pdb=" N GLU h 58 " --> pdb=" O GLU h 52 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP h 48 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'h' and resid 74 through 77 removed outlier: 4.566A pdb=" N SER h 74 " --> pdb=" O ALA h 130 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS h 127 " --> pdb=" O VAL h 103 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL h 103 " --> pdb=" O ILE h 126 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'i' and resid 5 through 11 removed outlier: 4.344A pdb=" N LYS i 60 " --> pdb=" O GLY i 24 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LYS i 27 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU i 63 " --> pdb=" O LYS i 27 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.272A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 65, first strand: chain 'k' and resid 29 through 36 removed outlier: 4.150A pdb=" N ASN k 29 " --> pdb=" O SER k 26 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'l' and resid 29 through 33 removed outlier: 5.203A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N HIS l 96 " --> pdb=" O ARG l 83 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY l 85 " --> pdb=" O ARG l 94 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG l 94 " --> pdb=" O GLY l 85 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'l' and resid 36 through 41 removed outlier: 3.518A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'p' and resid 4 through 10 Processing sheet with id= 69, first strand: chain 'q' and resid 7 through 11 removed outlier: 7.174A pdb=" N GLU q 60 " --> pdb=" O VAL q 76 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'q' and resid 19 through 31 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain 's' and resid 30 through 34 1821 hydrogen bonds defined for protein. 5397 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3827 hydrogen bonds 5928 hydrogen bond angles 0 basepair planarities 1526 basepair parallelities 2740 stacking parallelities Total time for adding SS restraints: 249.93 Time building geometry restraints manager: 62.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 13133 1.30 - 1.44: 70495 1.44 - 1.57: 63843 1.57 - 1.71: 9301 1.71 - 1.84: 266 Bond restraints: 157038 Sorted by residual: bond pdb=" C1 ERY 7 101 " pdb=" C2 ERY 7 101 " ideal model delta sigma weight residual 1.558 1.369 0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" C10 ERY 7 101 " pdb=" C9 ERY 7 101 " ideal model delta sigma weight residual 1.542 1.404 0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" N3 U A2604 " pdb=" C4 U A2604 " ideal model delta sigma weight residual 1.380 1.265 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C8 ERY 7 101 " pdb=" C9 ERY 7 101 " ideal model delta sigma weight residual 1.523 1.417 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C1 ERY 7 101 " pdb=" O2 ERY 7 101 " ideal model delta sigma weight residual 1.459 1.354 0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 157033 not shown) Histogram of bond angle deviations from ideal: 95.72 - 104.32: 18945 104.32 - 112.92: 95860 112.92 - 121.52: 81489 121.52 - 130.13: 36283 130.13 - 138.73: 2506 Bond angle restraints: 235083 Sorted by residual: angle pdb=" N ALA g 65 " pdb=" CA ALA g 65 " pdb=" C ALA g 65 " ideal model delta sigma weight residual 114.56 104.21 10.35 1.27e+00 6.20e-01 6.64e+01 angle pdb=" C ILE m 4 " pdb=" N ALA m 5 " pdb=" CA ALA m 5 " ideal model delta sigma weight residual 120.82 130.77 -9.95 1.50e+00 4.44e-01 4.40e+01 angle pdb=" N ILE T 2 " pdb=" CA ILE T 2 " pdb=" C ILE T 2 " ideal model delta sigma weight residual 111.77 105.32 6.45 1.04e+00 9.25e-01 3.85e+01 angle pdb=" C LYS H 8 " pdb=" N VAL H 9 " pdb=" CA VAL H 9 " ideal model delta sigma weight residual 121.97 133.12 -11.15 1.80e+00 3.09e-01 3.84e+01 angle pdb=" C GLN H 2 " pdb=" N VAL H 3 " pdb=" CA VAL H 3 " ideal model delta sigma weight residual 121.97 132.44 -10.47 1.80e+00 3.09e-01 3.38e+01 ... (remaining 235078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 88422 35.99 - 71.97: 10984 71.97 - 107.96: 1176 107.96 - 143.94: 31 143.94 - 179.93: 47 Dihedral angle restraints: 100660 sinusoidal: 84449 harmonic: 16211 Sorted by residual: dihedral pdb=" CA GLU U 88 " pdb=" C GLU U 88 " pdb=" N ASP U 89 " pdb=" CA ASP U 89 " ideal model delta harmonic sigma weight residual -180.00 -118.27 -61.73 0 5.00e+00 4.00e-02 1.52e+02 dihedral pdb=" CA LEU 1 34 " pdb=" C LEU 1 34 " pdb=" N GLU 1 35 " pdb=" CA GLU 1 35 " ideal model delta harmonic sigma weight residual -180.00 -125.83 -54.17 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA GLY d 39 " pdb=" C GLY d 39 " pdb=" N GLN d 40 " pdb=" CA GLN d 40 " ideal model delta harmonic sigma weight residual -180.00 -126.07 -53.93 0 5.00e+00 4.00e-02 1.16e+02 ... (remaining 100657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.133: 30061 1.133 - 2.266: 0 2.266 - 3.399: 0 3.399 - 4.532: 0 4.532 - 5.665: 4 Chirality restraints: 30065 Sorted by residual: chirality pdb=" C12 ERY 7 101 " pdb=" C11 ERY 7 101 " pdb=" C13 ERY 7 101 " pdb=" C35 ERY 7 101 " both_signs ideal model delta sigma weight residual False -2.75 2.92 -5.67 2.00e-01 2.50e+01 8.02e+02 chirality pdb=" C6 ERY 7 101 " pdb=" C32 ERY 7 101 " pdb=" C5 ERY 7 101 " pdb=" C7 ERY 7 101 " both_signs ideal model delta sigma weight residual False -2.75 2.80 -5.56 2.00e-01 2.50e+01 7.72e+02 chirality pdb=" C16 ERY 7 101 " pdb=" C15 ERY 7 101 " pdb=" C17 ERY 7 101 " pdb=" C19 ERY 7 101 " both_signs ideal model delta sigma weight residual False 2.68 -2.85 5.53 2.00e-01 2.50e+01 7.64e+02 ... (remaining 30062 not shown) Planarity restraints: 12481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD BARG 7 6 " -1.017 9.50e-02 1.11e+02 4.56e-01 1.26e+02 pdb=" NE BARG 7 6 " 0.060 2.00e-02 2.50e+03 pdb=" CZ BARG 7 6 " 0.014 2.00e-02 2.50e+03 pdb=" NH1BARG 7 6 " -0.005 2.00e-02 2.50e+03 pdb=" NH2BARG 7 6 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A2061 " -0.056 2.00e-02 2.50e+03 2.21e-02 1.47e+01 pdb=" N9 G A2061 " 0.041 2.00e-02 2.50e+03 pdb=" C8 G A2061 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G A2061 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G A2061 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G A2061 " -0.010 2.00e-02 2.50e+03 pdb=" O6 G A2061 " -0.018 2.00e-02 2.50e+03 pdb=" N1 G A2061 " -0.009 2.00e-02 2.50e+03 pdb=" C2 G A2061 " 0.006 2.00e-02 2.50e+03 pdb=" N2 G A2061 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A2061 " 0.014 2.00e-02 2.50e+03 pdb=" C4 G A2061 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP b 82 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C ASP b 82 " -0.065 2.00e-02 2.50e+03 pdb=" O ASP b 82 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA b 83 " 0.022 2.00e-02 2.50e+03 ... (remaining 12478 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.14: 1 2.14 - 2.83: 40977 2.83 - 3.52: 186370 3.52 - 4.21: 476850 4.21 - 4.90: 625938 Nonbonded interactions: 1330136 Sorted by model distance: nonbonded pdb=" C LEU 7 7 " pdb=" O3' A 8 87 " model vdw 1.444 3.270 nonbonded pdb=" NH1 ARG 5 59 " pdb=" OP1 A a1311 " model vdw 2.159 2.520 nonbonded pdb=" N7 A A1912 " pdb=" O4 U A1917 " model vdw 2.182 3.120 nonbonded pdb=" N6 A A2590 " pdb=" O4 U A2604 " model vdw 2.188 2.520 nonbonded pdb=" N2 G A 27 " pdb=" O2' G A 512 " model vdw 2.190 2.520 ... (remaining 1330131 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.130 Extract box with map and model: 15.260 Check model and map are aligned: 1.580 Set scattering table: 1.040 Process input model: 540.650 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 576.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.008 0.189 157038 Z= 0.466 Angle : 0.992 17.045 235083 Z= 0.515 Chirality : 0.082 5.665 30065 Planarity : 0.008 0.456 12481 Dihedral : 23.585 179.926 90190 Min Nonbonded Distance : 1.444 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.10 % Favored : 92.61 % Rotamer: Outliers : 0.67 % Allowed : 8.93 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.55 % 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: -3.62 (0.09), residues: 5593 helix: -2.78 (0.09), residues: 1833 sheet: -1.40 (0.15), residues: 1074 loop : -2.49 (0.10), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP b 23 HIS 0.015 0.002 HIS j 56 PHE 0.031 0.003 PHE F 175 TYR 0.023 0.003 TYR f 59 ARG 0.022 0.001 ARG Q 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1371 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1340 time to evaluate : 6.114 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: C 203 ARG cc_start: 0.8262 (ptp90) cc_final: 0.8019 (ptm160) REVERT: D 179 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7561 (ttp80) REVERT: E 100 MET cc_start: 0.8066 (mtp) cc_final: 0.7736 (mtm) REVERT: F 96 MET cc_start: 0.7716 (tmm) cc_final: 0.7365 (ttp) REVERT: G 58 TYR cc_start: 0.6442 (m-80) cc_final: 0.6186 (m-80) REVERT: J 120 ARG cc_start: 0.8006 (mtt180) cc_final: 0.6870 (mpp-170) REVERT: K 13 ASN cc_start: 0.7976 (p0) cc_final: 0.7729 (p0) REVERT: L 27 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8574 (pp) REVERT: N 107 ASN cc_start: 0.8467 (t0) cc_final: 0.8266 (t0) REVERT: P 29 LYS cc_start: 0.8157 (mttp) cc_final: 0.7940 (mmtm) REVERT: Q 11 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7651 (ttm-80) REVERT: R 35 PHE cc_start: 0.8204 (m-80) cc_final: 0.7971 (m-80) REVERT: V 8 VAL cc_start: 0.7937 (m) cc_final: 0.7716 (t) REVERT: Y 29 ARG cc_start: 0.8081 (ptt-90) cc_final: 0.7876 (ptt-90) REVERT: 0 37 LYS cc_start: 0.8281 (mmtp) cc_final: 0.8064 (mmtp) REVERT: 2 31 LEU cc_start: 0.9070 (mp) cc_final: 0.8818 (mp) REVERT: c 44 THR cc_start: 0.7563 (m) cc_final: 0.7302 (m) REVERT: e 70 ASN cc_start: 0.7270 (m-40) cc_final: 0.7003 (p0) REVERT: e 138 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8272 (mtt-85) REVERT: g 60 GLU cc_start: 0.6011 (pm20) cc_final: 0.5459 (pm20) REVERT: h 22 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7813 (mmtt) REVERT: h 27 MET cc_start: 0.7960 (ptp) cc_final: 0.7752 (ptm) REVERT: h 36 ILE cc_start: 0.9030 (mt) cc_final: 0.8769 (mt) REVERT: m 73 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8490 (mp) REVERT: n 86 GLU cc_start: 0.6513 (mt-10) cc_final: 0.6224 (mt-10) REVERT: q 15 ASP cc_start: 0.6564 (p0) cc_final: 0.6296 (p0) REVERT: t 18 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7925 (ttt-90) outliers start: 31 outliers final: 13 residues processed: 1362 average time/residue: 2.2617 time to fit residues: 4325.5557 Evaluate side-chains 1071 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1056 time to evaluate : 6.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain m residue 73 ILE Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 852 optimal weight: 1.9990 chunk 764 optimal weight: 5.9990 chunk 424 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 515 optimal weight: 7.9990 chunk 408 optimal weight: 9.9990 chunk 790 optimal weight: 0.0980 chunk 306 optimal weight: 3.9990 chunk 480 optimal weight: 0.9980 chunk 588 optimal weight: 0.9980 chunk 916 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 49 GLN D 130 GLN D 164 GLN E 41 GLN E 94 GLN E 136 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN G 73 ASN G 104 ASN H 128 HIS J 40 HIS K 13 ASN N 62 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN P 75 GLN Q 71 GLN R 86 GLN R 89 HIS S 61 ASN T 15 HIS U 40 ASN U 53 ASN U 69 ASN W 12 ASN Y 27 ASN Y 58 ASN 0 5 GLN 1 19 HIS 1 26 ASN 2 29 GLN 3 28 ASN ** 5 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 39 HIS b 227 GLN c 190 HIS d 40 GLN ** d 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 97 GLN e 148 ASN f 11 HIS ** f 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS f 63 ASN ** f 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN g 68 ASN g 148 ASN h 4 GLN h 18 GLN h 118 GLN j 64 GLN k 15 GLN k 24 HIS k 28 ASN n 4 GLN n 60 GLN n 66 GLN ** o 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 GLN p 29 ASN p 63 GLN q 31 HIS q 51 ASN s 14 HIS s 52 HIS t 70 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 157038 Z= 0.136 Angle : 0.607 26.102 235083 Z= 0.314 Chirality : 0.041 2.097 30065 Planarity : 0.005 0.099 12481 Dihedral : 23.800 178.963 78995 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.74 % Favored : 94.06 % Rotamer: Outliers : 3.97 % Allowed : 20.60 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.10), residues: 5593 helix: -0.89 (0.11), residues: 1871 sheet: -1.01 (0.15), residues: 1070 loop : -2.11 (0.10), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 213 HIS 0.008 0.001 HIS k 24 PHE 0.022 0.001 PHE R 93 TYR 0.015 0.001 TYR Q 47 ARG 0.009 0.000 ARG c 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1182 time to evaluate : 6.226 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: E 100 MET cc_start: 0.8013 (mtp) cc_final: 0.7758 (mtm) REVERT: E 127 GLU cc_start: 0.6370 (mp0) cc_final: 0.6087 (mp0) REVERT: E 184 ASP cc_start: 0.7296 (m-30) cc_final: 0.7065 (m-30) REVERT: F 63 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6831 (mm110) REVERT: F 96 MET cc_start: 0.7711 (tmm) cc_final: 0.7383 (ttp) REVERT: G 35 ARG cc_start: 0.6082 (OUTLIER) cc_final: 0.5863 (tpt-90) REVERT: G 58 TYR cc_start: 0.6393 (m-80) cc_final: 0.6127 (m-80) REVERT: J 118 MET cc_start: 0.8078 (ptm) cc_final: 0.7613 (mtp) REVERT: L 27 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8377 (pp) REVERT: M 18 ARG cc_start: 0.8029 (mtp180) cc_final: 0.7825 (mtp180) REVERT: N 107 ASN cc_start: 0.8451 (t0) cc_final: 0.8246 (t0) REVERT: O 12 THR cc_start: 0.8012 (p) cc_final: 0.7582 (t) REVERT: P 29 LYS cc_start: 0.7849 (mttp) cc_final: 0.7581 (mmtm) REVERT: P 71 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7431 (mt-10) REVERT: Q 11 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7555 (ttm110) REVERT: T 33 LYS cc_start: 0.8096 (tttt) cc_final: 0.7881 (tttp) REVERT: 0 36 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.5868 (mp0) REVERT: 2 9 VAL cc_start: 0.8719 (p) cc_final: 0.8378 (t) REVERT: b 88 ASP cc_start: 0.4475 (m-30) cc_final: 0.4058 (t0) REVERT: c 5 VAL cc_start: 0.8435 (p) cc_final: 0.8046 (t) REVERT: c 44 THR cc_start: 0.7671 (m) cc_final: 0.7395 (m) REVERT: e 70 ASN cc_start: 0.7452 (m-40) cc_final: 0.7181 (p0) REVERT: g 26 PHE cc_start: 0.8387 (t80) cc_final: 0.8102 (t80) REVERT: g 48 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.6015 (pm20) REVERT: h 36 ILE cc_start: 0.8921 (mt) cc_final: 0.8646 (mt) REVERT: i 61 LEU cc_start: 0.6360 (pt) cc_final: 0.5960 (pt) REVERT: j 10 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8036 (pp) REVERT: k 56 ARG cc_start: 0.7307 (mtm-85) cc_final: 0.7100 (mtm-85) REVERT: k 61 PHE cc_start: 0.8136 (t80) cc_final: 0.7821 (t80) REVERT: p 21 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8588 (p) REVERT: t 18 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7647 (ttt-90) REVERT: t 82 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7245 (mm-40) REVERT: u 21 ARG cc_start: 0.7039 (mmp80) cc_final: 0.6783 (mmp-170) REVERT: u 33 ARG cc_start: 0.6725 (ttm110) cc_final: 0.6235 (tpt170) outliers start: 184 outliers final: 71 residues processed: 1264 average time/residue: 2.0852 time to fit residues: 3801.7382 Evaluate side-chains 1140 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1061 time to evaluate : 5.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain U residue 35 ILE Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 29 SER Chi-restraints excluded: chain 0 residue 36 GLU Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 57 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 59 ASP Chi-restraints excluded: chain t residue 82 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 509 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 762 optimal weight: 10.0000 chunk 623 optimal weight: 20.0000 chunk 252 optimal weight: 10.0000 chunk 917 optimal weight: 0.2980 chunk 991 optimal weight: 8.9990 chunk 817 optimal weight: 8.9990 chunk 910 optimal weight: 8.9990 chunk 312 optimal weight: 9.9990 chunk 736 optimal weight: 20.0000 overall best weight: 7.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN C 239 ASN D 150 GLN D 173 GLN F 27 GLN ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN K 82 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS R 86 GLN S 61 ASN T 15 HIS T 48 GLN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 ASN V 49 ASN Y 27 ASN 0 42 HIS 1 19 HIS 2 29 GLN 3 28 ASN 3 43 HIS ** 5 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 177 ASN d 40 GLN ** d 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 164 GLN ** f 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 ASN h 4 GLN i 126 GLN k 28 ASN m 14 HIS ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 GLN ** o 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 GLN p 29 ASN q 51 ASN r 54 GLN t 70 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 157038 Z= 0.533 Angle : 0.838 27.096 235083 Z= 0.417 Chirality : 0.052 2.032 30065 Planarity : 0.007 0.078 12481 Dihedral : 23.897 179.313 78985 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.49 % Favored : 92.29 % Rotamer: Outliers : 7.50 % Allowed : 22.21 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.10), residues: 5593 helix: -0.52 (0.11), residues: 1874 sheet: -1.05 (0.15), residues: 1056 loop : -1.99 (0.11), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 23 HIS 0.010 0.002 HIS j 56 PHE 0.025 0.003 PHE p 32 TYR 0.015 0.003 TYR l 38 ARG 0.009 0.001 ARG i 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1412 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1064 time to evaluate : 6.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: C 132 MET cc_start: 0.7886 (mtm) cc_final: 0.7623 (mtp) REVERT: C 154 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8581 (mt) REVERT: C 181 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7246 (mpp) REVERT: F 63 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7255 (mm110) REVERT: G 27 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5806 (mtpp) REVERT: G 58 TYR cc_start: 0.6499 (m-80) cc_final: 0.6236 (m-80) REVERT: H 12 LEU cc_start: 0.5177 (OUTLIER) cc_final: 0.4959 (pp) REVERT: J 58 ASN cc_start: 0.8022 (m-40) cc_final: 0.7751 (m-40) REVERT: J 106 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7740 (ttpt) REVERT: J 118 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7602 (mtp) REVERT: O 4 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7541 (tptp) REVERT: Q 11 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7719 (ttm-80) REVERT: Q 30 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8258 (mtt-85) REVERT: S 59 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6464 (tp30) REVERT: T 1 MET cc_start: -0.0510 (ptt) cc_final: -0.1110 (mtp) REVERT: U 21 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7184 (ttpp) REVERT: V 79 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7728 (mmt90) REVERT: 0 5 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8444 (mm110) REVERT: 2 41 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6442 (mpp-170) REVERT: c 3 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.6857 (mm-40) REVERT: c 152 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: d 57 GLU cc_start: 0.7145 (tp30) cc_final: 0.6923 (tp30) REVERT: e 70 ASN cc_start: 0.7506 (m-40) cc_final: 0.7157 (p0) REVERT: e 138 ARG cc_start: 0.8483 (mtp85) cc_final: 0.8254 (mtt-85) REVERT: g 48 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6336 (pm20) REVERT: g 70 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7016 (tpt90) REVERT: j 10 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8354 (pp) REVERT: k 56 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7116 (mtm-85) REVERT: k 82 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6808 (pp) REVERT: k 122 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7578 (ttt180) REVERT: k 126 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7681 (tptp) REVERT: l 80 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.9024 (pp) REVERT: l 94 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7848 (ptt180) REVERT: m 93 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6734 (mtt90) REVERT: t 16 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8291 (tttp) REVERT: t 18 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7902 (ttt-90) outliers start: 348 outliers final: 168 residues processed: 1247 average time/residue: 2.0426 time to fit residues: 3673.4329 Evaluate side-chains 1214 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1018 time to evaluate : 5.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 84 LYS Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 21 LYS Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 73 LYS Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 5 GLN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 22 LEU Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 3 residue 4 ILE Chi-restraints excluded: chain 3 residue 57 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 93 ASP Chi-restraints excluded: chain c residue 136 ARG Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 105 MET Chi-restraints excluded: chain d residue 124 MET Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 46 VAL Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 165 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 17 LYS Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 70 ARG Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 56 ARG Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 122 ARG Chi-restraints excluded: chain k residue 126 LYS Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 98 LYS Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 59 MET Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 77 GLU Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 60 LYS Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 16 LYS Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 59 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 906 optimal weight: 0.9990 chunk 690 optimal weight: 8.9990 chunk 476 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 438 optimal weight: 0.0770 chunk 616 optimal weight: 20.0000 chunk 921 optimal weight: 4.9990 chunk 975 optimal weight: 4.9990 chunk 481 optimal weight: 3.9990 chunk 873 optimal weight: 6.9990 chunk 262 optimal weight: 2.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN C 153 GLN D 136 ASN E 195 GLN G 30 ASN G 104 ASN J 47 HIS ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN T 15 HIS V 49 ASN 2 29 GLN 3 28 ASN ** 5 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 HIS f 58 HIS f 81 ASN g 28 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN k 28 ASN m 14 HIS n 62 ASN n 66 GLN ** o 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 GLN p 29 ASN q 51 ASN r 54 GLN t 61 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 157038 Z= 0.180 Angle : 0.614 26.389 235083 Z= 0.315 Chirality : 0.042 2.101 30065 Planarity : 0.005 0.060 12481 Dihedral : 23.696 179.725 78983 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.03 % Favored : 93.79 % Rotamer: Outliers : 5.67 % Allowed : 25.13 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.11), residues: 5593 helix: 0.11 (0.12), residues: 1868 sheet: -0.92 (0.15), residues: 1069 loop : -1.79 (0.11), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 213 HIS 0.005 0.001 HIS 3 31 PHE 0.022 0.001 PHE 5 60 TYR 0.023 0.001 TYR N 112 ARG 0.010 0.000 ARG 4 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1080 time to evaluate : 6.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 132 MET cc_start: 0.7796 (mtm) cc_final: 0.7595 (mtp) REVERT: C 251 GLN cc_start: 0.8088 (tp40) cc_final: 0.7831 (tm-30) REVERT: F 63 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7111 (mm110) REVERT: F 153 ASP cc_start: 0.7753 (p0) cc_final: 0.7455 (p0) REVERT: G 58 TYR cc_start: 0.6508 (m-80) cc_final: 0.6209 (m-80) REVERT: J 58 ASN cc_start: 0.7981 (m-40) cc_final: 0.7767 (m-40) REVERT: J 118 MET cc_start: 0.8160 (ptm) cc_final: 0.7799 (mtp) REVERT: L 117 THR cc_start: 0.6091 (OUTLIER) cc_final: 0.5165 (m) REVERT: O 4 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7435 (tptp) REVERT: O 12 THR cc_start: 0.7931 (p) cc_final: 0.7705 (p) REVERT: O 62 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6119 (pp) REVERT: Q 30 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8328 (mtt-85) REVERT: R 24 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7901 (tttp) REVERT: T 1 MET cc_start: -0.0692 (ptt) cc_final: -0.1015 (mtp) REVERT: W 68 LYS cc_start: 0.8118 (tttm) cc_final: 0.7866 (tttt) REVERT: Y 1 MET cc_start: 0.5360 (OUTLIER) cc_final: 0.5007 (tmm) REVERT: 0 5 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8326 (mm-40) REVERT: 2 9 VAL cc_start: 0.8796 (p) cc_final: 0.8487 (t) REVERT: b 21 ARG cc_start: 0.7311 (ttp-170) cc_final: 0.7056 (ptm160) REVERT: c 3 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.6473 (mm-40) REVERT: c 5 VAL cc_start: 0.8380 (p) cc_final: 0.8030 (t) REVERT: c 152 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: e 138 ARG cc_start: 0.8437 (mtp85) cc_final: 0.8008 (mtt-85) REVERT: e 165 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5917 (mt) REVERT: g 26 PHE cc_start: 0.8468 (t80) cc_final: 0.8210 (t80) REVERT: g 48 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.6033 (pm20) REVERT: g 70 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7089 (tpt90) REVERT: g 96 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.5954 (ttm-80) REVERT: g 120 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7660 (tp) REVERT: k 61 PHE cc_start: 0.8262 (t80) cc_final: 0.7912 (t80) REVERT: k 82 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.6924 (pp) REVERT: k 114 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8202 (t) REVERT: k 122 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7322 (ttt180) REVERT: k 126 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7454 (tttp) REVERT: l 80 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8934 (pp) REVERT: l 94 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7766 (ptt180) REVERT: q 19 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7906 (tttp) REVERT: q 21 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8839 (pp) REVERT: t 18 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7941 (ttt-90) outliers start: 263 outliers final: 132 residues processed: 1211 average time/residue: 2.1033 time to fit residues: 3676.6677 Evaluate side-chains 1199 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1046 time to evaluate : 5.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 35 ILE Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 73 LYS Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 5 GLN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 29 SER Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 3 residue 57 LEU Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 14 LYS Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 165 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 70 ARG Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 96 ARG Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 22 LYS Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 93 ARG Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 122 ARG Chi-restraints excluded: chain k residue 126 LYS Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 98 LYS Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 59 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 812 optimal weight: 0.7980 chunk 553 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 726 optimal weight: 30.0000 chunk 402 optimal weight: 9.9990 chunk 832 optimal weight: 0.7980 chunk 674 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 498 optimal weight: 2.9990 chunk 875 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN D 150 GLN D 173 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN Q 71 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN T 15 HIS 2 29 GLN 3 28 ASN e 43 ASN ** e 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 148 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN m 14 HIS n 49 GLN n 66 GLN o 35 GLN o 62 GLN p 29 ASN q 51 ASN r 54 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 157038 Z= 0.236 Angle : 0.626 26.371 235083 Z= 0.319 Chirality : 0.042 2.092 30065 Planarity : 0.005 0.059 12481 Dihedral : 23.645 177.782 78983 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.90 % Favored : 92.95 % Rotamer: Outliers : 6.53 % Allowed : 25.86 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.11), residues: 5593 helix: 0.32 (0.12), residues: 1866 sheet: -0.84 (0.15), residues: 1043 loop : -1.65 (0.11), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 97 HIS 0.007 0.001 HIS 3 31 PHE 0.022 0.002 PHE 5 60 TYR 0.022 0.002 TYR N 112 ARG 0.010 0.001 ARG Y 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1378 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1075 time to evaluate : 6.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: C 251 GLN cc_start: 0.8181 (tp40) cc_final: 0.7964 (tm-30) REVERT: D 17 GLU cc_start: 0.6614 (tp30) cc_final: 0.6361 (tp30) REVERT: E 1 MET cc_start: 0.5306 (OUTLIER) cc_final: 0.4176 (ppp) REVERT: F 4 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6535 (mm) REVERT: F 63 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7027 (mm110) REVERT: F 153 ASP cc_start: 0.7768 (p0) cc_final: 0.7472 (p0) REVERT: G 58 TYR cc_start: 0.6476 (m-80) cc_final: 0.6161 (m-80) REVERT: H 2 GLN cc_start: 0.5168 (OUTLIER) cc_final: 0.4845 (mm-40) REVERT: J 58 ASN cc_start: 0.7972 (m-40) cc_final: 0.7751 (m-40) REVERT: J 106 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7711 (ttpt) REVERT: J 118 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7821 (mtp) REVERT: L 117 THR cc_start: 0.5885 (OUTLIER) cc_final: 0.5297 (m) REVERT: N 110 MET cc_start: 0.8125 (mmm) cc_final: 0.7841 (mmm) REVERT: O 62 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6073 (pp) REVERT: Q 30 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8324 (mtt-85) REVERT: R 24 LYS cc_start: 0.8264 (ttpp) cc_final: 0.7872 (tttp) REVERT: W 68 LYS cc_start: 0.8120 (tttm) cc_final: 0.7863 (tttt) REVERT: Y 27 ASN cc_start: 0.8168 (m-40) cc_final: 0.7782 (m110) REVERT: 0 5 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8419 (mm110) REVERT: 2 41 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6568 (mpp-170) REVERT: 4 24 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7736 (mtp180) REVERT: 5 1 MET cc_start: 0.6757 (mtm) cc_final: 0.6230 (mtt) REVERT: b 21 ARG cc_start: 0.7307 (ttp-170) cc_final: 0.7030 (ptm160) REVERT: c 3 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.6690 (mm-40) REVERT: c 14 ILE cc_start: 0.5631 (OUTLIER) cc_final: 0.5276 (mp) REVERT: c 58 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6038 (mm-30) REVERT: c 152 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: d 21 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7112 (pt) REVERT: e 138 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8011 (mtt-85) REVERT: g 26 PHE cc_start: 0.8584 (t80) cc_final: 0.8363 (t80) REVERT: g 48 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.6117 (pm20) REVERT: g 59 LEU cc_start: 0.7136 (tm) cc_final: 0.6455 (tp) REVERT: g 120 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7716 (tp) REVERT: j 10 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8189 (pp) REVERT: k 56 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7087 (mtm-85) REVERT: k 61 PHE cc_start: 0.8328 (t80) cc_final: 0.7986 (t80) REVERT: k 82 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.6913 (pp) REVERT: k 93 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.4710 (mtp85) REVERT: k 126 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7472 (tttp) REVERT: l 80 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8920 (pp) REVERT: l 94 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7789 (ptt180) REVERT: q 19 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7970 (tttp) REVERT: t 18 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7923 (ttt-90) outliers start: 303 outliers final: 177 residues processed: 1225 average time/residue: 2.0739 time to fit residues: 3705.6267 Evaluate side-chains 1230 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1026 time to evaluate : 6.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 103 ILE Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 73 LYS Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 5 GLN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 29 SER Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 3 residue 4 ILE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 57 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 24 ARG Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 157 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 58 GLU Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 124 MET Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 22 LYS Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 56 ARG Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 93 ARG Chi-restraints excluded: chain k residue 126 LYS Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 12 HIS Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 79 ARG Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 98 LYS Chi-restraints excluded: chain o residue 59 MET Chi-restraints excluded: chain o residue 67 LEU Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 59 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 328 optimal weight: 9.9990 chunk 878 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 572 optimal weight: 0.9990 chunk 240 optimal weight: 10.0000 chunk 976 optimal weight: 4.9990 chunk 810 optimal weight: 10.0000 chunk 452 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 322 optimal weight: 0.9980 chunk 512 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN F 135 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN Q 71 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN T 15 HIS 2 29 GLN 3 28 ASN e 43 ASN ** e 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 148 ASN f 81 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN l 77 HIS m 14 HIS n 49 GLN n 66 GLN o 62 GLN p 29 ASN q 51 ASN r 54 GLN u 56 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 157038 Z= 0.225 Angle : 0.616 26.226 235083 Z= 0.313 Chirality : 0.042 2.099 30065 Planarity : 0.005 0.059 12481 Dihedral : 23.600 178.094 78983 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.49 % Favored : 93.36 % Rotamer: Outliers : 6.72 % Allowed : 26.78 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.11), residues: 5593 helix: 0.45 (0.12), residues: 1877 sheet: -0.76 (0.15), residues: 1050 loop : -1.62 (0.11), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 39 HIS 0.006 0.001 HIS 3 31 PHE 0.024 0.002 PHE V 56 TYR 0.031 0.002 TYR o 78 ARG 0.011 0.000 ARG Y 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1371 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1059 time to evaluate : 6.194 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: C 82 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7001 (mt-10) REVERT: C 181 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7301 (mpp) REVERT: E 1 MET cc_start: 0.5540 (OUTLIER) cc_final: 0.4453 (ppp) REVERT: F 63 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7042 (mm110) REVERT: F 153 ASP cc_start: 0.7730 (p0) cc_final: 0.7458 (p0) REVERT: G 58 TYR cc_start: 0.6486 (m-80) cc_final: 0.6175 (m-80) REVERT: H 2 GLN cc_start: 0.4943 (OUTLIER) cc_final: 0.4726 (mm-40) REVERT: J 58 ASN cc_start: 0.7971 (m-40) cc_final: 0.7750 (m-40) REVERT: J 106 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7711 (ttpt) REVERT: J 118 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7835 (mtp) REVERT: L 117 THR cc_start: 0.6031 (OUTLIER) cc_final: 0.5293 (m) REVERT: N 110 MET cc_start: 0.8030 (mmm) cc_final: 0.7680 (mmm) REVERT: P 102 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5616 (mp0) REVERT: Q 30 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8325 (mtt-85) REVERT: R 24 LYS cc_start: 0.8278 (ttpp) cc_final: 0.7878 (tttp) REVERT: W 68 LYS cc_start: 0.8125 (tttm) cc_final: 0.7861 (tttt) REVERT: 0 5 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8412 (mm110) REVERT: 2 41 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6566 (mpp-170) REVERT: 4 24 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7675 (mtp180) REVERT: 5 1 MET cc_start: 0.6775 (mtm) cc_final: 0.6280 (mtt) REVERT: b 11 LYS cc_start: 0.6338 (mmtt) cc_final: 0.6057 (mtpt) REVERT: b 21 ARG cc_start: 0.7294 (ttp-170) cc_final: 0.7069 (ptm160) REVERT: c 3 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.6807 (mm-40) REVERT: c 14 ILE cc_start: 0.5632 (OUTLIER) cc_final: 0.5302 (mp) REVERT: c 58 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6016 (mm-30) REVERT: c 152 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: d 8 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7980 (mtpp) REVERT: d 21 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7128 (pt) REVERT: e 138 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8014 (mtt-85) REVERT: f 13 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.5450 (t0) REVERT: g 26 PHE cc_start: 0.8610 (t80) cc_final: 0.8397 (t80) REVERT: g 48 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6110 (pm20) REVERT: k 56 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7089 (mtm-85) REVERT: k 61 PHE cc_start: 0.8299 (t80) cc_final: 0.7964 (t80) REVERT: k 82 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6904 (pp) REVERT: k 122 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7374 (ttt180) REVERT: k 126 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7478 (tttp) REVERT: l 80 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8920 (pp) REVERT: l 94 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7827 (ptt180) REVERT: q 19 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7945 (tttp) REVERT: t 18 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7925 (ttt-90) outliers start: 312 outliers final: 187 residues processed: 1231 average time/residue: 2.1193 time to fit residues: 3773.6355 Evaluate side-chains 1225 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1011 time to evaluate : 6.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 35 ILE Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 5 GLN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 29 SER Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 57 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 24 ARG Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 7 residue 7 LEU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 58 GLU Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 14 LYS Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 56 ARG Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 93 ARG Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 122 ARG Chi-restraints excluded: chain k residue 126 LYS Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain o residue 59 MET Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 59 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 941 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 chunk 556 optimal weight: 8.9990 chunk 712 optimal weight: 8.9990 chunk 552 optimal weight: 6.9990 chunk 821 optimal weight: 10.0000 chunk 545 optimal weight: 9.9990 chunk 972 optimal weight: 10.0000 chunk 608 optimal weight: 5.9990 chunk 592 optimal weight: 7.9990 chunk 448 optimal weight: 0.0040 overall best weight: 6.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN D 173 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS R 86 GLN T 15 HIS Y 31 GLN 2 29 GLN 3 28 ASN d 196 ASN e 43 ASN ** e 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 148 ASN f 94 HIS g 68 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN m 14 HIS n 49 GLN n 66 GLN ** o 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 GLN p 29 ASN r 54 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 157038 Z= 0.441 Angle : 0.762 26.202 235083 Z= 0.381 Chirality : 0.049 2.056 30065 Planarity : 0.006 0.069 12481 Dihedral : 23.721 178.752 78983 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.74 % Favored : 92.11 % Rotamer: Outliers : 7.45 % Allowed : 26.76 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.11), residues: 5593 helix: 0.19 (0.12), residues: 1878 sheet: -0.82 (0.16), residues: 1006 loop : -1.66 (0.11), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 97 HIS 0.010 0.002 HIS 3 31 PHE 0.024 0.002 PHE 5 60 TYR 0.034 0.002 TYR o 78 ARG 0.013 0.001 ARG Y 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 1026 time to evaluate : 6.142 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: C 82 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7122 (mt-10) REVERT: C 251 GLN cc_start: 0.8196 (tp40) cc_final: 0.7987 (tm-30) REVERT: E 1 MET cc_start: 0.5610 (OUTLIER) cc_final: 0.5035 (ppp) REVERT: F 63 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7238 (mm110) REVERT: F 153 ASP cc_start: 0.7840 (p0) cc_final: 0.7497 (p0) REVERT: G 58 TYR cc_start: 0.6507 (m-80) cc_final: 0.6248 (m-80) REVERT: H 58 LEU cc_start: 0.5691 (OUTLIER) cc_final: 0.4802 (mp) REVERT: J 58 ASN cc_start: 0.8063 (m-40) cc_final: 0.7812 (m-40) REVERT: J 106 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7731 (ttpt) REVERT: J 118 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7635 (mtp) REVERT: L 117 THR cc_start: 0.5817 (OUTLIER) cc_final: 0.5189 (m) REVERT: N 110 MET cc_start: 0.8125 (mmm) cc_final: 0.7812 (mmm) REVERT: O 4 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7563 (tptp) REVERT: P 102 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5700 (mp0) REVERT: Q 30 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8355 (mtt-85) REVERT: R 24 LYS cc_start: 0.8416 (ttpp) cc_final: 0.7969 (tttp) REVERT: V 79 ARG cc_start: 0.8085 (mmt90) cc_final: 0.7880 (mmt90) REVERT: W 66 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8364 (mppt) REVERT: Y 1 MET cc_start: 0.5256 (OUTLIER) cc_final: 0.4734 (tmm) REVERT: 0 5 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8489 (mm-40) REVERT: 2 41 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6624 (mpp-170) REVERT: 3 33 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7870 (mp) REVERT: 4 24 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7783 (mtp180) REVERT: b 11 LYS cc_start: 0.6591 (mmtt) cc_final: 0.6235 (mtpt) REVERT: b 41 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6544 (pp) REVERT: c 3 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.6859 (mm-40) REVERT: c 14 ILE cc_start: 0.5914 (OUTLIER) cc_final: 0.5537 (mp) REVERT: c 58 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6006 (mm-30) REVERT: c 72 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6193 (ttp-110) REVERT: c 152 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: d 8 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8078 (mtpp) REVERT: d 21 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7397 (pt) REVERT: d 73 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6545 (ttm170) REVERT: e 138 ARG cc_start: 0.8452 (mtp85) cc_final: 0.8203 (mtt-85) REVERT: g 26 PHE cc_start: 0.8723 (t80) cc_final: 0.8516 (t80) REVERT: g 48 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6265 (pm20) REVERT: g 111 ARG cc_start: 0.6271 (OUTLIER) cc_final: 0.5841 (ppp80) REVERT: h 41 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8039 (ttmm) REVERT: j 10 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8271 (pp) REVERT: k 56 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7169 (mtm-85) REVERT: k 61 PHE cc_start: 0.8442 (t80) cc_final: 0.8141 (t80) REVERT: k 82 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.6935 (pp) REVERT: k 122 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7522 (ttt180) REVERT: k 126 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7688 (tptp) REVERT: l 80 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8981 (pp) REVERT: l 94 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7901 (ptt180) REVERT: n 30 ILE cc_start: 0.7979 (tp) cc_final: 0.7674 (tp) REVERT: p 52 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7930 (mm) REVERT: q 19 LYS cc_start: 0.8324 (mtpt) cc_final: 0.7991 (tttp) REVERT: q 21 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8813 (pp) REVERT: t 18 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7949 (ttt-90) outliers start: 346 outliers final: 212 residues processed: 1218 average time/residue: 2.0978 time to fit residues: 3687.5821 Evaluate side-chains 1251 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1003 time to evaluate : 6.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 5 GLN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 29 SER Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 3 residue 4 ILE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 55 LEU Chi-restraints excluded: chain 3 residue 57 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 24 ARG Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 7 residue 7 LEU Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 58 GLU Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 29 ASP Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 105 MET Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 14 LYS Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain e residue 165 LEU Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 111 ARG Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 96 MET Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 22 LYS Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 56 ARG Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 93 ARG Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 122 ARG Chi-restraints excluded: chain k residue 126 LYS Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 79 ARG Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 98 LYS Chi-restraints excluded: chain o residue 59 MET Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 26 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 59 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 601 optimal weight: 0.8980 chunk 388 optimal weight: 1.9990 chunk 580 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 618 optimal weight: 20.0000 chunk 662 optimal weight: 10.0000 chunk 480 optimal weight: 0.0870 chunk 90 optimal weight: 10.0000 chunk 764 optimal weight: 6.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN D 173 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN H 2 GLN H 11 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN Q 71 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN T 15 HIS U 99 ASN Y 31 GLN Y 58 ASN 2 29 GLN 3 28 ASN e 148 ASN g 28 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN m 14 HIS n 49 GLN n 66 GLN o 62 GLN p 29 ASN q 51 ASN r 54 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 157038 Z= 0.234 Angle : 0.656 26.454 235083 Z= 0.336 Chirality : 0.044 2.086 30065 Planarity : 0.005 0.073 12481 Dihedral : 23.717 179.939 78983 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.90 % Favored : 92.97 % Rotamer: Outliers : 6.66 % Allowed : 27.60 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.11), residues: 5593 helix: 0.31 (0.12), residues: 1885 sheet: -0.85 (0.15), residues: 1029 loop : -1.63 (0.11), residues: 2679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 97 HIS 0.008 0.001 HIS 3 31 PHE 0.027 0.002 PHE O 92 TYR 0.034 0.002 TYR o 78 ARG 0.015 0.001 ARG q 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 1019 time to evaluate : 6.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7034 (mt-10) REVERT: E 1 MET cc_start: 0.5550 (OUTLIER) cc_final: 0.4633 (ppp) REVERT: F 63 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7188 (mm110) REVERT: F 153 ASP cc_start: 0.7916 (p0) cc_final: 0.7551 (p0) REVERT: G 58 TYR cc_start: 0.6488 (m-80) cc_final: 0.6229 (m-80) REVERT: H 58 LEU cc_start: 0.5733 (OUTLIER) cc_final: 0.4816 (mp) REVERT: J 58 ASN cc_start: 0.8017 (m-40) cc_final: 0.7788 (m-40) REVERT: J 106 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7743 (ttpt) REVERT: J 118 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7679 (mtp) REVERT: L 117 THR cc_start: 0.5811 (OUTLIER) cc_final: 0.5224 (m) REVERT: N 110 MET cc_start: 0.8111 (mmm) cc_final: 0.7742 (mmm) REVERT: O 62 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6126 (pp) REVERT: P 102 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5598 (mp0) REVERT: Q 30 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8386 (mtt-85) REVERT: R 24 LYS cc_start: 0.8366 (ttpp) cc_final: 0.7955 (tttp) REVERT: 0 5 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8369 (mm110) REVERT: 2 41 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6581 (mpp-170) REVERT: 4 24 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7785 (mtp180) REVERT: 5 1 MET cc_start: 0.6550 (mtm) cc_final: 0.6070 (mtt) REVERT: b 11 LYS cc_start: 0.6509 (mmtt) cc_final: 0.6204 (mtpt) REVERT: c 3 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.6737 (mm-40) REVERT: c 14 ILE cc_start: 0.5876 (OUTLIER) cc_final: 0.5476 (mp) REVERT: c 58 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5993 (mm-30) REVERT: c 152 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: d 8 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8015 (mtpp) REVERT: d 21 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7236 (pt) REVERT: d 73 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6484 (ttm170) REVERT: e 138 ARG cc_start: 0.8424 (mtp85) cc_final: 0.8176 (mtt-85) REVERT: g 44 TYR cc_start: 0.7039 (m-10) cc_final: 0.6823 (m-10) REVERT: g 48 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6188 (pm20) REVERT: g 111 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5289 (ppp80) REVERT: h 41 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7999 (ttmm) REVERT: k 56 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7146 (mtm-85) REVERT: k 61 PHE cc_start: 0.8356 (t80) cc_final: 0.8074 (t80) REVERT: k 82 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.6834 (pp) REVERT: k 114 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8266 (m) REVERT: k 122 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7465 (ttt180) REVERT: k 126 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7471 (tttp) REVERT: l 80 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8949 (pp) REVERT: n 30 ILE cc_start: 0.7919 (tp) cc_final: 0.7638 (tp) REVERT: p 52 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7889 (mm) REVERT: q 19 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7854 (tttp) REVERT: q 21 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8732 (pp) REVERT: s 61 PHE cc_start: 0.7580 (t80) cc_final: 0.7232 (t80) REVERT: t 18 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7944 (ttt-90) outliers start: 309 outliers final: 198 residues processed: 1196 average time/residue: 2.0887 time to fit residues: 3628.8769 Evaluate side-chains 1228 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 999 time to evaluate : 6.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 27 LEU 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 117 THR Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 5 GLN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 55 LEU Chi-restraints excluded: chain 3 residue 57 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 24 ARG Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 58 GLU Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 111 ARG Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 56 ARG Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 93 ARG Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 122 ARG Chi-restraints excluded: chain k residue 126 LYS Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 79 ARG Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 49 GLN Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 98 LYS Chi-restraints excluded: chain o residue 59 MET Chi-restraints excluded: chain o residue 67 LEU Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 59 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 884 optimal weight: 0.9990 chunk 931 optimal weight: 0.5980 chunk 850 optimal weight: 5.9990 chunk 906 optimal weight: 4.9990 chunk 545 optimal weight: 9.9990 chunk 394 optimal weight: 10.0000 chunk 711 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 818 optimal weight: 9.9990 chunk 857 optimal weight: 6.9990 chunk 903 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN D 173 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN Q 59 GLN Q 71 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN T 15 HIS Y 31 GLN 2 29 GLN 3 28 ASN 5 41 HIS e 148 ASN g 28 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN m 14 HIS ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 GLN o 62 GLN p 29 ASN r 54 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 157038 Z= 0.301 Angle : 0.674 26.291 235083 Z= 0.342 Chirality : 0.044 2.084 30065 Planarity : 0.005 0.072 12481 Dihedral : 23.664 179.918 78983 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.26 % Favored : 92.61 % Rotamer: Outliers : 6.46 % Allowed : 28.16 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.11), residues: 5593 helix: 0.31 (0.12), residues: 1886 sheet: -0.91 (0.15), residues: 1074 loop : -1.65 (0.11), residues: 2633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP b 23 HIS 0.007 0.001 HIS 3 31 PHE 0.031 0.002 PHE O 92 TYR 0.028 0.002 TYR N 112 ARG 0.014 0.001 ARG Y 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1018 time to evaluate : 5.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: E 1 MET cc_start: 0.5547 (OUTLIER) cc_final: 0.4683 (ppp) REVERT: F 63 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7190 (mm110) REVERT: F 153 ASP cc_start: 0.7937 (p0) cc_final: 0.7558 (p0) REVERT: G 58 TYR cc_start: 0.6491 (m-80) cc_final: 0.6233 (m-80) REVERT: H 58 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.4765 (mp) REVERT: J 58 ASN cc_start: 0.8039 (m-40) cc_final: 0.7807 (m-40) REVERT: J 106 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7707 (ttpt) REVERT: J 118 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7688 (mtp) REVERT: L 117 THR cc_start: 0.5803 (OUTLIER) cc_final: 0.5233 (m) REVERT: N 110 MET cc_start: 0.8128 (mmm) cc_final: 0.7760 (mmm) REVERT: O 62 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.6133 (pp) REVERT: P 102 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5588 (mp0) REVERT: Q 30 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8339 (mtt-85) REVERT: R 24 LYS cc_start: 0.8391 (ttpp) cc_final: 0.7969 (tttp) REVERT: 0 5 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8412 (mm110) REVERT: 2 41 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6587 (mpp-170) REVERT: 4 24 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7764 (mtp180) REVERT: 5 1 MET cc_start: 0.6493 (mtm) cc_final: 0.6005 (mtt) REVERT: b 11 LYS cc_start: 0.6522 (mmtt) cc_final: 0.6255 (mtpt) REVERT: c 3 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.6908 (mm-40) REVERT: c 14 ILE cc_start: 0.5802 (OUTLIER) cc_final: 0.5421 (mp) REVERT: c 58 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6022 (mm-30) REVERT: c 152 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: d 8 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8073 (mtpp) REVERT: d 21 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7212 (pt) REVERT: d 73 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6498 (ttm170) REVERT: e 138 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8215 (mtt-85) REVERT: g 48 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6181 (pm20) REVERT: g 111 ARG cc_start: 0.6243 (OUTLIER) cc_final: 0.5297 (ppp80) REVERT: h 41 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8001 (ttmm) REVERT: j 10 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8232 (pp) REVERT: k 34 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8529 (mt) REVERT: k 56 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7155 (mtm-85) REVERT: k 61 PHE cc_start: 0.8353 (t80) cc_final: 0.8073 (t80) REVERT: k 82 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6822 (pp) REVERT: k 114 THR cc_start: 0.8578 (t) cc_final: 0.8362 (m) REVERT: k 122 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7506 (ttt180) REVERT: k 126 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7478 (tttp) REVERT: l 80 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8955 (pp) REVERT: n 30 ILE cc_start: 0.7948 (tp) cc_final: 0.7636 (tp) REVERT: p 52 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7909 (mm) REVERT: q 19 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7890 (tttp) REVERT: q 21 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8738 (pp) REVERT: t 18 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7951 (ttt-90) outliers start: 300 outliers final: 219 residues processed: 1191 average time/residue: 2.1020 time to fit residues: 3616.4739 Evaluate side-chains 1257 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1006 time to evaluate : 6.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 27 LEU 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 117 THR Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 35 ILE Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 5 GLN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 22 LEU Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 55 LEU Chi-restraints excluded: chain 3 residue 57 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 24 ARG Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 174 LYS Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 58 GLU Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain d residue 8 LYS Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 29 ASP Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 118 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 165 LEU Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 111 ARG Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 22 LYS Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 56 ARG Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 93 ARG Chi-restraints excluded: chain k residue 122 ARG Chi-restraints excluded: chain k residue 126 LYS Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 35 ASN Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 98 LYS Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 59 MET Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 59 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 595 optimal weight: 2.9990 chunk 958 optimal weight: 5.9990 chunk 584 optimal weight: 8.9990 chunk 454 optimal weight: 0.7980 chunk 666 optimal weight: 10.0000 chunk 1005 optimal weight: 0.6980 chunk 925 optimal weight: 2.9990 chunk 800 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 618 optimal weight: 20.0000 chunk 490 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN Q 71 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN T 15 HIS Y 31 GLN 2 29 GLN 3 28 ASN e 148 ASN g 28 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN m 14 HIS ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 GLN ** o 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 GLN p 29 ASN r 54 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 157038 Z= 0.232 Angle : 0.653 26.611 235083 Z= 0.332 Chirality : 0.043 2.093 30065 Planarity : 0.005 0.077 12481 Dihedral : 23.671 179.680 78983 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.08 % Favored : 92.79 % Rotamer: Outliers : 5.80 % Allowed : 28.93 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.11), residues: 5593 helix: 0.33 (0.12), residues: 1887 sheet: -0.91 (0.15), residues: 1061 loop : -1.62 (0.11), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 248 HIS 0.007 0.001 HIS 3 31 PHE 0.039 0.002 PHE R 53 TYR 0.054 0.002 TYR o 78 ARG 0.015 0.001 ARG Y 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11186 Ramachandran restraints generated. 5593 Oldfield, 0 Emsley, 5593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1013 time to evaluate : 6.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: E 1 MET cc_start: 0.5525 (OUTLIER) cc_final: 0.4609 (ppp) REVERT: F 63 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7175 (mm110) REVERT: F 153 ASP cc_start: 0.7922 (p0) cc_final: 0.7550 (p0) REVERT: G 58 TYR cc_start: 0.6485 (m-80) cc_final: 0.6226 (m-80) REVERT: H 58 LEU cc_start: 0.5673 (OUTLIER) cc_final: 0.4745 (mp) REVERT: J 58 ASN cc_start: 0.8014 (m-40) cc_final: 0.7792 (m-40) REVERT: J 106 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7727 (ttpt) REVERT: J 118 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7699 (mtp) REVERT: L 117 THR cc_start: 0.5999 (OUTLIER) cc_final: 0.5252 (m) REVERT: O 62 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.6112 (pp) REVERT: P 102 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5672 (mp0) REVERT: P 110 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7920 (pt) REVERT: Q 30 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8365 (mtt-85) REVERT: R 24 LYS cc_start: 0.8365 (ttpp) cc_final: 0.7951 (tttp) REVERT: 0 5 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8384 (mm110) REVERT: 2 41 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6573 (mpp-170) REVERT: 4 24 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7752 (mtp180) REVERT: 5 1 MET cc_start: 0.6469 (mtm) cc_final: 0.5977 (mtt) REVERT: b 11 LYS cc_start: 0.6505 (mmtt) cc_final: 0.6258 (mtpt) REVERT: c 3 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.6866 (mm-40) REVERT: c 14 ILE cc_start: 0.5816 (OUTLIER) cc_final: 0.5433 (mp) REVERT: c 58 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5999 (mm-30) REVERT: c 72 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6092 (ttp-110) REVERT: c 152 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: d 21 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7148 (pt) REVERT: d 73 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6479 (ttm170) REVERT: e 138 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8219 (mtt-85) REVERT: g 48 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6184 (pm20) REVERT: g 111 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5285 (ppp80) REVERT: h 41 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7974 (ttmm) REVERT: j 10 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8211 (pp) REVERT: k 34 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8516 (mt) REVERT: k 56 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7143 (mtm-85) REVERT: k 61 PHE cc_start: 0.8329 (t80) cc_final: 0.8051 (t80) REVERT: k 82 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.6788 (pp) REVERT: k 122 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7456 (ttt180) REVERT: k 126 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7478 (tttp) REVERT: l 80 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8956 (pp) REVERT: n 30 ILE cc_start: 0.7904 (tp) cc_final: 0.7592 (tp) REVERT: q 19 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7848 (tttp) REVERT: q 21 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8718 (pp) REVERT: t 18 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7945 (ttt-90) outliers start: 269 outliers final: 209 residues processed: 1165 average time/residue: 2.0776 time to fit residues: 3490.3949 Evaluate side-chains 1242 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1001 time to evaluate : 6.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 27 LEU 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 117 THR Chi-restraints excluded: chain L residue 136 GLU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 59 ARG Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 30 SER Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 5 GLN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 22 LEU Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 55 LEU Chi-restraints excluded: chain 3 residue 57 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 24 ARG Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 174 LYS Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 58 GLU Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 29 ASP Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 191 LEU Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 17 LYS Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 111 ARG Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 51 VAL Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 56 ARG Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 93 ARG Chi-restraints excluded: chain k residue 122 ARG Chi-restraints excluded: chain k residue 126 LYS Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 5 ASN Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 11 VAL Chi-restraints excluded: chain n residue 35 ASN Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 82 ILE Chi-restraints excluded: chain n residue 98 LYS Chi-restraints excluded: chain o residue 59 MET Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 59 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 635 optimal weight: 10.0000 chunk 852 optimal weight: 0.4980 chunk 245 optimal weight: 6.9990 chunk 738 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 801 optimal weight: 4.9990 chunk 335 optimal weight: 6.9990 chunk 823 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN Q 59 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN T 15 HIS Y 31 GLN 2 29 GLN 3 28 ASN e 148 ASN g 28 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN m 14 HIS ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 GLN o 62 GLN p 29 ASN r 54 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.157909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126751 restraints weight = 198283.336| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.26 r_work: 0.3112 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 157038 Z= 0.407 Angle : 0.749 26.110 235083 Z= 0.376 Chirality : 0.048 2.053 30065 Planarity : 0.006 0.065 12481 Dihedral : 23.712 178.094 78983 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.91 % Favored : 91.95 % Rotamer: Outliers : 5.86 % Allowed : 29.32 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.11), residues: 5593 helix: 0.16 (0.12), residues: 1884 sheet: -0.97 (0.15), residues: 1022 loop : -1.70 (0.11), residues: 2687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 23 HIS 0.010 0.001 HIS 3 31 PHE 0.026 0.002 PHE g 18 TYR 0.035 0.002 TYR o 78 ARG 0.016 0.001 ARG Y 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50229.13 seconds wall clock time: 869 minutes 45.81 seconds (52185.81 seconds total)